13306: Unicode fixes for the conformance tests

Arvados-DCO-1.1-Signed-off-by:  Eric Biagiotti <ebiagiotti@veritasgenetics.com>

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 09deabd22de45609f8920b7928529523b4ec4f69..52fd4d21a115f29ee7fb388c11ebeb0564b40ae2 100644 (file)
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -69,9 +69,9 @@ def versionstring():
 def arg_parser():  # type: () -> argparse.ArgumentParser
     parser = argparse.ArgumentParser(description='Arvados executor for Common Workflow Language')
 
-    parser.add_argument("--basedir", type=str,
+    parser.add_argument("--basedir",
                         help="Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line).")
-    parser.add_argument("--outdir", type=str, default=os.path.abspath('.'),
+    parser.add_argument("--outdir", default=os.path.abspath('.'),
                         help="Output directory, default current directory")
 
     parser.add_argument("--eval-timeout",
@@ -102,9 +102,9 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=True, dest="enable_reuse",
                         help="Disable job or container reuse")
 
-    parser.add_argument("--project-uuid", type=str, metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
-    parser.add_argument("--output-name", type=str, help="Name to use for collection that stores the final output.", default=None)
-    parser.add_argument("--output-tags", type=str, help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None)
+    parser.add_argument("--project-uuid", metavar="UUID", help="Project that will own the workflow jobs, if not provided, will go to home project.")
+    parser.add_argument("--output-name", help="Name to use for collection that stores the final output.", default=None)
+    parser.add_argument("--output-tags", help="Tags for the final output collection separated by commas, e.g., '--output-tags tag0,tag1,tag2'.", default=None)
     parser.add_argument("--ignore-docker-for-reuse", action="store_true",
                         help="Ignore Docker image version when deciding whether to reuse past jobs.",
                         default=False)
@@ -131,7 +131,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     exgroup.add_argument("--no-log-timestamps", action="store_false", help="No timestamp on logging lines",
                         default=True, dest="log_timestamps")
 
-    parser.add_argument("--api", type=str,
+    parser.add_argument("--api",
                         default=None, dest="work_api",
                         choices=("jobs", "containers"),
                         help="Select work submission API.  Default is 'jobs' if that API is available, otherwise 'containers'.")
@@ -144,7 +144,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="RAM (in MiB) required for the workflow runner job (default 1024)",
                         default=None)
 
-    parser.add_argument("--submit-runner-image", type=str,
+    parser.add_argument("--submit-runner-image",
                         help="Docker image for workflow runner job, default arvados/jobs:%s" % __version__,
                         default=None)
 
@@ -153,11 +153,11 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=False)
 
     exgroup = parser.add_mutually_exclusive_group()
-    exgroup.add_argument("--submit-request-uuid", type=str,
+    exgroup.add_argument("--submit-request-uuid",
                          default=None,
                          help="Update and commit to supplied container request instead of creating a new one (containers API only).",
                          metavar="UUID")
-    exgroup.add_argument("--submit-runner-cluster", type=str,
+    exgroup.add_argument("--submit-runner-cluster",
                          help="Submit workflow runner to a remote cluster (containers API only)",
                          default=None,
                          metavar="CLUSTER_ID")
@@ -166,7 +166,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=None,
                         help="Collection cache size (in MiB, default 256).")
 
-    parser.add_argument("--name", type=str,
+    parser.add_argument("--name",
                         help="Name to use for workflow execution instance.",
                         default=None)
 
@@ -178,7 +178,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
     parser.add_argument("--enable-dev", action="store_true",
                         help="Enable loading and running development versions "
                              "of CWL spec.", default=False)
-    parser.add_argument('--storage-classes', default="default", type=str,
+    parser.add_argument('--storage-classes', default="default",
                         help="Specify comma separated list of storage classes to be used when saving workflow output to Keep.")
 
     parser.add_argument("--intermediate-output-ttl", type=int, metavar="N",
@@ -211,7 +211,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         default=False, dest="trash_intermediate",
                         help="Do not trash intermediate outputs (default).")
 
-    parser.add_argument("workflow", type=str, default=None, help="The workflow to execute")
+    parser.add_argument("workflow", default=None, help="The workflow to execute")
     parser.add_argument("job_order", nargs=argparse.REMAINDER, help="The input object to the workflow.")
 
     return parser

diff --git a/sdk/cwl/arvados_cwl/arvcontainer.py b/sdk/cwl/arvados_cwl/arvcontainer.py
index 47fbfa5a7910c56e1d427f150d8410a08b23dddd..a45321d37834f1ddcdb214b848e2a5dfd00f3962 100644 (file)
--- a/sdk/cwl/arvados_cwl/arvcontainer.py
+++ b/sdk/cwl/arvados_cwl/arvcontainer.py
@@ -162,7 +162,7 @@ class ArvadosContainer(JobBase):
                                 }
                             else:
                                 with vwd.open(p.target, "w") as n:
-                                    n.write(p.resolved.encode("utf-8"))
+                                    n.write(p.resolved)
 
                 def keepemptydirs(p):
                     if isinstance(p, arvados.collection.RichCollectionBase):

diff --git a/sdk/cwl/arvados_cwl/fsaccess.py b/sdk/cwl/arvados_cwl/fsaccess.py
index dbcc66245d41ed2ece2b43637ffb2c365eb2433a..fc0bbb80b9ea05715770c2d3142e7208ca19dcb2 100644 (file)
--- a/sdk/cwl/arvados_cwl/fsaccess.py
+++ b/sdk/cwl/arvados_cwl/fsaccess.py
@@ -288,21 +288,21 @@ pipeline_template_uuid_pattern = re.compile(r'[a-z0-9]{5}-p5p6p-[a-z0-9]{15}')
 
 def collectionResolver(api_client, document_loader, uri, num_retries=4):
     if uri.startswith("keep:") or uri.startswith("arvwf:"):
-        return uri
+        return uri.encode("utf-8").decode()
 
     if workflow_uuid_pattern.match(uri):
-        return "arvwf:%s#main" % (uri)
+        return u"arvwf:%s#main" % (uri)
 
     if pipeline_template_uuid_pattern.match(uri):
         pt = api_client.pipeline_templates().get(uuid=uri).execute(num_retries=num_retries)
-        return "keep:" + viewvalues(pt["components"])[0]["script_parameters"]["cwl:tool"]
+        return u"keep:" + viewvalues(pt["components"])[0]["script_parameters"]["cwl:tool"]
 
     p = uri.split("/")
     if arvados.util.keep_locator_pattern.match(p[0]):
-        return "keep:%s" % (uri)
+        return u"keep:%s" % (uri)
 
     if arvados.util.collection_uuid_pattern.match(p[0]):
-        return "keep:%s%s" % (api_client.collections().
+        return u"keep:%s%s" % (api_client.collections().
                               get(uuid=p[0]).execute()["portable_data_hash"],
                               uri[len(p[0]):])
 

diff --git a/sdk/cwl/arvados_cwl/pathmapper.py b/sdk/cwl/arvados_cwl/pathmapper.py
index 2be850c5cdb2c2d7499b1d74c2fb0ee6733ed43b..e0445febdc9a0731314607417739747c8f0e632c 100644 (file)
--- a/sdk/cwl/arvados_cwl/pathmapper.py
+++ b/sdk/cwl/arvados_cwl/pathmapper.py
@@ -120,7 +120,7 @@ class ArvPathMapper(PathMapper):
             remap.append((obj["location"], path + "/" + obj["basename"]))
         elif obj["location"].startswith("_:") and "contents" in obj:
             with c.open(path + "/" + obj["basename"], "w") as f:
-                f.write(obj["contents"].encode("utf-8"))
+                f.write(obj["contents"])
             remap.append((obj["location"], path + "/" + obj["basename"]))
         else:
             raise SourceLine(obj, "location", WorkflowException).makeError("Don't know what to do with '%s'" % obj["location"])