feat!: implement new workflow system

bento-platform · Nov 14, 2023 · 0993d31 · 0993d31
1 parent 1a9760b
commit 0993d31
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Showing 2 changed files with 36 additions and 28 deletions.
diff --git a/src/api/workflows/main.go b/src/api/workflows/main.go
@@ -13,14 +13,20 @@ var WORKFLOW_VARIANT_SCHEMA WorkflowSchema = map[string]interface{}{
 			"name":        "Compressed-VCF Elasticsearch Indexing",
 			"description": "This ingestion workflow will validate and ingest a BGZip-Compressed-VCF into Elasticsearch.",
 			"data_type":   "variant",
+			"tags":        []string{"variant"},
 			"file":        "vcf_gz.wdl",
-			"action":     "ingestion",
+			"type":        "ingestion",
 			"inputs": []map[string]interface{}{
 				{
-					"id":         "vcf_gz_file_names",
-					"type":       "file[]",
-					"required":   true,
-					"extensions": []string{".vcf.gz"},
+					"id":       "project_dataset",
+					"type":     "project:dataset",
+					"required": true,
+				},
+				{
+					"id":       "vcf_gz_file_names",
+					"type":     "file[]",
+					"required": true,
+					"pattern":  "^.*\\.vcf\\.gz$",
 				},
 				{
 					"id":       "assembly_id",
@@ -37,26 +43,15 @@ var WORKFLOW_VARIANT_SCHEMA WorkflowSchema = map[string]interface{}{
 					"default":  "false",
 				},
 				{
-					"id":		"gohan_url",
-					"type":		"string",
-					"required":	true,
-					"value":	"FROM_CONFIG",
-					"hidden":	true,
-				},
-			},
-			"outputs": []map[string]interface{}{
-				{
-					"id":    "txt_output",
-					"type":  "file",
-					"value": "{txt_output}",
-				},
-				{
-					"id":    "err_output",
-					"type":  "file",
-					"value": "{err_output}",
+					"id":           "gohan_url",
+					"type":         "service-kind",
+					"required":     true,
+					"injected":     true,
+					"service_kind": "gohan",
 				},
 			},
 		},
 	},
 	"analysis": map[string]interface{}{},
+	"export":   map[string]interface{}{},
 }
diff --git a/src/api/workflows/vcf_gz.wdl b/src/api/workflows/vcf_gz.wdl
@@ -2,24 +2,37 @@ workflow vcf_gz {
     String gohan_url
     Array[File] vcf_gz_file_names
     String assembly_id
-    String project_id
-    String dataset_id
+    String project_dataset
     String filter_out_references
-    String secret__access_token
+    String access_token
+
+    call project_and_dataset_id {
+        input: project_dataset = project_dataset
+    }
 
     scatter(file_name in vcf_gz_file_names) {
         call vcf_gz_gohan {
             input: gohan_url = gohan_url,
                    vcf_gz_file_name = file_name,
                    assembly_id = assembly_id,
-                   project = project_id,
-                   dataset = dataset_id,
+                   project = project_and_dataset_id.out[0],
+                   dataset = project_and_dataset_id.out[1],
                    filter_out_references = filter_out_references,
-                   access_token = secret__access_token,
+                   access_token = access_token,
         }
     }
 }
 
+task project_and_dataset_id {
+    input {
+        String project_dataset
+    }
+    command <<< python3 -c 'import json; print(json.dumps("~{project_dataset}".split(":")))' >>>
+    output {
+        Array[String] out = read_json(stdout())
+    }
+}
+
 task vcf_gz_gohan {
     String gohan_url
     String vcf_gz_file_name