Make workflow type optional in store, remove references to WDL in Swa…

…gger.
broadinstitute · 655112961cc49775bc01654a560f172543976407 · mcovarr committed with mcovarr Jun 12, 2017 · Jun 12, 2017 · 6551129
1 parent c0289dc
commit 655112961cc49775bc01654a560f172543976407
diff --git a/database/migration/src/main/resources/changesets/workflow_store_type_and_version.xml b/database/migration/src/main/resources/changesets/workflow_store_type_and_version.xml
@@ -14,10 +14,4 @@
         </addColumn>
     </changeSet>
 
-    <changeSet author="mcovarr" id="not-null-workflow-store-type">
-        <addNotNullConstraint columnDataType="VARCHAR(30)"
-                              columnName="WORKFLOW_TYPE"
-                              defaultNullValue="WDL"
-                              tableName="WORKFLOW_STORE_ENTRY"/>
-    </changeSet>
 </databaseChangeLog>
diff --git a/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala b/database/sql/src/main/scala/cromwell/database/slick/tables/WorkflowStoreEntryComponent.scala
@@ -15,7 +15,7 @@ trait WorkflowStoreEntryComponent {
 
     def workflowExecutionUuid = column[String]("WORKFLOW_EXECUTION_UUID")
 
-    def workflowType = column[String]("WORKFLOW_TYPE", O.Length(30))
+    def workflowType = column[Option[String]]("WORKFLOW_TYPE", O.Length(30))
 
     def workflowTypeVersion = column[Option[String]]("WORKFLOW_TYPE_VERSION")
 
diff --git a/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala b/database/sql/src/main/scala/cromwell/database/sql/tables/WorkflowStoreEntry.scala
@@ -6,7 +6,7 @@ case class WorkflowStoreEntry
 (
   workflowExecutionUuid: String,
   workflowDefinition: Option[Clob],
-  workflowType: String,
+  workflowType: Option[String],
   workflowTypeVersion: Option[String],
   workflowInputs: Option[Clob],
   workflowOptions: Option[Clob],
diff --git a/engine/src/main/resources/swagger/cromwell.yaml b/engine/src/main/resources/swagger/cromwell.yaml
@@ -58,33 +58,33 @@ paths:
           type: string
           in: path
           default: v1
-        - name: wdlSource
-          description: WDL Source
+        - name: workflowSource
+          description: Workflow source file
           required: true
           type: file
           in: formData
         - name: workflowInputs
-          description: WDL Inputs JSON, 1
+          description: Workflow Inputs JSON, 1
           required: false
           type: file
           in: formData
         - name: workflowInputs_2
-          description: WDL Inputs JSON, 2
+          description: Workflow Inputs JSON, 2
           required: false
           type: file
           in: formData
         - name: workflowInputs_3
-          description: WDL Inputs JSON, 3
+          description: Workflow Inputs JSON, 3
           required: false
           type: file
           in: formData
         - name: workflowInputs_4
-          description: WDL Inputs JSON, 4
+          description: Workflow Inputs JSON, 4
           required: false
           type: file
           in: formData
         - name: workflowInputs_5
-          description: WDL Inputs JSON, 5
+          description: Workflow Inputs JSON, 5
           required: false
           type: file
           in: formData
@@ -93,13 +93,23 @@ paths:
           required: false
           type: file
           in: formData
+        - name: workflowType
+          description: Type of workflow
+          required: false
+          type: string
+          in: formData
+        - name: workflowTypeVersion
+          description: Version of workflow type
+          required: false
+          type: string
+          in: formData
         - name: customLabels
           description: Custom Labels JSON
           required: false
           type: file
           in: formData
         - name: workflowDependencies
-          description: Zip file containing WDL dependencies
+          description: Zip file containing workflow dependencies
           required: false
           type: file
           in: formData
@@ -129,13 +139,13 @@ paths:
           type: string
           in: path
           default: v1
-        - name: wdlSource
-          description: WDL Source
+        - name: workflowSource
+          description: Workflow Source
           required: true
           type: file
           in: formData
         - name: workflowInputs
-          description: WDL Inputs JSON as an array
+          description: Workflow Inputs JSON as an array
           required: true
           type: file
           in: formData
@@ -144,13 +154,23 @@ paths:
           required: false
           type: file
           in: formData
+        - name: workflowType
+          description: Type of workflow
+          required: false
+          type: string
+          in: formData
+        - name: workflowTypeVersion
+          description: Version of workflow type
+          required: false
+          type: string
+          in: formData
         - name: customLabels
           description: Custom Labels JSON
           required: false
           type: file
           in: formData
         - name: workflowDependencies
-          description: Zip file containing WDL dependencies
+          description: Zip file containing workflow dependencies
           required: false
           type: file
           in: formData
diff --git a/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala b/engine/src/main/scala/cromwell/engine/workflow/workflowstore/SqlWorkflowStore.scala
@@ -56,7 +56,7 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase) extends Workf
   private def fromWorkflowStoreEntry(workflowStoreEntry: WorkflowStoreEntry): WorkflowToStart = {
     val sources = WorkflowSourceFilesCollection(
       workflowSource = workflowStoreEntry.workflowDefinition.toRawString,
-      workflowType = Option(workflowStoreEntry.workflowType),
+      workflowType = workflowStoreEntry.workflowType,
       workflowTypeVersion = workflowStoreEntry.workflowTypeVersion,
       inputsJson = workflowStoreEntry.workflowInputs.toRawString,
       workflowOptionsJson = workflowStoreEntry.workflowOptions.toRawString,
@@ -76,8 +76,7 @@ case class SqlWorkflowStore(sqlDatabase: WorkflowStoreSqlDatabase) extends Workf
     WorkflowStoreEntry(
       workflowExecutionUuid = WorkflowId.randomId().toString,
       workflowDefinition = workflowSourceFiles.workflowSource.toClobOption,
-      // TODO ensure safety
-      workflowType = workflowSourceFiles.workflowType.get,
+      workflowType = workflowSourceFiles.workflowType,
       workflowTypeVersion = workflowSourceFiles.workflowTypeVersion,
       workflowInputs = workflowSourceFiles.inputsJson.toClobOption,
       workflowOptions = workflowSourceFiles.workflowOptionsJson.toClobOption,
diff --git a/scripts/test_upgrade/test_upgrade.sh b/scripts/test_upgrade/test_upgrade.sh
@@ -67,7 +67,7 @@ do
 	echo -n "submitting job ${i}a and ${i}b..."
 	RESULT_FILE="$OUT_DIR/submitResult_${i}_ab.json"
 	curl -X POST --header "Accept: application/json" "http://localhost:8000/api/workflows/v1/batch" \
-	  -F wdlSource=@scatter_files.wdl \
+	  -F workflowSource=@scatter_files.wdl \
 	  -F workflowInputs=@scatter_files_input_part1_ab.json \
 	  -F workflowInputs_2=@scatter_files_input_part2.json \
 	  -F workflowInputs_3=@scatter_files_input_part3.json \
@@ -80,7 +80,7 @@ do
 	echo -n "submitting job ${i}c..."
 	RESULT_FILE="$OUT_DIR/submitResult_${i}_c.json"
 	curl -X POST --header "Accept: application/json" "http://localhost:8000/api/workflows/v1/batch" \
-	  -F wdlSource=@scatter_files.wdl \
+	  -F workflowSource=@scatter_files.wdl \
 	  -F workflowInputs=@scatter_files_input_part1_c.json \
 	  -F workflowInputs_2=@scatter_files_input_part2.json \
 	  -F workflowInputs_3=@scatter_files_input_part3.json \
@@ -125,7 +125,7 @@ i=3
 echo -n "submitting job ${i}a and ${i}b..."
 RESULT_FILE="$OUT_DIR/submitResult_${i}_ab.json"
 curl -X POST --header "Accept: application/json" "http://localhost:8000/api/workflows/v1/batch" \
-  -F wdlSource=@scatter_files.wdl \
+  -F workflowSource=@scatter_files.wdl \
   -F workflowInputs=@scatter_files_input_part1_ab.json \
   -F workflowInputs_2=@scatter_files_input_part2.json \
   -F workflowInputs_3=@scatter_files_input_part3.json \
@@ -138,7 +138,7 @@ echo "done (Response in: $RESULT_FILE)."
 echo -n "submitting job ${i}c..."
 RESULT_FILE="$OUT_DIR/submitResult_${i}_c.json"
 curl -X POST --header "Accept: application/json" "http://localhost:8000/api/workflows/v1/batch" \
-  -F wdlSource=@scatter_files.wdl \
+  -F workflowSource=@scatter_files.wdl \
   -F workflowInputs=@scatter_files_input_part1_c.json \
   -F workflowInputs_2=@scatter_files_input_part2.json \
   -F workflowInputs_3=@scatter_files_input_part3.json \
diff --git a/services/src/test/scala/cromwell/services/ServicesStoreSpec.scala b/services/src/test/scala/cromwell/services/ServicesStoreSpec.scala
@@ -621,5 +621,5 @@ object ServicesStoreSpec {
     }
   }
 
-  private val WdlWorkflowType = "WDL"
+  private val WdlWorkflowType = Option("WDL")
 }