8784: Link directly to keep-web when sharing collections.

[arvados.git] / crunch_scripts / run-command

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index ae2233e4913dc9c51591d5935b17ae6585c1ff83..74793d4fce40ae84a820a72db74b69a6c92f3ec4 100755 (executable)
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -331,6 +331,13 @@ try:
         if not args.dry_run:
             stdoutfile = open(stdoutname, "wb")
 
+    if "task.env" in taskp:
+        env = copy.copy(os.environ)
+        for k,v in taskp["task.env"].items():
+            env[k] = subst.do_substitution(taskp, v)
+    else:
+        env = None
+
     logger.info("{}{}{}".format(' | '.join([' '.join(c) for c in cmd]), (" < " + stdinname) if stdinname is not None else "", (" > " + stdoutname) if stdoutname is not None else ""))
 
     if args.dry_run:
@@ -363,7 +370,7 @@ try:
             # this is an intermediate command in the pipeline, so its stdout should go to a pipe
             next_stdout = subprocess.PIPE
 
-        sp = subprocess.Popen(cmd[i], shell=False, stdin=next_stdin, stdout=next_stdout)
+        sp = subprocess.Popen(cmd[i], shell=False, stdin=next_stdin, stdout=next_stdout, env=env)
 
         # Need to close the FDs on our side so that subcommands will get SIGPIPE if the
         # consuming process ends prematurely.
@@ -390,12 +397,19 @@ try:
     active = 1
     pids = set([s.pid for s in subprocesses])
     while len(pids) > 0:
-        (pid, status) = os.wait()
-        pids.discard(pid)
-        if not taskp.get("task.ignore_rcode"):
-            rcode[pid] = (status >> 8)
+        try:
+            (pid, status) = os.wait()
+        except OSError as e:
+            if e.errno == errno.EINTR:
+                pass
+            else:
+                raise
         else:
-            rcode[pid] = 0
+            pids.discard(pid)
+            if not taskp.get("task.ignore_rcode"):
+                rcode[pid] = (status >> 8)
+            else:
+                rcode[pid] = 0
 
     if sig.sig is not None:
         logger.critical("terminating on signal %s" % sig.sig)
@@ -415,7 +429,7 @@ signal.signal(signal.SIGQUIT, signal.SIG_DFL)
 
 logger.info("the following output files will be saved to keep:")
 
-subprocess.call(["find", ".", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr, cwd=outdir)
+subprocess.call(["find", "-L", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"], stdout=sys.stderr, cwd=outdir)
 
 logger.info("start writing output to keep")
 
@@ -426,14 +440,14 @@ if "task.vwd" in taskp and "task.foreach" in jobp:
             if stat.S_ISLNK(s.st_mode):
                 os.unlink(os.path.join(root, f))
 
-outcollection = vwd.checkin(outdir).manifest_text()
+(outcollection, checkin_error) = vwd.checkin(outdir)
 
 # Success if we ran any subprocess, and they all exited 0.
-success = rcode and all(status == 0 for status in rcode.itervalues())
+success = rcode and all(status == 0 for status in rcode.itervalues()) and not checkin_error
 
 api.job_tasks().update(uuid=arvados.current_task()['uuid'],
                                      body={
-                                         'output': outcollection,
+                                         'output': outcollection.manifest_text(),
                                          'success': success,
                                          'progress':1.0
                                      }).execute()