X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/529a648458ceefc02d77abf470a2005a099d9907..36360d1f2987cea89ce217a2519c01da7456d533:/sdk/python/arvados/commands/run.py

diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index 7a298b4c17..860fc8f805 100644
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -11,22 +11,38 @@ import put
 import time
 import subprocess
 import logging
+import sys
 import arvados.commands._util as arv_cmd
 
+from arvados._version import __version__
+
 logger = logging.getLogger('arvados.arv-run')
 logger.setLevel(logging.INFO)
 
 arvrun_parser = argparse.ArgumentParser(parents=[arv_cmd.retry_opt])
-arvrun_parser.add_argument('--dry-run', action="store_true", help="Print out the pipeline that would be submitted and exit")
-arvrun_parser.add_argument('--local', action="store_true", help="Run locally using arv-run-pipeline-instance")
-arvrun_parser.add_argument('--docker-image', type=str, help="Docker image to use, otherwise use instance default.")
-arvrun_parser.add_argument('--ignore-rcode', action="store_true", help="Commands that return non-zero return codes should not be considered failed.")
-arvrun_parser.add_argument('--no-reuse', action="store_true", help="Do not reuse past jobs.")
-arvrun_parser.add_argument('--no-wait', action="store_true", help="Do not wait and display logs after submitting command, just exit.")
-arvrun_parser.add_argument('--project-uuid', type=str, help="Parent project of the pipeline")
-arvrun_parser.add_argument('--git-dir', type=str, default="", help="Git repository passed to arv-crunch-job when using --local")
-arvrun_parser.add_argument('--repository', type=str, default="arvados", help="repository field of component, default 'arvados'")
-arvrun_parser.add_argument('--script-version', type=str, default="master", help="script_version field of component, default 'master'")
+arvrun_parser.add_argument('--dry-run', action="store_true",
+                           help="Print out the pipeline that would be submitted and exit")
+arvrun_parser.add_argument('--local', action="store_true",
+                           help="Run locally using arv-run-pipeline-instance")
+arvrun_parser.add_argument('--docker-image', type=str,
+                           help="Docker image to use, otherwise use instance default.")
+arvrun_parser.add_argument('--ignore-rcode', action="store_true",
+                           help="Commands that return non-zero return codes should not be considered failed.")
+arvrun_parser.add_argument('--no-reuse', action="store_true",
+                           help="Do not reuse past jobs.")
+arvrun_parser.add_argument('--no-wait', action="store_true",
+                           help="Do not wait and display logs after submitting command, just exit.")
+arvrun_parser.add_argument('--project-uuid', type=str,
+                           help="Parent project of the pipeline")
+arvrun_parser.add_argument('--git-dir', type=str, default="",
+                           help="Git repository passed to arv-crunch-job when using --local")
+arvrun_parser.add_argument('--repository', type=str, default="arvados",
+                           help="repository field of component, default 'arvados'")
+arvrun_parser.add_argument('--script-version', type=str, default="master",
+                           help="script_version field of component, default 'master'")
+arvrun_parser.add_argument('--version', action='version',
+                           version="%s %s" % (sys.argv[0], __version__),
+                           help='Print version and exit.')
 arvrun_parser.add_argument('args', nargs=argparse.REMAINDER)
 
 class ArvFile(object):
@@ -110,7 +126,7 @@ def statfile(prefix, fn, fnPattern="$(file %s/%s)", dirPattern="$(dir %s/%s/)"):
 def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPattern="$(file %s/%s)", name=None):
     # Find the smallest path prefix that includes all the files that need to be uploaded.
     # This starts at the root and iteratively removes common parent directory prefixes
-    # until all file pathes no longer have a common parent.
+    # until all file paths no longer have a common parent.
     n = True
     pathprefix = "/"
     while n:
@@ -155,9 +171,13 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPatter
                 collection.start_new_stream(stream)
             collection.write_file(f.fn, sp[1])
 
-        exists = api.collections().list(filters=[["owner_uuid", "=", project],
-                                                 ["portable_data_hash", "=", collection.portable_data_hash()],
-                                                 ["name", "=", name]]).execute(num_retries=num_retries)
+        filters=[["portable_data_hash", "=", collection.portable_data_hash()],
+                 ["name", "like", name+"%"]]
+        if project:
+            filters.append(["owner_uuid", "=", project])
+
+        exists = api.collections().list(filters=filters).execute(num_retries=num_retries)
+
         if exists["items"]:
             item = exists["items"][0]
             logger.info("Using collection %s", item["uuid"])
@@ -171,6 +191,7 @@ def uploadfiles(files, api, dry_run=False, num_retries=0, project=None, fnPatter
         pdh = item["portable_data_hash"]
 
     for c in files:
+        c.keepref = "%s/%s" % (pdh, c.fn)
         c.fn = fnPattern % (pdh, c.fn)
 
     os.chdir(orgdir)