adding comments

helm/audit/templates/deployment.yaml

@@ -90,6 +90,7 @@ spec:
                 readOnly: true
                 mountPath: "/src/audit-service-config.yaml"
                 subPath: "audit-service-config.yaml"
+              # Added an additional volume mount for new images using the /<app-name> directory, while retaining the 'src' mount for backward compatibility.
               - name: "config-volume"
                 readOnly: true
                 mountPath: "/audit/audit-service-config.yaml"
@@ -138,12 +139,14 @@ spec:
           args:
             - "-c"
             - |
+              # Managing virtual environments via poetry instead of python since the AL base image update, but retaining backwards compatibility 
               poetry run alembic upgrade head || /env/bin/alembic upgrade head
           volumeMounts:
             - name: "config-volume"
               readOnly: true
               mountPath: "/src/audit-service-config.yaml"
               subPath: "audit-service-config.yaml"
+            # Added an additional volume mount for new images using the /<app-name> directory, while retaining the 'src' mount for backward compatibility.
             - name: "config-volume"
               readOnly: true
               mountPath: "/audit/audit-service-config.yaml"

helm/metadata/README.md

@@ -25,7 +25,7 @@ A Helm chart for gen3 Metadata Service
 | affinity.podAntiAffinity.preferredDuringSchedulingIgnoredDuringExecution[0].podAffinityTerm.topologyKey | string | `"kubernetes.io/hostname"` | Value for topology key label. |
 | aggMdsConfig | string | `"{\n  \"configuration\": {\n    \"schema\": {\n      \"_subjects_count\": {\n        \"type\": \"integer\"\n      },\n      \"__manifest\": {\n        \"description\": \"an array of filename (usually DRS ids and its size\",\n        \"type\": \"array\",\n        \"properties\": {\n          \"file_name\": {\n            \"type\": \"string\"\n          },\n          \"file_size\": {\n            \"type\": \"integer\"\n          }\n        }\n      },\n      \"tags\": {\n        \"type\": \"array\"\n      },\n      \"_unique_id\": {},\n      \"study_description\": {},\n      \"study_id\": {},\n      \"study_url\": {},\n      \"project_id\": {},\n      \"short_name\": {\n        \"default\": \"not_set\"\n      },\n      \"year\": {\n        \"default\": \"not_set\"\n      },\n      \"full_name\": {},\n      \"commons_url\": {},\n      \"commons\": {}\n    },\n    \"settings\": {\n      \"cache_drs\": true\n    }\n  },\n  \"adapter_commons\": {\n    \"Gen3\": {\n      \"mds_url\": \"https://gen3.datacommons.io/\",\n      \"commons_url\": \"gen3.datacommons.io/\",\n      \"adapter\": \"gen3\",\n      \"config\": {\n        \"guid_type\": \"discovery_metadata\",\n        \"study_field\": \"gen3_discovery\"\n      },\n      \"keep_original_fields\": false,\n      \"field_mappings\": {\n        \"tags\": \"path:tags\",\n        \"_unique_id\": \"path:_unique_id\",\n        \"study_description\": \"path:summary\",\n        \"full_name\": \"path:study_title\",\n        \"short_name\": \"path:short_name\",\n        \"year\": \"path:year\",\n        \"accession_number\": \"path:accession_number\",\n        \"commons\": \"Gen3 Data Commons\",\n        \"study_url\": {\n          \"path\": \"link\",\n          \"default\": \"unknown\"\n        }\n      }\n    }\n  }\n}\n"` |  |
 | aggMdsNamespace | string | `"default"` | Namespae to use if AggMds is enabled. |
-| args | list | `["-c","poetry run alembic upgrade head || /env/bin/alembic upgrade head\n"]` | Arguments to pass to the init container. |
+| args | list | `["-c","# Managing virtual environments via poetry instead of python since the AL base image update, but retaining backwards compatibility \npoetry run alembic upgrade head || /env/bin/alembic upgrade head\n"]` | Arguments to pass to the init container. |
 | automountServiceAccountToken | bool | `false` | Automount the default service account token |
 | autoscaling | map | `{"enabled":false,"maxReplicas":100,"minReplicas":1,"targetCPUUtilizationPercentage":80}` | Configuration for autoscaling the number of replicas |
 | autoscaling.enabled | bool | `false` | Whether autoscaling is enabled |

helm/metadata/values.yaml

@@ -253,6 +253,7 @@ volumeMounts:
     readOnly: true
     mountPath: /src/.env
     subPath: metadata.env
+  # Added an additional volume mount for new images using the /<app-name> directory, while retaining the 'src' mount for backward compatibility.
   - name: config-volume-g3auto
     readOnly: true
     mountPath: /mds/.env
@@ -290,6 +291,7 @@ initVolumeMounts:
     readOnly: true
     mountPath: /src/.env
     subPath: metadata.env
+  # Added an additional volume mount for new images using the /<app-name> directory, while retaining the 'src' mount for backward compatibility.
   - name: config-volume-g3auto
     readOnly: true
     mountPath: /mds/.env
@@ -308,6 +310,7 @@ command: ["/bin/sh"]
 args:
   - "-c"
   - |
+    # Managing virtual environments via poetry instead of python since the AL base image update, but retaining backwards compatibility 
     poetry run alembic upgrade head || /env/bin/alembic upgrade head
 
 # Service and Pod

helm/requestor/README.md

@@ -23,7 +23,7 @@ A Helm chart for gen3 Requestor Service
 | affinity.podAntiAffinity.preferredDuringSchedulingIgnoredDuringExecution[0].podAffinityTerm.labelSelector.matchExpressions[0].values | list | `["requestor"]` | Value for the match expression key. |
 | affinity.podAntiAffinity.preferredDuringSchedulingIgnoredDuringExecution[0].podAffinityTerm.topologyKey | string | `"kubernetes.io/hostname"` | Value for topology key label. |
 | arboristUrl | string | `"http://arborist-service"` | Arborist service URL. |
-| args | list | `["-c","poetry run alembic upgrade head || /env/bin/alembic upgrade head\n"]` | Arguments to pass to the init container. |
+| args | list | `["-c","# Managing virtual environments via poetry instead of python since the AL base image update, but retaining backwards compatibility \npoetry run alembic upgrade head || /env/bin/alembic upgrade head\n"]` | Arguments to pass to the init container. |
 | automountServiceAccountToken | bool | `false` | Automount the default service account token |
 | autoscaling | map | `{"enabled":false,"maxReplicas":100,"minReplicas":1,"targetCPUUtilizationPercentage":80}` | Configuration for autoscaling the number of replicas |
 | autoscaling.enabled | bool | `false` | Whether autoscaling is enabled |

helm/requestor/values.yaml

@@ -190,6 +190,7 @@ volumeMounts:
   #   readOnly: true
   #   mountPath: "/src/requestor-config.yaml"
   #   subPath: "requestor-config.yaml"
+  # Added an additional volume mount for new images using the /<app-name> directory, while retaining the 'src' mount for backward compatibility.
   # - name: "config-volume"
   #   readOnly: true
   #   mountPath: "/requestor/requestor-config.yaml"
@@ -227,6 +228,7 @@ command: ["/bin/sh"]
 args:
   - "-c"
   - |
+    # Managing virtual environments via poetry instead of python since the AL base image update, but retaining backwards compatibility 
     poetry run alembic upgrade head || /env/bin/alembic upgrade head
 
 # Service and Pod

helm/wts/templates/deployment.yaml

@@ -185,6 +185,7 @@ spec:
             if hash alembic 2>/dev/null; then
               echo "Running DB migration"
               cd /wts
+              # Managing virtual environments via poetry instead of python since the AL base image update, but retaining backwards compatibility 
               poetry run alembic upgrade head || alembic upgrade head
             else
               echo "Alembic not installed - not running DB migration"