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: Ross 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: Ross 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: Ross 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: Ross 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: dependabot[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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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: Ross 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
	deleted:    admin/src/main/resources/static/fonts/fontawesome-webfont.woff
	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