X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/0e5198142fdba0ce2af6eb2852d45dff46ffb2e2..5fc627d22b47723289251e1e1d9dc45c0e1bd49e:/sdk/cwl/arvados_cwl/__init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index ba89951317..a22b075ce4 100644
--- a/sdk/cwl/arvados_cwl/__init__.py
+++ b/sdk/cwl/arvados_cwl/__init__.py
@@ -30,6 +30,7 @@ from .arvworkflow import ArvadosWorkflow, upload_workflow
 from .fsaccess import CollectionFsAccess
 from .perf import Perf
 from .pathmapper import FinalOutputPathMapper
+from ._version import __version__
 
 from cwltool.pack import pack
 from cwltool.process import shortname, UnsupportedRequirement, getListing
@@ -123,7 +124,8 @@ class ArvCwlRunner(object):
                     try:
                         self.cond.acquire()
                         j = self.processes[uuid]
-                        logger.info("Job %s (%s) is %s", j.name, uuid, event["properties"]["new_attributes"]["state"])
+                        txt = self.work_api[0].upper() + self.work_api[1:-1]
+                        logger.info("%s %s (%s) is %s", txt, j.name, uuid, event["properties"]["new_attributes"]["state"])
                         with Perf(metrics, "done %s" % j.name):
                             j.done(event["properties"]["new_attributes"])
                         self.cond.notify()
@@ -181,7 +183,7 @@ class ArvCwlRunner(object):
             for v in obj:
                 self.check_writable(v)
 
-    def make_output_collection(self, name, outputObj):
+    def make_output_collection(self, name, outputObj, tagsString):
         outputObj = copy.deepcopy(outputObj)
 
         files = []
@@ -232,6 +234,11 @@ class ArvCwlRunner(object):
                     final.api_response()["name"],
                     final.manifest_locator())
 
+        final_uuid = final.manifest_locator()
+        tags = tagsString.split(',')
+        for tag in tags:
+             self.api.links().create(body={"head_uuid": final_uuid, "link_class": "tag", "name": tag}).execute()
+
         self.final_output_collection = final
 
     def set_crunch_output(self):
@@ -388,7 +395,7 @@ class ArvCwlRunner(object):
         else:
             if self.output_name is None:
                 self.output_name = "Output of %s" % (shortname(tool.tool["id"]))
-            self.make_output_collection(self.output_name, self.final_output)
+            self.make_output_collection(self.output_name, self.final_output, kwargs.get("output_tags", ""))
             self.set_crunch_output()
 
         if self.final_status != "success":
@@ -408,7 +415,7 @@ def versionstring():
     arvpkg = pkg_resources.require("arvados-python-client")
     cwlpkg = pkg_resources.require("cwltool")
 
-    return "%s %s, %s %s, %s %s" % (sys.argv[0], arvcwlpkg[0].version,
+    return "%s %s %s, %s %s, %s %s" % (sys.argv[0], __version__, arvcwlpkg[0].version,
                                     "arvados-python-client", arvpkg[0].version,
                                     "cwltool", cwlpkg[0].version)
 
@@ -446,6 +453,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     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("--ignore-docker-for-reuse", action="store_true",
                         help="Ignore Docker image version when deciding whether to reuse past jobs.",
                         default=False)
@@ -467,7 +475,7 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
 
     parser.add_argument("--api", type=str,
                         default=None, dest="work_api",
-                        help="Select work submission API, one of 'jobs' or 'containers'.")
+                        help="Select work submission API, one of 'jobs' or 'containers'. Default is 'jobs' if that API is available, otherwise 'containers'.")
 
     parser.add_argument("--compute-checksum", action="store_true", default=False,
                         help="Compute checksum of contents while collecting outputs",