Merge branch '10534-go-systemd-sdnotify-v14' of https://github.com/wtsi-hgi/arvados

[arvados.git] / sdk / cwl / arvados_cwl / __init__.py

diff --git a/sdk/cwl/arvados_cwl/__init__.py b/sdk/cwl/arvados_cwl/__init__.py
index 936f445c50be22d1d3318bd5b82b20e8c600f720..92be92d6e0469fba63a1504a5f0c834fb4a9b2b7 100644 (file)
--- 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
@@ -200,14 +201,28 @@ class ArvCwlRunner(object):
 
         srccollections = {}
         for k,v in generatemapper.items():
+            if k.startswith("_:"):
+                if v.type == "Directory":
+                    continue
+                if v.type == "CreateFile":
+                    with final.open(v.target, "wb") as f:
+                        f.write(v.resolved.encode("utf-8"))
+                    continue
+
+            if not k.startswith("keep:"):
+                raise Exception("Output source is not in keep or a literal")
             sp = k.split("/")
             srccollection = sp[0][5:]
             if srccollection not in srccollections:
-                srccollections[srccollection] = arvados.collection.CollectionReader(
-                    srccollection,
-                    api_client=self.api,
-                    keep_client=self.keep_client,
-                    num_retries=self.num_retries)
+                try:
+                    srccollections[srccollection] = arvados.collection.CollectionReader(
+                        srccollection,
+                        api_client=self.api,
+                        keep_client=self.keep_client,
+                        num_retries=self.num_retries)
+                except arvados.errors.ArgumentError as e:
+                    logger.error("Creating CollectionReader for '%s' '%s': %s", k, v, e)
+                    raise
             reader = srccollections[srccollection]
             try:
                 srcpath = "/".join(sp[1:]) if len(sp) > 1 else "."
@@ -217,7 +232,7 @@ class ArvCwlRunner(object):
 
         def rewrite(fileobj):
             fileobj["location"] = generatemapper.mapper(fileobj["location"]).target
-            for k in ("basename", "size", "listing"):
+            for k in ("basename", "listing", "contents"):
                 if k in fileobj:
                     del fileobj[k]
 
@@ -233,7 +248,13 @@ class ArvCwlRunner(object):
                     final.api_response()["name"],
                     final.manifest_locator())
 
-        self.final_output_collection = final
+        def finalcollection(fileobj):
+            fileobj["location"] = "keep:%s/%s" % (final.portable_data_hash(), fileobj["location"])
+
+        adjustDirObjs(outputObj, finalcollection)
+        adjustFileObjs(outputObj, finalcollection)
+
+        return (outputObj, final)
 
     def set_crunch_output(self):
         if self.work_api == "containers":
@@ -389,7 +410,7 @@ 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.final_output, self.final_output_collection = self.make_output_collection(self.output_name, self.final_output)
             self.set_crunch_output()
 
         if self.final_status != "success":
@@ -409,7 +430,7 @@ 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)
 
@@ -468,7 +489,7 @@ 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",