1. 26 Mar, 2021 1 commit
  2. 19 Mar, 2021 2 commits
  3. 09 Mar, 2021 1 commit
  4. 03 Mar, 2021 2 commits
  5. 01 Mar, 2021 1 commit
  6. 27 Feb, 2021 4 commits
  7. 17 Feb, 2021 3 commits
  8. 16 Feb, 2021 3 commits
  9. 15 Feb, 2021 2 commits
  10. 13 Feb, 2021 2 commits
  11. 09 Feb, 2021 2 commits
    • Dalibor Stuchlík's avatar
      deleted: .github/ISSUE_TEMPLATE/bug_report.md · 44d7a28f
      Dalibor Stuchlík authored
      	deleted:    .github/ISSUE_TEMPLATE/custom.md
      	deleted:    .github/ISSUE_TEMPLATE/feature_request.md
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/updog/TSV.java
      	deleted:    indexer/src/test/resources/ogm.properties
      	deleted:    web/src/main/resources/static/js/chart.bundle.js
      	deleted:    web/src/main/resources/static/js/date.js
      44d7a28f
    • Dalibor Stuchlík's avatar
      deleted: admin/.classpath · 818824ce
      Dalibor Stuchlík authored
      	deleted:    admin/.factorypath
      	deleted:    admin/.project
      	modified:   admin/src/main/app-ui/package-lock.json
      	modified:   admin/src/main/app-ui/src/app/datasource-summary/datasource-summary.component.html
      	modified:   admin/src/main/app-ui/src/pdxfinder/pattern-library/style.css
      new file:   admin/src/main/java/org/pdxfinder/controllers/TransController.java
      	deleted:    admin/src/main/resources/static/css/animate.css
      	deleted:    admin/src/main/resources/static/css/bootstrap.css
      	deleted:    admin/src/main/resources/static/css/font-awesome.css
      	deleted:    admin/src/main/resources/static/css/style.css
      	deleted:    admin/src/main/resources/static/images/icons/Jira2.png
      	deleted:    admin/src/main/resources/static/images/icons/Reports-icon.png
      	deleted:    admin/src/main/resources/static/images/icons/SOPs.png
      	deleted:    admin/src/main/resources/static/images/icons/cdp.png
      	deleted:    admin/src/main/resources/static/images/icons/contact.png
      	deleted:    admin/src/main/resources/static/images/icons/finder.png
      	deleted:    admin/src/main/resources/static/images/icons/github.jpg
      	deleted:    admin/src/main/resources/static/images/icons/vms.png
      	deleted:    admin/src/main/resources/static/images/icons/zoomaa.png
      	deleted:    admin/src/main/resources/static/images/profile_small.jpg
      	deleted:    admin/src/main/resources/static/js/bootstrap.min.js
      	deleted:    admin/src/main/resources/static/js/jquery-2.1.1.js
      	deleted:    admin/src/main/resources/static/js/pdxAdmin.js
      	deleted:    admin/src/main/resources/static/js/plugins/chart/3dbar.js
      	deleted:    admin/src/main/resources/static/js/plugins/chart/amcharts.js
      	deleted:    admin/src/main/resources/static/js/plugins/chart/export.css
      	deleted:    admin/src/main/resources/static/js/plugins/chart/export.min.js
      	deleted:    admin/src/main/resources/static/js/plugins/chart/light.js
      	deleted:    admin/src/main/resources/static/js/plugins/chart/serial.js
      	deleted:    admin/src/main/resources/static/js/plugins/metisMenu/jquery.metisMenu.js
      	deleted:    admin/src/main/resources/static/js/plugins/slimscroll/jquery.slimscroll.js
      	deleted:    admin/src/main/resources/static/js/plugins/slimscroll/jquery.slimscroll.min.js
      	deleted:    admin/src/main/resources/templates/fragments/components.html
      	deleted:    admin/src/main/resources/templates/fragments/footer.html
      	deleted:    admin/src/main/resources/templates/fragments/header.html
      	deleted:    admin/src/main/resources/templates/fragments/sidenav.html
      	deleted:    admin/src/main/resources/templates/fragments/topnav.html
      	deleted:    admin/src/main/resources/templates/index.html
      modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/DataProjectionRepository.java
      	new file:   data-model/src/test/java/org/pdxfinder/graph/repositories/AllLookupNodeRepositoriesTest.java
      	new file:   data-model/src/test/java/org/pdxfinder/graph/repositories/PatientRepositoryTest.java
      	new file:   data-model/src/test/java/org/pdxfinder/graph/repositories/PlatformRepositoryTest.java
      	new file:   data-model/src/test/java/org/pdxfinder/graph/repositories/SampleRepositoryTest.java
      	new file:   data-model/src/test/resources/logback.xml
      	new file:   data-model/src/test/resources/ogm.properties
      	modified:   data-services/pom.xml
      	modified:   data-services/src/main/java/org/pdxfinder/services/AutoCompleteService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/search/OneParamCheckboxSearch.java
      	new file:   data-services/src/test/java/org/pdxfinder/services/MolcharTableTest.java
      	new file:   data-services/src/test/java/org/pdxfinder/services/SearchServiceTest.java
      	new file:   data-services/src/test/java/org/pdxfinder/services/ds/SearchDSTest.java
      	new file:   data-services/src/test/resources/logback.xml
      	new file:   data-services/src/test/resources/ogm.properties
      	deleted:    data-services/target/maven-archiver/pom.properties
      	deleted:    data-services/target/maven-status/maven-compiler-plugin/compile/default-compile/createdFiles.lst
      	deleted:    data-services/target/maven-status/maven-compiler-plugin/compile/default-compile/inputFiles.lst
      818824ce
  12. 08 Feb, 2021 1 commit
  13. 05 Feb, 2021 1 commit
    • Dalibor Stuchlík's avatar
      Squashed commit of the following: · 754f66a1
      Dalibor Stuchlík authored
      commit edcd8b9115e1312eb48b5e7b96ab59a9c7ce932e
      Merge: 0633c8dde 942cb9bfe
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Jan 13 15:17:17 2021 +0000
      
          Merge pull request #478 from PDXFinder/beta
      
          Beta
      
      commit 942cb9bfef30adb25f4e695dca4a3e3ef647d980
      Merge: 2c59a2793 58e92cda0
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Jan 12 19:11:24 2021 +0000
      
          Merge pull request #475 from PDXFinder/publication_fix
      
          Publication fix
      
      commit 58e92cda0f3fd09bbdd9b42d4532f1b9704fd756
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 12 15:46:53 2021 +0000
      
          Update api url in test
      
      commit 67baf840957b66222335cd9405edf5cc49bcfc83
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 12 15:38:46 2021 +0000
      
          Use external id for looking up publication
      
      commit 00c207c36b5b4e492f7cd7d89c999933bb68d0a4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 12 15:34:20 2021 +0000
      
          Remove PMID case insensitive
      
      commit 0633c8dde7cf2582678d660d3915c9bc9eb3cf3c
      Author: Zina Perova <38244059+zperova@users.noreply.github.com>
      Date:   Thu Dec 17 14:32:24 2020 +0000
      
          Added links to resources
      
      commit d2bec0480f9823d801e83a403512c2dee3b96dbc
      Author: Zina Perova <38244059+zperova@users.noreply.github.com>
      Date:   Thu Dec 17 14:30:09 2020 +0000
      
          Update README.md
      
      commit 2df9dda42feca4879e3882c931030eb9a4938999
      Author: Zina Perova <38244059+zperova@users.noreply.github.com>
      Date:   Tue Dec 15 16:01:27 2020 +0000
      
          Added links to publications
      
      commit 4b0f5b0781eb5b8423097be4718f06fb8d43d013
      Author: Zina Perova <38244059+zperova@users.noreply.github.com>
      Date:   Tue Dec 15 15:56:06 2020 +0000
      
          Created issue templates
      
      commit d56591f2e79ca527560ccfb92b52ca6cd763c8b4
      Merge: c5bdf87b1 2c59a2793
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Dec 9 12:23:54 2020 +0000
      
          Merge pull request #454 from PDXFinder/beta
      
          Fix two param linked filter update error
      
      commit 2c59a2793849a79adc8d8eb1d200603d59b096a9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Dec 4 10:41:40 2020 +0000
      
          Fix two param linked filter update error
      
      commit c5bdf87b1b9b60d4eaee806e6a2c17c0d7d79207
      Merge: 43ed7a914 b05b37e69
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Oct 28 12:12:18 2020 +0000
      
          Merge pull request #371 from PDXFinder/beta
      
          Beta
      
      commit b05b37e699a0d419a1fc0d35d10f6874846c0bda
      Merge: 44019c81b c836bc6b0
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Oct 26 19:19:50 2020 +0000
      
          Merge pull request #370 from PDXFinder/dev
      
          Dev
      
      commit c836bc6b0234d1b05241319b1f7286b8122b848a
      Merge: 24ca22f5f aaa88a058
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Oct 26 09:21:51 2020 +0000
      
          Merge pull request #368 from PDXFinder/stats-fix
      
          Add nullchecks for keys
      
      commit 24ca22f5f0e5df4333359c8c1e58e8134ad96aeb
      Merge: 89473fd89 d9f2b6003
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Sat Oct 24 10:36:59 2020 +0100
      
          Merge pull request #367 from PDXFinder/thymeLeafFix-Dev
      
          Fix broken rawDataLabel by updating Thymeleaf
      
      commit d9f2b6003e4595d35ba35b8421a1dcaa98d0436d
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Oct 23 14:55:08 2020 +0100
      
          Fix broken rawDataLabel by updating Thymeleaf
      
          Because
          - it broke
      
      commit aaa88a05864f564cf877cc2f3e07c32156f21a2b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 23 13:49:40 2020 +0100
      
          Add nullchecks for keys
      
      commit 89473fd89de0e1863ce3c18a4943f7243e922262
      Merge: c4ca531d8 f2ec86593
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Oct 21 18:14:12 2020 +0100
      
          Merge pull request #365 from PDXFinder/molchartable-limit
      
          Molchartable limit
      
      commit f2ec86593e0431f2ae1da0ed16c6271fdba73d65
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 21 14:07:05 2020 +0100
      
          Add test to details service
      
      commit 4d408a785d6fd807570c11f9c5335a5b8fb50b20
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 21 14:06:39 2020 +0100
      
          Return big datasets for export only
      
      commit c4ca531d84382221e3e3568eab9655aaf4ab8a14
      Merge: bca08db5f ac38824d4
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Oct 20 09:41:15 2020 +0100
      
          Merge pull request #359 from PDXFinder/redirect
      
          Redirect
      
      commit bca08db5f2aa2b54667e01feffb26452287d58b1
      Merge: 28cf64655 64890b633
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Fri Oct 16 16:05:18 2020 +0100
      
          Merge pull request #355 from PDXFinder/patientTreatment-Xdog
      
          Alexs_custom_retirement_plan_with_the_Xdog
      
      commit 64890b633a0af27c0940aa33f416ac0be3ea9dd6
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Oct 16 15:56:35 2020 +0100
      
          made final variable static as per code smell review
      
      commit 8a423ba7a5fc6c3d8c78ede940f216de543b1a00
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Oct 16 15:55:04 2020 +0100
      
          made final variable static as per code smell review
      
      commit 6f5760f1e1753267c4f0b926f5fe3b2d0929598d
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Oct 16 15:50:32 2020 +0100
      
          Patched bug in Xdog. Retired PDXNet custom loaders
      
      commit 498a362ca812f7ad0a3f1304855c0cfebf96b59b
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Oct 16 15:24:39 2020 +0100
      
          Wrote tests for Drug Dosing and Patient Treatment Feature
      
      commit e7fe8d6f4deef94be1097dc9ffda5a1ba55310cc
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Oct 16 13:52:11 2020 +0100
      
          Fixed failing tests
      
      commit ac38824d485e044ab1d43333aa38ad23bc0ae0e7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 16 13:21:41 2020 +0100
      
          Add csv test
      
      commit a88b817a4746f4e58aa8eb31dd37ede0e234c9ad
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 16 12:47:49 2020 +0100
      
          Add csv test
      
      commit cdfd2504d171e651c2554624085ad73afbb3d115
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 16 12:28:22 2020 +0100
      
          Make method public
      
      commit 9feb4427e7e89439e7d56c7d35486bed6060c5a8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 16 12:25:00 2020 +0100
      
          Fix sonar issue
      
      commit 28cf64655e785c33a359cf23e13546002817db4e
      Merge: 5e0656895 94dd3187e
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Oct 16 12:09:35 2020 +0100
      
          Merge pull request #356 from PDXFinder/dev_frommaster_update
      
          Dev frommaster update
      
      commit a854c169261fce220d7f406c88026ceb5cada2e4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 16 12:06:45 2020 +0100
      
          Add redirect test
      
      commit f5d3b65775dd0d0ac21922745fb43eab2fd351f5
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 15 14:58:12 2020 +0100
      
          Redirect /data to /data/search
      
      commit 94dd3187e6bcc25082485c90139f335fb5a90d0a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 15 11:05:39 2020 +0100
      
          Cleanup
      
      commit 7e00f96363d7cb77af1c1551c985e86df0af1ad4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 15 10:58:56 2020 +0100
      
          Rename id
      
      commit 184e4a651bee5ce9328c06fbe172f19c43d8aa4b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 15 10:56:17 2020 +0100
      
          Cleanup
      
      commit 902e7900e1305bcf77a9f79f25dfc5feb2dcfa7f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 15 10:50:06 2020 +0100
      
          Update deprecated annotations
      
      commit 1b5dcbdc8cc8ea3dd9b6c5d7a09d8be0ae78c34d
      Merge: 5e0656895 43ed7a914
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 15 10:37:53 2020 +0100
      
          Merge branch 'beta_test' into dev_frommaster_update
      
          # Conflicts:
          #	data-model/src/main/java/org/pdxfinder/graph/dao/PatientSnapshot.java
          #	data-model/src/main/java/org/pdxfinder/graph/repositories/PatientRepository.java
          #	dependencies/pom.xml
          #	indexer/src/main/java/org/pdxfinder/dataloaders/UniversalLoader.java
      
      commit 6de3302faea0ce6949499c2b1bdaf63040750d6d
      Merge: 53c6d498d f32d8f86d
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Oct 14 17:08:34 2020 +0100
      
          Merge branch 'custom-retirment-plan' into patientTreatment-Xdog
      
      commit 53c6d498d6deda39786dd97e8623a029fb046b3a
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Oct 14 17:08:30 2020 +0100
      
          added support for Patient Treatment and Drug Dosing to Xdog
      
      commit 5e0656895c515c0e1450022cb2f0bc8b949bfda2
      Merge: 96d0d6af6 d0dfa7af8
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Oct 14 08:46:30 2020 +0100
      
          Merge pull request #352 from PDXFinder/change_dataset_visibility
      
          Hide Curie LC and BC datasets
      
      commit d0dfa7af8d2467bbcb3b604517e30404082ee697
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 14 08:38:20 2020 +0100
      
          Hide Curie LC and BC datasets
      
      commit 01c81282d07cbbacb110f0c21cc463d9343fb067
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Oct 7 16:29:20 2020 +0100
      
          added support for Patient Treatment and Drug Dosing to Xdog
      
      commit f32d8f86df3691b8bac01ab30eb53d78d0cf3053
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Oct 13 14:38:43 2020 +0100
      
          Updated BrokenRelationErrorCreator to have clearer ERROR MSG
      
      commit f26dbe4748d792a27e25484012718350570f6199
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Oct 13 14:37:11 2020 +0100
      
          update to FinderLoader to remove PDXNet loaders.
      
          Because:
          --These sets are being moved to Updog
      
          Added PDXNet group to the PDXNet sets. PDXNet has been removed from their name for simplicity. A minor fix to the xDog here to allow xDog to construct the export folder correctly
      
      commit 96d0d6af68339c44b78b1e07877721772e56c163
      Merge: eeff16571 21e288eb1
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Oct 9 14:55:35 2020 +0100
      
          Merge pull request #349 from PDXFinder/bugfixes
      
          Bugfixes
      
      commit eeff16571340ad06638c5257a67f594f520c80a3
      Merge: 627e44544 3990ff71e
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Oct 8 09:31:50 2020 +0100
      
          Merge pull request #346 from PDXFinder/extend-search
      
          Extend search
      
      commit 3990ff71e1f67b42ba2e2b32ffce5f660ee1f427
      Merge: 0c3da61bf 247dc953c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 7 11:11:50 2020 +0100
      
          Merge branch 'button-fix' into extend-search
      
      commit 247dc953c1e61888b03a2059adf5c15c307b7ade
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 7 11:02:52 2020 +0100
      
          Register onclick event for OR button via attr
      
      commit 627e44544facdeeea42768c82d6a19cda514fc8f
      Merge: f563fa91d cde6b4733
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Oct 7 10:19:40 2020 +0100
      
          Merge pull request #323 from PDXFinder/cbioportalUpdate
      
          Made changes to parse HGNC symbol from Detail JSON.
      
      commit cde6b473345a5f043cfa32c952cb85c7fc46506a
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Oct 6 13:43:01 2020 +0100
      
          Removed unnecessary declaration of Throw IOException
      
      commit 015b7c4ad530b39dcffdb49daf713e9ae5e5ddbd
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Oct 6 13:31:56 2020 +0100
      
          Fixed sonarQube bug regarding Workbook.close()
      
      commit 572ebe37bbeff5449b59045483da61620191eedd
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Oct 6 12:59:15 2020 +0100
      
          Fixed SonarQube blockers in MappingService
      
          Because:
          - There is a directory traversal attack vulnerability
      
          Checks the input for special characters and throws illegalArgumentException if
          it finds any. Characters can be any case alphanumeric including underscore and
          hyphen
      
      commit 2135fe43ac8816a0255220c0a07d83bb51987362
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Oct 6 12:59:15 2020 +0100
      
          Fixed SonarQube blockers in MappingService
      
          Because:
          - There is a directory traversal attack vulnerability
      
          Checks the input for special characters and throws illegalArgumentException if
          it finds any.
      
      commit 7c126c198b3eab11e1d78c58ffab8bcac50d1611
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Tue Oct 6 11:09:10 2020 +0100
      
          Update application.properties
      
          remove unintended edit
      
      commit 47ff518122de30b733bb59d6490c45a943cb73b2
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Oct 5 17:22:02 2020 +0100
      
          Added test to check that the nest Json is parsed correctly
      
      commit 0c3da61bfd8850c064fa2ff61f871187b72f9e2f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Oct 6 10:05:35 2020 +0100
      
          Add search by model id functionality
      
      commit b2e6632f42a467677810ea7ace73293ba7a94ea9
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Sep 29 16:37:36 2020 +0100
      
          Made changes to parse HGNC symbol from Detail JSON.
      
          Because:
          HGNC markers did complete Entrez mappings
      
          Changed code to parse "detailed" json that includes HGNC symbols. THis is collected from
          cbioportal.ca using the "detailed" parameter on the swagger API. Other changes are included
          to clean up the cbioportal exporter for shifted templates and incorrect file structure.
      
      commit 21e288eb1d9017736a33ae20fc815ad9f40e13c9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 9 17:45:46 2020 +0100
      
          Add h2 dependency to data services as well
      
      commit af83f96c8972f9f8ae4a79e2457f58a40a147380
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 9 15:46:32 2020 +0100
      
          Move h2 dependency from data services to individual modules
      
      commit 542941a66e8bb9d178ae6738a9a98459fa25793b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 9 11:50:37 2020 +0100
      
          h2 db version to set to 197
      
      commit 59d2caa5b4c6e9619fda0ac8d2a6446754a91d39
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 9 11:47:36 2020 +0100
      
          Downgrade h2
      
      commit 1777ee129a714ad7110899cc3db668ca5e3a7884
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 9 10:28:02 2020 +0100
      
          Enable env for admin
      
      commit b8439757d1e210ef43621a58b16e6558f6cb7fe7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 9 09:22:08 2020 +0100
      
          Enable neo4j bolt for admin
      
      commit f563fa91dc83b23177ee432818985d80b63ac645
      Merge: 286208801 01784fbb4
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Sep 7 09:43:14 2020 +0100
      
          Merge pull request #307 from PDXFinder/acutators
      
          Enable env endpoint for server management
      
      commit 01784fbb429cc0862c99b904445b2951890c57ee
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Sep 4 15:24:27 2020 +0100
      
          Enable env endpoint for server management
      
      commit 286208801a40110d88e30738c5c40d66679fb968
      Merge: b3acace25 02fd01cac
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Sep 4 13:04:27 2020 +0100
      
          Merge pull request #305 from PDXFinder/frontend-fix
      
          Refactor window opening logic in Thymeleaf and Javascript
      
      commit 02fd01cac8b99061a50a30abed6ec2ca5cef451f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Sep 4 10:55:58 2020 +0100
      
          Refactor window opening logic in Thymeleaf and Javascript
      
      commit b3acace2591a65468f9b70bc51587b2ed4f5f63a
      Merge: 981178e2b 80c7a1767
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Aug 28 14:01:48 2020 +0100
      
          Merge pull request #295 from PDXFinder/upgrade-spring-boot-2.3.1
      
          Upgrade spring boot 2.3.3
      
      commit 80c7a1767cd7f0399336ac6d0e9dbddfb8e7156e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 25 12:54:48 2020 +0100
      
          Solving the problems of the universe
      
      commit 5e0e71249ca5a3187f499dd1b147f379f2e2a553
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 25 12:18:37 2020 +0100
      
          Refactor embedded and bolt drivers
      
      commit 80e65745abf2c07e6552f8ecf53a931acbae31f3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 25 12:17:32 2020 +0100
      
          Fix thymeleaf errors
      
      commit 981178e2bdb2a4cae0fd80ea36c8fc082967f3ba
      Merge: e3ee69771 43d82fe0f
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Tue Aug 25 11:04:18 2020 +0100
      
          Merge pull request #293 from PDXFinder/dev-PPTC-enabled2
      
          Dev pptc enabled
      
      commit 43d82fe0fd5e73182bb2064e32e2cbb4606551ec
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Aug 25 10:08:31 2020 +0100
      
          Removed DataProviderTest.java
      
          Because:
          *It was a brittle test that would hamper normal configuration changes
      
      commit 6a32a449e00f65764a095f0d848fc55a5c3c15df
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Aug 24 10:04:23 2020 +0100
      
          Remove unique restriction
      
      commit 8522701a424953f145d38ccea7695dab7291ce2e
      Merge: 40c9e5a27 de6ef8c2b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Aug 24 10:01:21 2020 +0100
      
          Merge branch 'loadtime-fix' into upgrade-spring-boot-2.3.1
      
      commit 92162fbea57c79e7d483c1db2bfc0e0e841c1aa7
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Aug 21 16:49:44 2020 +0100
      
          Enabled PPTC provider for UPDOG
      
      commit 40c9e5a278bdb07e7e9f5f48b902223c4b5527fb
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Aug 20 19:36:23 2020 +0100
      
          Update tests
      
      commit 85aa91ff334509dc91386912bb9909cca132ecf3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Aug 20 18:33:53 2020 +0100
      
          Update Neo4j dependencies
      
      commit de6ef8c2b1ebfd4590a0e5e438668282a0f3bf61
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Aug 19 13:45:20 2020 +0100
      
          Remove dependency
      
      commit 023d38554f8eb0c0101670f78c15510dce51c39d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Aug 19 09:56:56 2020 +0100
      
          Fix thymeleaf fragment error
          Update deprecated properties
      
      commit 382c903f7b95e99378309fc8e82f2c6c559c030d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 18 14:38:32 2020 +0100
      
          Add Gson dependency
      
      commit 22a768f977dc5be485141072f937c67d3d636565
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Aug 17 09:19:38 2020 +0100
      
          Add custom sessionFactory
      
      commit 92ededa597069f432a379f35537a7eb3c73a64e4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Aug 17 09:19:25 2020 +0100
      
          Fix paging
      
      commit 6f08ff5f4655feb9b66f6828bca531eb5eb13084
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Aug 17 09:19:02 2020 +0100
      
          Change Spring boot version to 2.3.3
      
      commit e3ee69771a4c05afdd33ad244fe093b054e40597
      Merge: 86725b89a 95d1a5b86
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Aug 14 12:51:29 2020 +0100
      
          Merge pull request #283 from PDXFinder/dev-cleanup
      
          dev cleanup
      
      commit 95d1a5b8602bede990ae32666d2a1558e41fc738
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 14 11:00:28 2020 +0100
      
          Get rid of code smells
      
      commit 707fde7f50eb4c3bad8a79b6b50e29b8085192c5
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 14 10:47:55 2020 +0100
      
          Remove old universal loader and ircc loader
      
      commit a02cfa766961cea97f461f3bbb1d2c2a53b78898
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 14 10:47:26 2020 +0100
      
          Service cleanup
      
      commit 33dd5eb7a12cc1bea6cb982024d1a4b8a80d5182
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 14 10:46:43 2020 +0100
      
          Repository methods cleanup
      
      commit 0d977b2b298c8f1e8ce92b335fd78e85f9ee51bc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 14 10:05:37 2020 +0100
      
          Remove unused imports
      
      commit 3d93df5c1f76d511efed0f6bb8b143e078266533
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 14 10:05:06 2020 +0100
      
          Remove unused methods
      
      commit 9972af3c8f66055f1a7b55342a25a466cbcfe3ea
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 14 09:16:34 2020 +0100
      
          Remove old db validator
      
      commit 86725b89a0fa8942bb569839065e302467c3f81f
      Merge: fc2fda805 148c1d6d5
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Aug 13 17:58:01 2020 +0100
      
          Merge pull request #280 from PDXFinder/h2-fix
      
          H2 fix
      
      commit 148c1d6d581b817ac6805945340ce031a71c9010
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 11 21:36:10 2020 +0100
      
          Fix qualityassurrance query error
      
      commit d4356e11fe1ae29ea77fa5fc0d41d3ec6a633d82
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 11 17:36:40 2020 +0100
      
          Remove url from config
      
      commit fc2fda80552e7b27046fa711747211b9a1ba80e0
      Merge: 4273e0319 c4db1c54b
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Fri Jul 31 08:07:10 2020 +0100
      
          Merge pull request #198 from PDXFinder/dev-upgrade-test
      
          Dev upgrade test
      
      commit c4db1c54b9dfdb64bb851bf8311206d9a089083c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 29 15:38:29 2020 +0100
      
          Test whole datavisibility process
      
      commit 677f94e79b011da81c7df2c0152036172c60198c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 29 15:37:54 2020 +0100
      
          Rename
      
      commit c6c1dfa92b541f7eb9d42b391ee9bdf1d29dcb3b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 29 14:49:23 2020 +0100
      
          Add test to datavisibility logic
      
      commit 3c7cdaa9657cf470eecbfe7685d622fe3426fb8f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 29 14:31:33 2020 +0100
      
          Refactor datavisibility method
      
      commit cec871d2d3addad58c1a67521879d148d01c16d3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 29 14:00:49 2020 +0100
      
          Add test to markerassociation
      
      commit 4e67ecc3718919b51c58fb9e2fa132beef48026c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 29 10:50:22 2020 +0100
      
          Add test to treatment linking
      
      commit b4ba02c947aa0f7ee9b5b0708afbdc8b676cf2cc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 29 09:53:23 2020 +0100
      
          Add test to model drug dosing
      
      commit dae3f8d56e073c943c31dee3e96df17028cf616b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 29 09:18:24 2020 +0100
      
          Reduce complexity for model drug projection
      
      commit 1161c24eddd989e6034bd4a865b7d7b1c430cae0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 21:50:53 2020 +0100
      
          Test dataprojection save
      
      commit 97a3368ff13914b5407968201cf67074e7a40383
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 21:17:24 2020 +0100
      
          Remove unused imports
      
      commit 6f6f2c8948113025c0527c68675a127946dad61e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 21:17:05 2020 +0100
      
          Additional tests to save logic
      
      commit 60a4a59cb4de58a13c2f44850d2d608d00636eb9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 20:54:52 2020 +0100
      
          Add test to projections
      
      commit 098f4f1f2757da8e4feafec2fe876cce4c644766
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 20:25:55 2020 +0100
      
          Remove potential exception in catch
      
      commit 517b36ed65c3291fca9c288e1515f7283f162b68
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 16:39:21 2020 +0100
      
          Initial commit
      
      commit 4618c55aed55aebcc511f7ebbb6fb0ecdeba032c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 16:38:27 2020 +0100
      
          Add getters and setters
      
      commit 7fab4f9b8d685e192c0043886ed3ba33070757f4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 16:24:20 2020 +0100
      
          Return dataprojection on save
      
      commit 8892a9faf9159658ba16d4ba32a929682950fd8d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 15:59:51 2020 +0100
      
          Remove unused imports
      
      commit c0735c8d79ad93ca425b107ed62cd9bde3b02da6
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 15:32:28 2020 +0100
      
          Refactor saving logic
      
      commit dd7ff4a1cff5796ac6aa6c841c3f5be25d0e67d8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 14:52:50 2020 +0100
      
          Add equals test
      
      commit a13f672f35966f12af8a09e7240a874760854ab0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 11:53:01 2020 +0100
      
          Extend age tests
      
      commit 2518998c5b6a9131e1f3c728f90a94a2c99fb94c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 10:21:41 2020 +0100
      
          Fix age calculation
      
      commit 329e23062639fa85fc4704b1a538f2394d79df5e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 28 09:57:17 2020 +0100
      
          Test paediatric age calculation
      
      commit f82fb8b75a32babbfd92eaacf04167516f42c5d8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 27 10:02:16 2020 +0100
      
          Fix tests
      
      commit 6d99ecbd087527210f6fe20c0fb959eaf14d101c
      Merge: 2ed8896ab 4273e0319
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 27 09:53:19 2020 +0100
      
          Merge branch 'dev' into dev-upgrade-test
      
          # Conflicts:
          #	indexer/src/main/java/org/pdxfinder/dataloaders/updog/Updog.java
          #	indexer/src/test/java/org/pdxfinder/commandline/FinderCommandLineTest.java
          #	indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreatorTest.java
      
      commit 4273e0319e643b8f052ff56022fb2cd3fda9c8b8
      Merge: 1d1b1924c 24c7eb1fd
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Mon Jul 27 09:47:38 2020 +0100
      
          Merge pull request #211 from PDXFinder/xdog-changes
      
          Xdog changes
      
      commit 24c7eb1fd397d9b9c878160737d60e81a5bfa397
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Jul 27 09:39:50 2020 +0100
      
          Changed dataImportService.findModelWithMolecularDataByDSAndIdAndMolcharType to findModelsWithMolecularDataByDSAndMolcharType
      
          Because:
          *The new name better reflects the function
      
          Renamed the query in the ModelCreationRepository as well.
      
      commit 0b3307fba8ff62e4726a565af6627f0414e551ed
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Jul 24 16:28:14 2020 +0100
      
          Changed logs to be more uniform and provider better information.
      
      commit cc71325b9e9900ef7dc145e47a5d07400fd89dad
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Jul 24 12:07:07 2020 +0100
      
          Fixed saving Metadata. Fixed samplePlatform name
      
      commit 2ed8896ab1ff1dc5fd5c349752475df4acc0318e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 24 11:13:25 2020 +0100
      
          Back to 2.0.9
      
      commit 19c17f8ab0883c3930338e274e6abd3b12581284
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Jul 23 15:06:22 2020 +0100
      
          Fixed tests. Removed Group parameter in MetadataSheets. Renamed UniversalDataExtractionUtilites to UniversalDataExtractionServices.
      
      commit 3768cf6395265ce64608e27ff8f65d9357d6e5ad
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jul 23 15:03:26 2020 +0100
      
          Upgrade Spring to 2.3.1
      
      commit daff2960962e92ce63a03a0f8d685a8def0292ae
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jul 23 13:48:53 2020 +0100
      
          Remove log entry
      
      commit 8fe77f16f408d3fe2ac8b2b07e5ff2cafa18baa1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jul 23 13:21:59 2020 +0100
      
          Update classpath
      
      commit feaa7bf342c75353fb338906606add2c7a4d9db7
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Jul 22 18:02:02 2020 +0100
      
          Fixed code smells. Updated query for retrieving models with molecular data. Fixed minor issues
      
      commit fba12f7541e37e0ccd0cc8ce19884f5c5a2184bf
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 22 14:43:41 2020 +0100
      
          Remove unused imports
      
      commit e55a1cacacfbc086b85a9a5d5364b188cde56fc6
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 22 14:37:08 2020 +0100
      
          Add missing method
      
      commit 00185b913ba401bb743ee76e01c079659a78df46
      Merge: 1d1b1924c 299f6958f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 22 14:19:46 2020 +0100
      
          Merge branch 'upgrade-spring-boot-2.0.9' into dev-upgrade-test
      
          # Conflicts:
          #	data-services/src/main/java/org/pdxfinder/services/UtilityService.java
          #	indexer/src/main/java/org/pdxfinder/dataloaders/updog/Updog.java
      
      commit 1b107904af2c2f6755c12944c38449ad65045834
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Jul 21 15:29:18 2020 +0100
      
          Fixed code smells. Removed several class variables in UniversalDataExtractionUtilities
      
      commit 17e2407835d34f0ddab5665f1a9807a2aa5b967e
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Jul 21 14:30:05 2020 +0100
      
          Wrote and tested ExporterTemplates harmonized/unharmonized toggle
      
      commit c3262e046fcc18c60ba69357a138e84956a58383
      Merge: 745106171 1d1b1924c
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Jul 20 14:36:32 2020 +0100
      
          Merge branch 'dev' into xdog-refactor
      
      commit 7451061712bd7f32204e151c15a6e536eb72e8e3
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Jul 20 14:34:42 2020 +0100
      
          Updated CbpTransformer tests
      
      commit 5f7aab874aa61d74afba223db1d63722092c45e1
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Jul 20 13:48:54 2020 +0100
      
          Added tests for UniversalDataExporter to increase coverage. Fixed failing tests.
      
      commit 5161aa9c6af3cc7afc9f62df73dbf7881faa7495
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Jul 17 17:04:52 2020 +0100
      
          Finnished changing code base. Test completed for both utilites. Start writing tests for UniversalDataExporter
      
      commit d568b8459f653cd577e52b8fd496b3cbecb94b35
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Jul 16 17:50:59 2020 +0100
      
          Added new class to utilize the Xdog utilities and allow for saving of Omic data by batch
      
          Because
          *Omic data is two large to save in memory all at once
          *Utilities needed to be separated from higher logic
      
          Made extensive changes to UniversalDataExtractionUtilities and UniversalDataWriterUtilities. The aim is to both be extensible to the future code base while allowing for increased functionality on the Xdog.
          the Cbioportal transform used the UniversalDataWriterUtilities to save data. The way omic data is read and saved was change throughout extensively.
      
      commit 9a356caf8af55cbe8f4fed32bf53bec18f414f15
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Jul 15 12:05:40 2020 -0600
      
          Refactored extractOmicdata type functions in UniversalDataExtractor to be more extendable, behavior driven, and robust
      
      commit b9eede57c663ba0bb0ecc066fddcfaf834fa313f
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Jul 15 11:51:43 2020 -0600
      
          Merge branch 'dev' into xdog-refactor
      
          # Conflicts:
          #	indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
          #	web/src/main/resources/templates/details.html
      
      commit 97fd099c9bb7df9332c9c49c178b19aa891f087e
      Merge: e95e8a424 70a33a187
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Jul 13 12:27:14 2020 -0600
      
          Merge branch 'dev' into xdog-refactor
      
          # Conflicts:
          #	indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
          #	web/src/main/resources/templates/details.html
      
      commit 1d1b1924c0d91dc8c7c508cb6a72b60411576861
      Merge: 70a33a187 4b0654334
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Jul 13 14:22:16 2020 +0100
      
          Merge pull request #168 from PDXFinder/cli-extension
      
          Add mapping exporter to cli
      
      commit 4b06543345739e58cb23b606dd5ef57185f33569
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Sun Jul 5 11:43:19 2020 +0100
      
          Add mapping exporter to cli
      
      commit 299f6958f006235c5ad537433772e6315df57939
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jul 2 00:13:18 2020 +0100
      
          Tidy up application properties
      
      commit 895c798d063e48f184d36675fe6c3729fbb5bb90
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jul 1 23:54:14 2020 +0100
      
          Send validation logs to html report
      
      commit 61191a8db49d4a28922915f77dbf17b88fe17db2
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 30 20:54:30 2020 +0100
      
          Separate datasource configuration
      
      commit d6b49042cf36ed8f223adc9a421a273b0103d6f3
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 30 18:21:28 2020 +0100
      
          Remove gson dependency
      
      commit 19113a07b013fdb80893eb2ea3feac38efb03608
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 30 13:39:03 2020 +0100
      
          Use com.github.open-json
      
          To avoid com.json classpath collisions and avid non-Evil licence issues
      
      commit ccad5bbec1322ebe5ce74283b93a01b176f405fc
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 30 11:54:40 2020 +0100
      
          Clean up console logging and programatically define non web components
      
      commit 44b5dfda3ce9593d4aada5d088a794f4c40cfb61
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 29 20:10:20 2020 +0100
      
          Tidy up startup logging
      
      commit dd68a2d2624089b8b33f69270719599727183997
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jun 26 16:42:45 2020 +0100
      
          Fix failing tests and organise module dependencies
      
      commit d090ac6cd480958dfe0e68ff725f794427bda2c9
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jun 25 19:20:46 2020 +0100
      
          Fix H2 datasource configuration
      
      commit 43ed7a914e86a222dde1c363283e8e94d37fecf2
      Merge: 985cd0fa8 44019c81b
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Jun 25 16:45:30 2020 +0100
      
          Merge pull request #167 from PDXFinder/beta
      
          Beta
      
      commit 44019c81bd84763a961c753e2d4e20d547b82efa
      Merge: e85ca8801 dc116ec8b
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Jun 25 14:00:18 2020 +0100
      
          Merge pull request #166 from PDXFinder/beta-release
      
          Beta release
      
      commit dc116ec8b76fe035837324cec8c05af10e72448c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 25 12:40:45 2020 +0100
      
          Add export supporting methods
      
      commit e33e6fd0dafb59ec306e2946bca3e88ef9bd3a9f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 25 12:40:16 2020 +0100
      
          Add missing queries
      
      commit 624ae6091385d40ee3511577f0bba9d0eef7dad1
      Merge: e85ca8801 70a33a187
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 25 12:31:15 2020 +0100
      
          Merge branch 'dev' into beta-release
      
          # Conflicts:
          #	data-model/src/main/java/org/pdxfinder/graph/dao/EngraftmentMaterial.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/EngraftmentSite.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/EngraftmentType.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/Group.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/HostStrain.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/Marker.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/ModelCreation.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/MolecularCharacterization.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/Patient.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/Sample.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/Specimen.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/Tissue.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentProtocol.java
          #	data-model/src/main/java/org/pdxfinder/graph/dao/TumorType.java
          #	data-model/src/main/java/org/pdxfinder/graph/repositories/ModelCreationRepository.java
          #	data-model/src/test/java/org/pdxfinder/integration/PatientIntegrationTest.java
          #	data-services/pom.xml
          #	indexer/pom.xml
          #	indexer/src/main/java/org/pdxfinder/dataexport/ModelDetails.java
          #	indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
          #	indexer/src/main/java/org/pdxfinder/envload/LoadNCIT.java
          #	indexer/src/main/java/org/pdxfinder/postload/SetDataVisibility.java
          #	indexer/src/test/java/org/pdxfinder/dataexport/DataExportTest.java
      
      commit 70a33a187a73d8e25f9b6362fa59e0104af65363
      Merge: d91a59559 446a4a89a
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Jun 25 12:17:15 2020 +0100
      
          Merge pull request #165 from NatConte/patch-1
      
          Update README.md
      
      commit 446a4a89af4dd46cf5bacc27dfb58f758ad7bf5d
      Author: nathalie conte <nconte@ebi.ac.uk>
      Date:   Thu Jun 25 12:11:10 2020 +0100
      
          Update README.md
      
      commit d91a595596975b0893d0bd2ced38bb102cdeab98
      Merge: cda88b8cc bf89d7d57
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Jun 25 11:28:08 2020 +0100
      
          Merge pull request #164 from PDXFinder/fix-molecular-data-download
      
          Fix molecular data download
      
      commit bf89d7d57dec5e021f83fc91bb62ed8a9287d8c7
      Merge: 4a54e7a5a ca3df4847
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 25 11:24:24 2020 +0100
      
          Merge branch 'fix-molecular-data-download' of https://github.com/PDXFinder/pdxfinder into fix-molecular-data-download
      
      commit 4a54e7a5a8c20f0e87f286d7a4ac504930bb6d86
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 25 11:23:22 2020 +0100
      
          Enhance molecular download button tpo escape samples having no dataset
      
      commit cda88b8ccf3abbb9a017e505d7a75f14c0b5839e
      Merge: acf56a17a ca3df4847
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Wed Jun 24 16:46:46 2020 +0100
      
          Merge pull request #163 from PDXFinder/fix-molecular-data-download
      
          Fix molecular data download
      
      commit ca3df4847c5dc7bec0514a4cff5f8a39fd92a3b5
      Merge: 5d312c3c3 acf56a17a
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Wed Jun 24 15:25:30 2020 +0100
      
          Merge branch 'dev' into fix-molecular-data-download
      
      commit acf56a17a8292523798b54c0c39b694c703d1a6d
      Merge: d1e8a657c 8d8a077cb
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Jun 24 15:14:20 2020 +0100
      
          Merge pull request #162 from PDXFinder/pediatric-filter-fix
      
          Missing space, boy!
      
      commit 8d8a077cbc49d6873864fb494ee6d301b5694b2f
      Merge: 2f6a9b1c2 d1e8a657c
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Jun 24 15:07:04 2020 +0100
      
          Merge branch 'dev' into pediatric-filter-fix
      
      commit d1e8a657ce35caa1757ce21ef94c34f7f29bf2eb
      Merge: c1affae63 b2c1dfa41
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Wed Jun 24 15:03:29 2020 +0100
      
          Merge pull request #161 from PDXFinder/remove-providers-menu
      
          Remove providers menu & fix UI bugs
      
      commit 5d312c3c35ae27e111916ffa5cbdd8adfc8df8f2
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 24 14:59:28 2020 +0100
      
          remove unused code segment
      
      commit 2f6a9b1c2c8830a2519aee9fe084293c25dde6e3
      Merge: 8a9701544 c1affae63
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Jun 24 14:56:17 2020 +0100
      
          Merge branch 'dev' into pediatric-filter-fix
      
      commit 8a97015448539653f4b26f031c84c67a6c1b63d8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 24 14:54:49 2020 +0100
      
          Missing space, boy!
      
      commit b2c1dfa4162833f2eaf29ddebdfff6692249079b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 24 14:29:57 2020 +0100
      
          create break points and media rule for the expanding text field bug
      
      commit 60fdc6fd495311d06032f9a836e967bcaa817b23
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 24 09:03:44 2020 +0100
      
          remove links to data providers from top menu
      
      commit 8ccc365dc729ba190b493c0e2f2bccfb8e120270
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 24 08:50:23 2020 +0100
      
          remove spaces
      
      commit c1affae63ebdd2dc7364e16975b26c3c44afd72b
      Merge: 20cf97695 e6d2fa9a1
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Jun 23 18:16:59 2020 +0100
      
          Merge pull request #159 from PDXFinder/pediatric-filter-fix
      
          Pediatric filter fix
      
      commit e6d2fa9a116c61c9b79b460161431682272a5c12
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 23 15:30:19 2020 +0100
      
          Add LIH provider
      
      commit 3e019869e3ae5a093dd74b8f685d6962472cb61e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 23 14:43:15 2020 +0100
      
          Fix treatment duration and dose string
      
      commit 78d96918da8b15622ba67593f9f7fc12b00cbbdd
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 23 14:24:32 2020 +0100
      
          Fix neo4j dependency version setting
      
      commit 0ac0c32fcc65f8fd7522fc3d60acfcc393a46d0b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 23 13:49:32 2020 +0100
      
          Remove month reference from age value before calculating age
      
      commit e56644d18008e731da90367b188c9d95ebad3e3b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 22 23:20:22 2020 +0100
      
          Fix molecular data download on details page
      
      commit 522516cc3e7c2f472d394d4f2a3dec6f1902c3fa
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 22 23:18:35 2020 +0100
      
          Reference urls are not required in csv, so sanitize molecular data row for csv export
      
      commit 2db3f83638f59905cff04e3a5940f4b7459d1bbe
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 22 21:54:14 2020 +0100
      
          Add new helpers for serializing csv data for response header
      
      commit 638a080c443884b8f0408adc8b0a80f5bafebcd7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 22 21:53:27 2020 +0100
      
          refactor detail service replace old molchar data csv download methods
      
      commit 20cf97695dca963c6f37f924260e8641689fcc0e
      Merge: c05ab896d 407f629ec
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Jun 22 18:26:42 2020 +0100
      
          Merge pull request #158 from PDXFinder/contact-fix
      
          Do not allow empty contacts to be included
      
      commit 407f629ecd527fd8b00109a89cad5bf8444cca63
      Merge: 20624f34d c05ab896d
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Jun 22 18:08:35 2020 +0100
      
          Merge branch 'dev' into contact-fix
      
      commit c05ab896db8f70dba087e077f711b78f1871230b
      Merge: ac40643c7 9cdb36eaf
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Jun 22 17:45:18 2020 +0100
      
          Merge pull request #157 from PDXFinder/jaxload-fix
      
          Jaxload fix
      
      commit 9cdb36eaf9387e80890e40c721bbbf9e16adb309
      Merge: 946ad2a71 ac40643c7
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Jun 22 17:33:09 2020 +0100
      
          Merge branch 'dev' into jaxload-fix
      
      commit 20624f34d7cb866d7f86172f3b19b52f84c08dfc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jun 22 12:00:24 2020 +0100
      
          Do not allow empty contacts to be included
      
      commit 6135779a974f10bf6e54cffa9ac96574653805d1
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jun 19 12:09:07 2020 +0100
      
          Deduplicate embedded driver dependency, update logging for fixing exception
      
      commit ac40643c7e588b673219bfc9a3cf48a7d90f9f34
      Merge: a4517b2b2 87ad6ee19
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Jun 19 10:39:45 2020 +0100
      
          Merge pull request #156 from PDXFinder/exportedPdmrMods
      
          Removed PDMR-XDOG from data providers. Removed call to PDMR customer …
      
      commit 87ad6ee19cf4af655681a75e0c0938d6cc78e556
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Jun 18 21:55:03 2020 -0600
      
          Removed PDMR-XDOG from data providers. Removed call to PDMR customer loader from cmdline.
      
          Because
          * PDMR data has been exported to template
      
          Also, removed the PDMR special case Thyme Leaf behavior.
      
      commit e44156fc5462e12726a26e4f6a3bf2be3493908c
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Jun 18 21:25:34 2020 -0600
      
          Removed PDMR-XDOG from data providers. Removed call to PDMR customer loader from cmdline.
      
          Because
          * PDMR data has been exported to template
      
          Also, removed the PDMR special case Thyme Leaf behavior.
      
      commit 946ad2a71cacf7c75b5025eaf275cd33954c4d14
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 18 15:26:56 2020 +0100
      
          Simplify methods for readability
      
      commit 6bf8002bfc953b41d374427cbca0a7a671113e89
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 18 15:13:51 2020 +0100
      
          Revert changes in old omic
      
      commit 6ef59ea674de6056663ba351b73eb21ca33bc29e
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jun 17 15:21:46 2020 +0100
      
          Explicitly depend on embedded drive for database config
      
      commit 8df8896127f6c5f044f3b6fe006a5e8cea5742b2
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 16 15:30:15 2020 +0100
      
          Update database configuration to use new builders
      
      commit a5f3ebfe0657f3ec1d3a021e715fb0dbbc2bfbd4
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 16 15:29:43 2020 +0100
      
          Use new thymeleaf template engine and tidy
      
      commit 73774986f66b8d91fec8796467b7e50ea979eff4
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 16 15:28:47 2020 +0100
      
          Use org.json instead of org.neo4j.ogm.json
      
      commit 72fc1976ca963fe9ef31bd5b391dd95b63de999b
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 16 15:26:22 2020 +0100
      
          Fix updated repository methods
      
      commit d4261dbe025b2838ceaf30291e1ef80b5d4ae786
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 16 13:41:18 2020 +0100
      
          Use new template engine for Thymeleaf
      
      commit 6121c3409950e4923a43e9084150ba4b51b062f5
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 16 11:46:25 2020 +0100
      
          Use org.json instead of the removed org.neo4j.ogm.json
      
      commit a4517b2b264aae2d9c9b17bbe3d34b74ad5f6069
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jun 12 10:49:21 2020 +0100
      
          Validation error limit (#155)
      
          * Set limit
          * Log errors with limit
          * Add tests
      
      commit 6e77c6880f3e1b104a893312f64c1ba39f0fe581
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jun 11 20:42:49 2020 +0100
      
          Add spring-boot-starter-web dependency to data-services
      
      commit 5973b0d4153693a6bcaaaff45b2490a7d47fa11c
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jun 11 20:41:55 2020 +0100
      
          Construct database OGM configuration using builders
      
      commit 2d2078577eaa5f58e25d0831f9fbc3d16f79eb72
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jun 11 20:40:58 2020 +0100
      
          Bump Spring Boot version to 2.0.9
      
      commit 67706d3b90468c06a81ec3f9abff188e41385304
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jun 11 18:23:52 2020 +0100
      
          Clean up application properties
      
      commit d14539fd4dfd5475b944cf1e986471fde4ecd9e7
      Merge: 0c1d7a7b0 337f1b588
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Jun 11 14:27:39 2020 +0100
      
          Merge pull request #152 from PDXFinder/release-2020-04
      
          Release 2020 04
      
      commit 337f1b588ae4e9b2c8c65d03500793880bc82610
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 11 09:45:26 2020 +0100
      
          Fix broken Test
      
      commit 32b09f6576f12e39e5c5ba7f694af2a7b38c1596
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 11 09:41:45 2020 +0100
      
          undo rename
      
      commit 8cf16ad399e3a0ffa5d76a33d7b163a089340b19
      Merge: 518e80578 428f88772
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 11 09:31:11 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 518e80578c1b665f029b8ef2e623ba1ddcdb83f4
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 11 01:14:24 2020 +0100
      
          Add feature to retrieve variant data from Kubernetes and link required amino acid to civicdb
      
      commit d928ed2e1cd1395196caa8d2a3762e6b6e4b1907
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 11 01:12:44 2020 +0100
      
          Add feature to generate url and link to open cravat
      
      commit 23535cf7f674273849fea5db0200c8e2d47bf694
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jun 10 15:43:42 2020 +0100
      
          Remove unecessary files
      
      commit 96143bb8dd458b7b80cf3dab558f8ccdbaa27ce0
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jun 10 15:41:24 2020 +0100
      
          Remove uncessary comments and dependency entries
      
      commit 428f887722d89456b91a7db23d14e82f1866c1ce
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 10 15:22:41 2020 +0100
      
          Add VHIO-PC
      
      commit 794bc5241044b24c89a50c8059a2c99ffb56330c
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 9 19:06:41 2020 +0100
      
          Upgrade to Spring Boot 1.5.22
      
      commit 29245cf1ee9c4c3cc6e2252cc233fe3dd68c5de4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 9 18:32:50 2020 +0100
      
          Remove log entry
      
      commit ad5be2950ed10ee7cf8693902465be7e71c26590
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 9 18:32:25 2020 +0100
      
          Define method for security reasons
      
      commit ddae7c636997a5106ca25f1f3bf3d2bd05360ba9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 9 18:19:12 2020 +0100
      
          Test disease and treatment terms separately
      
      commit 1a3dd5dabe96db0ae16467c17e1105aa1c5a71cc
      Merge: 65437a7c8 6ab35e3b9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 9 18:09:16 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 65437a7c8cced3ea45627ba2999ebf62aaa8ca25
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 9 18:09:08 2020 +0100
      
          Enable Ontolia
      
      commit 11e61cad09d36c373facb186f12935de3100534d
      Merge: 65b9d1480 6ab35e3b9
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jun 9 12:09:59 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 6ab35e3b9421c6e80b3057b5c263f0c39fa78902
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 9 11:55:01 2020 +0100
      
          Add table creation from string
      
      commit 65b9d1480343867d6d61b740ac71fd9fbecfdb38
      Merge: b3a364379 bce71cea3
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jun 9 11:18:11 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit b3a3643791211e18a27b582db1ecbf91a90722fd
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jun 9 10:31:06 2020 +0100
      
          dev server config fixed, restore restTemplate
      
      commit bce71cea31f8e11b6064192918fadc692c50eb5b
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jun 5 10:43:33 2020 +0100
      
          Add assertions for null tests
      
      commit 6ffdc31bc3e75c3aaf232e424b4f2621b234b180
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jun 5 10:40:01 2020 +0100
      
          Add tests for null tables
      
      commit ca16eaa5e3283ff7d9ce44ec860554925d851885
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jun 5 10:12:29 2020 +0100
      
          Add UMCG to test
      
      commit 59e0b229c362ad69ba80e5df9e9ef4aaa2b26525
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jun 5 10:06:21 2020 +0100
      
          Do not validate missing tables
      
      commit eef8487c6bd92bb7b2db0db6442471386b1c9b33
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jun 5 08:47:51 2020 +0100
      
          Add UMCG dataprovider
      
      commit 957a878893ac23ef09a02a44866061c9c9d34f15
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 4 17:01:00 2020 +0100
      
          replace restTemplate with oktaHttp because it doesn't time out on server
      
      commit 667288d9f7d482ca3e6fa59149099dd518aa604d
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 4 15:27:06 2020 +0100
      
          increase restTemplate connection timeout configuration
      
      commit 0db344ffd7188fb1356c0491e987b2f0933e90f7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 4 14:45:27 2020 +0100
      
          replace restTemplate with okhttpClient
      
      commit 61f049842bbecef22aa77a5515b2d8d0bb4ee40a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 4 14:16:34 2020 +0100
      
          temporary k8 test call on impc gentar from pdxfinder
      
      commit 79586f7295ea1dc26f907a81da50608741f7eefe
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 4 11:10:23 2020 +0100
      
          temporary disable kubernetes linking
      
      commit b61f104a9d3482def9ffd2cd9b35b396ba46bf7f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 4 10:32:47 2020 +0100
      
          temporary disable kubernetes linking
      
      commit e72a9ec6d6f7760c65bc9319daeaa3611b506634
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 4 10:03:51 2020 +0100
      
          variant type object column should be nullable, for some molchar data types
      
      commit af86214078bee9b97011871f2688fd22e0238e6c
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 4 04:24:14 2020 +0100
      
          Add feature to return cosmic reference db urls
      
      commit aa6648c71e51794059f523b4082b95fc09a912ac
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 4 02:18:42 2020 +0100
      
          change variant type column label
      
      commit 03cda47f45f9482766537dd5d8e1baaae45a0677
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 3 17:28:01 2020 +0100
      
          fixing connection refused error
      
      commit 82758007a87e833a40a761dd2987ed22f33c18b8
      Merge: c0016da64 c92f4f3bd
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 3 16:24:26 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit c0016da64b784b343c3b63c278b3a75c94600c1b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 3 16:24:18 2020 +0100
      
          temporary display full exception on server for failing remote call
      
      commit c92f4f3bd0c1d0438ac2a192a5952390ed03f395
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 3 16:22:57 2020 +0100
      
          Fix exception logging
      
      commit 6bd2e801bc4d7d1db77ef9013387e1234ac31d46
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 3 16:03:46 2020 +0100
      
          Fix sonarqube flagged bugs
      
      commit f5672c812a287390757fc9b97df1090357d30672
      Merge: 08072f0e5 cac417ee9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 3 15:39:41 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 08072f0e5c64211acfa87bb750e05e2e8a39c6a7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 3 15:39:25 2020 +0100
      
          Add drug dosing counter projection
      
      commit cac417ee9f2b250c6edee40dd147b5218ba8cdf1
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 3 13:44:27 2020 +0100
      
          Add fault tolerance to PDXFinder -> PDx-gun interaction
      
      commit 86cf00389910827a64cff0e3ea4543645b337a01
      Merge: 9254c9355 27b363abd
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Jun 3 10:27:08 2020 +0100
      
          Merge pull request #153 from PDXFinder/nullPointerFix
      
          Added two null checks to prevent NullPointerExceptions.
      
      commit 9254c93551b6529b34e18404b2617c9afe6d4726
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 2 19:44:12 2020 +0100
      
          Add Text column type
      
      commit a4c600a3f89af7a3cf4e2d0d62741fecd65aea63
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 2 16:32:33 2020 +0100
      
          Log validation errors in debug
      
      commit 62a042de2ccbbe097a251f1cfab0d65b1bddde98
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 2 16:25:59 2020 +0100
      
          Fix month string
      
      commit 27b363abd77d2facae99be13e6a7acd765cecf1a
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Jun 2 16:15:16 2020 +0100
      
          Added two null checks to prevent NullPointerExceptions.
      
          Because
          *The front end was hanging on NullPointerExceptions
      
          Added a null check in getAuthorString that will return a blank string if the value is null.  Added a null check to setRawDataLabelAndLink to return a blank string if RawDataLabel value is null.
      
      commit f6e536a3f4577e49e68da0ce4fab1b6a07a51f20
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 2 14:53:37 2020 +0100
      
          Add paediatric age calculation and bin
      
      commit d98d034c7196c56795733cd476374fdee1659bff
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 2 14:52:33 2020 +0100
      
          Disable tests temporarily
      
      commit c25cd409fa3c7c418a76aaa63fcb66ea57625fce
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jun 2 09:18:59 2020 +0100
      
          Re-enable relation validation and clean up ontology logging
      
      commit 7576fd3dc7e7331edcec74b1ca143ed1a4c9507e
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 1 23:13:32 2020 +0100
      
          disable setRawDataLabelAndLink in Details Service which is breaking the details page
      
      commit efb01230e0be699b801aecaeaf9d6c6e5c9883c4
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 1 22:37:30 2020 +0100
      
          update Details Service to retrieve reference db data
      
      commit 32e52abb7771ee4d2b8543604596668cb32bfd06
      Merge: f6a1b2703 15f915575
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 1 22:31:09 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
           Conflicts:
          	data-services/src/main/java/org/pdxfinder/services/DetailsService.java
      
      commit f6a1b270374286f0a839ed8a15b040e2993d821a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 1 22:25:54 2020 +0100
      
          Link hgnc to reference datbases on details page
      
      commit de7270aa17ddeaaaa65c33226ee8c6bb0f782505
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 1 19:33:50 2020 +0100
      
          Change Hgnc data structure from string to MarkerData Object
      
      commit 4b06123948ede75796fcf925b7eb15d8bd196f2f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 1 19:30:23 2020 +0100
      
          Add back end service to retrieve reference data
      
      commit 288391ec60c012954dbbb4246d7db5df5f203e37
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 1 19:25:44 2020 +0100
      
          Add dto to consume reference database data
      
      commit 15f91557565f28461d1ef4fdea900e209ccd79ef
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 1 19:15:27 2020 +0100
      
          Remove -k parameter and clean createMarkers
      
      commit bed7fdd27026cd026ff7643e6fa2db68eb1aedaf
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 1 18:23:10 2020 +0100
      
          Update readme
      
      commit 53cab91b413ae622a94995337f7cfa0327395939
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 1 18:18:11 2020 +0100
      
          Update readme
      
      commit b3148d238e52ea52854eb5e6b2d3ca4f6005589d
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 1 17:15:02 2020 +0100
      
          Fix unit tests
      
      commit a84ee0b9e3616f6e2113eb00a7922275c93ec530
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jun 1 16:54:48 2020 +0100
      
          Add graphQl query builder
      
      commit c76217e028850f30ecf173bf21be9f9d2cda319c
      Merge: 4d74731db 4ff8490e0
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 1 16:33:37 2020 +0100
      
          Merge branch 'release-2020-04' of github.com:PDXFinder/pdxfinder into release-2020-04
      
      commit 4d74731dbe5a4592343b663b7b8aa9c3b20a3d94
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 1 16:33:26 2020 +0100
      
          Refactor LoadMarkers, reduce load time by using saveAllMarkers()
      
      commit 4ff8490e024637b60770ac8e075b5864e8a9ac1a
      Merge: d0873fde6 08cb47a33
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jun 1 14:55:59 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit d0873fde6639c661a3f141c7c99690361b4388ea
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jun 1 14:55:51 2020 +0100
      
          Refactor old omic loader to merge samples at the same passage
      
      commit 08cb47a33c0ba65d5d2963feeeeaf9c46957fa51
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 1 12:39:39 2020 +0100
      
          Initialise Publication resultList correctly
      
      commit f18eeea5cacf4780c798c24e773f8d2b1063ee31
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 1 11:55:17 2020 +0100
      
          Refactor marker creation
      
      commit 9827060b2ff1d2df7a849858a406f4632425bacf
      Merge: 6b9afb306 7d4238e3f
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jun 1 11:29:35 2020 +0100
      
          Merge branch 'release-2020-04' of github.com:PDXFinder/pdxfinder into release-2020-04
      
      commit 7d4238e3f46319971624f4ef6beff5443750b6cf
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Jun 1 09:46:19 2020 +0100
      
          Created a more robust approach to linking Raw Data Urls
      
          Because
          *Multiple accession types are available for linking to different resources
          *The template contain heaps and heap of rubbish in this column that needs filtering
      
          Created the formatAccesionsToURL function in the DomainObjectCreator. This function will proccess a select few accession with the ENA, EGA, and GEO returning a built URL and the original accession. If not, it will return and empty string to avoid filling the pdxFinder with rubbish. An additional variable on MolecularDataEntryDTO was created to store the link and is then retrieved by Thyme Leaf to generated the front end link. An empty string "" in the raw data url will cause a "Not Available to show up on the front end"
      
      commit 6b9afb306568134ac3d7bfcb7869e55b206b3422
      Merge: 9fa74be69 93b4f6235
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 29 15:23:13 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 9fa74be695ae60b53c3615da7efd3897324c982f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 29 15:22:54 2020 +0100
      
          Add Illumina HGEA Exp
      
      commit 93b4f623589c697cd6e82007cd0028164f046745
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu May 28 21:22:03 2020 +0100
      
          re-organized  patient tab on details page
      
      commit 6fae884a6280b85be18f24a7af488a6a0e6264c0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu May 28 20:41:45 2020 +0100
      
          Autowire RestTemplate
      
      commit e85cc123d0107c8e8a41e2d375f858fb255fd36a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu May 28 20:41:19 2020 +0100
      
          Add configuration to data-services
      
      commit 167dc16206c2d540c6facd8fd0c575f9e73da256
      Merge: edeccff73 1c1202e77
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu May 28 20:03:38 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit edeccff730b0825523c4d6f53cb24bde7c3a2f5b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu May 28 20:03:27 2020 +0100
      
          Add publications to models
      
      commit 1c1202e771febd38ab97b5452f924d3941b00915
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu May 28 19:57:55 2020 +0100
      
          Fix DataProvider Unit test for SJCRH
      
      commit 654a8e15544afed30b0e1d95ba5faa3f55f2e632
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu May 28 19:52:56 2020 +0100
      
          Create project group only if name is not blank
      
      commit 517f025e289f9f78f22c633c46916b36f47c336c
      Merge: e42ac8563 d055b1c08
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu May 28 19:52:55 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit e42ac8563a7fc45007fdde9a92c3ae04ce63e611
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu May 28 19:52:06 2020 +0100
      
          Fix DataUrl Unit test
      
      commit d055b1c08d22f201fbb283eb35fb2c8693840ee1
      Merge: c527b3845 e4287181f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu May 28 19:46:23 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit c527b38454b7a676d602a1bf51f4452d709aa9c3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu May 28 19:46:15 2020 +0100
      
          Do not throw exception on missing patient
      
      commit e4287181f7ebb8d1fa2de9febc35dd2a22bb926e
      Merge: 66062ca32 1263d9af1
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu May 28 19:32:46 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 66062ca32e9f69777416d0d9026d77f3cfc047a7
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu May 28 19:32:26 2020 +0100
      
          Add UI for publication feature
      
      commit ab41f9b40e1907419b8c9d45cb4b57c20367a12e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu May 28 19:25:30 2020 +0100
      
          Add SJCRH dataset
      
      commit 9d0fe327d0e9d7cf79d1ab5deed59b21f1239212
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu May 28 15:10:51 2020 +0100
      
          Configure restTemplate for UnitTest
      
      commit 5f3c55282646ea571e7fe3c55b60f5f3a53bba17
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu May 28 15:06:29 2020 +0100
      
          Fix publication abstract retrieval
      
      commit 9fdb8cfb857345cee1148456be4b06decb3104d0
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu May 28 14:31:41 2020 +0100
      
          Retrieve publication from europepmc
      
      commit e52ff08bb6d8157e33ae6892aed88df47e8d29b8
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu May 28 14:26:27 2020 +0100
      
          Add publicationService unit test
      
      commit a0b77a6cdd099ab2218ab405a719f604407c70a1
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu May 28 13:15:14 2020 +0100
      
          Added restTemplate Bean
      
      commit 1453dd42cc7725611d95b85608fc475c32ef99c1
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu May 28 13:06:36 2020 +0100
      
          Add europe-pmc publication dto
      
      commit 1263d9af10de9176c37cd0999aed0780aee7fd46
      Merge: 7f9f3e335 7aaa8d055
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu May 28 12:55:15 2020 +0100
      
          Merge branch 'release-2020-04' of github.com:PDXFinder/pdxfinder into release-2020-04
      
      commit 7f9f3e33595ccd3c26a3dbc5ed660a76444f94c6
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu May 28 12:55:09 2020 +0100
      
          Add getCellAsText() for conversion of different column types to strings
      
      commit 7aaa8d055f110c03b7f2f7e525d6996b807abf76
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 27 20:07:40 2020 +0100
      
          Fix sonarqube flagged issues
      
      commit 03cc6b7a336b397817f2d8906a9ae0003aae0da8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 27 18:43:47 2020 +0100
      
          Do not print out molchar linking rules
      
      commit f291828fc00573f2dc129726de26bd97c1e8678f
      Merge: 7bcf22c56 55cf09dc3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 27 18:34:17 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 7bcf22c5679c1d759bc9dac8bf6cd0936f7c634a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 27 18:34:10 2020 +0100
      
          Add a check to platform urls
      
      commit 55cf09dc39d2a01775c70b923c8ff6b7b8e0d6eb
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed May 27 17:23:52 2020 +0100
      
          Remove redundant enum comments
      
      commit 1e02cf8297e1da83e6f331842ca3fda5a874d6bb
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed May 27 17:14:04 2020 +0100
      
          Refactor isMarkerSymbolNullOrEmpty()
      
      commit 176bc5576a4ae3d0255aef49b4bc5dd6bdff5d4c
      Merge: 86df5d10f 2175f215e
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed May 27 17:13:04 2020 +0100
      
          Merge branch 'release-2020-04' of github.com:PDXFinder/pdxfinder into release-2020-04
      
      commit 86df5d10f3b443a44ab4d5c5644cf862be24db45
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed May 27 17:05:26 2020 +0100
      
          Remove commented code
      
      commit 2175f215e08f7cd8b650e736117fe9fd8795ebed
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 27 16:26:31 2020 +0100
      
          Remove special characters when comparing platforms
      
      commit 7b676058ffca8238fac9a75a9f9f33aa599c1869
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 27 16:25:56 2020 +0100
      
          Persist molchars with data in first cycle, persist all remaining in last
      
      commit f36a51131caca107af351d4fcbc9ab2595b16cea
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 27 15:37:26 2020 +0100
      
          Use stringutils empty check
      
      commit 01ac17a12eaa7f5d1db7d060ebd195e3a756595a
      Merge: a6f6dd89f 6c92b2087
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed May 27 12:40:06 2020 +0100
      
          Merge pull request #151 from PDXFinder/devTestFix
      
          fixed failing test given_DataProviderEnumListCount_EnsureListIntegrit…
      
      commit a6f6dd89f405cce783dc9d60401877b0732020ed
      Merge: 5b751772a 1a4ebe785
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed May 27 12:39:25 2020 +0100
      
          Merge branch 'release-2020-04' of github.com:PDXFinder/pdxfinder into release-2020-04
      
      commit 5b751772aaa8c863352e030c0b17140cce201b69
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed May 27 12:36:28 2020 +0100
      
          Tidy up UPDOG
      
      commit 6c92b2087d846670ef2c092e276207e54fcb2896
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed May 27 12:30:09 2020 +0100
      
          fixed failing test given_DataProviderEnumListCount_EnsureListIntegrity() by removing
      
      commit 1a4ebe785c3b2e76e82af267dc3fb461a906e865
      Merge: 9fd5dd612 b028b6d36
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed May 27 12:13:13 2020 +0100
      
          Merge pull request #150 from PDXFinder/RawDataUrlAndXdogPatch
      
          Raw data url and xdog patch
      
      commit b028b6d36af2bae85d69effbc7a7b9721b7171ad
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed May 27 12:12:35 2020 +0100
      
          Update Validator.java
      
      commit 7936514b4b35d5c2eb9c31596757c217cd8b60ff
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed May 27 12:03:59 2020 +0100
      
          Added JAX-XDOG provider. Added check for 'Not Available' in ThymeLeaf
      
      commit 9fd5dd61264809af6eba89ca3f48e2828d24ad84
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 27 11:01:39 2020 +0100
      
          Null check for model in expression data
      
      commit 33128b3a79a5c58630848fb929af06344f6ab6e7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 27 09:38:38 2020 +0100
      
          Null check for model
      
      commit a4e766dea8d76d447f06f13a0c2233087cc74472
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue May 26 18:57:39 2020 +0100
      
          Added test to initOmic in Xdog
      
      commit 1d02094d491cba5993d39b45c0af9e324db8f90c
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue May 26 12:28:56 2020 +0100
      
          Added test to the domainObjectcreator to test for bug
      
          Because
          * Null pointer existed with the new Raw Data URL
          * Sample Id inconsistency existed
      
          Added behavior to overwrite sourceSampleId if blank here. Tests for lack of overwrite.
      
      commit dad61ef08b01b0135bb79dd11260ed86e363f541
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri May 22 19:09:41 2020 +0100
      
          Updated UniversalDataExtractor to take the exportSheets object
      
          Because
          *The old xDog was heavily coupled to data structures
      
          init() on the UniversalDataExtractor now initializes sheets from an passed exportSheets object. This includes Group information.
      
      commit e95e8a424846c332c6da5b78308e99ac4f3b786e
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri May 22 11:44:52 2020 +0100
      
          Updated UniversalDataExtractor to take the exportSheets object
      
          Because
          *The old xDog was heavily coupled to data structures
      
          init() on the UniversalDataExtractor now initializes sheets from an passed exportSheets object. This includes Group information.
      
      commit c0e4908bfd2db336be51f12b380a15a3de516f8c
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri May 22 09:52:19 2020 +0100
      
          Made changes to tests to accommodate a new provider
      
      commit 7b5bb642d08e31e4cb67362366c588d604fd772f
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri May 22 09:15:25 2020 +0100
      
          Thyme Leaf Modifications to display RawDataURl on front end
      
      commit 9644e81c8bf0b3cb3b46ba0e1d40aca731b986a2
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri May 22 09:11:29 2020 +0100
      
          Not working refactoring changes.
      
      commit d8ee8bbd113b3646fa655ea30b4db05d03ed5c48
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed May 20 11:40:37 2020 +0100
      
          Thyme Leaf Modifications to display RawDataURl on front end
      
      commit 1f33afdbfa12fb0206262bf4c2595d981aac8042
      Merge: 67ef9bc52 3a61a2e93
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue May 19 15:49:30 2020 +0100
      
          Merge branch 'xDog-unharmonized' of https://github.com/PDXFinder/pdxfinder into xDog-unharmonized
      
      commit 3a61a2e938f6b6304b7c9108878c4d0342ef3624
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue May 19 14:55:52 2020 +0100
      
          Add raw data url to sample
      
      commit 67ef9bc52356fdce816f5a671eef7a0bd3fda669
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue May 19 14:51:09 2020 +0100
      
          Updated column headers for Xdog mutation data
      
      commit f8afe384c52e2b027a13b8fe950e578edb1cabe9
      Merge: e7a0f8195 d6eac7eb1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue May 19 13:54:03 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit e7a0f81955366e2a257f4631c947d9a860858a2a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue May 19 13:53:45 2020 +0100
      
          Implement batch data visibility load
      
      commit 457652792c50b6184e11488fcc0c1dbe3894c2a6
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue May 19 12:59:11 2020 +0100
      
          Fixed commandLine bug for parsing providers. Add PMDR-XDOG to providers
      
      commit d6eac7eb1ffaec5520dd9d5f9e2d0db1083a7805
      Merge: b52c07739 774aa952e
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Mon May 18 18:04:20 2020 +0100
      
          Merge pull request #149 from PDXFinder/xdog-exprAndCyto
      
          Xdog expr and cyto
      
      commit 774aa952e5bf4d6ffec7ccb19974b7a883896b8b
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon May 18 17:52:34 2020 +0100
      
          Added tests to OmicTransformationService. Refactored where needed.
      
      commit 059f1c136dab154d5665560de4a4aea52c9da0bc
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon May 18 17:40:38 2020 +0100
      
          Added tests to OmicTransformationService. Refactored where needed.
      
      commit 6c5e104dd8fc1a0496961160df33151abd13c2f8
      Merge: 1cd2277f8 717d5ccc6
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon May 18 16:34:59 2020 +0100
      
          Merge branch 'xdog-exprAndCyto' of https://github.com/PDXFinder/pdxfinder into xdog-exprAndCyto
      
      commit 1cd2277f8e303cd89c9cd5f433bd01c59ec86253
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon May 18 16:34:29 2020 +0100
      
          Refactored LoadMarkers class. Made code review recommendations
      
          Because
          *Reduces redundant code
          *Clarify try-catch exceptions
          *Increase readability
      
          Broke down load genes into three additional methods. downloadDataFromURL has it's own try-catch as well as the while loop that reads the file. Prior, one catch for both network and file parsing was being used. Further fixed code smells
      
      commit 19b3d5b448c71b47bad3724aac9ecdcf8900b9b4
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon May 18 13:56:32 2020 +0100
      
          Refactored LoadMarkers class
      
          Because
          *Reduces redundant code
          *Clarify try-catch exceptions
          *Increase readability
      
          Broke down load genes into three additional methods. downloadDataFromURL has it's own try-catch as well as the while loop that reads the file. Prior, one catch for both network and file parsing was being used. Further fixed code smells
      
      commit b52c07739e00dafee69718fd2eaaa526453d0503
      Merge: a7a484b45 accb4f1d7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 15 21:01:58 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit a7a484b45af171ca5d10a7abfd0d59d719759273
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 15 21:01:44 2020 +0100
      
          Implement batch loading of molecular data
      
      commit 5357466c7e66e89526780f000e00a05415bf9e65
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 15 20:57:20 2020 +0100
      
          Error check for molecular data projections
      
      commit 0906b610e17a0aaecb9a0973e05d49a91d4e080d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 15 20:56:38 2020 +0100
      
          Query for batch molchars
      
      commit cd69c03787b09df746ba568cf6600ccf35aef919
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 15 12:17:37 2020 +0100
      
          Remove post data load for CRL
      
      commit 6352eb497502223a921aa6e211ffde701608ceea
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 15 12:14:18 2020 +0100
      
          Return node id upon save
      
      commit accb4f1d719b360e022c9ae6ec55c0049c744429
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri May 15 10:59:24 2020 +0100
      
          Refine datatype identification
      
      commit 2344d41b482fac272d32962e9bccd2c2412d4d86
      Merge: f0d88663a aef15e0dc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 15 10:34:56 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit f0d88663a2d3148c248823aa5c3905358e0f94dc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri May 15 10:34:44 2020 +0100
      
          Get specimen with sample
      
      commit aef15e0dc2d3692b474864216f7879f097a07c6c
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu May 14 19:13:00 2020 +0100
      
          Add batch loading file methods
      
      commit 717d5ccc65b3ae17ee78b3884a223821a2f7432b
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Thu May 14 17:37:00 2020 +0100
      
          Update Marker.java
      
      commit 3efb7d989c2699a2b3e68d2c70c7db1cb6e354b6
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 13 20:49:28 2020 +0100
      
          Add DS_Store to gitignore
      
      commit 61cd0978bcf449afb3fff1ea30436c61f3b2ea3d
      Merge: 8a65e78ae 3398afee0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 13 20:48:13 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 8a65e78aef7ab30b95936d05621f09e3631b31aa
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 13 20:40:50 2020 +0100
      
          Add two omic processing approaches
      
      commit 8e9fd3afaaf87b8780bae71be2e5eb54a0afdfd5
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed May 13 17:28:10 2020 +0100
      
          Fixed Sonar Code Smells
      
      commit b49f3ce239df405a7a1198aa20f1ff5b19e60922
      Merge: 8adb1e708 7f42b4b37
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed May 13 17:15:37 2020 +0100
      
          Merge remote-tracking branch 'origin/xdog-exprAndCyto' into xdog-exprAndCyto
      
          # Conflicts:
          #	indexer/src/main/java/org/pdxfinder/dataloaders/UniversalLoader.java
      
      commit 8adb1e708ddb479c5462fa37a56235a9e0f3c1e8
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed May 13 17:11:26 2020 +0100
      
          Fixed Sonar Code Smells
      
      commit 7f42b4b37f099915fdb5b504c35130bbd45073b3
      Merge: ccf79f89f 3398afee0
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed May 13 12:46:15 2020 +0100
      
          Merge branch 'release-2020-04' into xdog-exprAndCyto
      
      commit ccf79f89fcdcb9eacde53c1012e5acd35e054527
      Merge: 82010b4c1 5c2b6c1a8
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed May 13 11:57:24 2020 +0100
      
          Merge branch 'xdog-exprAndCyto' of https://github.com/PDXFinder/pdxfinder into xdog-exprAndCyto
      
           Conflicts:
          	indexer/src/main/java/org/pdxfinder/commandline/FinderExporter.java
      
      commit 82010b4c1773409b8032453ed9ab72169172e9f2
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed May 13 11:55:19 2020 +0100
      
          updated test in CbpTransformer and DataExport
      
      commit 5c2b6c1a856158b0ef039fe61c54cbbf51d5e091
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed May 13 10:28:07 2020 +0100
      
          Pass data provider argument correctly
      
      commit 3398afee0ee684c0664c750387bba98273085e9d
      Merge: fd89284da 962087ec1
      Author: abayomi <abayomi@sprintell.org>
      Date:   Wed May 13 10:19:04 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 962087ec1c56af9ba69c6c8347af745db48c151f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 13 10:10:31 2020 +0100
      
          Add per model/patient persisting option
      
      commit fd89284da989f1348e2ff2b3483b2ff712c7d32b
      Author: abayomi <abayomi@sprintell.org>
      Date:   Tue May 12 23:43:27 2020 +0100
      
          Display Platform used when it is not OncoKB Gene Panel
      
      commit 47fa7007d813b553a712642e1a66f3038ae85324
      Author: abayomi <abayomi@sprintell.org>
      Date:   Tue May 12 23:35:22 2020 +0100
      
          Change links to PDMR variation data
      
      commit 4e06329aa391fb1380f2cd8f382a3280f402182b
      Author: abayomi <abayomi@sprintell.org>
      Date:   Mon May 11 02:53:50 2020 +0100
      
          update unit test
      
      commit 0c69d13b83b835d5e5072b61059dcd792dc72816
      Author: abayomi <abayomi@sprintell.org>
      Date:   Mon May 11 02:51:06 2020 +0100
      
          Update details service
      
      commit a23cddd5c746e0826b7c485ead489f5d8fc87f7c
      Merge: 482af7c47 0af6850e7
      Author: abayomi <abayomi@sprintell.org>
      Date:   Mon May 11 01:59:12 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 482af7c479f95c71c90985618bab2d6e43206a61
      Author: abayomi <abayomi@sprintell.org>
      Date:   Mon May 11 01:59:02 2020 +0100
      
          Refactor molecular data api structure
      
      commit e1cd565c68b85a410c8fdee81555a9a1d971a6b7
      Author: abayomi <abayomi@sprintell.org>
      Date:   Mon May 11 01:58:03 2020 +0100
      
          Extend front end for the new moleular data structure
      
      commit 0af6850e715338e154758eec633d950cd4f848da
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu May 7 17:01:11 2020 +0100
      
          TODOs for batch molecular data load
      
      commit c6c412f3f948ca6a584cd11f45b09e300d606808
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 6 21:09:13 2020 +0100
      
          Add gene expression and cytogenetics filter
      
      commit 953c526b89c7dab171fbbb8a3f5bd98e40b7946e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 6 21:07:57 2020 +0100
      
          Fix missing key bug
      
      commit 07dea1e4a9464a8a51bc8e68316b6b0b3671254f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 6 16:24:35 2020 +0100
      
          Disable validation due to exception
      
      commit 48eb64b6b0c3f0bf9512f4768b0ad88b9ae94e57
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 6 16:24:08 2020 +0100
      
          Revert "Disable validation due to exception"
          This reverts commit 51a7e47a
      
      commit 51a7e47a5195319ee26608ad76d6bc74552e8692
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 6 16:19:28 2020 +0100
      
          Disable validation due to exception
      
      commit 7a322c80e5daf3d88281b8425971a43a5bd77c09
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed May 6 15:39:40 2020 +0100
      
          Add rnaseq count to table
      
      commit 43f7f05b7a89fad7dec68570f06f914d1d4973d4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue May 5 18:30:14 2020 +0100
      
          Rename breast cancer markers dp
      
      commit 13c2fbef26c469dde547bbce694b59043334021a
      Merge: fcb355241 e8b905664
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon May 4 19:23:02 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit fcb355241d699361fbe61d7da6853e5308ef3f69
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon May 4 19:22:27 2020 +0100
      
          Add expression dp
      
      commit e8b905664238511c0fdd2054ceac4676416cd5f4
      Merge: c1fed5635 e87735436
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon May 4 14:13:14 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit c1fed5635b748d7fd7ec9e888043a8c4923f1444
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon May 4 14:13:11 2020 +0100
      
          Update Omic validation rules and reporting
      
      commit 0073aa14a448338b3e6455d0beb0d837480671b4
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon May 4 12:59:18 2020 +0100
      
          if-else statment into switch-case
      
      commit e877354365163cfcf7d28e4a843cae3456a71f93
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon May 4 12:51:18 2020 +0100
      
          Add cytogenetics dp
      
      commit 03cbf1b49fabeb6aa14ff642cb7cda04fd3c848c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon May 4 12:50:56 2020 +0100
      
          Rename marker_name to symbol
      
      commit d253fe4401102b4fa07206d75287bc4cf1baac2e
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Apr 30 15:05:58 2020 +0100
      
          Support short validation error messages to aid debugging
      
      commit 248147595b3f89cc308b4770994503dc7058ba36
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Apr 30 13:29:45 2020 +0100
      
          Add validation rules for omic expression data and fix error creation
      
      commit bd3719c6c49cb7acfc2f8190a2ada4f3ebf12a4c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Apr 28 23:18:09 2020 +0100
      
          Use expression instead of transcriptomics
      
      commit e500f88e4e478bdcc43f633b23602b7c48c2998a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Apr 28 23:13:18 2020 +0100
      
          Update copy number alteration molchar type
      
      commit 309464c7d43a7b1335e70d5b7b7d76b56e463ec9
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Apr 28 16:06:48 2020 +0100
      
          adjusted templates to new templates, expr and cyto
      
      commit 1354e9c4821053878465afc10c83d15debef28b7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Apr 28 15:37:38 2020 +0100
      
          Use debug message instead of info
      
      commit cc05f6c60a7217c955da2fc06503422e427221ff
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Apr 28 15:24:20 2020 +0100
      
          Create marker set before encoding
      
      commit e5bc7ad3c4e776451d8e788bfb8ad8892607c0f3
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Apr 28 14:29:30 2020 +0100
      
          Added NKI to DataProviderGroup.UPDOG and updated tests
      
      commit 9ec0066c534d6145b20036d346dda27408d0b5be
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Apr 28 13:45:56 2020 +0100
      
          Added NKI to DataProvider Enums to run with the Loader picoClient
      
      commit 181fdfae89886a147d24d83131da0a885ffb2f3e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Apr 27 15:13:35 2020 +0100
      
          Fix combined passages bug
      
      commit e5a0bc78c6422a1403b8b30a27b3fbff0cc0f179
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Apr 24 11:35:17 2020 +0100
      
          Add expression functionality to xdog
      
      commit 93b86b95c13bb103d51cb7d0bd6d5c0b138f8edd
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Apr 23 16:28:16 2020 +0100
      
          Add group for custom loaders
      
      commit d3f9585a8c0e32181c22097b7631ec65d2eb2639
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Apr 23 16:27:48 2020 +0100
      
          Fix missing specimen sample bug in custom loaders
      
      commit cc8a50c3253dfe6fdd13b6eba4302343947298da
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Apr 22 20:41:48 2020 +0100
      
          Fix missing specimen sample bug
      
      commit a2100fbd9c8457eabbbcd43998366e736511c1e9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Apr 22 19:53:42 2020 +0100
      
          Enable expression data loading
      
      commit 78e4ec2a6e8b315dfff695e58bfa95cdbef432ab
      Merge: 8f80d8df3 e6967fe0a
      Author: abayomi <abayomi@sprintell.org>
      Date:   Tue Apr 21 22:19:07 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit 8f80d8df3a60dc5c7d5374e82888a6e1c9f71aa7
      Author: abayomi <abayomi@sprintell.org>
      Date:   Tue Apr 21 22:19:00 2020 +0100
      
          Fix PDMR missing PDX model Engraftment data
      
      commit e6967fe0a5eb46de8250f61ebbf9cb0cc16e4135
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Apr 21 20:37:04 2020 +0100
      
          Move validator tests and refactor
      
      commit 1f086a0405f90748266f1d690ccefb950db2de46
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Apr 21 08:38:19 2020 +0100
      
          Prepare validator extension for new errors
      
      commit e5051ca16eb23287110a69b22ec97d2458dda1fa
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Sat Apr 18 17:48:54 2020 +0100
      
          Fix logging arguments
      
      commit 339f6a9c86dcd222fe0f2739bbfa51bdb3e6622b
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Sat Apr 18 17:43:52 2020 +0100
      
          Fix too few args bug
      
      commit 54818a570c97b02c69a0590fcfdb3ffe349a2753
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Sat Apr 18 16:14:26 2020 +0100
      
          Refactor validation tests
      
      commit fe2c8b6cbfdc7197bdd25320b8df04e825617aeb
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Apr 17 23:54:03 2020 +0100
      
          Refactor validation - wrap column reference and relation in classes
      
      commit c88518fb612ace74323582be6b103ed664227961
      Merge: 41afa78bc f70fdc462
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu Apr 16 15:39:20 2020 +0100
      
          Merge branch 'release-2020-04' of https://github.com/PDXFinder/pdxfinder into release-2020-04
      
      commit f70fdc46244bf1d0ad6ed186452971a216923a24
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Apr 16 15:09:50 2020 +0100
      
          Add exception handling to patient treatment
      
      commit 41afa78bc2bcbc779c8da6052fc3a540e32ac8e6
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu Apr 16 15:04:37 2020 +0100
      
          Add --db-refresh command to the CLI
      
      commit 55adb5ac30f976e49ea1ba1a24b631cbcbe7e5dd
      Author: abayomi <abayomi@sprintell.org>
      Date:   Thu Apr 16 15:04:00 2020 +0100
      
          Add feature to automate refreshing of embeddedDB from developer's machine and copy cache directory if it exists
      
      commit d74ae10ac26c3ce25aabcd6f51d2f229e265f349
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Apr 16 11:29:06 2020 +0100
      
          Adds untested functionality to ncbiGeneToHGNCSymbol.
          adds cyto functionality to xdog and unfinished expr
      
      commit cde18e9f5fb64467c5da26fed4d2964144e4d40f
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Apr 9 18:08:02 2020 +0100
      
          Adds untested functionality to ncbiGeneToHGNCSymbol.
          adds cyto functionality to xdog and unfinished expr
      
      commit 56c0d94086ba39ea8b3c10470692009eaa102f94
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Apr 9 17:22:08 2020 +0100
      
          Disable expression loading temporarily
      
      commit fc4cce11ceb45eef94725eafa8253c7e26f0703e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Apr 9 11:59:52 2020 +0100
      
          Fix molchar creation bug
      
      commit 18668ec8080dc7aaa6ac1da407b3493e7b1e57ae
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Apr 8 11:18:06 2020 +0100
      
          Load marker status for cyto
      
      commit 85fb6c050d7c02cba0f9c5df7992347c8cd3d181
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Apr 8 11:14:01 2020 +0100
      
          Get expression properties
      
      commit 0b66ae08fbe191e03413379958e1916c0ced779e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Apr 8 11:08:40 2020 +0100
      
          Read expression data
      
      commit 05b0f10a6505cb7ecd52d12fb0c36667536dda21
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Apr 8 11:07:37 2020 +0100
      
          Add expression headers
      
      commit f9c23d0c3b14c4c71d826ac94bbe469cf20119c3
      Author: abayomi <abayomi@sprintell.org>
      Date:   Tue Apr 7 00:49:43 2020 +0100
      
          Properly handle double quoted comma in csv
      
      commit 80a5be15b52bd117c0e9ee655c3f5f91f929efad
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Apr 6 14:03:54 2020 +0100
      
          Add skeeleton for expression data loading
      
      commit 92071f7da0eea70d40aa76ef2ff96355abc60f61
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Apr 6 13:00:12 2020 +0100
      
          Use print instead of log for clearer display
      
      commit 4dc2d8a10528f46b41e67802b8f7d9f1b9e4e5b0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Sun Apr 5 16:14:33 2020 +0100
      
          Enable drug dosing loading
      
      commit 0c1d7a7b05ae7e0810d294f38d5f2de8f568dd99
      Merge: ef1187f1c 68f578bc1
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Fri Apr 3 12:43:57 2020 +0100
      
          Merge pull request #146 from PDXFinder/CbpTransformer
      
          Cbp transformer
      
      commit 68f578bc159fe1986a5e0707e4eb309828c7520d
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Apr 2 18:41:59 2020 +0100
      
          Changed if..else if.. to switch statment
      
      commit c1b2e0585381669c39bafe645409ec7b5e23ea40
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Apr 2 18:28:47 2020 +0100
      
          Changed if..else if.. to switch statment
      
      commit 87b0790614b41e1a27338b39b9aa0f38d2b71b57
      Merge: 08bbbc1a6 a84293ad6
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Apr 2 18:06:31 2020 +0100
      
          Merge branch 'CbpTransformer' of https://github.com/PDXFinder/pdxfinder into updatedCbio
      
      commit 104abd43197bcc895c69dd4cb942aa5e81cce4e7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Apr 2 14:32:47 2020 +0100
      
          Enable treatment loading
      
      commit e95e0fb1eff8dc65b2771f9116c939be958ede1e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Apr 2 14:32:08 2020 +0100
      
          Add treatment headers
      
      commit 3e4c56011fc961e6ee43d90368257fd6822af818
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Apr 2 14:03:01 2020 +0100
      
          Clean treatment files during read
      
      commit 08bbbc1a654d0a092a8fb3b833869d9cd5d4ad43
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Apr 1 16:38:44 2020 +0100
      
          split resolveDirEnv into multiple methods
      
      commit a84293ad658a6a2b3ee89f373a710f3f024a3359
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Apr 1 16:23:03 2020 +0100
      
          Update indexer/src/test/java/org/pdxfinder/commandline/FinderExporterTest.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit 333463457959a786b67ea0504a73393a89f0ca48
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Apr 1 16:22:41 2020 +0100
      
          Update indexer/src/test/java/org/pdxfinder/commandline/FinderExporterTest.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit 036be48085862558bb00b47bd5ad86232a260366
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Apr 1 16:22:27 2020 +0100
      
          Update indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit bf7acdc357cfbd9dd0b369b1995f9fd7767b4369
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Apr 1 16:08:16 2020 +0100
      
          Update indexer/src/main/java/org/pdxfinder/commandline/FinderTransformer.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit 6a73b41f739ae183a4e650d79a5329e846165927
      Author: abayomi <abayomi@sprintell.org>
      Date:   Wed Apr 1 16:04:56 2020 +0100
      
          update admin db details
      
      commit 73bd26c4bb32b4af78024638b27bb94f15b06205
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Apr 1 13:09:21 2020 +0100
      
          one code smell fixed
      
      commit c27896aa1ebeacba1d2669c3f84011ce49a06ba8
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Apr 1 10:27:05 2020 +0100
      
          Fixed failing tests
      
      commit de36f38ce07ec7afd7c8f3b6fe8afe286bd8cc89
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Apr 1 10:13:09 2020 +0100
      
          Split classes in FinderCommandLine into Exporter and Transformer. Added changed/added appropriate tests.
      
      commit 4ac21f613baac87ccc4900749976b6940febf11a
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Mar 31 15:58:38 2020 +0100
      
          removed cognitive complexity.
      
      commit 32d2cd8b8f6bb07b00b077e218a8edde80a43987
      Author: abayomi <abayomi@sprintell.org>
      Date:   Tue Mar 31 12:39:26 2020 +0100
      
          add feature to purge admin-db before intiliazing with unti test
      
      commit b2ed629ea6b25eb4a81f9b0ae335fb007c299439
      Author: abayomi <abayomi@sprintell.org>
      Date:   Tue Mar 31 12:37:50 2020 +0100
      
          add option to purge and initialize admin-db to cli
      
      commit 4815d67af83a119c9962de9ecb00cc83552f8f12
      Author: abayomi <abayomi@sprintell.org>
      Date:   Mon Mar 30 22:43:41 2020 +0100
      
          update unit test
      
      commit ad1c5f62a26bddc8466281d989b1221df04e837b
      Author: abayomi <abayomi@sprintell.org>
      Date:   Mon Mar 30 22:36:19 2020 +0100
      
          updated unit test
      
      commit 3e77d928c8582efb7b3cf7f8081535a24add6803
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 30 14:48:27 2020 +0100
      
          removed cognitive complexity.
      
      commit 472798589d8fdb2e332a8cbd6a65e9eb5442a04c
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 30 14:29:17 2020 +0100
      
          Fixed Code smells and Bug
      
      commit 0210ef32d7312e4f179d7d055a9665587f73f7d2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Mar 30 14:07:03 2020 +0100
      
          Remove objects during loop
      
      commit 2abeaee849c9d8854d34573944825d2f02cc7a58
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 30 13:58:20 2020 +0100
      
          Fixed Code smells
      
      commit 4c6252e3f01230f16837162fd39804f0829583ba
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Mar 30 13:31:26 2020 +0100
      
          Remove objects from map after persisting
      
      commit 0ca8091c7222688430b73640207393b0548b5b2f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Mar 27 21:35:38 2020 +0000
      
          Simplify mapping key
      
      commit bfa813a6cb1f19b933b93c96afde79230110d561
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Mar 27 21:34:51 2020 +0000
      
          Trim diagnosis
      
      commit 1b0cadd299b160f2ffcee72d42f8216cc57c06f2
      Merge: 26a0335be ef1187f1c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Mar 27 09:37:05 2020 +0000
      
          Merge branch 'dev' into release-2020-04
      
          # Conflicts:
          #	indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/DomainObjectCreator.java
      
      commit 93040a028558de6eef1f88369a6c945c0af2ac0d
      Merge: 2d15dfb5c 73b7141d7
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Mar 26 13:52:43 2020 +0000
      
          Merge branch 'CbpTransformer' of https://github.com/PDXFinder/pdxfinder into CbpTransformer
      
      commit 73b7141d7fdd6ca16750f8cc269a1767ec277ea8
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Mar 26 12:46:39 2020 +0000
      
          Register transform subcommand and fix typos, add linewraps
      
      commit 2d15dfb5c2f3c52ad55e9aa8dc840c9858bd39ee
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Mar 26 11:21:00 2020 +0000
      
          Refactored tests/code to pass. finished cbioportal cmd line interface
      
          Because
          * cbioportal needed to be updated
          * tests were failing with new code base
      
          Refactored tests/code so that test are all passing. Includes adding setters to the xDog/DownDog in lieu of a larger refactor.
      
      commit e6bdd012474926ad882c46024097e8d63b10ce8c
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Mar 26 09:54:33 2020 +0000
      
          Refactored tests/code to pass. finished cbioportal cmd line interface
      
          Because
          * cbioportal needed to be updated
          * tests were failing with new code base
      
          Refactored tests/code so that test are all passing. Includes adding setters to the xDog/DownDog in lieu of a larger refactor.
      
      commit d9ec382e6e1dae50069251e63ac847bae851dd84
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Mar 25 15:14:22 2020 +0000
      
          Merge branch 'cbioTransformer-xDog' into dev. Added cbioportal cmd
      
          Because
          * Cbioportal was could not run without cmd integration.
      
          command line options were expanded. Finder transformer was expanded to integrate cbioTransformer too. Test have been provided.
      
          # Conflicts:
          #	indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
      
      commit 26a0335beb23be13ee706df78f1b4d1d34452aef
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 25 08:58:07 2020 +0000
      
          Disable log message
      
      commit e99e7f20436d8d4af80f27adb846a9f505ef7a2a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 25 08:57:46 2020 +0000
      
          Print error message instead of throwing and exception
      
      commit 567dc077d3a3418a75b81394813a3d57cb614f8f
      Merge: 2ee05c70c ef1187f1c
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Mar 24 10:59:17 2020 +0000
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 2ee05c70c6737cb771892231bea661236b6c643a
      Merge: 881cb85b4 14bb06b0b
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Mar 24 10:59:07 2020 +0000
      
          Merge branch 'cbioTransformer-xDog' into dev
      
          # Conflicts:
          #	indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
      
      commit ef1187f1c31f023cf9f3a9f9393f56f202ea89f4
      Merge: 881cb85b4 49fdfd8e0
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Tue Mar 24 10:31:23 2020 +0000
      
          Merge pull request #144 from PDXFinder/xDogChanges
      
          X dog changes
      
      commit 49fdfd8e0a9f3299957d2a95b6c70032a17291ec
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Mar 24 09:35:32 2020 +0000
      
          Fixes code smells
      
      commit cdc145ed69f2b7fc9e5cf01373af4ff82a872cc0
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 23 18:14:02 2020 +0000
      
          Fixes code smells
      
      commit eaf1092dab876481608a1365f3e91e51ae86e8fd
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 23 18:08:17 2020 +0000
      
          Removed vulnerability caused by stdout an IOException
      
          Because
          * SonarQube recommended it.
      
      commit 8e85efdb9e127abc4d09981ab10febee3019e645
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 23 17:58:11 2020 +0000
      
          Removed vulnerability caused by stdout an IOException
      
          Because
          * SonarQube recommended it.
      
      commit 5145c960bfd81acd2f625aaca67acb9f2a64e1b5
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 23 17:56:10 2020 +0000
      
          Changed "transcriptomic" to "expression" in the Jax loader
      
          Because
          * Currently the language is not defined in the Finder
          * Both transcriptomic and expression exist as MolecularCharacterizations
      
          Changed the String datatype that is passed to the loadOmicdata() (deprecated) from "transcriptomic" to "expression" Changed the file folder to from "trans" to "expr". Changed loadOmicData where absolutely neccessary
      
      commit 790b0cbb9acd7ca88cbd255af596bae25541adc9
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 23 17:17:27 2020 +0000
      
          Added Tests for FinderTransformer and FinderCommandLine
      
          Because
          * Testing is good
      
          Also recreated ExportDataToTemplate to increase ease of testing the FinderTransformer. I have not writtent tests for the ExportDataToTemplate class yet.
      
      commit b3efcd04528554783a6558750c5f1d69fdb5bd8d
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 23 15:14:30 2020 +0000
      
          Added commands for xDog(down dogs) to picoclient
      
          Because
          * xDog used command line clients, but not the pico
          * xDog runner was crashing container
      
          Added logic to new inner class in FinderCommandLine. added finderTransformer that contain the now deleted ExportDataToTemplate.java behaviors. Added tests for the new arguments for the FinderCommandLine
      
      commit 7b36b213eb3a21100d1efeec051b150536c2e1c5
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 23 15:03:22 2020 +0000
      
          Added commands for xDog(down dogs) to picoclient
      
          Because
          * xDog used command line clients, but not the pico
          * xDog runner was crashing container
      
          Added logic to new inner class in FinderCommandLine. added finderTransformer that contain the now deleted ExportDataToTemplate.java behaviors. Added tests for the new arguments for the FinderCommandLine
      
      commit e5cca24ee2d965fdd6799e7abe420ce0502c11b3
      Merge: 2a74a9fe5 881cb85b4
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 23 10:04:48 2020 +0000
      
          Merge branch 'dev' into xdog
      
      commit 881cb85b4329ca5c4c9058b14b5952acadf343c5
      Merge: 98551535d 0e1ba7df3
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Mar 17 10:07:27 2020 +0000
      
          Merge pull request #145 from PDXFinder/loader-fixes
      
          Loader fixes
      
      commit 0e1ba7df387d0e28cccef10a28204eaee2cd18b6
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 17 09:32:51 2020 +0000
      
          Fix missing DPs due to marker change
      
      commit 23442657b9c68ea24301c46630d43a26c47ecc1d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 17 09:32:18 2020 +0000
      
          Fix incorrect molecular data creation sequence
      
      commit f927a00241c610bbe0c4f0fe78c88153f54e616e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 17 09:31:17 2020 +0000
      
          Adds equals and hashcode
      
      commit 14bb06b0b5b6b7ea922ae4a3d5b31553c61011f2
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Mar 16 14:33:19 2020 +0000
      
          Added functions to Down Dog (X-Dog) to not export data. Refactored
           Because
           *Down Dog needs to stop making useless files
           *Complexity needed to refactor
           * Both Cbportal and Xdog share code. Therefore, there is a higher need to maintain it.
      
           Added checks to sheets so file are not created when there is null data being imported. Refactored to reduce complexity in one method.
      
      commit 58218236177813e2b0d56e81f6391c236c4e0c06
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Feb 18 16:30:28 2020 +0000
      
          Has one integration test for the CbpTransformer
      
      commit 5c71bef3f7e0bd28a74e15e4994a649448b39bce
      Author: afollette <follette.alex@gmail.com>
      Date:   Sun Feb 16 17:44:10 2020 +0000
      
          Has one integration test for the CbpTransformer
      
      commit 2cc69062ec08dbf17b13696001a64cb3cb19a5b3
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Feb 10 16:53:23 2020 +0000
      
          Added tests and two methods in UtilityService.
      
      commit fae78c97e6f3ee4e3364e3c6f399703c9ae69a4d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Mar 16 08:49:29 2020 +0000
      
          Fix missing markers in DP
      
      commit ca50270350892e30541bbb454302a8bec25d2d09
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Mar 16 08:49:08 2020 +0000
      
          Do not look for markers linked to MA
      
      commit cf4894130f23b80e5ca71d295010d66098b54635
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Mar 16 08:48:04 2020 +0000
      
          Store marker set on MC
      
      commit b1915c8952b478ae8aa1d7d27df9cbd67c9cdc58
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Mar 13 12:12:37 2020 +0000
      
          Add error messages
      
      commit 543f950a7d4fa196211c13b016eb796c045d2d07
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Mar 13 09:19:15 2020 +0000
      
          Add DFCI data provider
      
      commit 453c5df2627958c28b048b5e3962d9b8f87be62b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Mar 13 09:09:49 2020 +0000
      
          Add DFCI data provider
      
      commit 98551535d249dd421542aba4abd24957fe281cef
      Merge: d9ca33e0e f600a853e
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Mar 11 10:22:46 2020 +0000
      
          Merge pull request #143 from PDXFinder/loader-fixes
      
          Loader fixes
      
      commit f600a853e4b3344ffd170dfea87abf564192c095
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 11 09:59:05 2020 +0000
      
          Load IRCC-CRC with updog
      
      commit 62d2787158774d3a840e686d91a7241a06a06aa1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 11 09:55:45 2020 +0000
      
          Fix molecular data load for HCI
      
      commit 3b89fb420429bea48b6fb1a5f4f9d9e8951a8751
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 11 09:37:56 2020 +0000
      
          Do not throw exception on unknown patient treatment just skip loading
      
      commit b96a5ea016569badb0cd9976d075167e5cbc4617
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 11 08:40:56 2020 +0000
      
          Check the presence of sampleExtractionMethod
      
      commit d9ca33e0e75f4b6aa158e755c6f989909078c1c7
      Merge: b53b91a38 e8a733e1f
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Mar 10 15:02:13 2020 +0000
      
          Merge pull request #142 from PDXFinder/loader-fixes
      
          Loader fixes
      
      commit e8a733e1f3db8caae285a2bdd5b076cb350022be
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 10 14:24:32 2020 +0000
      
          Populate marker set on molchar
      
      commit 68e651ba42b9c6ebb45b7c8eb483282fea89d97c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 10 14:24:04 2020 +0000
      
          Change loading order for breast cancer markers
      
      commit c2f9f14ef4f23f6571714041614d3ed09f9145df
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 10 14:23:16 2020 +0000
      
          Fix molchar table content
      
      commit 4101ea1ed6c7b11e97ad99187dfbda42f89dad3e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 10 12:31:54 2020 +0000
      
          Add new attributes to DAO
      
      commit b53b91a3819d94e0e0510fb3ad15f38654e50b60
      Merge: 92b648aae 34ce8cf0e
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Mar 10 10:21:29 2020 +0000
      
          Merge pull request #141 from PDXFinder/loader-fixes
      
          Loader fixes
      
      commit 34ce8cf0ec37e2e7eb05c7913a824a7f54a4c0b2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 10 10:02:30 2020 +0000
      
          Change test not to rely on equals
      
      commit fffae05b6f952156a5de054d046fc7305209cbde
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 10 09:49:41 2020 +0000
      
          Disable testing equals on samples
      
      commit 34cde92cd2be6626447e3f6eec203928a0506ba1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 10 09:43:27 2020 +0000
      
          Remove equals and hashcode
      
      commit f40d3993534a3946d844621ae8db25078abffba6
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Mar 10 09:42:20 2020 +0000
      
          Remove log message
      
      commit 81701b9c42dd6a64f9fc4214a12439f7e786db26
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Mar 9 15:18:33 2020 +0000
      
          Add exception handling for missing mappings
      
      commit b0fb481cc52b7b196f9e30f35d43cdb52e69f5d7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Mar 9 15:18:14 2020 +0000
      
          Store ds abbrev ref on patient sample as per projection requirement
      
      commit 444ca18d38263a9e2797d8155068ec181b1fef1d
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Mar 9 11:45:00 2020 +0000
      
          Fix header rows not being removed
      
          This was due to the 'Field' column being removed before
          removeHeaderRowsIfPresent, which relies on this value being present
          to test if there are description rows present or not.
      
      commit 1a7f4bcbb29c5ca2dd491532b47a80ecbb57b308
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Mar 9 11:28:58 2020 +0000
      
          Remove description column if present for omic tables
      
      commit 9e8ed69bb4f38193394752820b5202f3dc44fd41
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Sat Mar 7 10:36:31 2020 +0000
      
          Update old omic loader to use markerassociations appropriately
      
      commit 92b648aaebff7e46a1c11c5a02f63e5a29bcc9ce
      Merge: c82f7d4b3 c04670b48
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Mar 5 10:20:02 2020 +0000
      
          Merge pull request #140 from PDXFinder/updog_refactoring
      
          Updog refactoring
      
      commit c04670b48d18a47fab76f888f7e511ec98e56e15
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Mar 4 22:54:03 2020 +0000
      
          Link PicoCli to refactored UPDOG
      
      commit 1155ec101a2ffcc4d741a2520ec79b54451e7526
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Mar 4 14:47:39 2020 +0000
      
          Fix some broken find/replace artifacts, delete comments
      
      commit b3047c5ffdc3666da1ad3bd496597678a96fede9
      Merge: de1d58dd7 1104aa518
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Mar 4 13:52:20 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit de1d58dd713b7d463d3ca98469e17a62816715ce
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Mar 4 13:52:11 2020 +0000
      
          Add load all option to minimal load runner
      
      commit 1104aa518411fc3e1adef9281e62455fe31c3a1f
      Merge: 6a2c158d3 c82f7d4b3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 4 13:24:19 2020 +0000
      
          Merge branch 'dev' into updog_refactoring
      
          # Conflicts:
          #	indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java
          #	indexer/src/main/java/org/pdxfinder/postload/ValidateDB.java
      
      commit 6a2c158d3b87a746619b942d05247b2681b73eb2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 4 11:54:49 2020 +0000
      
          Decode molecular data before presenting
      
      commit 776cf30b32e598dc697d5bf1dff4d655ff9b4953
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 4 11:53:58 2020 +0000
      
          Include association data when getting molchar
      
      commit 37ce72cb5072d31cf2ae9ece779d966503593fa4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 4 11:52:22 2020 +0000
      
          Store datapoints on MA
      
      commit 723c6a2369e88c6b1b342bff662210ef376b046d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 4 10:48:10 2020 +0000
      
          Fix dataprovider key in tests
      
      commit 24cdd96e4dd9518d024d62a0f5f531c67ebfac18
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Mar 4 10:25:33 2020 +0000
      
          Check if marker was harmonized before adding it to MA
      
      commit c82f7d4b35f18cabbf72c4da5ae5650859c5faef
      Merge: 21d48fa0f 1d63596d1
      Author: Sprintell <abayomi@sprintell.org>
      Date:   Wed Mar 4 09:40:18 2020 +0000
      
          Merge pull request #138 from PDXFinder/PicoCli
      
          Pico cli
      
      commit 1d63596d1e60263680e4003b32b7f16185f525f5
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Mar 4 03:11:40 2020 +0000
      
          Reactor to fix CLI Loading Problems
      
      commit 20d4669bc098588756d6a4bba4116689fd8d40fe
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Mar 4 03:10:44 2020 +0000
      
          Reactor to fix CLI Loading Problems
      
      commit f66021063b2bfe49d9f865d0e1a968fc7ff392c6
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Mar 3 15:59:27 2020 +0000
      
          Refactor and clean up
      
      commit 2d1a35c781d56d1ffbc672e9a0e09f2970a5fd34
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Mar 3 10:31:16 2020 +0000
      
          Fix and refactor encodeMolecularData
      
      commit 119b73f521afffef1c679c5ab0e7c0e1ef5b23e2
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Mar 2 22:35:05 2020 +0000
      
          Load omic data from single table into domain object pool
      
      commit 58492fe1ead6647e2905da7bbc2d3eca63e62afa
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Mar 2 14:24:23 2020 +0000
      
          Add molecular characterisations to object pool
      
      commit 76799432640d9c91ab5c612440b1f6dd6a9fe5e0
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Mar 2 08:18:26 2020 +0000
      
          ModelCreation domain object refactor
      
          (null specimens still added to models, TODO fix)
      
      commit 1b09b470e0eed7d6a6548e4fe24ead7a00100d9d
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Feb 28 16:22:01 2020 +0000
      
          LinkSampleToNCITTerms respond to new CLI calls
      
      commit 2bfe992760cea91a7333c56e82e93ba1710234bc
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Feb 28 14:27:02 2020 +0000
      
          Remove call to validateGeneSymbols
      
      commit 642449af628c8636b28ea4bb94d0fafa74ad7b47
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Feb 28 13:20:29 2020 +0000
      
          Update Finder Post Load Steps to respond PicoCli commands
      
      commit 958acf1eec6c076a9c6d5c39069a3013edd194e3
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 27 15:47:16 2020 +0000
      
          Refactor patient creation
      
      commit 21d48fa0fb27210e5c4821ea16e7e65219b62b9d
      Merge: 5b7c274ad 3efbb59c8
      Author: Sprintell <abayomi@sprintell.org>
      Date:   Thu Feb 27 12:55:04 2020 +0000
      
          Merge pull request #137 from PDXFinder/PicoCli
      
          Fix Curie_OV replace with Curie_OC
      
      commit 3efbb59c893237f27ed4bf8ba974ca172ec10cad
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Feb 27 10:54:33 2020 +0000
      
          Fix Curie_OV replace with Curie_OC
      
      commit eb92dfb757c10cb49bad394ec2359e549fa61d0c
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Feb 26 22:40:54 2020 +0000
      
          Refactor provider group creation
      
      commit 2a74a9fe582b36f4c4e35255e004d355487cb04c
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Feb 26 17:12:18 2020 +0000
      
          Commit to fix very broken exportAll functions. Null checks to prevent breaking on exportAll
      
      commit 5b7c274ad5e891cc2e5c15cf447438537929fe07
      Merge: 2eff7bdaa bc53d2f6b
      Author: Sprintell <abayomi@sprintell.org>
      Date:   Wed Feb 26 11:56:35 2020 +0000
      
          Merge pull request #136 from PDXFinder/PicoCli
      
          add other required Spring Boot configurable parameters to picoCli Cal…
      
      commit bc53d2f6b292cd677234d84fc3aa5bc27042a22c
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Feb 26 11:36:42 2020 +0000
      
          add other required Spring Boot configurable parameters to picoCli Callable element
      
      commit 2eff7bdaaba49ca37f3c06b8907edde2a5ce51c0
      Merge: d54a77154 d808abf4a
      Author: Sprintell <abayomi@sprintell.org>
      Date:   Wed Feb 26 10:36:43 2020 +0000
      
          Merge pull request #135 from PDXFinder/PicoCli
      
          New Command Line Interface
      
      commit dcb83afa37b9ffdd33193573b95fc039f1c1c164
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Feb 26 10:14:25 2020 +0000
      
          Tidy up and add toStrings on DAOs
      
      commit d808abf4a55d86563480563c569456d9559c1796
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Feb 26 10:10:54 2020 +0000
      
          remove unused data directory parameter
      
      commit e7b33ee153b001b71a568dedde7b8ec9ec8fb089
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 25 17:49:02 2020 +0000
      
          Default Data set requested to load should not be all
      
      commit 8323a01f8517600ec1ff2e2ba1e15aea6833d724
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 25 17:22:13 2020 +0000
      
          Add Universal Loader Data Loading Group (-g UPDOG)
      
      commit ed997b5bbda658278d06cbc36376223bbf7b6f6f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 25 17:20:49 2020 +0000
      
          Update LoadUniversal for PicoCLI changes
      
      commit defac7d2fb1375706fbb1932122f38ba7f07bc87
      Merge: e606e87c5 d54a77154
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 25 16:09:56 2020 +0000
      
          Resolve conflicts with dev
      
      commit 44d2eea2e85af8a923267a648df04dbf53037496
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 25 13:36:54 2020 +0000
      
          Refactor getListOfRequestedProviders to avoid errors when no dataProvider or dataProviderGroup is supplied e.g during load All or caching
      
      commit c07e9328cd4860898e10c4a4ae6f008a99499b56
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 25 13:33:28 2020 +0000
      
          Change the multiplicity of the Exclusive -g and -o to make it optional cos of cache
      
      commit 11b1d7d1721370cb22468cffabf4815829211ad4
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 25 13:31:10 2020 +0000
      
          Restore enforcement of previously implemented mutually exclusive commands dataProvider and dataProvidergroup
      
      commit 445d86d214033e0ca872c019c7e640856898393b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 25 12:49:36 2020 +0000
      
          Add loading cache PicoCLI feature and fix loading specified list of dataproviders
      
      commit b3031ad8b66358cad8015ee2da716e7d001f88b0
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Feb 25 11:59:33 2020 +0000
      
          Down Dog changes. One to the modelRepository to includ Hoststrain information. Another for exportAll functionality
      
      commit e606e87c5ab7efb6217a15081e3977c0a4d8b4d3
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 25 09:32:32 2020 +0000
      
          Start multi file validation for omic data
      
      commit ce9e1d83797b36203dfda4b74723f608066620a0
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 20 17:01:39 2020 +0000
      
          Factor out ColumnSpecification
      
      commit d99ff46b16f13a20cbcbb529e453ad0dad14e435
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 20 14:54:52 2020 +0000
      
          Allow validation without object creation and persistance
      
      commit 67e65059c8f7377d23d46e819eca418fa21fc659
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 20 10:56:22 2020 +0000
      
          Refactor validation rule creation
      
      commit e6d9df3785eec600abedf792df0f0bcb642d0206
      Merge: ec3d056f8 9e605927b
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 20 09:48:21 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit ec3d056f825e3965138cd832af682d8b842793ab
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 20 09:46:37 2020 +0000
      
          Inject dependencies for DomainObjectCreator
      
      commit e0acaf1c97468e84188625e950a4cb6cd458d6fe
      Merge: f1d169be7 177e5d2a9
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Feb 19 13:30:21 2020 +0000
      
          Fix new CLI loading
      
      commit 177e5d2a92229ee3ae98edcddbbee66505122521
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 18 18:29:36 2020 +0000
      
          Fix broken tests
      
      commit f1d169be7bb2eface393f34453a39d9f03f7ec86
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 18 18:06:30 2020 +0000
      
          Rename loader and remove delete data command
      
      commit 9e605927be52f3be2016a8c9403d30af23812458
      Author: afollette <follette.alex@gmail.com>
      Date:   Tue Feb 18 17:58:31 2020 +0000
      
          Made changes to the MolecularData variables for updated template
      
          Because
          *These variables reflect the data on the template
      
          Changed MolecularData to include multiple variables that were not included on the previous template. Change getMutProperties to set these variables from row data.
      
      commit 5ddb8600454d28162633089bbfaa649e85c36594
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 18 17:50:12 2020 +0000
      
          Support loading groups of data providers
      
      commit d675429a1c61fac6abc09cb368aa73377bb27147
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 18 17:47:50 2020 +0000
      
          Updated unit test for String fileDirectory
      
      commit 06cebb9e889b8eaa2277d42903dccb850245f00b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 18 17:47:14 2020 +0000
      
          Updated LoaderNew, FinderCommandline and DataProviders
      
      commit 2101f7fc61ace9a4c68ce59dd20b6fa3a072c28e
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 18 17:44:40 2020 +0000
      
          update configuration file for new data directory data-dir
      
      commit 62ffd2bcc98a4b24767460189a641b58832eefaa
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Feb 18 17:43:53 2020 +0000
      
          Refactor custom loaders for new CLI
      
      commit a0ea7b4665816d91db3001bd44567d87d19163a2
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 18 16:50:56 2020 +0000
      
          Test getProvidersFrom
      
      commit 0f7778080588bcbef76be16cfa72787f5ad5a023
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 18 14:47:02 2020 +0000
      
          Set correct success code
      
      commit 8b620c3aa2bcefbd96b581090f81503de962e994
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Feb 18 14:19:34 2020 +0000
      
          Use marker hashmaps for marker harmonization
      
      commit 1a755c0d5506b7c578e8031c91b245523989d6af
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Feb 18 14:18:11 2020 +0000
      
          Cleanup
      
      commit e85ca88011fba186d195642325c9826c8af68628
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 18 10:11:11 2020 +0000
      
          Remove IRCC embargo, set data to be visible
      
      commit b6b0c323f6db1624f596a1c4353f98188a0c348d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Feb 18 08:27:37 2020 +0000
      
          Load cna
      
      commit abe31d117b72c674112f39edbf94a15e0b0743e0
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Feb 17 15:22:52 2020 +0000
      
          Extract load logic to separate class, add unit tests
      
      commit b2c3d7fd5950caff67859ac9a2abea353469c422
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Feb 17 12:35:07 2020 +0000
      
          Read cna files
      
      commit dcb181978b14ee94d1d6eadc90e39162d2dfff2e
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Feb 14 15:27:24 2020 +0000
      
          Inject ontology mocks for testing
      
      commit 7943e3f2a4705b406b6bb61236beb840dc859fd8
      Merge: 76fc72689 5c4d54c83
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Feb 14 09:52:54 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 76fc7268991bbf80ab9c0db0b15bd8852b89496f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Feb 14 09:52:44 2020 +0000
      
          Refactor molecular loading
      
      commit c0eaf520ad5d62f4aa21fd900b5075065f2ad9e5
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 13 20:57:45 2020 +0000
      
          Fix CreateBaseCommand dependency error
      
      commit d768f7c0de31d5c62071bc7680866e7bed83f1bf
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 13 16:53:47 2020 +0000
      
          Revert loader deletions
      
      commit dee00ea4234312ab641fb8375d5f5c3b0778ab4b
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 13 16:03:34 2020 +0000
      
          Call new ontology loaders
      
      commit 254e85cb6b6a43c872ce34c718a9431bc1f5f0c8
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Feb 12 15:04:07 2020 +0000
      
          Add pico CLI
      
      commit 5c4d54c8394ac3b66a6d254cd1a0e184dbf95947
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Feb 12 11:51:49 2020 +0000
      
          Override equals() and hashCode() for ValidationError
      
      commit 862b0b74338eb06d30ccfe7d1de254106a24b473
      Merge: cc235a96f f32390f19
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Feb 12 08:34:37 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit f32390f19b2f3ab09a5f0de84a93c0ef4d775e0d
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 11 12:40:56 2020 +0000
      
          Fix provider name removal
      
      commit 586f7e884a22d2d6f324170fa7d088ef22339385
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 11 11:35:06 2020 +0000
      
          Sample entire column for type inference
      
      commit cc235a96f61bbf0731a5347d43ac20335d56d550
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Feb 10 14:28:29 2020 +0000
      
          Implement drug dosing for models
      
      commit a9dfda1f15dec3494a925bf7cbebf5ae391b2228
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Feb 10 14:23:34 2020 +0000
      
          Make sample platform loading optional
      
      commit 9866c6358d50f5c21af25b9d4b0ceafeada68b0f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Feb 7 08:51:19 2020 +0000
      
          Remove header rows from treatment files
      
      commit 14e3607eae3585f2e89e0899403fc9234be68367
      Merge: 807ec0d12 b5653a472
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 6 15:28:28 2020 +0000
      
          Resolve merge conflicts
      
      commit 807ec0d125467bc7a474ae9bde60fb6f815dbb96
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 6 15:25:08 2020 +0000
      
          Conditionally remove omics file header rows
      
      commit b5653a47214b6667a1982770622de3c41778f36d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Feb 6 14:35:59 2020 +0000
      
          Add cna to test
      
      commit 44a3200cfad7adecb19942a9cd7e42dc523213e0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Feb 6 14:19:20 2020 +0000
      
          Load treatments
      
      commit 55b427ed52c0e8ec3f63adbe8d534d05d8fc9eaa
      Merge: b15f1b8c0 6f6c4a8c2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Feb 6 14:14:23 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
           Conflicts:
          	indexer/src/main/java/org/pdxfinder/dataloaders/updog/Updog.java
      
      commit b15f1b8c09afb792818265ecd51d0c658077121b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Feb 6 14:13:48 2020 +0000
      
          Load CNA
      
      commit 76ea903d5be83462807388baf786003ab05f9f50
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Feb 6 14:13:35 2020 +0000
      
          Add cna attributes
      
      commit 7972c007ae3bea721183a867ccc9c20dfb7671f7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Feb 6 13:39:51 2020 +0000
      
          Convert molecular data for patients before persisting
      
      commit 59be0f25908b7935d863e182d58d05879fffa99e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Feb 6 13:39:12 2020 +0000
      
          Read treatment data
      
      commit 6f6c4a8c2803c0287bfbcafb132e7e0766c101c0
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Feb 6 13:04:12 2020 +0000
      
          Refactor ColumnSetSpecification creation
      
      commit 9d91003f6a8e0091c3d00db3c2cb8e9671c6135e
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Feb 5 14:39:12 2020 +0000
      
          Remove provider name from table name
      
      commit b17539d6eb2169234d1ea3edecfcf3fe6c821684
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Feb 5 14:31:07 2020 +0000
      
          Clean up provider name
      
      commit 627712ea1d315acc1324514ba79c80d9cb21e984
      Merge: fd33549e5 aed1a8026
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Feb 5 14:08:20 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit fd33549e5c892732b49169ac597fe5a35f892fde
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Feb 5 14:08:10 2020 +0000
      
          Add patient treatment loading
      
      commit aed1a80267f597481b01682d17ec05d8623a9657
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Feb 5 14:07:16 2020 +0000
      
          Remove provider from filename in TableSet
      
      commit 1021b74e76af19c45a1391caa0e88917a4bcfe3d
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 4 18:13:54 2020 +0000
      
          Add all validation rules for metadata
      
      commit f066928a9e969d33cc6f050d563ddb3af935ee5a
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 4 16:17:54 2020 +0000
      
          Add test for valid file with required non-missing values
      
      commit eee269aa2ad408b8af267c579e0628aff929fd17
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 4 15:55:36 2020 +0000
      
          Validate relations and remove relation type specificity
      
      commit 08ff0a29d5fefa6ac6c4e4f20a01eee49dbaf718
      Merge: c1afae2b7 30067263f
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 4 14:47:50 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit c1afae2b7ee34e35d750b2e2228fd5c55304ae0e
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Feb 4 14:47:45 2020 +0000
      
          Add validation for missing values in relations
      
      commit 2e4ef3ee69e6f9c50f58b74ef1f6501e697285cb
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Feb 4 14:14:08 2020 +0000
      
          Add cna and transcriptomic skeleton
      
      commit d01bbc32835408e17de5369b5019f545e4058167
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Feb 4 09:55:51 2020 +0000
      
          Add cytogenetics
      
      commit 30067263fddf60d64119b38afe7bacc2739f05a5
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Feb 3 13:26:04 2020 +0000
      
          Persist molecular data
      
      commit b9e09aa933720e8794c52929e5cf455813e37066
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Feb 3 08:39:04 2020 +0000
      
          Cleanup
      
      commit 76b54b0d63a34678f70a02c427d5c55f7d8948c9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Feb 3 08:38:38 2020 +0000
      
          Add mutation test table
      
      commit b87424b0a549556d48f0594e2159d5942a1457e7
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jan 31 17:36:19 2020 +0000
      
          Fix validation messages
      
      commit a0671173d1ad383d162417442305a13cd0d7ed69
      Merge: 800b05c01 6c054dd18
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jan 31 16:04:11 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 800b05c013b97f404c61ae1d0431e079192454c0
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jan 31 16:03:58 2020 +0000
      
          Pass table column names to validation rule creation
      
      commit 6c054dd185c5e570ebd84026074a1225ca63235a
      Merge: 43dc53159 096d0b4ad
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 31 11:32:28 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 43dc53159c168867b16f0077ed3870ac5c0bed9a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 31 11:32:13 2020 +0000
      
          Create mutation data
      
      commit 096d0b4ad40d2a7162858130069de995650e3792
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 30 20:46:09 2020 +0000
      
          Tidy up after rename
      
      commit 4a386b33e4966cbf7d5d151c172df6dbf095caa2
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 30 20:40:10 2020 +0000
      
          Rename TableValidationError to ValidationError
      
      commit c65638d1e48b6b1862b9e0a4a0ea0482be6ee7e5
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 30 20:34:44 2020 +0000
      
          Add message formatting for broken relation errors
      
      commit 44a4a3a4dd5539b1af7d45bf41a93bcc47d50dc6
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 30 18:44:38 2020 +0000
      
          Fix tests
      
      commit bea5593775a3356294e99590fffb988714f6a552
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 30 18:40:37 2020 +0000
      
          Refactor validation errors
      
      commit a5bfe20c0efa7a6a36b87c1cb6bbdc5a7c4506a1
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 30 11:50:13 2020 +0000
      
          Report missing values in right column for one to many relations
      
      commit 985cd0fa8eab06aca68bd2fd31783f004e434be6
      Merge: f1701f324 f9246742c
      Author: Sprintell <abayomi@sprintell.org>
      Date:   Wed Jan 29 19:50:36 2020 +0000
      
          Merge pull request #127 from PDXFinder/dependabot/npm_and_yarn/admin/src/main/app-ui/handlebars-4.5.3
      
          Bump handlebars from 4.1.2 to 4.5.3 in /admin/src/main/app-ui
      
      commit 4b3e939011c11a29ab6f671dccf25aaa41b43146
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jan 29 14:35:22 2020 +0000
      
          Refactor tests
      
      commit 55a040c430b21f20246a6eb54d50ac7ce65c43df
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jan 29 13:50:44 2020 +0000
      
          Clean omics tables
      
      commit 30245ac5cc2b035f856166980b673671817c4b4e
      Merge: 6a9dab1c9 95f65f7cf
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jan 29 11:42:04 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 6a9dab1c9cb3a7065575163f540b8642820831c5
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jan 29 11:41:54 2020 +0000
      
          Add molecular data creation
      
      commit 95f65f7cf19651473cd80b13577d62bc325c860d
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jan 29 11:40:47 2020 +0000
      
          Allow Reader to import mutation files
      
      commit df2bd2a3d1bf8a956f40a1f6be2d636ee43c44f5
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jan 29 11:29:47 2020 +0000
      
          Add relation validation for missing columns
      
      commit a158f05a9162e6981ea910629dbaf845c904443f
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jan 28 17:20:09 2020 +0000
      
          Add validation for unique values
      
      commit 6fa18b9162adeee2777e16f3eeb8a52e13136f0f
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jan 28 13:57:44 2020 +0000
      
          Refactor and rename
      
      commit c9c52bf0f185a781ee12d38560f1c6969183e394
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jan 28 10:18:02 2020 +0000
      
          Use Apache commons Pair
      
          Because:
          - Needed to use a tuple datatype, originally tried javafx.util.Pair
          - Development server uses OpenJDK 1.8 and therefore lacks JavaFX
          - Used org.apache.commons.lang3.tuple.Pair instead
      
          JDK version should be standardised across machines to prevent this
          occuring again (I was running JDK 1.8, which compiled fine)
      
      commit 4528ee766c846c10247f8ec77b0c95d2e9bf277f
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jan 27 20:42:36 2020 +0000
      
          Add validation for missing required values
      
      commit 700f54bcb37fbe061f3f4580c706f6d0b882c1cc
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jan 27 18:31:44 2020 +0000
      
          Refactor missing required column validation
      
      commit 079a43f32d87e29cce716df4390c6406e8259414
      Merge: 47228b7d8 25a68a77e
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jan 27 14:51:50 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 47228b7d8f5165ad7393d392c480816a2da467e5
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jan 27 14:51:39 2020 +0000
      
          Refactor fileset specification to separate class
      
      commit 25a68a77eaa38cf81e68b4f0951ea39f420df632
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 27 13:46:13 2020 +0000
      
          Add test data for sampleplatform
      
      commit c47ccc9ea2612cfe1f13f15758ae8f5ba7acaae9
      Merge: ec7ad82ac 546671685
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 27 13:35:11 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit ec7ad82acd01e26c9b13fc576c2d997f62e59008
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 27 13:34:56 2020 +0000
      
          Create link mc and platform to sample
      
      commit 7cd1eabb30d975d0450280462cbffc1ee7d617b2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 27 13:28:32 2020 +0000
      
          Load sample platform data into dataframe
      
      commit 546671685da61f3a3e3e8008aa77544e78bd8b9f
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jan 27 11:54:17 2020 +0000
      
          Update missing required value to return readable row number
      
      commit 408fdc6a4b910da0f7d3343f0a5b1b256718b53e
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jan 27 11:36:04 2020 +0000
      
          Add validation error for missing required value
      
      commit d2ecef8a2f79e5739ef18918b344f1f32b2ce3b6
      Merge: c560e03f9 c016417b3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 27 08:09:52 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
           Conflicts:
          	indexer/src/main/java/org/pdxfinder/dataloaders/updog/DomainObjectCreator.java
      
      commit c560e03f91e323badbbd08ad3d9a83b7e5249679
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 27 08:09:03 2020 +0000
      
          Add molecular load skeleton
      
      commit a923ea3b1adc8f7d5a0a90566a9bb8f366a684b8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 27 08:08:29 2020 +0000
      
          Support mutation
      
      commit c016417b3fb730b173e9fafa2a0522014dc965b3
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Sun Jan 26 22:22:24 2020 +0000
      
          Refactor validator and tests
      
      commit 9bd85efa2a734aa53f5dfa7372007fa4aa870e84
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Sun Jan 26 19:06:56 2020 +0000
      
          Add validation error factory method
      
      commit d54a77154e6e1b368979cb0b49a0a30efb8a9d36
      Merge: 437b1e3fe 74a126ff6
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Fri Jan 24 17:43:07 2020 +0000
      
          Merge pull request #131 from PDXFinder/xdog-SampePlatform-adj
      
          Xdog sampe platform adj
      
      commit c89ad587c6d448bb2f3e14d136a59f10146a9fed
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jan 24 10:38:16 2020 +0000
      
          Check for Group if accessbility or access modality present
      
      commit 437b1e3fef7e91aba0c9bdb15e40688a72fe139b
      Merge: 22a082051 47e7c6a89
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Jan 24 09:50:54 2020 +0000
      
          Merge pull request #128 from PDXFinder/marker-and-ontology-catching
      
          Marker and ontology catching
      
      commit 9853e29ff6f7a5225f751eafd1bb11ce8764741b
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 23 21:08:24 2020 +0000
      
          Add tests and refactor
      
      commit 47e7c6a89f6f17a756211e6a175d98b3ac2eae20
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jan 23 14:03:39 2020 +0000
      
          Added unit test cases for file handler utilities
      
      commit 213205c40f9a7e0c55542342a3d750b46a687d74
      Merge: 5df806d04 8d16f6117
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 23 13:40:56 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 5df806d04b8c25d23ea8c41154f8cf65408869de
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 23 13:40:53 2020 +0000
      
          Remove missing rows by id columns
      
      commit a9353352a0836d5385ed8b48dd9bcc89509f178a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jan 23 10:52:28 2020 +0000
      
          Added unit test cases for utility Service
      
      commit d1d2aa61f6fcdfdeea15f30a3a5f57e83e735c4e
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jan 23 10:51:29 2020 +0000
      
          Added unit test cases for utility Service
      
      commit 8d16f61179fef83fb0db8cd7e1933e62440a6c57
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jan 23 09:19:22 2020 +0000
      
          Do not autofail testcases
      
      commit 9373a0d9e019978e69b1a34278be48ecc10871e5
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jan 23 09:14:15 2020 +0000
      
          Disable test
      
      commit d113f5f5ecaf7dad2ee6256e72d3fbee4ccc28e4
      Merge: b22ef4944 ead6d3f09
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jan 23 09:11:30 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit b22ef4944988ad1b2d07a9b691ff2d0f56a2f5f9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jan 23 09:11:20 2020 +0000
      
          Add metadata specifier to TSV
      
      commit ead6d3f09c1722bb61ae612bfa699df056f31bfc
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jan 23 00:17:24 2020 +0000
      
          Add header removal, collect in TableUtilities
      
      commit 4262c1fc84ffcb3f0343d854acf293d2c5012b87
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jan 22 16:03:18 2020 +0000
      
          Read cytogenetics data
      
      commit 8a3198adcff54a56bce479e8845f66f6a68e0d71
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jan 22 11:08:11 2020 +0000
      
          Test wrapper method
      
      commit 97c4082aa4a61f61b6a2b86dd4fc5fe2bb477c86
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 21 17:13:08 2020 +0000
      
          Fix bugs
      
      commit 47b3cce83851adb6aa6cddbdd152b921dd5b8aaf
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 21 16:37:08 2020 +0000
      
          Add more unit test cases
      
      commit 1d551aff60a5a5fecc6da8cfb89e0d12a61eb7e8
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 21 16:27:08 2020 +0000
      
          Add more unit test cases
      
      commit 90aa39248943c28249ec9cf3070e8b85bc01c208
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 21 16:14:03 2020 +0000
      
          Added unit test for NCIT Ontology loading steps
      
      commit d51d495bbbfc337e718e566c9b35ece52d808d69
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 21 14:56:56 2020 +0000
      
          Check accessibility of models
      
      commit 48daa9519763cef265b50db9511a68b91b083bda
      Merge: 1b6b07ac7 90040b528
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 21 14:40:12 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 1b6b07ac720e88ce30306761d0c5334ede730142
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 21 14:38:20 2020 +0000
      
          Add sharing related tests
      
      commit 1b15163614a07ac1e7772a1b511a99827d973c33
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 21 13:17:48 2020 +0000
      
          Add model related tests
      
      commit 0b319960b3d0865f28c980eeb84e957fa1a1124b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 21 13:17:21 2020 +0000
      
          Set missing sample attributes
      
      commit 90040b5284c55702d533c9defd1f1f66dd83f863
      Merge: 6909f4b99 33ce12330
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jan 21 12:01:54 2020 +0000
      
          Merge remote-tracking branch 'origin/updog_refactoring' into updog_refactoring
      
      commit 6909f4b994f23aa8a20c98a3016cf84d10508ad8
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Jan 21 12:01:34 2020 +0000
      
          Add validation for missing columns
      
      commit 33ce12330574785202bc7abc19136120c0c646b1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 21 11:45:17 2020 +0000
      
          Pass provider through the run method
      
      commit 7484cbeef3d1d75f138089d09b880ecb4d2cf122
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 21 11:34:16 2020 +0000
      
          Added unit test for DataUrl enum class
      
      commit 223daac219e1baa580627e6f1ce18741b89bd308
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 21 11:20:25 2020 +0000
      
          Update unit test for other data loading command line options
      
      commit bab44bf3114ab76c4e8a2bbc7b98c089d8034931
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 21 10:51:45 2020 +0000
      
          Added unit tests for Ontology and Marker Catching implementation
      
      commit fb88feed0a2e4327525391a8fd9631d55b73b562
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 21 10:50:34 2020 +0000
      
          Refactored the DataCommands to a single point of entry
      
      commit 3d2c62fc7b7cb83fe1ceb78e4c6391607d7627db
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 21 10:49:17 2020 +0000
      
          Refactored the Caching (LoadMarker,LoadNCIt,LoadNCITDrugs) Business Logic to service Layer for proper unit testing
      
      commit adc70cb7afdb91c8a8432495dc99482cece23dab
      Merge: 9313ab0e8 b542be099
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 20 13:32:28 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 9313ab0e82668f8e049f9b9ca7d6050e92764788
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 20 13:32:06 2020 +0000
      
          Add patient test
      
      commit 70fff0248dee08d8cd4e624163923c8609ab50b6
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 20 13:31:51 2020 +0000
      
          Initial commit for test
      
      commit 333998dd1c539a2bd39266bde00e97d2d1e464c2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 20 13:31:16 2020 +0000
      
          Change doc method visibilities
      
      commit b542be0990ff002f7bb0211603f156b6b8387c15
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Jan 20 11:35:06 2020 +0000
      
          Provide better context for missing file validation errors
      
      commit 91a58778a9500dda6c333d547e561cd24ab82573
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jan 20 09:59:45 2020 +0000
      
          Create sharing data
      
      commit 10c8730ed9678e181a456ccfb314a4f49f87d466
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jan 20 08:00:35 2020 +0000
      
          Fix save marker should return the new marker created
      
      commit 3a0106ab147bedf8bf7b05ad083c6bfe4c3f83f3
      Merge: 898efab6c 614b7b660
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Sun Jan 19 17:52:36 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 898efab6cf69b1b002f07810d3875e8db1307f04
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Sun Jan 19 17:52:32 2020 +0000
      
          Validate missing required files and rename tests
      
      commit 614b7b66093d05f8a280c7696369c1409e7ebff7
      Merge: 51060906d 81ff18717
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 17 15:25:06 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 51060906d20523eaccffb8706048c458bff43f97
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 17 15:24:45 2020 +0000
      
          Reduce CC for sample creation
      
      commit 6b8a6414c86574cbcbfdc337a3cdaafe9c4e279f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 17 15:00:04 2020 +0000
      
          Remove utilityservice
      
      commit 81ff18717d7179ee5d4ee7a025c3d641a00e0967
      Merge: 69ecfacb2 639a39c62
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jan 17 14:58:10 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 69ecfacb2ee972a9bc6e9fedb4839d2e511bff6c
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Jan 17 14:57:50 2020 +0000
      
          Add ColumnSpecification
      
      commit 639a39c62cd0f65cb2027394faaa1589f475181c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 17 13:59:26 2020 +0000
      
          Load model validations
      
      commit 3d0fe4e7f9def0b3af925ea7db1696c7d6a98d69
      Merge: de364315b a15fc9861
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 17 13:11:09 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit de364315ba32aefe2a65043f742ddf0e5389641a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 17 13:10:31 2020 +0000
      
          Load and save models
      
      commit e533491296c7299268143f6090064ce0b4d59832
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 17 13:09:36 2020 +0000
      
          Add dao ref to session
      
      commit 74a126ff6b90876925898439a0da609bffbf9b44
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Jan 17 10:02:18 2020 +0000
      
          Fixed failing test
      
          Shifted data structure in the test to accommodate new blank column in sheet.
      
      commit 5480f7ef0b62e2418aacfce67f1ca7bc3265a203
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Jan 16 16:34:55 2020 +0000
      
          Added single column to X-Dog fit SamplePlatform template correctly
      
          added a single empty string to first to list used to generate rows in SamplePlatform template.
          The template starts with a blank box and previously this was not accounted for.
      
      commit a15fc98610dca6314aeb1ee3359a9081183c7cc8
      Merge: 81c99c245 06146fec3
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jan 15 21:12:39 2020 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
      commit 81c99c24545cea26beab3ecdaddf61f4de315a6d
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Jan 15 21:12:29 2020 +0000
      
          Validate all required sheets are present
      
      commit 06146fec3c44530df1ac5493566426c7ca6ed06b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jan 15 14:09:20 2020 +0000
      
          Add enums for column headers
      
      commit 84cb1b1d3b502a255bc3d325225785977a65e9a8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jan 15 11:53:26 2020 +0000
      
          add sample to snapshot
      
      commit 63d6688be14fdf76cb4bc662149a81f5da197efa
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jan 15 11:51:25 2020 +0000
      
          Load sample data
      
      commit f1701f3240f97938512a014212053adc6c54601d
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jan 10 15:28:18 2020 +0000
      
          SUMMARY stats update
      
      commit cda09205814c02f0c7c70241073dfdacb067627c
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jan 10 15:14:19 2020 +0000
      
          SUMMARY stats update
      
      commit 00412f8eff31d6ad38e89809fdbbd1a7c168ea25
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jan 10 14:10:44 2020 +0000
      
          Refactored for code quality
      
      commit 105ae8ea48eb57302de4f0447170269985f90f41
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jan 10 11:23:27 2020 +0000
      
          Use column headers instead of positions
      
      commit d96c66dda41c724b1192da754c111976c4deefb3
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jan 9 13:49:03 2020 +0000
      
          Revert "Fix errors"
      
          This reverts commit 0f2c22aeb3d1b6b22333b0ae07284a1bbd55f588.
      
      commit 0f2c22aeb3d1b6b22333b0ae07284a1bbd55f588
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jan 9 13:44:27 2020 +0000
      
          Fix errors
      
      commit 49ebb95869c924c4c1fe161f74efb67f1d4f7c91
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jan 8 16:19:47 2020 +0000
      
          Fix code bugs and smells
      
      commit 34974c53f0a5faf807faf6338ba8621794eed66e
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jan 8 13:56:05 2020 +0000
      
          Fox the code smells in LoadNCItDrugs
      
      commit ac553cbe35e2a715331d90a477bc6d750c764899
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 7 16:51:03 2020 +0000
      
          Fix code smells:
          Duplicated String literals in Option Commands
          Dangling Javadoc comment
          More arguments provided than placeholders specified
          Remove unused imports e.t.c
          Reorder the modifiers to comply with the Java Language Specification. e.t.c
      
      commit 7d5b3cfbb9792816857dd2d475398192833000db
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jan 7 11:56:35 2020 +0000
      
          Added FEATURE to ensure whenever reloadCache command is issued, Markers and Ontologies (NCIT and NCITDrugs) are catched.
          When loadALL command is invoked LoadMarkers, LoadNCIT and LoadNCITDrugs are ignored except if there are no previously cached versions
      
      commit aec9456362b303bb5c67c14b4762887a999c573c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jan 8 10:25:50 2020 +0000
      
          Load providers and patients
      
      commit 8e3790212ae7b4680f6f0597f85cc429b537d958
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jan 7 12:32:52 2020 +0000
      
          Dinamically add directories to loaders
      
      commit f9246742c06893589625e4570c8c47d0015f9014
      Author: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
      Date:   Fri Dec 27 20:49:42 2019 +0000
      
          Bump handlebars from 4.1.2 to 4.5.3 in /admin/src/main/app-ui
      
          Bumps [handlebars](https://github.com/wycats/handlebars.js) from 4.1.2 to 4.5.3.
          - [Release notes](https://github.com/wycats/handlebars.js/releases)
          - [Changelog](https://github.com/wycats/handlebars.js/blob/master/release-notes.md)
          - [Commits](https://github.com/wycats/handlebars.js/compare/v4.1.2...v4.5.3)
      Signed-off-by: default avatardependabot[bot] <support@github.com>
      
      commit 804671e1d002dc51a6df61eddf89b39125f9bad8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Dec 20 10:49:39 2019 +0000
      
          Add requred services to constructors
      
      commit 88920ef8b51762b0452c5c04ea0418d6b6d2eeef
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Dec 19 15:56:14 2019 +0000
      
          Fix autowire error
      
      commit 62bbf90964fa2800b4ab65001114b13e841bd9df
      Merge: f87a57a15 8c043a0fd
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Dec 19 15:23:31 2019 +0000
      
          Merge branch 'updog_refactoring' of https://github.com/PDXFinder/pdxfinder into updog_refactoring
      
           Conflicts:
          	indexer/src/main/java/org/pdxfinder/dataloaders/updog/Updog.java
      
      commit f87a57a15789c7ab25d86376865043c6cff10e37
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Dec 19 15:23:02 2019 +0000
      
          Update skeleton
      
      commit 662869c4245ff2447ad1a91fdb22e696e840dea0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Dec 19 15:22:33 2019 +0000
      
          Update skeleton for new updog
      
      commit 8c043a0fdfba5a3f92a765d4fd4b2b931bd85c1a
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Dec 19 13:30:59 2019 +0000
      
          WIP Read tsv from stream
      
      commit de6def1848c4a54c86ca981062ae63af6a035929
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Dec 18 11:50:09 2019 +0000
      
          WIP load files with stream
      
      commit ceb3964064ba5fb41e85b3fab6102fbbee8a0816
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Dec 17 10:45:00 2019 +0000
      
          Add skeleton for new updog
      
      commit a4c7e4a35694a936f95077c5fb5aa88b6dca14db
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Dec 17 09:44:48 2019 +0000
      
          Use subpackages in sessionfactory
      
      commit 157d3ac064de4a2296568d37227bf8311f886f2b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Dec 17 09:36:09 2019 +0000
      
          Use subpackages in sessionfactory
      
      commit 03c601448e12cdc82f0059f0a5a48b2adf3ba509
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Dec 17 09:35:30 2019 +0000
      
          Allow to use unrecognised options to support root dir override
      
      commit 16a5c0d725e0c5e65928c891910fd828f230adcc
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Dec 16 16:00:47 2019 +0000
      
          WIP add tsv file reading
      
      commit 22a08205172f3d1436bdb14647d903ff03588f76
      Merge: bcaae837b 5a5bba0e9
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Mon Dec 16 15:01:10 2019 +0000
      
          Merge pull request #125 from PDXFinder/DownDogAddedColumnUpdate
      
          Down dog added column update
      
      commit 5a5bba0e95315bb78db29cc6eec7f54c89694c2d
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Dec 16 14:28:37 2019 +0000
      
          test the creation of files by the export method.
      
          because
      
          -- Tests covers the reading of excel sheets and the creation of desired file structure
          -- Gate requirments
      
          Added a single test that creates a several dummy xlsx sheets to feed to the UniversalDataExporter.export method.
          Then checks to see if the export method has created the correct data structure. Also tests for the creation of
          metadata.xlsx as a minimum requirement for export.
      
      commit e1f0edfb9abd004ac0c231928cbf79f2cec747ce
      Author: afollette <follette.alex@gmail.com>
      Date:   Mon Dec 16 14:25:38 2019 +0000
      
          test the creation of files by the export method
      
          because
      
          -- Tests covers the reading of excel sheets and the creation of desired file structure
          -- Gate requirments
      
          Added a single test that creates a several dummy xlsx sheets to feed to the UniversalDataExporter.export method.
          Then checks to see if the export method has created the correct data structure
      
      commit 842805923f19751e8e34d0d2a0c88e3abf9cdd9c
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Dec 11 14:16:22 2019 +0000
      
          added IOexception handling
      
          'cause
      
      commit fa6e3f4106119ee5a6e0a19401735ed90c2f2450
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Dec 11 13:38:51 2019 +0000
      
          Adjusted Down Dog to export files in a structure similiar to the UPDOG
      
          Because
      
          --This will greatly cut down on time needed to use the exported data.
      
          Used the provider name to create a directory in the export folder then placed mut and cna folders in that directory, if any of these files do not already exists. Ajusted the names in the Down Dog to match the UPDOG.
      
      commit a27ffec6325558dc830932a0fd4647642a562bcc
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Dec 11 11:45:35 2019 +0000
      
          Made adjustments to Down Dogs (X-dog) accommadate new column in templates.
      
          Because
          -- It is neccessary to updated to be with current template
      
          Reads in patient "EthnicityAssessment" and adds it to the patientSheetDataExport to be written as an excel sheet.
      
      commit bcaae837b52c7fd7dad01ae94d3c886cf1b34694
      Merge: 5685547c5 5e0ba9a2a
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Dec 11 11:36:33 2019 +0000
      
          Merge pull request #122 from PDXFinder/newColumnAdjustments
      
          Adds new column "ethnicityAssessment" to the Universal Loader
      
      commit 15ac444026aa2baf26ff89d3682e5a92994d1071
      Merge: 767ea140c db0303492
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Dec 11 10:22:53 2019 +0000
      
          Merge pull request #123 from PDXFinder/revert-121-newColumnAdjustments
      
          Revert "New column adjustments"
      
      commit db03034927a16edba89da01272537b489860f52f
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Dec 11 10:19:03 2019 +0000
      
          Revert "New column adjustments"
      
      commit 767ea140cae8d51370146ebb654cb3ead4d65f61
      Merge: 3814acfc1 5e0ba9a2a
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Dec 11 10:15:10 2019 +0000
      
          Merge pull request #121 from PDXFinder/newColumnAdjustments
      
          New column adjustments
      
      commit 5e0ba9a2a118296cab4ae0cac1f27900b911b442
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Dec 11 10:04:11 2019 +0000
      
          Adds new column "ethnicityAssessment" to the Universal Loader
      
          Because
      
          -- We will need to store this data in the future
          -- Templates break without this adjustment
      
          Added getter and setter and new variable "ethnicityAssessment" to patient model.
          Loader takes column from patient sheet and stores it in the patient using the setter method.
      
      commit 5685547c5f2523b6687b3ef60243ee15d8e16394
      Merge: 69bc1290b ec1209c98
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Dec 4 13:46:27 2019 +0000
      
          Merge pull request #118 from PDXFinder/ircc-gc-visibility
      
          Do not hide IRCC-GC molchar data
      
      commit ec1209c985d3fdec97606248675ea50a81d84067
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Dec 4 13:20:14 2019 +0000
      
          Do not hide IRCC-GC molchar data
      
      commit 64c957e229cc35a90159844830fbd980f1cfa628
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Dec 2 14:46:15 2019 +0000
      
          Fix missing value in MolcharData
      
      commit f881d6b152fe5265e36ec77b51be4c0dc18926ef
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Dec 2 14:00:53 2019 +0000
      
          Transition from MarkerAssociations to MolecularData
      
      commit e155ba9c0d30e5555d2a2e1cec3cc3fb50d14197
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Nov 28 14:42:10 2019 +0000
      
          Remove attributes, add moleculardata converting
      
      commit fe4bf2e6ae6558d3879c64d67e3303238a94d39c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Nov 28 14:28:29 2019 +0000
      
          Add marker references to mc
      
      commit e6773d05533673ac4ee14e8c23e9c7acd3618cd2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Nov 28 14:28:02 2019 +0000
      
          Add molecular data definition
      
      commit 69bc1290b6e20ef38b601090f86b68c5e2815204
      Merge: f95c8917c 6054927c4
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Nov 28 11:59:57 2019 +0000
      
          Merge pull request #117 from PDXFinder/universal_data_exporter
      
          Universal data exporter
      
      commit 6054927c4f4df81cc6dd495bb185a8f416d7fbb1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Nov 25 15:09:40 2019 +0000
      
          Add exception handling for wrong number formats
      
      commit 4c5e993c274bc87bd793a4eedc18aefa60a036eb
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Nov 25 15:09:09 2019 +0000
      
          Reset datarow per sample, not per snapshot
      
      commit f95c8917c24f303d7dd22fb3b0d290bee08759a3
      Merge: dc077560e c077bdc2c
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Nov 19 13:15:54 2019 +0000
      
          Merge pull request #115 from PDXFinder/universal_data_exporter
      
          Universal data exporter
      
      commit c077bdc2c6415c5f65314472e6651081ef5c4350
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 19 10:19:02 2019 +0000
      
          Test empty providers
      
      commit a1c84f6590bced9327829b5dd9b642d25d528b0e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 19 10:02:07 2019 +0000
      
          Test providergroups
      
      commit 827a12ea4a3f3e43161621e2d69064a285ac5d64
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 19 09:51:41 2019 +0000
      
          Test snapshots
      
      commit 6f1adce0b663a3c0f85789f4154acf11e4277b26
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 19 09:37:43 2019 +0000
      
          Additional tests for Patient
      
      commit be7f6423db6c2dd742401b11df83b8d842fe3f55
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 19 09:27:55 2019 +0000
      
          Remove duplicates
      
      commit 343f38bf9e94a254a0d2b302d5e20deb1f594393
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 19 09:19:28 2019 +0000
      
          Add ExternalUrl test
      
      commit aba5c6ad11f19c333a755831653a24550f909c6c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 19 09:18:22 2019 +0000
      
          Remove unused class
      
      commit 0c4f43bef2f4d3a8bdb2b0270ce1a8f791fb0834
      Merge: 7bbdcf125 18d0da96a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 19 08:48:21 2019 +0000
      
          Merge branch 'universal_data_exporter' of https://github.com/PDXFinder/pdxfinder into universal_data_exporter
      
      commit 7bbdcf125da1834aea2d87d6c2c637eb85884701
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 19 08:47:59 2019 +0000
      
          Code smell cleanups 2
      
      commit 18d0da96a761a7c5ca9c9ae891f671fd1a738e44
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Nov 19 00:16:17 2019 +0000
      
          Tidy and apply consistency to formatting
      
      commit 67134ff979c34800e3f91f2f2675ae9edfa1fc96
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Nov 18 09:37:01 2019 +0000
      
          Code smell cleanups
      
      commit 84d73e815439810413c77a54c0e8ff5ec78e72a8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Nov 18 09:31:31 2019 +0000
      
          Remove unused import
      
      commit 2c8032b4aebc2c028bdbcb47835c986cb58ef8b9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Nov 14 14:17:06 2019 +0000
      
          Rename tests
      
      commit ea74738638fe905b7a12465d9791b36412914edb
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Nov 14 13:43:10 2019 +0000
      
          Pass datasource to export as a parameter
      
      commit c5f3e72828fd2fc04389865598360d82b26507ab
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Nov 14 13:24:23 2019 +0000
      
          Update indexer/src/test/java/org/pdxfinder/dataexport/DataExportTest.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit 3f85a244eb90cfe9125618df08e36be055550ccd
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Nov 14 11:23:39 2019 +0000
      
          Import cleanup
      
      commit a64a4e00dd0c337a88f5a146660380ea1c2797cb
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Nov 14 11:17:28 2019 +0000
      
          Refactor last patientsnapshot method
      
      commit d0c72c4e7296f4997d4af7bf70327fdf557271f1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Nov 14 10:25:37 2019 +0000
      
          Add nullcheck to providerGroup
      
      commit 06e9268d00607bfd2adcef6e4e3db9edaa61b348
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Nov 13 14:46:18 2019 +0000
      
          Fix latest snapshot and test
      
      commit fd08ef13b3fcd6040a9417ad4959bf0744d9db73
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Nov 13 13:48:39 2019 +0000
      
          Remove unused import
      
      commit 63b8b871ceb1e36290d3121ee5e794f97dbff8b4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Nov 13 13:46:24 2019 +0000
      
          Test sheet updating
      
      commit 38649b6dd97268d880a7032edfdbf5aea9c2af2a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Nov 13 13:45:29 2019 +0000
      
          Merge export into one method
      
      commit 4218bc5ffe37401e3aa0cc91a303522ccc845eb1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Nov 13 12:56:59 2019 +0000
      
          Add patient integration test
      
      commit e435dba7408133d53f40a748c00214b24a725b56
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Nov 13 12:55:39 2019 +0000
      
          Merge conditions
      
      commit 44de0b591e634a6ab1ca1afa8967ad55c3481ef7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Nov 13 11:43:27 2019 +0000
      
          Remove duplicated dependencies
      
      commit 4ff269f8d1be3bf7930b68aabe046711447dd16b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Nov 13 10:52:24 2019 +0000
      
          Use XSSFWorkbook instead of interface
      
      commit 962d6384a7d5ed835472e4bebfe23ee8e1b89a1d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Nov 13 08:28:07 2019 +0000
      
          Test workbooks
      
      commit f60ae928991725613a29ae83a46eb37ef80f0ffc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 12 14:24:28 2019 +0000
      
          Remove unused imports
      
      commit 58c7cea10875c441bb2fc31246fd071a0752c894
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 12 13:21:09 2019 +0000
      
          Add tests
      
      commit c56fec3759824bf690cfec3a56a7e1fc24f81125
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 12 13:19:37 2019 +0000
      
          Enable all inits
      
      commit 131d3ee4dd0c21182639beddff0534c53bca9b30
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Nov 8 15:25:52 2019 +0000
      
          Enable testing patient and tumor collection data
      
      commit d584178dc652a159398e11b9b716d3a8e8f808a4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Nov 8 15:25:09 2019 +0000
      
          Add snapshot method
      
      commit 05757983e35148bb41e16d996ce33ebd86052fe1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Nov 8 11:10:36 2019 +0000
      
          Sonarcube cleanups
      
      commit eccb609966fc13f5a1cc9609d8769ea9ee45f7c0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Nov 7 09:31:39 2019 +0000
      
          Change export directory
      
      commit dc077560ef4f30c28d6b73ec3ea06d96ad90b042
      Merge: 2afef6128 607b9f0e4
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Nov 5 11:44:25 2019 +0000
      
          Merge pull request #114 from PDXFinder/diagnosis-terms
      
          Do not exclude Neoplasm by special category branch
      
      commit 607b9f0e403a77d2e03bc4e8a01297f99a0a804b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Nov 5 11:14:47 2019 +0000
      
          Do not exclude Neoplasm by special category branch
      
      commit ba27aad76c767e9b91caee71b746e8826fcbe3c6
      Merge: 122e6324f 0e2239333
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Nov 1 10:48:54 2019 +0000
      
          Merge branch 'dev' into universal_data_exporter
      
      commit 3814acfc1e8acba80e9c1b874c19bc6dd9a0140f
      Merge: 621fb24a 0d9d47180
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Oct 21 19:59:15 2019 +0100
      
          Merge pull request #113 from PDXFinder/beta
      
          Beta
      
      commit 0d9d4718010e1e35702f650231d9aa7f882f1642
      Merge: 94cf36466 2afef6128
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Oct 21 17:12:25 2019 +0100
      
          Merge pull request #112 from PDXFinder/dev
      
          Dev
      
      commit 2afef61281e4dc20b4ccaebdf4f827379abb6acb
      Merge: e6fbbbe47 14b17d059
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Oct 21 16:41:32 2019 +0100
      
          Merge pull request #111 from PDXFinder/summary-statistics
      
          Summary statistics
      
      commit 14b17d059378b6ef38d35f8726e9e4c9e539dcb7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Oct 21 15:08:36 2019 +0100
      
          Fix broken tests
      
      commit bd612d64b5f7fc9aa5ecaaf052d39a410c7ede27
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Oct 21 14:27:38 2019 +0100
      
          Update Java Menu for Data Summary Link
      
      commit d485839ea7f0f8ae58b4d252206086077792872a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Oct 21 14:18:48 2019 +0100
      
          Update Statistics Service Data
      
      commit 8d99e774e1d6b260be8bde9d7f4c4babe9138eda
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Oct 21 13:26:20 2019 +0100
      
          Remove unused code
      
      commit 94cf364666882c5ced99ed85b8c79618a3a99426
      Merge: 64987edc0 e6fbbbe47
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Mon Oct 21 12:13:43 2019 +0100
      
          Merge pull request #109 from PDXFinder/dev
      
          Dev
      
      commit e6fbbbe47f3d3512a8cdcaa53862b4cb9b7f5912
      Merge: a875d11db ed380aa93
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Oct 21 12:00:09 2019 +0100
      
          Merge pull request #108 from PDXFinder/ircc-links
      
          Add platform urls for ircc-crc
      
      commit ed380aa93768a8e99071f0d53198e8607e89ae16
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Oct 21 11:30:43 2019 +0100
      
          Add platform urls for ircc-crc
      
      commit 64987edc029efb08205d2fc68acf74e4551add86
      Merge: 3aa69e454 a875d11db
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Oct 21 09:29:41 2019 +0100
      
          Merge pull request #107 from PDXFinder/dev
      
          Dev
      
      commit a875d11dbb9ffc907e97b9a399579e57ae69cc81
      Merge: 0e2239333 8d142785d
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Oct 18 14:18:52 2019 +0100
      
          Merge pull request #106 from PDXFinder/project_group_fix
      
          Add IRCC-CRC models to EurOPDX project group
      
      commit 8d142785d37fd886db9738976b8f1fc31cca4b61
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 18 14:15:10 2019 +0100
      
          Throw exception when step is not applicable
      
      commit c1220aa7c4dcefc07b1ea9935ca08f7bb14584b1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 18 12:06:38 2019 +0100
      
          Add IRCC-CRC models to EurOPDX project group
      
      commit 3aa69e4547f1e08d40e569dfba4fd0c991ade601
      Merge: 1b202065 0e2239333
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Oct 18 09:17:40 2019 +0100
      
          Merge pull request #105 from PDXFinder/dev
      
          Dev
      
      commit 0d2ac45969819124bdd099012fb929a177312d8e
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Oct 17 17:48:24 2019 +0100
      
          Add data model to persist summary statistics
      
      commit 0e2239333a25395644d2da9d1438e4bc94aec6de
      Merge: 1e685b5b4 833b20186
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Wed Oct 16 16:47:44 2019 +0100
      
          Merge pull request #103 from PDXFinder/update-java-app-menu
      
          Update Finder Menu to synch with Word press menu
      
      commit 833b20186eae84899ec461a16474838da64e7cac
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Oct 16 16:31:50 2019 +0100
      
          Update Finder Menu to synch with Word press menu
      
      commit 1e685b5b4f246f7e9ca4ce25a17c34efde0bacbf
      Merge: 4a54fee90 fab36f76a
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Oct 16 09:49:38 2019 +0100
      
          Merge pull request #101 from PDXFinder/contact_fix
      
          Load contact form link when provided
      
      commit fab36f76a59031713c69eb7966d975d51fffb51b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 16 08:37:21 2019 +0100
      
          Load contact form link when provided
      
      commit 4a54fee9063b2c926b94affb4bc6941d3eb95c27
      Merge: c5d59fbbe 248791c02
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Oct 15 12:57:49 2019 +0100
      
          Merge pull request #100 from PDXFinder/hci-fix
      
          Fix url error for HCI
      
      commit 248791c02f919d4653763f2c7ffd9cdfb387714b
      Merge: c5946d7b6 c5d59fbbe
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Tue Oct 15 12:56:51 2019 +0100
      
          Merge branch 'dev' into hci-fix
      
      commit c5946d7b60532a03d1730f6d29166a232aa104ca
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Oct 15 12:50:22 2019 +0100
      
          Reset DTO for every iteration
      
      commit 864cc4c555dccf078289687d749a8cae2d80a198
      Merge: 41c03a22c 858e016e3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Oct 14 15:31:38 2019 +0100
      
          Merge branch 'hci-fix' of https://github.com/PDXFinder/pdxfinder into hci-fix
      
      commit 41c03a22ca50e64aefe45e27f2cee8c3e80596f3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Oct 14 15:31:02 2019 +0100
      
          Define platform url for pdmr
      
      commit 0c943f4db4d5926efbb09bf889286b16a7a6d6f5
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Oct 14 15:12:58 2019 +0100
      
          Update platform url only if its empty
      
      commit 858e016e383faa73970353e27090c74a6a007168
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Oct 14 15:11:26 2019 +0100
      
          Update indexer/src/main/java/org/pdxfinder/dataloaders/LoadHCI.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit 35d2cc0a84deab6fede5544cd17620b9828cc4e1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Oct 14 14:51:38 2019 +0100
      
          Fix url error for HCI
      
      commit c5d59fbbec72d0b18365210851c45186729962f2
      Merge: c22b84803 78cae8f4b
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Oct 11 11:36:55 2019 +0100
      
          Merge pull request #99 from PDXFinder/jax_and_platform_fix
      
          Optionally update platform urls
      
      commit 78cae8f4bcc158510830dd7a158d6c94f1f837ac
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 11 11:24:17 2019 +0100
      
          Optionally update platform urls
      
      commit c22b8480361fcd77d631b37ca97aa6e8f11edf7c
      Merge: d6ba178ba e390afdda
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Oct 9 13:56:23 2019 +0100
      
          Merge pull request #97 from PDXFinder/jax_and_platform_fix
      
          Jax and platform fix
      
      commit e390afddaea9fa40b9a2bffa7ff4fec5e9f43475
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 9 12:12:03 2019 +0100
      
          Set passage to NA when sample is not xenograft
      
      commit dfdf3edf01b4e04fdddaab38bd0edbfb999c58fa
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 9 12:11:25 2019 +0100
      
          Fix query to add missing patient molchar data
      
      commit 276e68ca3272f4bf5a55a4c4b8972d885345bcce
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 9 10:49:57 2019 +0100
      
          Add error message
      
      commit c2b7329fa6e899b2e3c0f9a9fbe5cd8d1cbeacc3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Oct 8 10:59:20 2019 +0100
      
          Reset node objects in dto for every interation to avoid duplicates
      
      commit af8ab97c41a9ec020322ac7dae1309ef636eb1e1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Oct 8 10:56:11 2019 +0100
      
          Seqstart = Seqend bug fix
      
      commit 122e6324f91d1368b043d4c819dc78a6f733abfc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Oct 7 14:46:27 2019 +0100
      
          Export mutation with DownDOG
      
      commit e116cd4bd4f03d1b4713caa04aadb3e8cd82d0af
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 4 11:42:40 2019 +0100
      
          Use template dir instead of individual files
      
      commit 7f9c1c5c77914ee3fd94395824c1d76907901ef5
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Oct 4 11:42:19 2019 +0100
      
          Export sample platforms
      
      commit c98adc710f43cf46385022d43751cb337c04acec
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 3 14:48:25 2019 +0100
      
          Fix nullpointers
      
      commit bf137eeab6d49e3f5f5792e90e185b21e6beeb91
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 3 14:37:35 2019 +0100
      
          Export finder related data
      
      commit 68199ab46c17a337e6efa6451367b1c0a2997e4b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 3 14:32:42 2019 +0100
      
          Export pdx details
      
      commit e702874faff679d74b006ae9f9d9673033da3b5c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 3 11:48:43 2019 +0100
      
          Export sharing and contact
      
      commit fff465acdc24077ed5a2346e6ac276d7eb005b92
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 3 10:59:01 2019 +0100
      
          Export model details
      
      commit c297a17a54fcf031430c1b7f8fc3ee254457d8c6
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 3 09:47:07 2019 +0100
      
          Replace GraphId annotations with @Id and @GeneratedValue
      
      commit 434df8bb8505c27dfcc594f8671b135c2f39b3d6
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Oct 3 08:17:56 2019 +0100
      
          Fix exception error
      
      commit 1427e849b0fdc17fe6c9357320fff8f409226e55
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 2 13:39:43 2019 +0100
      
          Method changes supporting data export
      
      commit 133ef00e9d0924dee714158a36386e5158b82a86
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 2 13:39:15 2019 +0100
      
          Command initial commit
      
      commit 92809111384e8816b4579421373a7a21e3109754
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 2 13:38:50 2019 +0100
      
          Initial commit
      
      commit d6ba178bab47b2c6d412321e304713cac7ff834f
      Merge: 27d0e56cd 1a8f94b19
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Oct 2 09:52:28 2019 +0100
      
          Merge pull request #96 from PDXFinder/platform_update
      
          Platform update
      
      commit 27d0e56cd54220d88c8b81389b483566f5912018
      Merge: 8fd6f5fca 7002eb769
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Wed Oct 2 09:50:20 2019 +0100
      
          Merge pull request #95 from PDXFinder/JAX-CNA-and-Expression-Loading
      
          Jax cna and expression loading
      
      commit 1a8f94b1982f4416d04d21a47e564bb79c23581d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Oct 2 09:46:39 2019 +0100
      
          Add save
      
      commit 9bf2f74dc2c3ad93caf719ad167e337546857c07
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Oct 1 15:47:16 2019 +0100
      
          Use equalsIgnoreCase
      
      commit 7002eb76912fbef17346a18365842855d1d5efae
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Oct 1 15:26:58 2019 +0100
      
          Remove unused comments
      
      commit b5af639ace86d00f618192a8395e71e45dceb66b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Oct 1 15:25:28 2019 +0100
      
          Remove unused test
      
      commit 25c330115ebd36618398cfb5f214490aa535d132
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Tue Oct 1 15:19:22 2019 +0100
      
          Update indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit a76ed388f2d909c560ff456dbe712df60875c8d7
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Tue Oct 1 15:19:14 2019 +0100
      
          Update indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit 73e60c7de1a8a8d816ec5bd6fbbb98c912e5b9d4
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Tue Oct 1 15:19:08 2019 +0100
      
          Update indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit 6335bab093149db32f9c8fadf8cbe1d5934cceff
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Tue Oct 1 15:14:36 2019 +0100
      
          Update indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit d6f57a7f2728a20651048259d654e7ed7623a724
      Author: Mosaku Abayomi <abayomi@sprintell.org>
      Date:   Tue Oct 1 15:12:00 2019 +0100
      
          Update indexer/src/main/java/org/pdxfinder/dataloaders/UniversalLoaderOmic.java
      Co-Authored-By: default avatarRoss Thorne <rthorne@ebi.ac.uk>
      
      commit d7f80d886ec58b3d505e99c3a742380c9991e338
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Oct 1 15:02:33 2019 +0100
      
          remove zooma wildcard imports
      
      commit 11911d5edb323485b9d005d6f87447ec3b2528bf
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Oct 1 15:01:56 2019 +0100
      
          Remove sql comments
      
      commit fc0a924ca41e343dea7455ea9e13f88412a8c098
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Oct 1 14:23:45 2019 +0100
      
          Fix nullcheck
      
      commit 93daa76ea6175505a1a62b26a5eb6fe670bdd293
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Oct 1 13:50:13 2019 +0100
      
          Add extra sample origin option
      
      commit 308a8192e39badea6a3aeec189bced8ddccee49f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Oct 1 12:46:07 2019 +0100
      
          Fix merge conflicts
      
      commit 238f26aabbb7a517b2e1cbba04f2105a3833109c
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Oct 1 12:25:05 2019 +0100
      
          Fix merge conflicts
      
      commit 47effddb1f9bf8f5bb38db6cd6154f2a56e62786
      Merge: 4f988b883 8fd6f5fca
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Oct 1 12:21:11 2019 +0100
      
          Fix merge conflicts
      
      commit 8fd6f5fca46cd7d51076c2d1472176ecc95e1cad
      Merge: 04be9585 566a04f73
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Sep 30 16:00:36 2019 +0100
      
          Merge pull request #94 from PDXFinder/SonarCloud
      
          Add static code analysis to CI
      
      commit 566a04f736dcfdbd9fd4cef6e00e5a5abfcbb736
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Sep 27 11:01:45 2019 +0100
      
          Add static code analysis to CI
      
      commit b2b9f711f61ebb29ec077615d0249704a60f24ef
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 30 14:07:14 2019 +0100
      
          Remove platform tag
      
      commit 5c7f41d51ed2e5bbe928f2dc1271a53b8629485f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 26 12:23:16 2019 +0100
      
          Update services and loaders to use platform type
      
      commit 2cc3338a1388489c15ed39a30bc3bed70c95c376
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 26 12:22:31 2019 +0100
      
          Add platform type to dao
      
      commit 621fb24a
      Merge: a9e56dd6 1b202065
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Sep 25 11:19:10 2019 +0100
      
          Merge pull request #92 from PDXFinder/beta
      
          Beta
      
      commit 1b202065
      Merge: f6106948 04be9585
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Sep 25 10:50:43 2019 +0100
      
          Merge pull request #91 from PDXFinder/dev
      
          Dev
      
      commit 04be9585
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 24 16:31:32 2019 +0100
      
          Trim sampleId
      
      commit 3051c5f8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 24 15:11:49 2019 +0100
      
          Use don't use platformtag for ihc
      
      commit 6c2b6103
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 24 15:05:53 2019 +0100
      
          Add _ihc tag for immunohistochemistry to avoid duplicates.
      
      commit ed6978d2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 24 11:51:43 2019 +0100
      
          Disable report saving
      
      commit cd6cdd4d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 24 07:52:41 2019 +0100
      
          Add nullcheck
      
      commit 2b478743
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 24 06:10:38 2019 +0100
      
          Fix sample origin ref
      
      commit f9310d53
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 23 22:35:31 2019 +0100
      
          Add tag to platform name
      
      commit 07973aaf
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 23 17:25:04 2019 +0100
      
          Passage conversion fix
      
      commit a3cc31e4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 23 16:34:10 2019 +0100
      
          Disable health check for mail
      
      commit 4f988b88390ecc063ed1e2504c320e2f1d94af58
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Sep 23 15:54:26 2019 +0100
      
          Add shut down hook for properly shutting down the admin app
      
      commit 91adb1ec068a690b92556c2f86ee126bf4be42a2
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Sep 23 15:48:26 2019 +0100
      
          Write Logs on Jenkins and dev server
      
      commit 32ce6a36
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 23 15:32:06 2019 +0100
      
          Add datasource to platformkey
      
      commit 04705640
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 23 15:31:44 2019 +0100
      
          Fix cytogenetics multiple mc nodes issue
      
      commit 7b984082acbf9e51db1af42b65857f214c42c5f9
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Sep 23 14:55:52 2019 +0100
      
          Cleaned up and Refactor Oracle Data Transformer
      
      commit 508deca0c95faa72bf1c759c7ad0bd0214b82134
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Sep 23 14:18:26 2019 +0100
      
          Transform and Load JAX cna and rna-seq data
      
      commit 6f784e6a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 23 12:11:56 2019 +0100
      
          Add  molchar type to molchar key
      
      commit cf9c95c2aafe958ea08768fa447674b4d9eec6d4
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Sep 23 11:16:50 2019 +0100
      
          Add Transcriptomics to data projection sprintell
      
      commit 0b934eec96c21f706c4a1f25e2741d51f87e4b00
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Sep 23 11:12:55 2019 +0100
      
          Add z-score column to details Page table
      
      commit bdb6ed09159bdd0db68eb03d46262c5c1fa3a31c
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Sep 23 11:11:49 2019 +0100
      
          Transform/Load JAX RNA-seq data
      
      commit a9e56dd6
      Merge: 3dae51b5 f6106948
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Sep 20 15:49:21 2019 +0100
      
          Merge pull request #90 from PDXFinder/beta
      
          Beta
      
      commit f6106948
      Merge: 20b04655 f8f0e59a
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Sep 20 15:40:51 2019 +0100
      
          Merge pull request #89 from PDXFinder/dev
      
          Dev
      
      commit f8f0e59a
      Merge: b43bb18d 91cdd8f7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Sep 20 15:08:04 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit b43bb18d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Sep 20 15:07:48 2019 +0100
      
          QA to be empty if missing
      
      commit 91cdd8f7
      Merge: 7d935c17 01d17172
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Sep 20 13:33:27 2019 +0100
      
          Merge pull request #88 from PDXFinder/Hotfix
      
          Fix format call
      
      commit 01d17172
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Sep 20 13:28:14 2019 +0100
      
          Fix format call
      
      commit 20b04655
      Merge: c2d0afb2 7d935c17
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Sep 20 12:52:21 2019 +0100
      
          Merge pull request #87 from PDXFinder/dev
      
          Dev
      
      commit 9a4881851480a274e2d6565a85dddbb037825de7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Sep 20 12:14:22 2019 +0100
      
          Extend MarkerAssociatin node with zscore attribute
      
      commit 7d935c17
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Sep 20 09:54:29 2019 +0100
      
          Add msg
      
      commit a234211d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Sep 20 08:13:43 2019 +0100
      
          Fix cypher as intended this time
      
      commit 217a8e68
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Sep 20 07:51:06 2019 +0100
      
          Fix cypher
      
      commit 1ddac190
      Merge: fe9e1593 71e3b438
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Sep 20 07:40:28 2019 +0100
      
          Merge pull request #86 from PDXFinder/HarmonisedTreatmentForPatient
      
          Fetch the harmonised treatment name for patient page
      
      commit 4a80b11a44330a867dd00dc67dfe024014daa01e
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Sep 19 17:59:25 2019 +0100
      
          Create Local feeds for JAX CNA and RNA-seq
      
      commit 33c82a63cf5ef860000e173853b5ded43f247dca
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Sep 19 16:08:27 2019 +0100
      
          Refactor data-transformer module
      
      commit 71e3b438
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Sep 19 15:25:58 2019 +0100
      
          Fetch the harmonised treatment name for patient page
      
      commit fe9e1593
      Merge: 1e14f888 eef0e39c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 19 15:22:30 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 1e14f888
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 19 15:22:22 2019 +0100
      
          Patient treatment can lead to multiple models
      
      commit eef0e39c
      Merge: 1079c174 2d8eb380
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Sep 19 14:19:26 2019 +0100
      
          Merge pull request #85 from PDXFinder/MappingExport
      
          Format export mappings for EuroPDX
      
      commit 2d8eb380
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Sep 19 13:58:23 2019 +0100
      
          Format export mappings for EuroPDX
      
      commit 1079c174
      Author: afollette <follette.alex@gmail.com>
      Date:   Thu Sep 19 13:39:42 2019 +0100
      
          Fixes Civic blank "Amino Acid Change" bug
      
          Removes alert("JESUS IS LORD")
      
      commit cca0b51a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 19 11:28:34 2019 +0100
      
          MappingService to be able to export treatment rules
      
      commit 759c53ff
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 19 11:04:38 2019 +0100
      
          Fix treatment number query bug
      
      commit 92e5ca65
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 19 08:39:58 2019 +0100
      
          Create a link to patient tab from search
      
      commit 03c759d0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 19 08:33:34 2019 +0100
      
          Add fold change to datamodel
      
      commit 6d934634
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 19 08:25:35 2019 +0100
      
          Add log info
      
      commit 751874ca
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Sep 19 08:24:48 2019 +0100
      
          Disable IRCC-GC mutation visibility
      
      commit ece19cb2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 18 16:18:11 2019 +0100
      
          Add nullcheck to ds name
      
      commit 37e1bfbf
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 18 16:12:18 2019 +0100
      
          Add nullcheck
      
      commit b222a231
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 18 15:37:40 2019 +0100
      
          Add attribute check to datasourceName
      
      commit 3d419a26
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 18 14:53:22 2019 +0100
      
          Use datasource name for ds filter
      
      commit 03d75496
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 18 10:07:06 2019 +0100
      
          Load clinical studies branch
      
      commit 1ab8ad81
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 17 15:03:49 2019 +0100
      
          Fix url
      
      commit cd1ed235
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 17 09:48:58 2019 +0100
      
          Load therapeutic procedures instead of radiotherapies
      
      commit b3a5fca1
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 17 09:02:25 2019 +0100
      
          Add patient treatment filter
      
      commit aee688f5
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 16 15:49:14 2019 +0100
      
          Order treatment string components alphabetically
      
      commit 288c6734
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 16 15:24:55 2019 +0100
      
          Add patient treatment filter
      
      commit 6d644842
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 16 15:24:31 2019 +0100
      
          Fix patient treatment dp bug
      
      commit 1745a7e24fd41fd16fac2ba03aad1cf25b3fa0aa
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Sep 16 14:13:18 2019 +0100
      
          Extend mapping suggestion to work for previously mapped terms
      
      commit e0a3bd6ea97c875efaecbb71cc475c462c5ae9c4
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Sep 16 14:12:28 2019 +0100
      
          Fix page size navigation to handle varying mapping status in the url
      
      commit 199a2192
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 16 10:58:38 2019 +0100
      
          Load additional treatment branches from NCIT
      
      commit 39b72cb6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Sep 13 18:33:10 2019 +0100
      
          Add orphaned mapping to summary table
      
      commit 64929516
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Sep 13 18:12:29 2019 +0100
      
          Extend back end to allow edit of old mappings
      
      commit f4765169
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Sep 13 17:01:35 2019 +0100
      
          ADMIN INTERFACE: Create a feature to allow editing of old mappings
      
      commit 1bf5bcbe
      Merge: f3d53b0f 7750481f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Sep 12 17:19:11 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit f3d53b0f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Sep 12 17:16:35 2019 +0100
      
          Add caching to speed up ontology suggestions
      
      commit 021c329a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Sep 12 15:30:24 2019 +0100
      
          Add ontology suggestion for treatment curation
      
      commit b2986f87
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Sep 12 11:15:16 2019 +0100
      
          Enable H2 Web access
      
      commit dbc3f813
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Sep 11 14:49:13 2019 +0100
      
          UX refining for the Admin Interface
      
      commit 7750481f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 11 13:55:07 2019 +0100
      
          Add patient treatment to DP
      
      commit aed0fa01
      Merge: d5edcabb 8f6c0df6
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Sep 6 14:56:32 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit d5edcabb
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Sep 6 14:56:20 2019 +0100
      
          Add Null check on ProjectName And Log.Info on patient creation
      
      commit 8f6c0df6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Sep 5 16:44:02 2019 +0100
      
          Change h2 directory for data laoder
      
      commit f21350d6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Sep 5 16:36:18 2019 +0100
      
          Change h2 directory in Loader
      
      commit 09967289
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Sep 5 12:01:29 2019 +0100
      
          Log operation when unmapped terms is saved
      
      commit eff8a01e
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Sep 4 15:59:05 2019 +0100
      
          Ensure mapping entity type is lowercase before save
      
      commit e916cef0
      Merge: 6acd8728 e68cab51
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Sep 4 15:30:59 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit e68cab51
      Merge: 94985dbc b5f54f9c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 15:21:21 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 94985dbc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 15:21:14 2019 +0100
      
          Use lowercase entity types
      
      commit b5f54f9c
      Merge: 9c941a9e 26916d9d
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 15:19:13 2019 +0100
      
          Merge pull request #83 from PDXFinder/UnitTests
      
          Unit tests
      
      commit 26916d9d
      Merge: 33f428d0 9c941a9e
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Sep 4 15:13:20 2019 +0100
      
          Merge branches 'dev' and 'UnitTests' of https://github.com/PDXFinder/pdxfinder into UnitTests
      
           Conflicts:
          	data-services/src/main/java/org/pdxfinder/services/DataImportService.java
      
      commit 6acd8728
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Sep 4 14:54:44 2019 +0100
      
          Get all ontology terms
      
      commit 9c941a9e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 14:39:03 2019 +0100
      
          H2 location change
      
      commit 4645305d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 14:38:11 2019 +0100
      
          Use no arg constructor for queryresult
      
      commit e66bdbdf
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 13:32:30 2019 +0100
      
          Change h2 dir
      
      commit 58f34f38
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 13:05:49 2019 +0100
      
          Enable disabled methods
      
      commit d093de96
      Merge: e0d1a082 15e5ae93
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 11:45:58 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit e0d1a082
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 11:45:26 2019 +0100
      
          Save frequently mutated genes in DP
          Service to use DP
      
      commit 15e5ae93
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Sep 4 11:39:07 2019 +0100
      
          Update Ontobee URL to OLS url in admin Interface
      
      commit 71d38875
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Sep 4 11:27:24 2019 +0100
      
          Update h2-db directory for data loader
      
      commit 33f428d0
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Sep 4 10:50:16 2019 +0100
      
          Changed Imports in DataImportService
      
          Instead of a static import wild card, only the necessary imports
          are imported
      
      commit d3036b27
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:46:21 2019 +0100
      
          Update TreatmentProtocolTest.java
      
          updated method name upper casing to match other tests
      
      commit fa32919d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 10:29:18 2019 +0100
      
          Include regimen combinations to projection
      
      commit 8e7929cd
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:25:50 2019 +0100
      
          Update BaseTestWithPersistence.java
      
      commit c51c096b
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:24:34 2019 +0100
      
          Update TreatmentComponent.java
      
      commit 3772f83b
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:23:02 2019 +0100
      
          Update DataImportServiceTests.java
      
          Changed type in line 69
      
      commit 7e519e32
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:17:03 2019 +0100
      
          Update data-model/src/test/java/org/pdxfinder/graph/dao/TreatmentProtocolTest.java
      Co-Authored-By: default avatarRoss Thorne <rmwthorne@googlemail.com>
      
      commit 57b863b8
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:16:48 2019 +0100
      
          Update data-model/src/test/java/org/pdxfinder/graph/dao/TreatmentProtocolTest.java
      Co-Authored-By: default avatarRoss Thorne <rmwthorne@googlemail.com>
      
      commit 70d226d1
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:16:33 2019 +0100
      
          Update data-model/src/test/java/org/pdxfinder/TestConfigWithPersistence.java
      Co-Authored-By: default avatarRoss Thorne <rmwthorne@googlemail.com>
      
      commit e51e1219
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:12:13 2019 +0100
      
          Update data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentProtocol.java
      Co-Authored-By: default avatarRoss Thorne <rmwthorne@googlemail.com>
      
      commit 7bfdff39
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:11:40 2019 +0100
      
          Update data-services/src/test/java/org/pdxfinder/DataImportServiceTests.java
      Co-Authored-By: default avatarRoss Thorne <rmwthorne@googlemail.com>
      
      commit e954e7bf
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:10:26 2019 +0100
      
          Update data-services/src/main/java/org/pdxfinder/services/DataImportService.java
      Co-Authored-By: default avatarRoss Thorne <rmwthorne@googlemail.com>
      
      commit 40d0ba26
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Wed Sep 4 10:09:37 2019 +0100
      
          Update data-services/src/test/java/org/pdxfinder/DataImportServiceTests.java
      Co-Authored-By: default avatarRoss Thorne <rmwthorne@googlemail.com>
      
      commit 4f3ea602
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Sep 4 09:39:26 2019 +0100
      
          Cleanup
      
      commit 052c20b7
      Merge: 998282f6 f4bdd570
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Sep 3 15:51:17 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 998282f6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Sep 3 15:51:08 2019 +0100
      
          Added back end feature to allow curator get suggestions from OLS and plug to UI
      
      commit f4bdd570
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 3 13:57:43 2019 +0100
      
          Fix not loaded treatments bug
      
      commit 59f95530
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 3 13:40:36 2019 +0100
      
          Disable sad node validation
      
      commit ce0eb32f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 3 13:00:05 2019 +0100
      
          Enforce skip if file is not present
      
      commit f00442d1
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Sep 3 12:24:31 2019 +0100
      
          Added front end feature to allow curator manually type terms with suggestions from OLS
      
      commit 6b325f1b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Sep 3 12:23:23 2019 +0100
      
          Added autocomplete libraries and styles
      
      commit a026a532
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Sep 3 12:20:50 2019 +0100
      
          Updated Angular dependencies for autocomplete
      
      commit e916e793
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 3 11:14:07 2019 +0100
      
          Load custom list with Ontolia
      
      commit 6e344b6b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 3 10:07:58 2019 +0100
      
          Create specimen in cytogen loading if hoststrain is already present
      
      commit 72e59f9c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 3 10:07:42 2019 +0100
      
          Get hoststrain by symbol
      
      commit 4490d309
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 3 09:20:35 2019 +0100
      
          Fix passage parsing error
      
      commit 6253c83c
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Sep 3 08:15:23 2019 +0100
      
          Reduce log noise
      
      commit 79e02d87
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 2 16:00:43 2019 +0100
      
          Load industrial aid branch as well
      
      commit f6620ab8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 2 13:19:23 2019 +0100
      
          Ontolia:
          - add scoring
          - implement bestCompleteMatch and bestMatch
      
      commit d143e378
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Sep 2 08:25:36 2019 +0100
      
          Don't allow loading duplicates for terms
      
      commit 76523023
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Aug 30 19:54:34 2019 +0100
      
          Added Angular Material Components
      
      commit f66bfed9
      Merge: a7e45567 95305782
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 30 15:51:34 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit a7e45567
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 30 15:50:39 2019 +0100
      
          Add OntoliaMatrix
      
      commit 83177248
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 30 15:49:56 2019 +0100
      
          Cleanup
      
      commit 95305782
      Merge: 94b8c167 4b5ca3d2
      Author: Ross Thorne <rmwthorne@googlemail.com>
      Date:   Fri Aug 30 15:04:29 2019 +0100
      
          Merge pull request #84 from PDXFinder/UpdogRefactorGetWorkbook
      
          Refactor opening excel files
      
      commit 94b8c167
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 30 14:40:54 2019 +0100
      
          Enable Ontolia
      
      commit 9e156243
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 30 14:40:22 2019 +0100
      
          Fix ircc omic loading directory error
      
      commit 4b5ca3d2
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Aug 30 14:30:14 2019 +0100
      
          Refactor opening excel files
      
      commit 9e59e928
      Merge: 2948727c 4902f685
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 30 11:40:02 2019 +0100
      
          Merge branch 'treatmentcombo' into dev
      
          # Conflicts:
          #	indexer/src/main/java/org/pdxfinder/envload/LoadNCITDrugs.java
      
      commit 5f80f67d
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Aug 30 11:29:03 2019 +0100
      
          Fixed byte to string conversion
      
      commit 18e0f99b
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Aug 30 11:27:18 2019 +0100
      
          Fixed byte to string conversion
      
      commit 4902f685
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 30 11:11:44 2019 +0100
      
          The birth of Ontolia
      
      commit 5de86b8c
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Aug 30 11:08:44 2019 +0100
      
          Made Given When Then naming convention consistent
      
          Added Null tests to getPatientSnapshot. Made added
          blank string checks to creatPatient and getPatientSnapshot
          in dataImportServices.
      
      commit 05f04739
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Aug 30 11:06:03 2019 +0100
      
          Made Given When Then naming convention consistent
      
          Added Null tests to getPatientSnapshot. Made added
          blank string checks to creatPatient and getPatientSnapshot
          in dataImportServices.
      
      commit 562b64b4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Aug 29 15:47:41 2019 +0100
      
          Save relationships for regimens
      
      commit 2948727c
      Merge: a828d76f eaa92d41
      Author: Ross Thorne <rmwthorne@googlemail.com>
      Date:   Thu Aug 29 10:17:50 2019 +0100
      
          Merge pull request #80 from PDXFinder/impcc_access_modalities
      
          Impcc access modalities
      
      commit a828d76f
      Merge: a1bfec5d b05e2e99
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 29 10:06:27 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit a1bfec5d
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 29 10:06:15 2019 +0100
      
          FRONT END UI ADJUSTMENT - PDXI-627
      
      commit 12a0ce1f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Aug 29 09:23:21 2019 +0100
      
          Add dash parsing and vocab filtering
      
      commit 1b075ab5
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 28 17:54:39 2019 +0100
      
          Add feature to click on suggested terms and see a detailed view as it is with Missing mapping table
      
      commit 3b02b7e1
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 28 16:13:12 2019 +0100
      
          Implement separate table area color for Missing Mapping table to clearly differentiate it from the table area that shows suggestions
      
      commit 022614a4
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Aug 28 16:12:37 2019 +0100
      
          Removed method getPatient() And changed naming conventions
      
          Refactored dependent methods. Put NullPointExceptions on
          GetPatientSnapshot and CreatePatient so they will
          quietly throw exceptions for creating a patient with
          a NULL id. Refactored TreatmentProtocols for readability
          changing their method names to clarify testing behaviors.
      
      commit eaa92d41
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Aug 28 13:49:55 2019 +0100
      
          Address QA and fix name spacing
      
          QA raised an issue with name spacing: `indexer/src/test/java/org.pdxfinder/commands/` existed.
          This was changed to `indexer/src/test/java/org/pdxfinder` directory was renamed and the contents of `commands` was moved into the parent directory.
      
      commit bd42b5c2
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Aug 28 13:36:41 2019 +0100
      
          Abstracted Byte to String Conversion
      
      commit 26fc401a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 28 13:14:18 2019 +0100
      
          Provide an option for curator to increase and reduce text size to desired size and reset to default size
      
      commit ab654e61
      Author: afollette <follette.alex@gmail.com>
      Date:   Wed Aug 28 12:20:45 2019 +0100
      
          Final refactoring
      
          Uppercased static finals. Clarified variables.
          Cleaned up code.
      
      commit 681ccf2b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 27 17:59:28 2019 +0100
      
          Properly handle error report on csv file upload
      
      commit e8ca92e4
      Merge: 1a454324 b05e2e99
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Aug 27 17:03:18 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into impcc_access_modalities
      
          Fix Conflicts:
           indexer/src/main/java/org/pdxfinder/commands/dataloaders/LoadIRCC.java
      
      commit 1a454324
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Aug 27 16:53:46 2019 +0100
      
          Fix code smell (test arguments wrong way round)
      
      commit 472e734b
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Aug 27 16:35:11 2019 +0100
      
          Add unit test for loading specimens
      
      commit 724f9a00
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Aug 27 16:33:30 2019 +0100
      
          Deal with trailing slashes in data dir option
      
      commit a222b8f1
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Aug 27 16:31:44 2019 +0100
      
          Add newline at end of files
      
      commit dbcbd74f
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Fri Aug 23 17:06:55 2019 +0100
      
          wip Add unit tests for load specimens
      
      commit 886536c4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 23 15:54:52 2019 +0100
      
          Link regimens to treatments using slash separator
      
      commit ed61766f
      Author: afollette <follette.alex@gmail.com>
      Date:   Fri Aug 23 15:19:01 2019 +0100
      
          Create load test on DataProjection
      
          Test Ignored by default. Created new tests configurations
          and base test for separation configurations for persistence.
      
      commit de4b3e99
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Aug 23 14:45:36 2019 +0100
      
          Extend front end to allow curator review uploaded csv content in browser before push to server
      
      commit b05e2e99
      Merge: 90d64653 4bae2546
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 23 09:22:23 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 90d64653
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 23 09:22:17 2019 +0100
      
          Add missing log msg
      
      commit 4bae2546
      Merge: a884f3f6 d4e3bddc
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 22 16:43:55 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit a884f3f6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 22 16:43:47 2019 +0100
      
          Extend front end for validation file upload
      
      commit 95d35f2c
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 22 16:42:07 2019 +0100
      
          Added feature to upload, validate and update validate terms in H2 DB
      
      commit 4512f688
      Merge: fe6646f5 22deb8f7
      Author: Ross Thorne <rmwthorne@googlemail.com>
      Date:   Thu Aug 22 16:12:43 2019 +0100
      
          Merge pull request #79 from PDXFinder/fix_indexer_mocks
      
          Move test resources in line with correct directory sturcture
      
      commit 22deb8f7
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Aug 22 16:11:06 2019 +0100
      
          Move test resources in line with correct directory sturcture
      
      commit d4e3bddc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Aug 22 15:19:45 2019 +0100
      
          Check write permission for log dir
      
      commit 5df45cca
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Aug 22 14:16:46 2019 +0100
      
          Omic loader to load from various file formats
      
      commit fe6646f5
      Merge: b3a24f8e 48b463f2
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Aug 22 14:10:38 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into impcc_access_modalities
      
      commit b3a24f8e
      Merge: 4de1485f 7a52bffa
      Author: Ross Thorne <rmwthorne@googlemail.com>
      Date:   Thu Aug 22 14:09:45 2019 +0100
      
          Merge pull request #78 from PDXFinder/fix_indexer_mocks
      
          Fix indexer mocks
      
      commit 7a52bffa
      Author: jmason-ebi <jmason@ebi.ac.uk>
      Date:   Thu Aug 22 13:42:27 2019 +0100
      
          Fix unit test
      
      commit a514ba77
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 22 12:28:18 2019 +0100
      
          Ensure treatment-mapping csv upload passes validation test
      
      commit 70a8d0cb
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 22 11:13:07 2019 +0100
      
          Add Validation rules for upload CSV headers and contents ensuring they originated from the database previously
      
      commit 770674e0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Aug 21 13:01:42 2019 +0100
      
          Save harmonization report in csv
      
      commit 6df82699
      Merge: 1b92590a 48b463f2
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 21 12:11:51 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 1b92590a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 21 11:13:15 2019 +0100
      
          Generate csv files with human readable header
      
      commit 3844ebf9
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 21 10:46:30 2019 +0100
      
          Add Camel Case converters to utilties
      
      commit 48b463f2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Aug 21 10:28:03 2019 +0100
      
          Shift treatment columns
      
      commit 9328ef0a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 20 15:12:11 2019 +0100
      
          Add uploaded MultipartFile serializer to UtilityService
      
      commit d5c7dadb
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 20 15:05:02 2019 +0100
      
          Added file upload page and angular service to transfer uploaded files
      
      commit 946dca27
      Author: afollette <afollette@ebi.ac.uk>
      Date:   Tue Aug 20 13:26:36 2019 +0100
      
          Refactored and cleaned code. Rearranged variables.
      
      commit 824b8a48
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 20 12:38:23 2019 +0100
      
          Add front End Components for managing validated curations based on providers approval
      
      commit 12d8048e
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 20 11:46:30 2019 +0100
      
          Sort missing mapped terms by 'unmapped column'
      
      commit 4dfe9b59
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 19 16:58:35 2019 +0100
      
          Add front end feature to export csv file of curations for data providers
      
      commit 0add53ad
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 19 16:11:24 2019 +0100
      
          Extend Admin back end service to allow download of csv file of curations for data providers
      
      commit 2debe667
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Aug 19 14:48:08 2019 +0100
      
          Start fixing indexer mocks
      
      commit 1c9e9802
      Merge: 4de1485f 6c597992
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Mon Aug 19 12:48:03 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into impcc_access_modalities
      
      commit 6c597992
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 19 12:18:19 2019 +0100
      
          Add templateResolver configuration to dataService TestConfig for Multipart HTML E-mail service
      
      commit 82e8fac6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 19 11:21:50 2019 +0100
      
          Add thymeleaf Email template for sending dynamically generated HTML E-mail
      
      commit dd8862fa
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 19 10:06:43 2019 +0100
      
          Add Email Notification Service - PDXI-368
      
      commit 6e0a53b0
      Author: alex <Follette.alex@gmail.com>
      Date:   Fri Aug 16 19:11:14 2019 +0100
      
          Refactored Unit Tests for DataImportServices
      
      commit 4f35b794
      Author: alex <Follette.alex@gmail.com>
      Date:   Fri Aug 16 09:40:11 2019 +0100
      
          Unit Tests for TreatmentProtocol DAO and DataImportService
      
      commit a871d58d
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Thu Aug 15 17:53:28 2019 +0100
      
          Delete DataImportServicesTests.java
      
      commit a0cf0aa4
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Thu Aug 15 17:52:38 2019 +0100
      
          Delete DataImportServiceTests.java
      
      commit 038b3a0c
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Thu Aug 15 17:50:53 2019 +0100
      
          Rename TreatmentProtocolTest.java to data-services/src/test/java/org/pdxfinder/services/DataImportServicesTests.java
      
      commit 93967b00
      Author: Alex Follette <45319940+Afollet@users.noreply.github.com>
      Date:   Thu Aug 15 17:47:02 2019 +0100
      
          Add files via upload
      
          Unit tests for TreatmentProtocol DAO and DataImportService
      
      commit 4de1485f
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Aug 15 17:21:11 2019 +0100
      
          wip tests
      
      commit bb8dd787
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Aug 15 17:18:46 2019 +0100
      
          Extend IRCC loader to set access modalities on all models
      
      commit 16cacc07
      Merge: 203115ff 566e19d2
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 15 16:31:31 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 203115ff
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 15 16:31:12 2019 +0100
      
          Add UI to manage orphaned terms skipped from unmapped terms
      
      commit 566e19d2
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Aug 15 15:16:26 2019 +0100
      
          Add Treatment similarity index rule
      
      commit f28b46fe
      Merge: 9dfde893 38403a3f
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Aug 15 13:28:02 2019 +0100
      
          Merge pull request #77 from PDXFinder/baseloader_access_modalities
      
          Extend BaseLoader to set access modality groups for models
      
      commit 1af5cf68
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 15 11:26:36 2019 +0100
      
          Refactor angular services and add badge notification for orphaned terms
      
      commit e068e3a6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 15 11:25:27 2019 +0100
      
          Add components for archive and skipped terms interface
      
      commit 0c582b65
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 15 10:04:00 2019 +0100
      
          Add feature to skip desired term during curation
      
      commit 61722cc1
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 15 10:03:23 2019 +0100
      
          Retrieve missing mapping data by status column, Allow submission of skipped curation terms
      
      commit 38403a3f
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Wed Aug 14 16:09:20 2019 +0100
      
          Extend BaseLoader to set access modality groups for models
      
      commit 9dfde893
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 13 16:13:54 2019 +0100
      
          Refactor mappingService and repository to allow multiple parameters on search filter
      
      commit 1051056a
      Merge: 9473b6c4 bcfcb740
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 13 16:10:22 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 9473b6c4
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 13 16:10:15 2019 +0100
      
          Add custom col-lg-2.5 to bootstrap grid system
      
      commit 6b48fca6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 13 13:54:44 2019 +0100
      
          Added feature for multiple filter query using Checkboxes in manage-curation component/template
      
      commit bcfcb740
      Merge: 6c516ad9 c62ef119
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Aug 13 13:02:48 2019 +0100
      
          Merge remote-tracking branch 'origin/dev' into dev
      
      commit 6c516ad9
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Tue Aug 13 13:02:28 2019 +0100
      
          Add Jacoco code coverage reporting
      
      commit c62ef119
      Merge: 874d44f9 e43dd1b3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 13 09:48:21 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 874d44f9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 13 09:43:26 2019 +0100
      
          Remove getDrugName
      
      commit e43dd1b3
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 12 14:45:47 2019 +0100
      
          Refactor harcoded list of curation filter to dynamically load from database
      
      commit b3bf9404
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Aug 12 13:57:49 2019 +0100
      
          Fix double conversion error
      
      commit 9038f995
      Merge: 2388ce8f 2a12f256
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 12 13:21:09 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 2388ce8f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 12 13:20:26 2019 +0100
      
          Add Search Filter and Filter Bar UI Components for manage-curations
      
      commit 75255267
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 12 13:16:52 2019 +0100
      
          Add pagination and feature to retrieve curated data status to manage-curation
      
      commit f0c8789c
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 12 12:45:44 2019 +0100
      
          Retrieve and present mappings created by curators but not yet approved by centers on maanage-curator page
      
      commit ee947f77
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Aug 9 16:02:17 2019 +0100
      
          Add Floating action Button Feature
      
      commit 7d6f37de
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Aug 9 11:59:40 2019 +0100
      
          ADMIN: Added components&interfaces to manage skipped terms, archive terms, and mappings created by curators but not yet approved by centers
      
      commit 2a12f256
      Merge: 7022a420 a24a8a61
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 9 11:14:33 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 7022a420
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Aug 9 11:13:57 2019 +0100
      
          Update urls for jax
      
      commit a24a8a61
      Merge: 3557c875 60047a61
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 8 14:31:42 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 3557c875
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 8 14:31:35 2019 +0100
      
          ADMIN: Added behaviour to request approval before submit curation
      
      commit b7c32eb5
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 8 10:25:27 2019 +0100
      
          ADMIN: Added behaviour to notify user of success or failure after submitting curation
      
      commit 0108d083
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 7 16:09:14 2019 +0100
      
          Avoid submission of empty mapping list
      
      commit 6ad4d0da
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 7 14:48:05 2019 +0100
      
          ADMIN INTERFACE 8 : Extend Service to retrieve mapping rules by status
      
      commit 60047a61
      Merge: d5d59191 8b28ee52
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Aug 7 13:54:32 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit d5d59191
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Aug 7 13:54:12 2019 +0100
      
          Make UPDOG load transcriptomics
      
      commit dc91a43a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Aug 7 13:20:21 2019 +0100
      
          Add transcriptomics attributes
      
      commit 8b28ee52
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 7 13:01:17 2019 +0100
      
          Write updated mapped terms to the file system and backup old file
      
      commit 2d10b245
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Aug 7 11:15:57 2019 +0100
      
          Extend utilityService file writer to allow caller to specify destination and append mode
      
      commit a66d6a70
      Merge: bb461e1c be2feb34
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 6 16:36:50 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit bb461e1c
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Aug 6 16:36:40 2019 +0100
      
          Save Curated Mapped Diagnosis in Admin - PDXI-469
      
      commit be2feb34
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 6 13:55:19 2019 +0100
      
          Add ontology term to treatment list
      
      commit f52dcc92
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 6 13:35:53 2019 +0100
      
          Remove unused methods
      
      commit c9f24ba0
      Merge: f39734a7 27cae193
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 6 10:24:40 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit f39734a7
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 6 10:24:26 2019 +0100
      
          Remove treatment type standardization
      
      commit 7e587c8b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Aug 6 10:20:31 2019 +0100
      
          Make component's type Drug by default
      
      commit 27cae193
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 5 14:21:28 2019 +0100
      
          Get suggestions only if mapped term is missing
      
      commit 1b556937
      Merge: 5c4176f6 30bc8ff6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 5 14:16:21 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 5c4176f6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Aug 5 12:07:24 2019 +0100
      
          Reposition the page size drop down selector to the far right
      
      commit 30bc8ff6
      Merge: b3acc97b 593be5ea
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Aug 5 10:38:01 2019 +0100
      
          Merge pull request #76 from PDXFinder/updog_refactoring
      
          Updog refactoring
      
      commit 36a23394
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Aug 2 21:40:48 2019 +0100
      
          Add data size to page navigation
      
      commit 68c1c7d7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Aug 2 19:58:19 2019 +0100
      
          Validate batch submission and discard unmapped terms
      
      commit 50b2acdd
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Aug 2 19:42:04 2019 +0100
      
          Allow part submission of curated terms
      
      commit b3acc97b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Aug 2 19:05:05 2019 +0100
      
          Load and manage Knowledge base from Finder on the curation interface
      
      commit ac903f85
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Aug 2 19:04:07 2019 +0100
      
          Create detailed notification view on curator selection of unmapped term
      
      commit 7c371903
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 1 21:34:16 2019 +0100
      
          Implement dynamic column for suggestion table
      
      commit 6aca0e74
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 1 20:30:05 2019 +0100
      
          Extend back end service to get MappingEntity By Id
      
      commit dd183119
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Aug 1 14:07:00 2019 +0100
      
          Fix mapping suggestions
      
      commit 74aae1ee
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 31 18:09:00 2019 +0100
      
          Fix misplaced text
      
      commit cae56711
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 31 18:06:46 2019 +0100
      
          Complete Pagination Navigation and make it respond to param changes on thesame route path
      
      commit 874e6f89
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 31 17:04:32 2019 +0100
      
          Add pagination feature in angular front end
      
      commit 06e7bc39
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 31 15:50:02 2019 +0100
      
          Extend the Data Transfer Object Interface in angular to capture pagination info
      
      commit a0d806b2
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 31 14:45:03 2019 +0100
      
          Dynamically retrieve center specific columns and row contents
      
      commit 9053d3d1
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 31 14:26:41 2019 +0100
      
          Show datasource specific table only if missing mapping entity exists
      
      commit 6ebd4455
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jul 30 17:13:55 2019 +0100
      
          Implement dynamic datasource-summary angular component and template for treatment, diagnosis and ...
      
      commit 593be5ea
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 30 14:46:53 2019 +0100
      
          Update loader to use new template format
      
      commit 803fe139
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 29 18:45:25 2019 +0100
      
          Create entitytype filter (treatment, diagnosis, ...) for mapping summary by data source
      
      commit c9d549f2
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 29 17:56:22 2019 +0100
      
          Refactor mapping summary page to use summary statistics data from the server
      
      commit 2dc7c733
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 29 16:15:59 2019 +0100
      
          Compute mapping summary statistics on the server for the angular client
      
      commit f99843e7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 29 16:12:34 2019 +0100
      
          ANgular UI, cleanup
      
      commit 096bf07f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 26 17:55:09 2019 +0100
      
          Add filter to mappings endpoint for retrieving all mapped terms
      
      commit b2c1d6dd
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 26 16:37:25 2019 +0100
      
          Angular Front end retrieves unmapped treatments and diagnosis and display on corresponding css badge
      
      commit c4d2cdfe
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 26 15:58:22 2019 +0100
      
          Get MappingedEntities By type from DB and Load mapping suggestions from Knowledge Base for unmapped terms
      
      commit c8f4ca0f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 26 15:50:19 2019 +0100
      
          Get MappingedEntities By type from DB and Load mapping suggestions from Knowledge Base for unmapped terms
      
      commit b86affdf
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 26 13:56:25 2019 +0100
      
          UPDOG separate metadata loading
      
      commit a57d245a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 17:02:12 2019 +0100
      
          Added filter to query for missing mappings
          Added filter to query for mapType
      
      commit f884b8c0
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 15:46:47 2019 +0100
      
          Validate page and size request to avoid negative page request error
      
      commit bd403d99
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 14:38:25 2019 +0100
      
          Reconfigure travisci dependency from oraclejdk8 to openjdk8 - oracle licensing has changed
      
      commit ad8cbaab
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 14:29:24 2019 +0100
      
          Save unmapped treatments into database during dataloading
      
      commit ff906404
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 14:16:23 2019 +0100
      
          Save unmapped treatments into database during dataloading
      
      commit e8963924
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 14:15:36 2019 +0100
      
          Properly handle any case combination in mapping entity filter search
      
      commit 1875fe32
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 11:41:00 2019 +0100
      
          Create mapping rest endpoint with search filters
          Added pagination services and pageable feature to H2 mapping services
      
      commit 7f86ff87
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 11:38:53 2019 +0100
      
          Write treatments to H2 DB
      
      commit 36b8fd8e
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 11:36:01 2019 +0100
      
          Create Search Filter for the Persisted Mapping Entities
      
      commit 1d00ca0d
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jul 25 11:33:02 2019 +0100
      
          Don't show mappingKey in the rest services
      
      commit 54faa5f5
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 24 17:40:02 2019 +0100
      
          Added Component and Services to Initialize H2 Database from mapping file
      
      commit 0fe195e3
      Merge: 6056d3b3 57db2e2f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 24 14:01:54 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 6056d3b3
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 24 14:00:41 2019 +0100
      
          Updated Statistics components and clean transformer and admin
      
      commit 57db2e2f
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 24 11:09:20 2019 +0100
      
          gitignore change
      
      commit c2f07316
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 24 11:07:40 2019 +0100
      
          Resolving additional conflicts + gitignore
      
      commit 03cdccda
      Merge: 494183f1 c8b45f9d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 24 10:56:37 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
          # Conflicts:
          #	admin/src/main/java/org/pdxfinder/admin/controllers/AjaxController.java
          #	data-services/src/main/java/org/pdxfinder/services/MappingService.java
          #	indexer/src/main/java/org/pdxfinder/commands/utils/UpdateMappings.java
      
      commit 494183f1
      Merge: e4362cfa e304ac99
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 24 10:22:43 2019 +0100
      
          Merge branch 'DrugLoading' into dev
      
      commit e304ac99
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 24 08:36:01 2019 +0100
      
          Url fix and log message change
      
      commit 4aa7d51e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 23 13:51:11 2019 +0100
      
          Fix treatment query and alter service to use new methods
      
      commit 85794a53
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 23 09:02:07 2019 +0100
      
          Remove unused methods
      
      commit 192ed383
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 23 08:57:35 2019 +0100
      
          Update queries to use treatments instead of drugs
      
      commit 7474117b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 22 13:07:13 2019 +0100
      
          Update url query
      
      commit 0b1fe342
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 22 11:10:11 2019 +0100
      
          OntologyTerm can be a sad node from the validation point of view
      
      commit 2e50d7f3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 22 11:07:58 2019 +0100
      
          Cleanup
      
      commit 76e63bf5
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 19 08:56:16 2019 +0100
      
          Entity type fix
      
      commit 8c265f19
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 19 08:55:58 2019 +0100
      
          Change toString for container to create json
      
      commit ded250f4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 19 08:07:34 2019 +0100
      
          Add -createDirectMappings command
      
      commit beb9ba35
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 19 08:07:09 2019 +0100
      
          Add ot methods
      
      commit 60e858f4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 19 07:52:31 2019 +0100
      
          Move queryresult class to corresponding package
      
      commit 7f1fb9bf
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 17 16:34:36 2019 +0100
      
          Add Pie with Legend to HighChart Components
      
      commit c8b45f9d
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jul 17 11:52:15 2019 +0100
      
          Fix Summary Statistics Display
      
      commit ba5d4b7c
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jul 16 17:29:24 2019 +0100
      
          AngularFrontend UI counts Missing Diagnosis Curation from H2 DB
      
      commit 21289392
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 16 14:47:51 2019 +0100
      
          Link drug dosing treatments too
      
      commit 8ec7c2bc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jul 16 14:47:10 2019 +0100
      
          Disable visibility for leaf nodes
      
      commit 08814ded
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jul 16 13:41:06 2019 +0100
      
          Add PieChart, doughnut and 3D doughnut Chart helpers to chart components
      
      commit 8b864081
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 15 16:28:37 2019 +0100
      
          Cleanup
      
      commit 43c3701a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 15 16:27:37 2019 +0100
      
          Rename method again to avoid mass confusion
      
      commit 66c12e80
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 15 16:17:40 2019 +0100
      
          Rename method to avoid confusion
      
      commit 92691f82
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 15 13:23:09 2019 +0100
      
          Do not delete terms when determining suggestions
      
      commit fc2c807b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 15 13:22:29 2019 +0100
      
          Allow suggestion flag
      
      commit d5d903e7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 15 11:13:28 2019 +0100
      
          Update Admin AjaxController to fix bug
      
      commit 7c7b8873
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 15 11:05:38 2019 +0100
      
          PDXI-594 : Read unmapped terms from H2 DB and Restore access to h2 repositories in data-services scope
      
      commit 74085ad2
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 15 10:57:16 2019 +0100
      
          Admin: Create Embedded in memory mode config for H2 Data Repositories in data-services testConfig
      
      commit e987b9c8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 12 13:10:18 2019 +0100
      
          No infinite loop bro
      
      commit 03668572
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 12 11:58:28 2019 +0100
      
          Disable usage of h2 repositories from within search-test scope till test configuration is extended to capture h2 database
      
      commit 0321eacf
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 12 10:11:37 2019 +0100
      
          Fix dependency injection ... in UpdateMappings
      
      commit 2ec577b1
      Merge: 0dd7d1a7 0a374e30
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 12 09:58:46 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 0dd7d1a7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 12 09:52:36 2019 +0100
      
          Admin Interface Update
      
      commit 8280d5f9
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 12 09:50:57 2019 +0100
      
          Service to read unmapped terms from H2
      
      commit 9b3be10d
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 12 09:45:39 2019 +0100
      
          Update rest endpoint and test cases
      
      commit 3878de81
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 12 09:32:28 2019 +0100
      
          Command to link treatments to ontology terms
      
      commit a812e18e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jul 11 15:05:10 2019 +0100
      
          Add relationship to Treatment
      
      commit 3fef351e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jul 11 11:49:12 2019 +0100
      
          Add treatment loading
      
      commit 0a374e30
      Author: Ross Thorne <rthorne@ebi.ac.uk>
      Date:   Thu Jul 11 11:17:21 2019 +0100
      
          Ignore target directories
      
      commit bd5bec12
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jul 11 09:36:29 2019 +0100
      
          Refactor mapping keys
      
      commit 28cd45f0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 10 14:16:32 2019 +0100
      
          Add treatment related services
      
      commit 5677343d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 5 14:50:38 2019 +0100
      
          Fix wrong url path
      
      commit 49cb19bf
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 5 14:48:49 2019 +0100
      
          Fix wrong url path
      
      commit 2ec1a023
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 5 13:06:03 2019 +0100
      
          Remove unused properties
      
      commit 392bf2dc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 5 13:05:47 2019 +0100
      
          Add finderRootDir property
      
      commit dc24bcef
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 5 13:05:15 2019 +0100
      
          Changes to use finderRootDir instead of data root dir
      
      commit c3a1d0b3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 5 13:04:12 2019 +0100
      
          Use new service
      
      commit 3e766fbd
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 5 13:03:44 2019 +0100
      
          Multi option initialization for service
      
      commit 06d1bebc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jul 5 13:02:54 2019 +0100
      
          Implement additional methods for container
      
      commit d7187744
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 5 11:24:19 2019 +0100
      
          Add BasicBar, StackedBar, and Clustered Bar Chart components to charts
      
      commit f5d44f50
      Author: sprintell <abayomi@sprintell.org>
      Date:   Fri Jul 5 09:43:16 2019 +0100
      
          Add test cases for molecular data/patients statistics endpoint
      
      commit b6b51e9d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jul 4 12:45:46 2019 +0100
      
          Add key generation for entity
      
      commit 0781ccd0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jul 3 09:02:10 2019 +0100
      
          Load Treatments from ncit
      
      commit 0997bdaf
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jul 2 12:38:20 2019 +0100
      
          Add Stacked Bar Chart Component to PDXFinder HighChart Wrapper
      
      commit a0b83935
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jul 2 11:01:10 2019 +0100
      
          Add 3D Pie and Doughnut Chart Component
      
      commit 4b0b8234
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jul 2 11:00:50 2019 +0100
      
          Add 3D Pie and Doughnut Chart Component
      
      commit 96b4e528
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jul 2 08:23:04 2019 +0100
      
          Update Java App for Summary Statistics
      
      commit a5167221
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jul 2 08:16:59 2019 +0100
      
          Add 3D Pie and Doughnut Chart Component
      
      commit c1773446
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 1 17:50:18 2019 +0100
      
          Fix subtitle description error and implemented 3D Pie Component
      
      commit 14f26a5f
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 1 17:20:07 2019 +0100
      
          Fix error in chart color
      
      commit 9062ba93
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 1 16:55:43 2019 +0100
      
          Add end point to retrieve Patient cout seprately from Drug count in Patient Treatment Statics
      
      commit fbfa794a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 1 13:26:26 2019 +0100
      
          Added barChart Components and endpoints for Providers count and Model Count Statistics
      
      commit aa99b70b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 1 13:09:35 2019 +0100
      
          Added ClusteredColumnChart Components
      
      commit 381fe8e7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Mon Jul 1 11:56:35 2019 +0100
      
          Added Enum Component for HTML Colors  according to the list at https://htmlcolorcodes.com/color-names
      
      commit 542a21c3
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 1 11:31:44 2019 +0100
      
          Add description
      
      commit 551a2215
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 1 11:26:46 2019 +0100
      
          Add type to terms when loading from api
      
      commit adef940d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jul 1 11:18:09 2019 +0100
      
          Add type attribute to ontologyterms
      
      commit 3dae51b5
      Merge: 43449029 c2d0afb2
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Jun 28 09:16:59 2019 +0100
      
          Merge pull request #75 from PDXFinder/beta
      
          Beta
      
      commit e4362cfa
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 27 17:55:19 2019 +0100
      
          Added Multiple Color for combinedColumnLineAndPieChart
      
      commit 702d0e2f
      Merge: a4df3320 ead16d91
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 27 17:35:56 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit a4df3320
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 27 17:35:37 2019 +0100
      
          Implemented Patient Treatment visualization with Fixed Placement Column Charts
      
      commit af7d9994
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 27 17:33:29 2019 +0100
      
          Added Components for Fixed Placement Column Charts
      
      commit c2d0afb2
      Merge: 2b700f23 ead16d91
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Thu Jun 27 11:11:48 2019 +0100
      
          Merge pull request #74 from PDXFinder/dev
      
          Dev
      
      commit 2b700f23
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 27 08:56:46 2019 +0100
      
          Fix CNA bug PDXI-592
      
      commit ead16d91
      Merge: 38349363 b9e032a0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 27 08:53:22 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 38349363
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 27 08:52:56 2019 +0100
      
          Fix CNA bug PDXI-592
      
      commit b90e1646
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 27 08:41:41 2019 +0100
      
          Retire Drug node and add Treatment node
      
      commit b9e032a0
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 26 17:23:29 2019 +0100
      
          Extended Chart Components / Added YAxis Helper
      
      commit f0c56263
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 26 16:53:47 2019 +0100
      
          Extended Chart XAxis, Title, Labels, and Added YAxis Component
      
      commit 0594a1b6
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 26 16:46:42 2019 +0100
      
          Extended Chart Labels Component
      
      commit 9f241b10
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 26 16:41:41 2019 +0100
      
          Add PlotOptions, Columns, Extended Series Components
      
      commit 4eb738d2
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 26 16:21:08 2019 +0100
      
          Extend Highchart Series Markers
      
      commit 3f826a1b
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 26 11:57:03 2019 +0100
      
          Restyled search table
      
      commit 43449029
      Merge: 9c37fbb7 a6c27c9f
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Jun 21 14:14:47 2019 +0100
      
          Merge pull request #73 from PDXFinder/beta
      
          Beta
      
      commit a6c27c9f
      Merge: 2e731e4f 790a6f88
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Fri Jun 21 13:56:43 2019 +0100
      
          Merge pull request #72 from PDXFinder/dev
      
          Dev
      
      commit 790a6f88
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 20 17:05:46 2019 +0100
      
          Added Enum Series Type, and Full Chart Data Holder
      
      commit 5ef60c09
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 20 16:59:43 2019 +0100
      
          Added Enum Series Type, and Full Chart Data Holder
      
      commit edd73cb3
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 20 16:58:40 2019 +0100
      
          Feature to convert statistics Data Object into highchart clustered Map format
      
      commit c768d46a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Thu Jun 20 16:20:10 2019 +0100
      
          Fix search filter bug due to space in treatments url
      
      commit 506c15a0
      Author: sprintell <abayomi@sprintell.org>
      Date:   Wed Jun 19 17:07:41 2019 +0100
      
          Added data Transfer Object for Statistics Summary
      
      commit 450d3a92
      Merge: 6c13dfff 3f3cf402
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Wed Jun 19 08:21:31 2019 +0100
      
          Merge pull request #71 from PDXFinder/dev
      
          Dev
      
      commit 5f9a6379
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jun 18 15:03:04 2019 +0100
      
          Added helper for HighChart label
      
      commit 8b561ec5
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jun 18 14:55:24 2019 +0100
      
          Added wrapper for HighChart Items, Labels and Styles
      
      commit 3f3cf402
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jun 18 14:41:11 2019 +0100
      
          Added components for HighChart Wrapper
      
      commit 9c37fbb7
      Merge: f7d670a1 2e731e4f
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Jun 17 09:45:49 2019 +0100
      
          Merge pull request #70 from PDXFinder/beta
      
          Beta
      
      commit 2e731e4f
      Merge: a65a5f4c c7bac640
      Author: Csaba Halmagyi <CsabaHalmagyi@users.noreply.github.com>
      Date:   Mon Jun 17 07:49:12 2019 +0100
      
          Merge pull request #69 from PDXFinder/dev
      
          Dev
      
      commit c7bac640
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jun 14 15:20:30 2019 +0100
      
          Add nullcheck
      
      commit d378fd9b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Fri Jun 14 13:28:55 2019 +0100
      
          Remove certain characters from platform url
      
      commit e44572ec
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Thu Jun 13 13:44:22 2019 +0100
      
          Add extra log messages for debugging
      
      commit c208d2fc
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 12 11:34:12 2019 +0100
      
          Add platform Urls to template
      
      commit 7b374590
      Merge: 3d94f8ba 03659eb4
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 11 15:49:26 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 03659eb4
      Merge: 8269b7b7 981cbd6a
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jun 11 15:46:06 2019 +0100
      
          Merge branch 'dev' of https://github.com/PDXFinder/pdxfinder into dev
      
      commit 8269b7b7
      Author: sprintell <abayomi@sprintell.org>
      Date:   Tue Jun 11 15:45:54 2019 +0100
      
          Fix missing Platform URL Link
      
      commit 3d94f8ba
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 11 15:31:38 2019 +0100
      
          Return distinct models only
      
      commit 981cbd6a
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 11 15:19:25 2019 +0100
      
          Add notes to methods
      
      commit cf9dd4a9
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 11 13:57:27 2019 +0100
      
          Change service to use projected data
      
      commit f33f077d
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 11 13:56:54 2019 +0100
      
          Rename treatment
      
      commit 09f9942e
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 11 13:41:17 2019 +0100
      
          Enable additional dataprojections
      
      commit 65eaa0b0
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 11 13:27:59 2019 +0100
      
          Save data available in a projection
      
      commit 1fd49c41
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Tue Jun 11 13:20:15 2019 +0100
      
          Remove comment
      
      commit 6c13dfff
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 5 13:38:38 2019 +0100
      
          Mapping manager initial commit
      
      commit 29c5cc3b
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 5 13:35:29 2019 +0100
      
          Treatment to NCIT command initial commit
      
      commit 075f96ed
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Wed Jun 5 13:27:21 2019 +0100
      
          OntologyTerm now can be linked to a treatment too
      
      commit 0cccf963
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jun 3 09:31:36 2019 +0100
      
          Add correspondinng treatment repo
      
      commit bf14e3a8
      Author: csaba <csaba@ebi.ac.uk>
      Date:   Mon Jun 3 09:30:21 2019 +0100
      
          Add Treatment and its relationship to dao
      
      	new file:   .github/ISSUE_TEMPLATE/bug_report.md
      	new file:   .github/ISSUE_TEMPLATE/custom.md
      	new file:   .github/ISSUE_TEMPLATE/feature_request.md
      	new file:   .gitignore
      	modified:   README.md
      	modified:   admin/pom.xml
      	modified:   admin/src/main/app-ui/src/app/datasource-specific/datasource-specific.component.html
      	modified:   admin/src/main/app-ui/src/app/mapping.service.ts
      	modified:   admin/src/main/java/org/pdxfinder/controllers/AjaxController.java
      	deleted:    admin/src/main/java/org/pdxfinder/controllers/TransController.java
      	modified:   admin/src/main/resources/application.properties
      	deleted:    admin/src/main/resources/static/fonts/FontAwesome.otf
      	deleted:    admin/src/main/resources/static/fonts/fontawesome-webfont.eot
      	deleted:    admin/src/main/resources/static/fonts/fontawesome-webfont.svg
      	deleted:    admin/src/main/resources/static/fonts/fontawesome-webfont.ttf
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      	deleted:    admin/src/main/resources/static/fonts/fontawesome-webfont.woff2
      	deleted:    admin/src/main/resources/static/images/4.png
      	modified:   data-model/pom.xml
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/CurrentTreatment.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/DataProjection.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/Drug.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/ExternalDataSource.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/ExternalUrl.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/Histology.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/Image.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/Marker.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/MarkerAssociation.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/OntologyTerm.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/PatientSnapshot.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/Platform.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/PlatformAssociation.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/QualityAssurance.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/Response.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/Sample.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/SampleToOntologyRelationship.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/Specimen.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/Treatment.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentComponent.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentProtocol.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentSummary.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/dao/TreatmentToOntologyRelationship.java
      	deleted:    data-model/src/main/java/org/pdxfinder/graph/dao/ValidationTechniques.java
      	deleted:    data-model/src/main/java/org/pdxfinder/graph/repositories/DrugRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/ExternalUrlRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/HostStrainRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerAssociationRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/MarkerRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/ModelCreationRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/MolecularCharacterizationRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/OntologyTermRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/PatientRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/PatientSnapshotRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/PlatformAssociationRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/QualityAssuranceRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/ResponseRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/SampleRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/SpecimenRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentProtocolRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/graph/repositories/TreatmentSummaryRepository.java
      	modified:   data-model/src/main/java/org/pdxfinder/rdbms/dao/MappingEntity.java
      	modified:   data-model/src/main/java/org/pdxfinder/rdbms/repositories/MappingEntityRepository.java
      	deleted:    data-model/src/test/java/org/pdxfinder/BaseTestWithPersistence.java
      	modified:   data-model/src/test/java/org/pdxfinder/TestConfig.java
      	deleted:    data-model/src/test/java/org/pdxfinder/TestConfigWithPersistence.java
      	modified:   data-model/src/test/java/org/pdxfinder/graph/dao/DataProjectionsTimeTest.java
      	new file:   data-model/src/test/java/org/pdxfinder/graph/dao/MarkerAssociationTest.java
      	new file:   data-model/src/test/java/org/pdxfinder/graph/dao/PatientSnapshotTest.java
      	modified:   data-services/pom.xml
      	modified:   data-services/src/main/java/org/pdxfinder/services/DataImportService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/DetailsService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/EmailService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/GraphService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/MappingService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/OmicTransformationService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/PlatformService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/PublicationService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/SearchService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/Statistics.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/TransformerService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/UtilityService.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/constants/DataProvider.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/constants/DataProviderGroup.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/constants/DataUrl.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/constants/OmicCSVColumn.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/ds/Harmonizer.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/ds/SearchDS.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/ds/SearchFacetName.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/ds/Standardizer.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/dto/LoaderDTO.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/dto/europepmc/Publication.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/dto/pdxgun/Reference.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/graphqlclient/Operator.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadMarkers.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/loader/envload/LoadNCIT.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/ontology/Ontolia.java
      	modified:   data-services/src/main/java/org/pdxfinder/services/pdf/Label.java
      	modified:   data-services/src/test/java/org/pdxfinder/DataImportServiceTests.java
      	modified:   data-services/src/test/java/org/pdxfinder/TestConfig.java
      	new file:   data-services/src/test/java/org/pdxfinder/services/DetailsServiceTest.java
      	modified:   data-services/src/test/java/org/pdxfinder/services/MappingServiceTest.java
      	modified:   data-services/src/test/java/org/pdxfinder/services/PublicationServiceTest.java
      	modified:   data-services/src/test/java/org/pdxfinder/services/UtilityServiceTest.java
      	deleted:    data-services/src/test/java/org/pdxfinder/services/constants/DataProviderTest.java
      	modified:   data-services/src/test/java/org/pdxfinder/services/loader/LoadMarkerTest.java
      	modified:   dependencies/pom.xml
      	deleted:    documentation/details_pdxfinder.pdf
      	deleted:    documentation/homepage_pdxfinder.pdf
      	deleted:    documentation/search_pdxfinder.pdf
      	modified:   indexer/pom.xml
      	deleted:    indexer/src/main/java/org/pdxfinder/DatasourceConfig.java
      	modified:   indexer/src/main/java/org/pdxfinder/LoadDiseaseOntology.java
      	modified:   indexer/src/main/java/org/pdxfinder/Loader.java
      	new file:   indexer/src/main/java/org/pdxfinder/TSV.java
      	modified:   indexer/src/main/java/org/pdxfinder/ValidateGeneSymbols.java
      	modified:   indexer/src/main/java/org/pdxfinder/commandline/FinderCommandLine.java
      	modified:   indexer/src/main/java/org/pdxfinder/commandline/FinderExporter.java
      	modified:   indexer/src/main/java/org/pdxfinder/commandline/FinderLoader.java
      	new file:   indexer/src/main/java/org/pdxfinder/commandline/FinderMappingExporter.java
      	new file:   indexer/src/main/java/org/pdxfinder/configuration/H2Configuration.java
      	new file:   indexer/src/main/java/org/pdxfinder/configuration/Neo4jConfiguration.java
      	new file:   indexer/src/main/java/org/pdxfinder/dataexport/ExporterTemplates.java
      	new file:   indexer/src/main/java/org/pdxfinder/dataexport/MetadataSheets.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExporter.java
      	new file:   indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataExtractionServices.java
      	new file:   indexer/src/main/java/org/pdxfinder/dataexport/UniversalDataWriterServices.java
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/LoadAdditionalDatasets.java
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/LoadHCI.java
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/LoadIRCC.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/LoadJAXData.java
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/LoadMDAnderson.java
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/LoadPDMRData.java
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/LoadUniversal.java
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/LoadWISTAR.java
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/LoadWUSTL.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/LoaderBase.java
      	deleted:    indexer/src/main/java/org/pdxfinder/dataloaders/UniversalLoader.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/Reader.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableSetUtilities.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/TableUtilities.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/Updog.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/DomainObjectCreator.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/GroupCreator.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreator.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/PatientCreator.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreator.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreator.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporter.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/Validator.java
      	modified:   indexer/src/main/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreator.java
      	modified:   indexer/src/main/java/org/pdxfinder/mapping/LinkSamplesToNCITTerms.java
      	modified:   indexer/src/main/java/org/pdxfinder/mapping/LinkTreatmentsToNCITTerms.java
      	modified:   indexer/src/main/java/org/pdxfinder/postload/CreateDataProjections.java
      	modified:   indexer/src/main/java/org/pdxfinder/postload/MolcharAPITest.java
      	modified:   indexer/src/main/java/org/pdxfinder/postload/SetDataVisibility.java
      	deleted:    indexer/src/main/java/org/pdxfinder/postload/ValidateDB.java
      	modified:   indexer/src/main/java/org/pdxfinder/reportmanager/ReportManager.java
      	modified:   indexer/src/main/java/org/pdxfinder/utils/CbpTransformer.java
      	modified:   indexer/src/main/java/org/pdxfinder/utils/CreateLocalFeeds.java
      	modified:   indexer/src/main/resources/application.properties
      	new file:   indexer/src/main/resources/datafeed.properties
      	modified:   indexer/src/main/resources/loader.properties
      	new file:   indexer/src/main/resources/logback.xml
      	modified:   indexer/src/test/java/org/pdxfinder/BaseTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/TestConfig.java
      	modified:   indexer/src/test/java/org/pdxfinder/commandline/FinderCommandLineTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/commandline/FinderExporterTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/commandline/FinderLoaderTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/commandline/FinderTransformerTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/dataexport/CbpTransformerTests.java
      	deleted:    indexer/src/test/java/org/pdxfinder/dataexport/DataExportTest.java
      	new file:   indexer/src/test/java/org/pdxfinder/dataexport/ExportTemplatesTest.java
      	new file:   indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataExportTests.java
      	new file:   indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataExtractorUtilitiesTest.java
      	new file:   indexer/src/test/java/org/pdxfinder/dataexport/UniversalDataWriterUtilitiesTests.java
      	deleted:    indexer/src/test/java/org/pdxfinder/dataloaders/LoadIRCCTest.java
      	deleted:    indexer/src/test/java/org/pdxfinder/dataloaders/UniversalLoaderTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/dataloaders/updog/UpdogTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/ModelCreationCreatorTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SampleCreatorTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/dataloaders/updog/domainobjectcreation/SpecimenCreatorTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/ErrorReporterTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/BrokenRelationErrorCreatorTest.java
      	modified:   indexer/src/test/java/org/pdxfinder/dataloaders/updog/tablevalidation/error/EmptyValueErrorCreatorTest.java
      	new file:   indexer/src/test/java/org/pdxfinder/mapping/LinkTreatmentsToNCITTermsTest.java
      	new file:   indexer/src/test/java/org/pdxfinder/postload/DataProjectionTest.java
      	new file:   indexer/src/test/java/org/pdxfinder/postload/SetDataVisibilityTest.java
      	deleted:    package-list
      	modified:   web/pom.xml
      	modified:   web/src/main/java/org/pdxfinder/web/controllers/AjaxController.java
      	modified:   web/src/main/java/org/pdxfinder/web/controllers/CBioController.java
      	modified:   web/src/main/java/org/pdxfinder/web/controllers/DetailsController.java
      	modified:   web/src/main/java/org/pdxfinder/web/controllers/SearchController.java
      	modified:   web/src/main/resources/application.properties
      	new file:   web/src/main/resources/static/css/validationLog.css
      	modified:   web/src/main/resources/static/js/pdxFinder.js
      	modified:   web/src/main/resources/templates/fragments/filter-components.html
      	modified:   web/src/test/java/org/pdxfinder/web/AjaxControllerTest.java
      	new file:   web/src/test/java/org/pdxfinder/web/IndexControllerTest.java
      754f66a1
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