X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/beaea7361fdfaf3dd220e3f5999fb3c0dfc3e61c..b29cc280e5220c7de3d24c3acc687be88bbcb29b:/sdk/python/arvados/commands/run.py

diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index ad442d5d9d..8403327b44 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):
@@ -34,6 +50,12 @@ class ArvFile(object):
         self.prefix = prefix
         self.fn = fn
 
+    def __hash__(self):
+        return (self.prefix+self.fn).__hash__()
+
+    def __eq__(self, other):
+        return (self.prefix == other.prefix) and (self.fn == other.fn)
+
 class UploadFile(ArvFile):
     pass
 
@@ -104,7 +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:
@@ -165,6 +187,7 @@ 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)