OSCAR workflow v1

OSCAR_flow/upload/upload.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: python
+arguments: [$(inputs.uploadScript),"--bucket",$(inputs.bucket),"--filename", $(inputs.file), "--endpoint",$(inputs.minioEndpoint),"--accesskey",$(inputs.minioAccesskey),"--secretkey",$(inputs.minioSecretkey)]
+inputs:
+  file:
+    type: File?
+  uploadScript:
+    type: File?
+  bucket:
+    type: string
+  minioEndpoint:
+    type: string
+  minioAccesskey:
+    type: string
+  minioSecretkey:
+    type: string
+outputs:
+  example_out:
+    type: stdout
+stdout: output.txt

OSCAR_flow/upload/upload.py

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+from minio import Minio
+import argparse
+
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument("--bucket")
+parser.add_argument("--filename")
+parser.add_argument("--endpoint")
+parser.add_argument("--accesskey")
+parser.add_argument("--secretkey")
+
+args = parser.parse_args()
+variables = vars(args)
+#print(variables)
+
+bucket=variables['bucket']
+filename=variables['filename']
+endpoint=variables['endpoint']
+accesskey=variables['accesskey']
+secretkey=variables['secretkey']
+
+#print (bucket.split("/")[0],)
+#print('/'.join(sys.argv[1].split("/")[1:]))
+#print(filename.split("/")[-1])
+#print(filename)
+
+# Create client with access and secret key.
+client = Minio(str(endpoint), accesskey, secretkey)
+
+result = client.fput_object(
+    bucket.split("/")[0], '/'.join(bucket.split("/")[1:])+"/"+filename.split("/")[-1], filename,
+)

OSCAR_flow/wait_output/wait.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: python
+arguments: [$(inputs.waitScript),"--bucket",$(inputs.bucket), "--endpoint",$(inputs.minioEndpoint),"--accesskey",$(inputs.minioAccesskey),"--secretkey",$(inputs.minioSecretkey)]
+inputs:
+  waitScript:
+    type: File?
+  bucket:
+    type: string
+  minioEndpoint:
+    type: string
+  minioAccesskey:
+    type: string
+  minioSecretkey:
+    type: string
+outputs:
+  example_out:
+    type: stdout
+stdout: output.txt

OSCAR_flow/wait_output/wait.py

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+from minio import Minio
+import argparse
+
+parser = argparse.ArgumentParser()
+
+parser.add_argument("--bucket")
+parser.add_argument("--filename")
+parser.add_argument("--endpoint")
+parser.add_argument("--accesskey")
+parser.add_argument("--secretkey")
+
+args = parser.parse_args()
+variables = vars(args)
+#print(variables)
+
+bucket=variables['bucket']
+filename=variables['filename']
+endpoint=variables['endpoint']
+accesskey=variables['accesskey']
+secretkey=variables['secretkey']
+
+
+# Create client with access and secret key.
+client = Minio(str(endpoint), accesskey, secretkey)
+
+with client.listen_bucket_notification(
+    bucket.split("/")[0],
+    prefix='/'.join(bucket.split("/")[1:]),
+    events=["s3:ObjectCreated:*", "s3:ObjectRemoved:*"],
+) as events:
+    for event in events:
+        print(event["Records"][0]["s3"]["object"]["key"])
+        break
+        #if(resultfile in event["Records"][0]["s3"]["object"]["key"]):
+        #    info=event
+        #    break

OSCAR_flow/workflow-minio.cwl

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+#!/usr/bin/env cwl-runner
+
+cwlVersion: v1.2
+class: Workflow
+
+requirements:
+  InlineJavascriptRequirement: {}
+
+inputs:
+  file:
+    type: File?
+  uploadScript:
+    type: File?
+  waitScript:
+    type: File?
+  minioEndpoint:
+    type: string
+  minioAccesskey:
+    type: string
+  minioSecretkey:
+    type: string
+  bucketInput:
+    type: string
+  bucketOutput:
+    type: string
+outputs:
+  out:
+    type: File?
+    outputSource: wait/example_out
+steps:
+  upload:
+    run: upload/upload.cwl
+    in:
+      file: file
+      uploadScript: uploadScript
+      bucket: bucketInput
+      minioEndpoint: minioEndpoint
+      minioAccesskey: minioAccesskey
+      minioSecretkey: minioSecretkey
+    out: [example_out]
+  wait:
+    run: wait_output/wait.cwl
+    in:
+      waitScript: waitScript
+      bucket: bucketOutput
+      minioEndpoint: minioEndpoint
+      minioAccesskey: minioAccesskey
+      minioSecretkey: minioSecretkey
+      data: 
+        source: upload/example_out
+    out: [example_out]

OSCAR_flow/workflow.yaml

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+file:
+  class: File
+  path: wflow_input.tar
+
+
+minioEndpoint: 
+minioAccesskey: 
+minioSecretkey: 
+
+
+bucketInput: wflow/in
+bucketOutput: wflow/out
+
+
+uploadScript:
+  class: File
+  path: upload/upload.py
+
+waitScript:
+  class: File
+  path: wait_output/wait.py