Merge pull request #580 from hms-dbmi-cellenics/add-sce-upload

rename seurat pipeline to obj2s
hms-dbmi-cellenics · Sep 20, 2024 · 72c4b51 · 72c4b51
2 parents cdf2b0b + 2c397ad
commit 72c4b51
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Showing 4 changed files with 8 additions and 5 deletions.
diff --git a/cf/irsa-api-role.yaml b/cf/irsa-api-role.yaml
@@ -149,10 +149,11 @@ Resources:
                   - "states:TagResource"
                 Resource:
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:biomage-pipeline-${Environment}-*"  # used to access old pipeline executions
+                  - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:biomage-seurat-${Environment}-*" # used to access old seurat executions
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:pipeline-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:biomage-qc-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:biomage-gem2s-${Environment}-*"
-                  - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:biomage-seurat-${Environment}-*"
+                  - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:biomage-obj2s-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:biomage-subset-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:stateMachine:biomage-copy-${Environment}-*"
 
@@ -167,11 +168,12 @@ Resources:
                   - "states:GetExecutionHistory"
                 Resource:
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:biomage-pipeline-${Environment}-*:*" # used to access old pipeline executions
+                  - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:biomage-seurat-${Environment}-*:*" # used to access old seurat executions
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:pipeline-${Environment}-*:*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:biomage-qc-${Environment}-*:*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:biomage-gem2s-${Environment}-*:*"
+                  - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:biomage-obj2s-${Environment}-*:*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:biomage-subset-${Environment}-*:*"
-                  - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:biomage-seurat-${Environment}-*:*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:execution:biomage-copy-${Environment}-*:*"
 
         - PolicyName: !Sub "can-create-activity-${Environment}"
@@ -184,7 +186,7 @@ Resources:
                 Resource:
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-qc-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-gem2s-${Environment}-*"
-                  - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-seurat-${Environment}-*"
+                  - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-obj2s-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-subset-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-copy-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:pipeline-${Environment}-*"

diff --git a/cf/irsa-pipeline-role.yaml b/cf/irsa-pipeline-role.yaml
@@ -150,6 +150,7 @@ Resources:
                 Resource:
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-qc-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-gem2s-${Environment}-*"
+                  - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-obj2s-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-subset-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:biomage-copy-${Environment}-*"
                   - !Sub "arn:aws:states:${AWS::Region}:${AWS::AccountId}:activity:pipeline-${Environment}-*"

diff --git a/cf/sns.yaml b/cf/sns.yaml
@@ -156,7 +156,7 @@ Resources:
             pipeline_type_mappings = {
                 "PipelineResponse": "/v2/pipelineResults",
                 "GEM2SResponse": "/v2/gem2sResults",
-                "SeuratResponse": "/v2/seuratResults"
+                "OBJ2SResponse": "/v2/obj2sResults"
             }
 
             if message_body.get("reason") == "BackOff":

diff --git a/infra/aws-elb-503-subscription-endpoint/templates/ingress.yaml b/infra/aws-elb-503-subscription-endpoint/templates/ingress.yaml
@@ -36,7 +36,7 @@ spec:
                 name: response-503
                 port:
                   name: use-annotation
-          - path: /v2/seuratResults
+          - path: /v2/obj2sResults
             pathType: ImplementationSpecific
             backend:
               service: