cwltool: upgrade to the latest version

closes reanahub/reana-workflow-engine-cwl#187

reana_client/cli/cwl_runner.py

@@ -19,10 +19,8 @@
 import click
 import yaml
 from bravado.exception import HTTPServerError
-from cwltool.context import LoadingContext
 from cwltool.load_tool import fetch_document
 from cwltool.main import printdeps
-from cwltool.workflow import findfiles
 
 from reana_client.cli.utils import add_access_token_options
 from reana_client.config import default_user
@@ -32,20 +30,32 @@
 PY3 = sys.version_info > (3,)
 
 
+def findfiles(wo, fn=None):
+    """Return a list CWL workflow files."""
+    if fn is None:
+        fn = []
+    if isinstance(wo, dict):
+        if wo.get("class") == "File":
+            fn.append(wo)
+            findfiles(wo.get("secondaryFiles", None), fn)
+        else:
+            for w in wo.values():
+                findfiles(w, fn)
+    elif isinstance(wo, list):
+        for w in wo:
+            findfiles(w, fn)
+    return fn
+
+
 def get_file_dependencies_obj(cwl_obj, basedir):
     """Return a dictionary which contains the CWL workflow file dependencies.
 
     :param cwl_obj: A CWL tool or job which might contain file dependencies.
     :param basedir: Workflow base dir.
     :returns: A dictionary composed of valid CWL file dependencies.
     """
-    # Load de document
-    loading_context = LoadingContext()
-    document_loader, workflow_obj, uri = fetch_document(
-        cwl_obj,
-        resolver=loading_context.resolver,
-        fetcher_constructor=loading_context.fetcher_constructor,
-    )
+    # Load the document
+    document_loader, workflow_obj, uri = fetch_document(cwl_obj)
     in_memory_buffer = io.StringIO() if PY3 else io.BytesIO()
     # Get dependencies
     printdeps(
@@ -73,6 +83,7 @@ def get_file_dependencies_obj(cwl_obj, basedir):
 @click.pass_context
 def cwl_runner(ctx, quiet, outdir, basedir, processfile, jobfile, access_token):
     """Run CWL files in a standard format <workflow.cwl> <job.json>."""
+    import json
     from reana_client.utils import get_api_url
     from reana_client.api.client import (
         create_workflow,
@@ -92,30 +103,29 @@ def cwl_runner(ctx, quiet, outdir, basedir, processfile, jobfile, access_token):
             with open(jobfile) as f:
                 reana_spec = {
                     "workflow": {"type": "cwl"},
-                    "inputs": {
-                        "parameters": {"input": yaml.load(f, Loader=yaml.FullLoader)}
-                    },
+                    "inputs": {"parameters": yaml.load(f, Loader=yaml.FullLoader)},
                 }
 
-            reana_spec["workflow"]["spec"] = load_workflow_spec(
+            reana_spec["workflow"]["specification"] = load_workflow_spec(
                 reana_spec["workflow"]["type"], processfile,
             )
         else:
             with open(jobfile) as f:
                 job = yaml.load(f, Loader=yaml.FullLoader)
             reana_spec = {"workflow": {"type": "cwl"}, "parameters": {"input": ""}}
 
-            reana_spec["workflow"]["spec"] = load_workflow_spec(
+            reana_spec["workflow"]["specification"] = load_workflow_spec(
                 reana_spec["workflow"]["type"], job["cwl:tool"]
             )
             del job["cwl:tool"]
-            reana_spec["inputs"]["parameters"] = {"input": job}
-        reana_spec["workflow"]["spec"] = replace_location_in_cwl_spec(
-            reana_spec["workflow"]["spec"]
+            reana_spec["inputs"]["parameters"] = job
+        reana_spec["workflow"]["specification"] = replace_location_in_cwl_spec(
+            reana_spec["workflow"]["specification"]
         )
 
         logging.info("Connecting to {0}".format(get_api_url()))
-        response = create_workflow(reana_spec, "cwl-test", access_token)
+        reana_specification = json.loads(json.dumps(reana_spec, sort_keys=True))
+        response = create_workflow(reana_specification, "cwl-test", access_token)
         logging.error(response)
         workflow_name = response["workflow_name"]
         workflow_id = response["workflow_id"]
@@ -157,11 +167,16 @@ def cwl_runner(ctx, quiet, outdir, basedir, processfile, jobfile, access_token):
                 # click.echo(response['status'])
                 break
         try:
-            out = re.search(r"success{[\S\s]*", logs).group().replace("success", "")
             import ast
-            import json
 
-            json_output = json.dumps(ast.literal_eval(str(out)))
+            index1 = logs.find("OUTPUTS")
+            index2 = logs.find("/OUTPUTS")
+            output = logs[index1:index2]
+            engine = output.rfind("reana-workflow-engine-cwl")
+            begin, end = output.find("{"), output.rfind("}", 0, engine)
+            output_str = f'"{output[begin: end+1]}"'
+            output_evl = ast.literal_eval(output_str)
+            json_output = str(output_evl).replace("\n", "").replace("'", '"')
         except AttributeError:
             logging.error("Workflow execution failed")
             sys.exit(1)