update workflowloow oscar

interTwin-eu · Oct 31, 2024 · be8170a · be8170a
1 parent 7c49c5c
commit be8170a
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Showing 6 changed files with 18 additions and 17 deletions.
diff --git a/DT_flood/workflows/cwl_OSCAR/upload/upload.cwl b/DT_flood/workflows/cwl_OSCAR/upload/upload.cwl
@@ -6,7 +6,7 @@ baseCommand: python
 arguments: [$(inputs.uploadScript),"--bucket",$(inputs.bucket),"--filename", $(inputs.file), "--endpoint",$(inputs.minioEndpoint),"--accesskey",$(inputs.minioAccesskey),"--secretkey",$(inputs.minioSecretkey)]
 inputs:
   file:
-    type: Directory?
+    type: File?
   uploadScript:
     type: File?
   bucket:

diff --git a/DT_flood/workflows/cwl_OSCAR/upload/upload.py b/DT_flood/workflows/cwl_OSCAR/upload/upload.py
@@ -28,10 +28,11 @@
 #print(filename)
 
 # Create client with access and secret key.
-with tarfile.open(filename+".tar", "w:gz") as tar:
-        tar.add(filename, arcname=os.path.basename(filename))
+#with tarfile.open(filename+".tar", "w:gz") as tar:
+#        tar.add(filename, arcname=os.path.basename(filename))
+
 client = Minio(str(endpoint), accesskey, secretkey)
 
 result = client.fput_object(
-    bucket.split("/")[0], '/'.join(bucket.split("/")[1:])+"/"+filename.split("/")[-1], filename+".tar",
+    bucket.split("/")[0], '/'.join(bucket.split("/")[1:])+"/"+filename.split("/")[-1], filename,
 )
diff --git a/DT_flood/workflows/cwl_OSCAR/wait_output/wait.cwl b/DT_flood/workflows/cwl_OSCAR/wait_output/wait.cwl
@@ -15,7 +15,7 @@ inputs:
     type: string
   minioSecretkey:
     type: string
+
 outputs:
-  example_out:
-    type: stdout
-stdout: output.txt
+    fa_database_out:
+        type: Directory
diff --git a/DT_flood/workflows/cwl_OSCAR/wflow_input.tar b/DT_flood/workflows/cwl_OSCAR/wflow_input.tar
diff --git a/DT_flood/workflows/cwl_OSCAR/workflow-minio.cwl b/DT_flood/workflows/cwl_OSCAR/workflow-minio.cwl
@@ -8,7 +8,7 @@ requirements:
 
 inputs:
   file:
-    type: Directory?
+    type: File?
   uploadScript:
     type: File?
   waitScript:
@@ -24,9 +24,9 @@ inputs:
   bucketOutput:
     type: string
 outputs:
-  out:
-    type: File?
-    outputSource: wait/example_out
+    fa_database_out:
+        type: Directory
+        
 steps:
 
   upload:
@@ -49,4 +49,4 @@ steps:
       minioSecretkey: minioSecretkey
       data: 
         source: upload/example_out
-    out: [example_out]
+    out: [fa_database_out]
diff --git a/DT_flood/workflows/cwl_OSCAR/workflow.yaml b/DT_flood/workflows/cwl_OSCAR/workflow.yaml
@@ -1,11 +1,11 @@
 file:
-  class: Directory
-  path: archive/
+  class: File
+  path: wflow_input.tar
 
 
-minioEndpoint: 
-minioAccesskey: 
-minioSecretkey: 
+minioEndpoint: minio.sleepy-lumiere4.im.grycap.net
+minioAccesskey: minio
+minioSecretkey: minio123
 
 bucketInput: wflow/in
 bucketOutput: wflow/out