Merge pull request #21 from ccdc-opensource/CSD-5638

Csd 5638

Author: rsimpson-ccdc

docker-compose.sample-db-config.yml

@@ -28,7 +28,7 @@ services:
   #      - ServiceSettings__Databases__N__Colour=#FF0000
   #      - ServiceSettings__Databases__N__Colour=red
   #      - ServiceSettings__Databases__N__Colour=rgba(255, 0, 0, 0.5)
-
+  #
   # Example:
   # If you have a database called test-db at the location /usr/local/data/test-db.csdsqlx
   # To use the test-db.csdsqlx database the file will look like this
@@ -41,6 +41,34 @@ services:
   #       - ServiceSettings__Databases__1__Name=test-db
   #       - ServiceSettings__Databases__1__ConnectionString=/csd-data/test-db.csdsqlx
   #       - ServiceSettings__Databases__1__Colour=red
+  #
+  # Structure File Links:
+  #   If you are using structure file links, include your .CSV file containg the mappings of links to structures
+  #   within the csd-data folder. See also section below for webcsd.
+  #
+  #########################################################################################################
+  # Kubernetes Users
+  # Please refer to the README regarding additional steps required for adding your in-house databases.
+  #########################################################################################################
+
+  webcsd:
+    volumes:
+      - ./path/to/structure/files:/structure-files
+  # Notes:
+  # If you are not using structure file links, then ignore this section and do not include the above snippet in your
+  # docker-compose file.
+  #
+  # If you are using structure file links, you need a .CSV file containing mappings of links to structures.
+  # Place the .CSV file in your csd-data folder along with your in-house database files for webcsdbackend (see above).
+  # When performing a docker-compose up, this will upload the file to the correct location.
+  #
+  # The associated files, that are linked to from the .CSV file, should be mapped to a folder in webcsd. Simply replace
+  # the /path/to/structure/files in the example above with your local path where the structure files are stored.
+
+  #########################################################################################################
+  # Kubernetes Users
+  # Please refer to the README regarding additional steps required for implementing Structure File links.
+  #########################################################################################################
 
   webcsd-theory:
     volumes:
@@ -52,6 +80,16 @@ services:
   # 2. A CSD-Theory metadata database containing additional theoretical data. This must be name CSPDatabase.db.
   # These 2 database are used in conjunction to create the CSD-Theory charts and reports.
 
+  #########################################################################################################
+  # Kubernetes Users
+  # When converting to Kubernetes, only specify the second setting, for example:
+  #   webcsd-theory:
+  #     volumes:
+  #       - /path/to/CSD-Theory Landscape Database:/app/databases
+  # This will create a persistent volume and claim for the location of the landscape database.
+  # Please refer to the README regarding additional steps required for implementing CSD Theory.
+  #########################################################################################################
+
   # IMPORTANT: The CSD Search database must also be included in the webcsdbackend volumes.
   #   The path in which the databases must be mounted is `/csd-data`.
   #   For each database there must be 2 corresponding environment variables:

docker-compose.yml

@@ -1,5 +1,8 @@
 version: "3.6"
 
+x-labels: &k8s-labels
+  kompose.image-pull-secret: pullsecret
+
 services:
   webcsd:
     environment:
@@ -13,7 +16,10 @@ services:
       - 80:80
     volumes:
       - ./userdata:/app/OnSite
-      - ./structure-files:/structure-files
+    labels:
+      <<: *k8s-labels
+      kompose.service.type: LoadBalancer
+      kompose.service.expose: "true"
 
   webcsdbackend:
     depends_on:
@@ -22,14 +28,24 @@ services:
     image: ccdcrepository.azurecr.io/webcsdbackend:0.1.6
     environment:
       - ServiceSettings__StructureInfoLocation=/csd-data/structure-links.csv
-      - CCDC_LICENSING_CONFIGURATION=${CCDC_LICENSING_CONFIGURATION};
+      - CCDC_LICENSING_CONFIGURATION=${CCDC_LICENSING_CONFIGURATION}
+    labels:
+      <<: *k8s-labels
+    expose:
+      - 80
 
   redis:
+    labels:
+      <<: *k8s-labels
     image: redis
     restart: always
     command: redis-server --requirepass ${CSD_CACHE_PASSWORD}
+    expose:
+      - 6379
 
   database-server:
+    labels:
+      <<: *k8s-labels
     image: ccdcrepository.azurecr.io/csd-database:2022.1.0.alpha2
     restart: always
     environment:
@@ -38,8 +54,12 @@ services:
       - "postgres"
       - "-c"
       - "max_connections=1000"
+    expose:
+      - 5432
 
   ccdc-csd-substructuresearch:
+    labels:
+      <<: *k8s-labels
     image: ccdcrepository.azurecr.io/ccdc-csd-substructuresearch:0.1.6
     depends_on:
       - database-server
@@ -49,73 +69,123 @@ services:
       - ccdc-csd-deposition
     environment:
       - StructureSearchReadConnection=Server=database-server;Port=5432;Database=csd-database;User Id=postgres;Password=${CSD_DB_PASSWORD};SearchPath=substructure
+    expose:
+      - 80
 
   ccdc-csd-deposition:
+    labels:
+      <<: *k8s-labels
     image: ccdcrepository.azurecr.io/ccdc-csd-deposition:0.1.6
     depends_on:
       - database-server
     environment:
       - CsdReadConnection=Server=database-server;Port=5432;Database=csd-database;User Id=postgres;Password=${CSD_DB_PASSWORD};SearchPath=csd_schema
+    expose:
+      - 80
 
   ccdc-csd-textnumericsearch:
+    labels:
+      <<: *k8s-labels
     depends_on:
       - database-server
     image: ccdcrepository.azurecr.io/ccdc-csd-textnumericsearch:0.1.6
     environment:
       - CsdReadConnection=Server=database-server;Port=5432;Database=csd-database;User Id=postgres;Password=${CSD_DB_PASSWORD};SearchPath=csd_schema
+    expose:
+      - 80
 
   ccdc-csd-searchservice:
+    labels:
+      <<: *k8s-labels
     depends_on:
       - ccdc-csd-textnumericsearch
       - ccdc-csd-substructuresearch
       - ccdc-csd-resultstore
     image: ccdcrepository.azurecr.io/ccdc-csd-searchservice:0.1.6
+    expose:
+      - 80
 
   csd-request-entry:
+    labels:
+      <<: *k8s-labels
     depends_on:
       - ccdc-csd-deposition
       - ccdc-csd-crystal-structure-export
       - database-server
     image: ccdcrepository.azurecr.io/csd-request-entry:0.1.6
     environment:
       - CsdReadConnection=Server=database-server;Port=5432;Database=csd-database;User Id=postgres;Password=${CSD_DB_PASSWORD};SearchPath=csd_schema
+    expose:
+      - 80
 
   ccdc-csd-formulasearch:
+    labels:
+      <<: *k8s-labels
     depends_on:
       - database-server
     image: ccdcrepository.azurecr.io/ccdc-csd-formulasearch:0.1.6
     environment:
       - FormulaSearchReadConnection=Server=database-server;Port=5432;Database=csd-database;User Id=postgres;Password=${CSD_DB_PASSWORD};SearchPath=formula
+    expose:
+      - 80
 
   ccdc-csd-unitcellsearch:
+    labels:
+      <<: *k8s-labels
     depends_on:
       - database-server
       - ccdc-csd-reducedcell-calculation-service
     image: ccdcrepository.azurecr.io/ccdc-csd-unitcellsearch:0.1.6
     environment:
       - UnitCellSearchReadConnection=Server=database-server;Port=5432;Database=csd-database;User Id=postgres;Password=${CSD_DB_PASSWORD};SearchPath=unitcell
+    expose:
+      - 80
 
   ccdc-csd-resultstore:
+    labels:
+      <<: *k8s-labels
     image: ccdcrepository.azurecr.io/ccdc-csd-resultstore:0.1.6
     environment:
       - OrderedCachePassword=${CSD_CACHE_PASSWORD}
+    expose:
+      - 80
 
   ccdc-csd-fingerprint:
+    labels:
+      <<: *k8s-labels
     image: ccdcrepository.azurecr.io/ccdc-csd-fingerprint-service:0.1.6
+    expose:
+      - 80
 
   ccdc-csd-substructure-filter:
+    labels:
+      <<: *k8s-labels
     image: ccdcrepository.azurecr.io/ccdc-csd-substructure-filter-service:0.1.6
+    expose:
+      - 80
 
   ccdc-csd-crystal-structure-export:
+    labels:
+      <<: *k8s-labels
     image: ccdcrepository.azurecr.io/ccdc-csd-crystal-structure-export-service:0.1.6
+    expose:
+      - 80
 
   ccdc-csd-reducedcell-calculation-service:
+    labels:
+      <<: *k8s-labels
     image: ccdcrepository.azurecr.io/ccdc-csd-reducedcell-calculation-service:0.1.6
+    expose:
+      - 80
 
   webcsd-theory:
-    image: ccdcrepository.azurecr.io/csd-theory:latest
+    labels:
+      <<: *k8s-labels
+    image: ccdcrepository.azurecr.io/csd-theory:1.0.160
     environment:
-      - CCDC_LICENSING_CONFIGURATION=${CCDC_LICENSING_CONFIGURATION};
+      - CCDC_LICENSING_CONFIGURATION=${CCDC_LICENSING_CONFIGURATION}
+    expose:
+      - 80
 
 volumes:
   csd_data: {}