Merge pull request #79 from ccdc-opensource/MMH-124_MMHub_In_House_Dbs

MMH-124 Add in-house protein database support

Author: AlexRajya

README.md

@@ -182,6 +182,9 @@ For details please see [Access Control To In-House Databases](https://github.com
 
 ### In-house Database Configuration
 
+:warning: **OnSite WebCSD assumes structure identifiers are unique across all registered in-house databases.
+You will likely encounter unexpected behaviour if this is not the case.**
+
 On-Site Lattice and WebCSD can be configured to read from in-house databases.
 
 Provided within the installation is a sample database `teaching-subset.csdsql` which can be found in the `sample-data` folder in the root of the installation.
@@ -193,6 +196,27 @@ To enable in-house databases:
 
 More information is given in the notes & example sections of the sample file. This acts as an [override file](https://docs.docker.com/compose/extends/) which you will have to include in the startup command.
 
+### In-house Protein Database Creation and Configuration
+
+If you have a Macromolecule Hub licence, you can also create and register in-house protein databases for use within OnSite WebCSD.
+
+To create an In-house Protein Database, you will need the Python Utilities. These can be downloaded from the [CCDC Downloads page](https://www.ccdc.cam.ac.uk/support-and-resources/csdsdownloads/)
+under `CSD Python API > Python CSD Python API Utilities`. If you do not see the CSD Python API listed in the available downloads, you may need to sign in.
+The relevant script can be found under `ccdc > utitities > create_protein_database`.
+You can run the script using the CSD Python API version 3.3.0 or later.
+
+Once you have created your protein database, you can register it by adding to your `docker-compose.db-config.yml` file following the instructions above.
+You must then mark the database as a protein database. Your database config should look something like this:
+
+```yml
+volumes:
+    - /path/to/ExampleProteinDb.csdsqlx:/csd-data/ExampleProteinDb.csdsqlx
+environment:
+    - ServiceSettings__Databases__2__Name=Example Protein DB
+    - ServiceSettings__Databases__2__ConnectionString=/csd-data/ExampleProteinDb.csdsqlx
+    - ServiceSettings__Databases__2__Speciality__0=Protein
+```
+
 ### CSD-Theory Web Database Configuration
 
 Instructions on setting up CSD-Theory Web can be found in the [wiki](https://github.com/ccdc-opensource/on-site-webcsd/wiki/Setting-up-CSD%E2%80%90Theory-Web).

docker-compose.disable-user-access.yml

@@ -1,8 +1,12 @@
 # On-Site Version 4.0
-# To disable User Access Control include this file in the startup command with -f docker-compose.disable-user-access.yml 
-version: '3.6'
+# To disable User Access Control include this file in the startup command with -f docker-compose.disable-user-access.yml
+version: "3.6"
 
 services:
+  csd-platform:
+    environment:
+      - DisableUserAccessControl=true
+
   webcsd:
     environment:
-      - ApplicationOnSiteSettings__DisableUserAccessControl=true
+      - ApplicationOnSiteSettings__DisableUserAccessControl=true

docker-compose.macromolecule-hub.yml

@@ -5,35 +5,33 @@ services:
   webcsd:
     environment:
       - CsdRepository__SketcherFeatures__1=Proteins
-   
+
   webcsdbackend:
     environment:
-      - CCDC_LICENSING_CONFIGURATION=${CCDC_LICENSING_CONFIGURATION}
       - ServiceSettings__Databases__1__Name=PDB Database
       - ServiceSettings__Databases__1__DbeName=pdb
       - ServiceSettings__Databases__1__ConnectionString=dbe
 
   ccdc-csd-substructuresearch:
     environment:
-      - PdbReadConnection=${DB_CONNECTIONSTRING};SearchPath=structure_optimisation;Database=${CSD_DATABASE}
       - SubstructureSearchDatabaseConfiguration__Databases__1__Name=pdb
-      - SubstructureSearchDatabaseConfiguration__Databases__1__SettingsKey=PdbReadConnection
+      - SubstructureSearchDatabaseConfiguration__Databases__1__ReadConnectionString=${DB_CONNECTIONSTRING};SearchPath=structure_optimisation;Database=${CSD_DATABASE}
+      - SubstructureSearchDatabaseConfiguration__Databases__1__WriteConnectionString=${DB_CONNECTIONSTRING};SearchPath=structure_optimisation;Database=${CSD_DATABASE}
 
   ccdc-csd-deposition:
     environment:
-      - DepositionPdbReadConnection=${DB_CONNECTIONSTRING};SearchPath=pdb_schema;Database=${CSD_DATABASE}
-      - DatabaseConfiguration__Databases__1__Name=pdb
-      - DatabaseConfiguration__Databases__1__SettingsKey=DepositionPdbReadConnection
+      - DepositionDatabaseConfiguration__Databases__1__Name=pdb
+      - DepositionDatabaseConfiguration__Databases__1__ReadConnectionString=${DB_CONNECTIONSTRING};SearchPath=pdb_schema;Database=${CSD_DATABASE}
+      - DepositionDatabaseConfiguration__Databases__1__WriteConnectionString=${DB_CONNECTIONSTRING};SearchPath=pdb_schema;Database=${CSD_DATABASE}
 
   ccdc-csd-textnumericsearch:
     environment:
       - PdbReadConnection=${DB_CONNECTIONSTRING};SearchPath=pdb_schema;Database=${CSD_DATABASE}
       - DatabaseConfiguration__Databases__1__Name=pdb
       - DatabaseConfiguration__Databases__1__SettingsKey=PdbReadConnection
 
-
   ccdc-csd-unitcellsearch:
     environment:
-      - UnitCellPdbReadConnection=${DB_CONNECTIONSTRING};SearchPath=pdb_cell_optimisation;Database=${CSD_DATABASE}
-      - DatabaseConfiguration__Databases__1__Name=pdb
-      - DatabaseConfiguration__Databases__1__SettingsKey=UnitCellPdbReadConnection
+      - UnitCellDatabaseConfiguration__Databases__1__Name=pdb
+      - UnitCellDatabaseConfiguration__Databases__1__ReadConnectionString=${DB_CONNECTIONSTRING};SearchPath=pdb_cell_optimisation;Database=${CSD_DATABASE}
+      - UnitCellDatabaseConfiguration__Databases__1__WriteConnectionString=${DB_CONNECTIONSTRING};SearchPath=pdb_cell_optimisation;Database=${CSD_DATABASE}

docker-compose.sample-csd-theory-db-config.yml

@@ -8,7 +8,7 @@ services:
     ports:
       - ${PLATFORM_PORT}:8443
       # This is required for csd theory ingestion python script to work
-      #- 80:8080
+      - 80:8080
 
   webcsdbackend:
     volumes: