reorganization

yaml/cbio-db/config.yml

-apiVersion: v1
-kind: ConfigMap
-metadata:
-  name: mysql-cbio-db
-  namespace: cbio-on-demand
-data:
-  mysql.conf: "# Copyright (c) 2014, 2016, Oracle and/or its affiliates. All rights
-    reserved.\n#\n# This program is free software; you can redistribute it and/or
-    modify\n# it under the terms of the GNU General Public License as published
-    by\n# the Free Software Foundation; version 2 of the License.\n#\n# This program
-    is distributed in the hope that it will be useful,\n# but WITHOUT ANY WARRANTY;
-    without even the implied warranty of\n# MERCHANTABILITY or FITNESS FOR A PARTICULAR
-    PURPOSE.  See the\n# GNU General Public License for more details.\n#\n# You
-    should have received a copy of the GNU General Public License\n# along with
-    this program; if not, write to the Free Software\n# Foundation, Inc., 51 Franklin
-    St, Fifth Floor, Boston, MA  02110-1301 USA\n\n#\n# The MySQL  Server configuration
-    file.\n#\n# For explanations see\n# http://dev.mysql.com/doc/mysql/en/server-system-variables.html\n\n[mysqld]\npid-file\t=
-    /var/run/mysqld/mysqld.pid\nsocket\t\t= /var/run/mysqld/mysqld.sock\ndatadir\t\t=
-    /var/lib/mysql\n#log-error\t= /var/log/mysql/error.log\n# By default we only
-    accept connections from localhost\n#bind-address\t= 127.0.0.1\n# Disabling symbolic-links
-    is recommended to prevent assorted security risks\nsymbolic-links=0\n\n#\n#
-    * Fine Tuning\n#\n\nkey_buffer_size         = 4G\nmax_heap_table_size     =
-    512M\ntmp_table_size          = 512M\nmax_allowed_packet      = 256M\nthread_stack
-    \           = 256K\nthread_cache_size       = 20\n# This replaces the startup
-    script and checks MyISAM tables if needed\n# the first time they are touched\nmyisam-recover-options
-    \ = BACKUP\nmax_connections        = 214\n#table_cache            = 64\n#thread_concurrency
-    \    = 10\n#\n# * Query Cache Configuration\n#\nquery_cache_limit       = 1M\nquery_cache_size
-    \       = 0\nquery_cache_type        = 0\n\n\njoin_buffer_size = 16M\ntable_open_cache
-    = 400\n"

yaml/cbio-db/secret.yml

-apiVersion: v1
-kind: Secret
-metadata:
-  name: mysql-env
-  namespace: cbio-on-demand
-data:
-  .env: TVlTUUxfUk9PVF9QQVNTV09SRD1QQHNzd29yZDEKTVlTUUxfVVNFUj1jYmlvCk1ZU1FMX1BBU1NXT1JEPVBAc3N3b3JkMQpNWVNRTF9EQVRBQkFTRT1jYmlvcG9ydGFsCgo=
-type: Opaque

yaml/complete/bind.yml

-apiVersion: rbac.authorization.k8s.io/v1
-kind: ClusterRoleBinding
-metadata:
-  name: cbio-api
-subjects:
-- kind: ServiceAccount
-  name: cbio-api
-  namespace: cbio-on-demand
-roleRef:
-  kind: ClusterRole
-  name: cbio-api
-  apiGroup: rbac.authorization.k8s.io
-
-
----
-
-apiVersion: rbac.authorization.k8s.io/v1beta1
-kind: ClusterRoleBinding
-metadata:
-  name: fabric8-rbac
-subjects:
-  - kind: ServiceAccount
-    # Reference to upper's `metadata.name`
-    name: cbio-api
-    # Reference to upper's `metadata.namespace`
-    namespace: cbio-on-demand
-roleRef:
-  kind: ClusterRole
-  name: cluster-admin
-  apiGroup: rbac.authorization.k8s.io

yaml/complete/cbiood.crt

------BEGIN CERTIFICATE-----
-MIIDszCCApugAwIBAgIUJMKNctTo0DplMqRD/9X5y3tbid8wDQYJKoZIhvcNAQEL
-BQAwaTELMAkGA1UEBhMCQVUxEzARBgNVBAgMClNvbWUtU3RhdGUxITAfBgNVBAoM
-GEludGVybmV0IFdpZGdpdHMgUHR5IEx0ZDEiMCAGA1UEAwwZY2Jpb29kLmVkaXJl
-eC5pY3MubXVuaS5jejAeFw0xOTA2MDcxNjQ5NTFaFw0yMDA2MDYxNjQ5NTFaMGkx
-CzAJBgNVBAYTAkFVMRMwEQYDVQQIDApTb21lLVN0YXRlMSEwHwYDVQQKDBhJbnRl
-cm5ldCBXaWRnaXRzIFB0eSBMdGQxIjAgBgNVBAMMGWNiaW9vZC5lZGlyZXguaWNz
-Lm11bmkuY3owggEiMA0GCSqGSIb3DQEBAQUAA4IBDwAwggEKAoIBAQDJfesKYdSq
-kb603X/O2tt1vfzNv2SEJQhJ7423vZQuKVxPD8zjouHuDP1X9qAVFm5kXABu3ysB
-4t/mmDYjD5TtMTO5qIvHc+i4I+vaLgGDN1BmdSrtSHkWP6PWAAES3PrH93TCD48b
-DiIwB8xLVX5xN8s/+gGvCR+a4ZfGiH2x36PI/LqnF2Fp7Za2QtFvnL1ED93FSSxg
-HKyBEyGn3tgZg0zbMPlACfLPPsSSBs23WfsU+pvwCbFJh1soSv7G0eIK3TYf4dzK
-10FCd/DQSRjhwADC39I++IO4WHaHtAXz7KyqYbXwIs1NSZ3IVUZRUq8bc5oHzIdP
-hYn95QPhi6yLAgMBAAGjUzBRMB0GA1UdDgQWBBQVa4WaF2IDcU/6W6n2B4zTz9WG
-+jAfBgNVHSMEGDAWgBQVa4WaF2IDcU/6W6n2B4zTz9WG+jAPBgNVHRMBAf8EBTAD
-AQH/MA0GCSqGSIb3DQEBCwUAA4IBAQBwdYhTxtf3z6ooF06MWkU2FnN/TphwP4+l
-/MB7aWtP/O05Wz2I/hel5ZimhgLJe0dmk/GFZxDLqMd7YlMuvqOjm2KNqh9sHAd4
-XyEBpie5ibv8prRxvZVukC2skiXwu7GX9HAlcnM/gzQZ3+CVRZtQfbsk+BLjsIb/
-aZHSokWWvEUI5EPixeOWLYyDvSH6Une9XezZzsRaQyiGuGqSXyH/O24uJ+FQVG+X
-yPTlCwuTbdmcEwBPEM8TjNzCTTyodDcTtTt1AKVbZDYid1BQpb0JVvgpVpWfuprA
-glzRYbtQY7Adrx45+UA3eNlEydjWTB2G/qpw7PR65pdwJn91OE9+
------END CERTIFICATE-----

yaml/complete/clusterRole.yml

-kind: ClusterRole
-apiVersion: rbac.authorization.k8s.io/v1
-metadata:
-  name: cbio-api
-rules:
-- apiGroups: [""]
-  resources: ["identifiers"]
-  verbs: ["VerbAll"]

yaml/complete/configMap.yml

-apiVersion: v1
-kind: ConfigMap
-metadata:
-  name: mysql-cbio-db
-  namespace: cbio-on-demand
-data:
-  mysql.conf: "# Copyright (c) 2014, 2016, Oracle and/or its affiliates. All rights
-    reserved.\n#\n# This program is free software; you can redistribute it and/or
-    modify\n# it under the terms of the GNU General Public License as published
-    by\n# the Free Software Foundation; version 2 of the License.\n#\n# This program
-    is distributed in the hope that it will be useful,\n# but WITHOUT ANY WARRANTY;
-    without even the implied warranty of\n# MERCHANTABILITY or FITNESS FOR A PARTICULAR
-    PURPOSE.  See the\n# GNU General Public License for more details.\n#\n# You
-    should have received a copy of the GNU General Public License\n# along with
-    this program; if not, write to the Free Software\n# Foundation, Inc., 51 Franklin
-    St, Fifth Floor, Boston, MA  02110-1301 USA\n\n#\n# The MySQL  Server configuration
-    file.\n#\n# For explanations see\n# http://dev.mysql.com/doc/mysql/en/server-system-variables.html\n\n[mysqld]\npid-file\t=
-    /var/run/mysqld/mysqld.pid\nsocket\t\t= /var/run/mysqld/mysqld.sock\ndatadir\t\t=
-    /var/lib/mysql\n#log-error\t= /var/log/mysql/error.log\n# By default we only
-    accept connections from localhost\n#bind-address\t= 127.0.0.1\n# Disabling symbolic-links
-    is recommended to prevent assorted security risks\nsymbolic-links=0\n\n#\n#
-    * Fine Tuning\n#\n\nkey_buffer_size         = 4G\nmax_heap_table_size     =
-    512M\ntmp_table_size          = 512M\nmax_allowed_packet      = 256M\nthread_stack
-    \           = 256K\nthread_cache_size       = 20\n# This replaces the startup
-    script and checks MyISAM tables if needed\n# the first time they are touched\nmyisam-recover-options
-    \ = BACKUP\nmax_connections        = 214\n#table_cache            = 64\n#thread_concurrency
-    \    = 10\n#\n# * Query Cache Configuration\n#\nquery_cache_limit       = 1M\nquery_cache_size
-    \       = 0\nquery_cache_type        = 0\n\n\njoin_buffer_size = 16M\ntable_open_cache
-    = 400\n"

yaml/complete/crd.yml

-apiVersion: apiextensions.k8s.io/v1beta1
-kind: CustomResourceDefinition
-metadata:
-  name: identifiers.example.com
-  annotations:
-    maintainer: Luboslav Pivarc <456130@muni.cz>
-spec:
-  scope: Namespaced
-  group: example.com
-  version: v1beta1
-  names:
-    kind: identifier
-    singular: identifier
-    plural: identifiers

yaml/complete/ingress-api.yml

-apiVersion: extensions/v1beta1
-kind: Ingress
-metadata:
-  name: cbio
-  namespace: cbio-on-demand
-spec:
-  rules:
-  - http:
-      paths:
-      - path: /api
-        backend:
-          serviceName: cbio-api
-          servicePort: 80

yaml/complete/ingress-proxy.yml

-apiVersion: extensions/v1beta1
-kind: Ingress
-metadata:
-  name: cbio-proxy
-  namespace: cbio-on-demand
-  annotations:
-    nginx.ingress.kubernetes.io/rewrite-target: /
-spec:
-  tls:
-  - hosts:
-    - cbiood.edirex.ics.muni.cz
-    secretName: ingress
-  rules:
-  - host: cbiood.edirex.ics.muni.cz
-    http:
-      paths:
-      - path: /
-        backend:
-          serviceName: cbio-proxy
-          servicePort: 80
-      - path: /api
-        backend:
-          serviceName: cbio-api
-          servicePort: 80

yaml/complete/namespace.yml

-apiVersion: v1
-kind: Namespace
-metadata:
-  name: cbio-on-demand

yaml/complete/secret.yml

-apiVersion: v1
-kind: Secret
-metadata:
-  name: mysql-env
-  namespace: cbio-on-demand
-data:
-  .env: TVlTUUxfUk9PVF9QQVNTV09SRD1QQHNzd29yZDEKTVlTUUxfVVNFUj1jYmlvCk1ZU1FMX1BBU1NXT1JEPVBAc3N3b3JkMQpNWVNRTF9EQVRBQkFTRT1jYmlvcG9ydGFsCgo=
-type: Opaque

yaml/complete/serviceAccount.yml

-apiVersion: v1
-kind: ServiceAccount
-metadata:
-  name: cbio-api
-  namespace: cbio-on-demand