Add ontology related files to the local Docker env

ebi-gene-expression-group · Mar 1, 2024 · 59b3aff · 59b3aff
1 parent 055a0f1
commit 59b3aff
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diff --git a/docker/dev.env b/docker/dev.env
@@ -5,6 +5,7 @@ GRADLE_RO_DEP_CACHE_VOL_NAME=gradle-ro-dep-cache
 
 ATLAS_DATA_BIOENTITY_PROPERTIES_VOL_NAME=atlas-data-bioentity-properties
 ATLAS_DATA_EXP_VOL_NAME=atlas-data-exp
+ATLAS_DATA_ONTOLOGY_VOL_NAME=atlas-data-ontology
 ATLAS_DATA_EXPDESIGN_VOL_NAME=atlas-data-expdesign
 ATLAS_DATA_VOL_NAME=gxa-data
 

diff --git a/docker/docker-compose-gradle.yml b/docker/docker-compose-gradle.yml
@@ -14,6 +14,7 @@ services:
       - bioentity-properties:/atlas-data/bioentity_properties:ro
       - gxa-exp:/atlas-data/exp:ro
       - gxa-expdesign:/atlas-data/expdesign
+      - gxa-ontology:/atlas-data/ontology
     depends_on:
       gxa-solrcloud-0:
         condition: service_started
@@ -36,6 +37,8 @@ volumes:
     name: ${PROJECT_NAME}_${ATLAS_DATA_EXP_VOL_NAME}
   gxa-expdesign:
     name: ${PROJECT_NAME}_${ATLAS_DATA_EXPDESIGN_VOL_NAME}
+  gxa-ontology:
+    name: ${PROJECT_NAME}_${ATLAS_DATA_ONTOLOGY_VOL_NAME}
 
 networks:
   atlas-test-net:

diff --git a/docker/docker-compose-tomcat.yml b/docker/docker-compose-tomcat.yml
@@ -19,6 +19,7 @@ services:
       - gxa-data:/atlas-data/exp
       - gxa-expdesign:/atlas-data/expdesign
       - gxa-exp:/atlas-data/exp
+      - gxa-ontology:/atlas-data/ontology
       - gxa-tomcat-conf:/usr/local/tomcat/conf
     depends_on:
       gxa-gradle-build:
@@ -46,6 +47,8 @@ volumes:
     name: ${PROJECT_NAME}_${ATLAS_DATA_EXP_VOL_NAME}
   gxa-expdesign:
     name: ${PROJECT_NAME}_${ATLAS_DATA_EXPDESIGN_VOL_NAME}
+  gxa-ontology:
+    name: ${PROJECT_NAME}_${ATLAS_DATA_ONTOLOGY_VOL_NAME}
 
 networks:
   atlas-test-net:

diff --git a/docker/prepare-dev-environment/volumes/Dockerfile b/docker/prepare-dev-environment/volumes/Dockerfile
@@ -10,5 +10,6 @@ RUN apt-get clean && \
 
 # Copy the auxiliary JSON files to the parent of the magetab directory
 COPY atlas-data/exp/* /atlas-data/exp/
+COPY atlas-data/ontology/* /atlas-data/ontology/
 
 ENTRYPOINT ["/bin/bash", "-c"]
diff --git a/docker/prepare-dev-environment/volumes/atlas-data/ontology/anatomical_systems.txt b/docker/prepare-dev-environment/volumes/atlas-data/ontology/anatomical_systems.txt
diff --git a/docker/prepare-dev-environment/volumes/atlas-data/ontology/organs.txt b/docker/prepare-dev-environment/volumes/atlas-data/ontology/organs.txt
diff --git a/docker/prepare-dev-environment/volumes/docker-compose.yml b/docker/prepare-dev-environment/volumes/docker-compose.yml
@@ -6,12 +6,13 @@ services:
     volumes:
       - atlas-data-bioentity-properties:/atlas-data/bioentity_properties
       - atlas-data-exp:/atlas-data/exp
+      - atlas-data-ontology:/atlas-data/ontology
     command:
       - |
         lftp -e \
         "mirror -vvv /pub/databases/microarray/data/atlas/bioentity_properties /atlas-data/bioentity_properties; exit" \
         ftp.ebi.ac.uk
-        
+
         # Create a directory for MAGETAB files
         mkdir -p /atlas-data/exp/magetab
         for EXP_ID in ${EXP_IDS}
@@ -26,3 +27,5 @@ volumes:
     name: ${PROJECT_NAME}_${ATLAS_DATA_BIOENTITY_PROPERTIES_VOL_NAME}
   atlas-data-exp:
     name: ${PROJECT_NAME}_${ATLAS_DATA_EXP_VOL_NAME}
+  atlas-data-ontology:
+    name: ${PROJECT_NAME}_${ATLAS_DATA_ONTOLOGY_VOL_NAME}
diff --git a/docker/prepare-dev-environment/volumes/run.sh b/docker/prepare-dev-environment/volumes/run.sh
@@ -77,4 +77,5 @@ printf '%b\n' "🙂 All done! You can inspect the volume contents attaching them
 printf '%b\n' "   docker run \\"
 printf '%b\n' "   -v ${PROJECT_NAME}_${ATLAS_DATA_BIOENTITY_PROPERTIES_VOL_NAME}:/${ATLAS_DATA_BIOENTITY_PROPERTIES_VOL_NAME} \\"
 printf '%b\n' "   -v ${PROJECT_NAME}_${ATLAS_DATA_EXP_VOL_NAME}:/${ATLAS_DATA_EXP_VOL_NAME} \\"
+printf '%b\n' "   -v ${PROJECT_NAME}_${ATLAS_DATA_ONTOLOGY_VOL_NAME}:/${ATLAS_DATA_ONTOLOGY_VOL_NAME} \\"
 printf '%b\n' "   --rm -it ubuntu:jammy bash"