Proof of concept web service for accepting CWL job requests.

Author: Peter Amstutz

cwl_client.py

@@ -0,0 +1,19 @@
+import argparse
+import requests
+
+def main():
+    parser = argparse.ArgumentParser()
+
+    parser.add_argument("--upload", action="store_true")
+    parser.add_argument("endpoint")
+    parser.add_argument("object")
+
+    args = parser.parse_args()
+
+    if args.upload:
+        r = requests.put(args.endpoint)
+    else:
+        r = requests.post(args.endpoint)
+
+if __name__ == "__main__":
+    main()

cwltool_flask.py

@@ -0,0 +1,42 @@
+import cwltool
+from flask import Flask
+from flask import request
+import os
+import StringIO
+
+app = Flask(__name__)
+
+@app.route("/<workflow>", methods=['GET', 'POST', 'PUT'])
+def runjob(workflow):
+    try:
+        if request.method == 'PUT':
+            with open(os.path.join("files", workflow), "w") as f:
+                f.write(request.stream.read())
+            return "Ok"
+
+        wf = os.path.join("files", workflow)
+
+        if not os.path.exists(wf):
+            return "Not found", 404
+
+        if request.method == 'POST':
+            out = StringIO.StringIO()
+            err = StringIO.StringIO()
+            if cwltool.main(args=[wf, "-"],
+                            stdin=request.stream.read(),
+                            stdout=out,
+                            stderr=err) != 0:
+                return err.getvalue(), 400
+            else:
+                return out.getvalue()
+
+        else:
+           with open(wf, "r") as f:
+               return f.read()
+    except Exception as e:
+        return str(e), 500
+
+if __name__ == "__main__":
+    if not os.path.exists("files"):
+        os.mkdir("files")
+    app.run()

cwltool_service.py

@@ -11,17 +11,19 @@
 README = os.path.join(SETUP_DIR, 'README')
 
 setup(name='cwltool_service',
-      version='1.0.2',
+      version='1.0.3',
       description='Common workflow language runner service',
       long_description=open(README).read(),
       author='Common workflow language working group',
       author_email='[email protected]',
       url="https://github.com/common-workflow-language/common-workflow-language",
       download_url="https://github.com/common-workflow-language/common-workflow-language",
       license='Apache 2.0',
-      py_modules=["cwltool_service"],
+      py_modules=["cwltool_stream", "cwltool_flask", "cwltool_client"],
       install_requires=[
-          'cwltool'
+          'cwltool >= 1.0.20151013135545',
+          'Flask',
+          'requests'
         ],
       entry_points={
           'console_scripts': [ "cwltool-service=cwltool_service:main" ]