Proof of concept flask service and client to accept CWL files and run CWL jobs.

Author: Peter Amstutz

cwl_client.py

@@ -1,19 +1,33 @@
 import argparse
 import requests
+import urlparse
+import os
 
 def main():
     parser = argparse.ArgumentParser()
 
-    parser.add_argument("--upload", action="store_true")
+    parser.add_argument("--upload", action="store_true", help="Upload new CWL tool or workflow.")
     parser.add_argument("endpoint")
-    parser.add_argument("object")
+    parser.add_argument("item", nargs="?")
 
     args = parser.parse_args()
 
+    if not args.item:
+        r = requests.get(args.endpoint)
+        print r.text
+        return
+
+    with open(args.item) as f:
+        data = f.read()
+
     if args.upload:
-        r = requests.put(args.endpoint)
+        dest = urlparse.urljoin(args.endpoint, os.path.basename(args.item))
+        r = requests.put(dest, data=data)
     else:
-        r = requests.post(args.endpoint)
+        r = requests.post(args.endpoint, data=data)
+
+    print r.text
+
 
 if __name__ == "__main__":
     main()

cwl_flask.py

@@ -0,0 +1,47 @@
+from flask import Flask
+from flask import request
+import os
+import subprocess
+import tempfile
+
+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':
+            with tempfile.NamedTemporaryFile() as f:
+                f.write(request.stream.read())
+                f.flush()
+                outdir = tempfile.mkdtemp()
+                proc = subprocess.Popen(["cwl-runner", os.path.abspath(wf), f.name],
+                                        stdout=subprocess.PIPE,
+                                        stderr=subprocess.PIPE,
+                                        close_fds=True,
+                                        cwd=outdir)
+                (stdoutdata, stderrdata) = proc.communicate()
+                proc.wait()
+                if proc.returncode == 0:
+                    return stdoutdata
+                else:
+                    return stderrdata, 400
+        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_flask.py

@@ -0,0 +1,42 @@
+#!/usr/bin/env python
+
+import sys
+import cwltool.main
+import tempfile
+import logging
+import StringIO
+import json
+
+_logger = logging.getLogger("cwltool")
+_logger.setLevel(logging.ERROR)
+
+def main(args=None):
+    if args is None:
+        args = sys.argv[1:]
+
+    if len(args) == 0:
+        print "Workflow must be on command line"
+        return 1
+
+    parser = cwltool.main.arg_parser()
+    parsedargs = parser.parse_args(args)
+
+    a = True
+    while a:
+        a = True
+        msg = ""
+        while a and a != "\n":
+            a = sys.stdin.readline()
+            msg += a
+
+        outdir = tempfile.mkdtemp("", parsedargs.tmp_outdir_prefix)
+
+        t = StringIO.StringIO(msg)
+        err = StringIO.StringIO()
+        if cwltool.main.main(["--outdir="+outdir] + args + ["-"], stdin=t, stderr=err) != 0:
+            sys.stdout.write(json.dumps({"cwl:error": err.getvalue()}))
+        sys.stdout.write("\n\n")
+        sys.stdout.flush()
+
+if __name__ == "__main__":
+    sys.exit(main(sys.argv[1:]))

cwltool_stream.py

@@ -19,7 +19,7 @@
       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_stream", "cwltool_flask", "cwltool_client"],
+      py_modules=["cwltool_stream", "cwl_flask", "cwltool_client"],
       install_requires=[
           'cwltool >= 1.0.20151013135545',
           'Flask',