3609: Added documentation page. Added to "arv" frontend command. Bug fix to

[arvados.git] / sdk / python / arvados / commands / run.py

diff --git a/sdk/python/arvados/commands/run.py b/sdk/python/arvados/commands/run.py
index 9301e3cb462c61f20c1af2aa1c7dfbadc026ef3b..a15a457c5e272cf85d2919d1f08955f16f7320ef 100644 (file)
--- a/sdk/python/arvados/commands/run.py
+++ b/sdk/python/arvados/commands/run.py
@@ -18,9 +18,9 @@ arvrun_parser = argparse.ArgumentParser()
 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-crunch-job")
 arvrun_parser.add_argument('--docker-image', type=str, default="arvados/jobs", help="Docker image to use, default arvados/jobs")
-arvrun_parser.add_argument('--git-dir', type=str, default="", help="Git directory to use to find run-command when using --local")
-arvrun_parser.add_argument('--repository', type=str, default="arvados", help="repository field of pipeline submission, default 'arvados'")
-arvrun_parser.add_argument('--script-version', type=str, default="master", help="script_version field of pipeline submission, default 'master'")
+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('args', nargs=argparse.REMAINDER)
 
 class ArvFile(object):
@@ -60,14 +60,22 @@ def statfile(prefix, fn):
 def main(arguments=None):
     args = arvrun_parser.parse_args(arguments)
 
+    if len(args.args) == 0:
+        arvrun_parser.print_help()
+        return
+
     reading_into = 2
 
     slots = [[], [], []]
     for c in args.args:
-        if c == '>':
+        if c.startswith('>'):
             reading_into = 0
-        elif c == '<':
+            if len(c) > 1:
+                slots[reading_into].append(c[1:])
+        elif c.startswith('<'):
             reading_into = 1
+            if len(c) > 1:
+                slots[reading_into].append(c[1:])
         elif c == '|':
             reading_into = len(slots)
             slots.append([])
@@ -156,23 +164,21 @@ def main(arguments=None):
 
     task_foreach = []
     group_parser = argparse.ArgumentParser()
-    group_parser.add_argument('--group', type=str)
+    group_parser.add_argument('--batch-size', type=int)
     group_parser.add_argument('args', nargs=argparse.REMAINDER)
 
     for s in xrange(2, len(slots)):
         for i in xrange(0, len(slots[s])):
             if slots[s][i] == '--':
-                inp = "input%i" % s
+                inp = "input%i" % (s-2)
                 groupargs = group_parser.parse_args(slots[2][i+1:])
-                component["script_parameters"][inp] = groupargs.args
-                if groupargs.group:
-                    inpgroups = inp+"_groups"
-                    component["script_parameters"][inpgroups] = {"group":inp, "regex":groupargs.group}
-                    slots[s] = slots[s][0:i] + [{"foreach": inpgroups, "command": "$(%s)" % inpgroups}]
-                    task_foreach.append(inpgroups)
+                if groupargs.batch_size:
+                    component["script_parameters"][inp] = {"batch":groupargs.args, "size":groupargs.batch_size}
+                    slots[s] = slots[s][0:i] + [{"foreach": inp, "command": "$(%s)" % inp}]
                 else:
+                    component["script_parameters"][inp] = groupargs.args
                     slots[s] = slots[s][0:i] + ["$(%s)" % inp]
-                    task_foreach.append(inp)
+                task_foreach.append(inp)
                 break
             if slots[s][i] == '\--':
                 slots[s][i] = '--'