[ARVADOS] created: 4689df784ce9702958361952b80f24076ea92039

git at public.curoverse.com git at public.curoverse.com
Thu Jul 3 11:03:42 EDT 2014


        at  4689df784ce9702958361952b80f24076ea92039 (commit)


commit 4689df784ce9702958361952b80f24076ea92039
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Wed Jul 2 14:27:25 2014 -0400

    Improve output messages a bit

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 9d4f361..6335523 100755
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -50,24 +50,24 @@ try:
         stdoutname = subst.do_substitution(p, p["stdout"])
         stdoutfile = open(stdoutname, "wb")
 
-    print("run-command {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
+    print("run-command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
 
     rcode = subprocess.call(cmd, stdout=stdoutfile)
 
-    print("run-command completed with exit code %i" % rcode)
+    print("run-command: completed with exit code %i" % rcode)
 
 except Exception as e:
-    print("run-command exception: {}".format(e))
+    print("run-command: caught exception: {}".format(e))
 
 finally:
     for l in links:
         os.unlink(l)
 
-    print("run-command output:")
+    print("run-command: the follow output files will be saved to keep:")
 
-    subprocess.call(["find", ".", "-type", "f", "-printf", "run-command %12.12s %h/%f\\n"])
+    subprocess.call(["find", ".", "-type", "f", "-printf", "run-command: %12.12s %h/%f\\n"])
 
-    print("run-command writing to keep")
+    print("run-command: start writing output to keep")
 
     out = arvados.CollectionWriter()
     out.write_directory_tree(".", max_manifest_depth=0)
@@ -83,8 +83,8 @@ if rcode == 0:
     os.chdir("..")
     shutil.rmtree("tmpdir")
     shutil.rmtree("output")
-    print("run-command success")
+    print("run-command: success")
 else:
-    print("run-command failed")
+    print("run-command: failed")
 
 sys.exit(rcode)

commit bcff555f9786f24ded842f1cf45e162f1a744c32
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jul 1 16:29:59 2014 -0400

    fix find

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 3fcbe2a..9d4f361 100755
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -65,7 +65,7 @@ finally:
 
     print("run-command output:")
 
-    subprocess.call(["find", ".", "-type", "f", "-printf", "run-command %12.12s %h/%f\\\n"])
+    subprocess.call(["find", ".", "-type", "f", "-printf", "run-command %12.12s %h/%f\\n"])
 
     print("run-command writing to keep")
 

commit 7f67cf41cb8f834debddc5c2a26abdd72e6278d4
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jul 1 14:16:38 2014 -0400

    More clever find

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 1351f3b..3fcbe2a 100755
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -65,7 +65,7 @@ finally:
 
     print("run-command output:")
 
-    subprocess.call(["find", "."])
+    subprocess.call(["find", ".", "-type", "f", "-printf", "run-command %12.12s %h/%f\\\n"])
 
     print("run-command writing to keep")
 

commit 3369c8fa24b8cb40c9f9da74a1744130e0aea83e
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jul 1 14:01:53 2014 -0400

    more status messages

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 39357d4..1351f3b 100755
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -50,7 +50,7 @@ try:
         stdoutname = subst.do_substitution(p, p["stdout"])
         stdoutfile = open(stdoutname, "wb")
 
-    print("run-command running: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
+    print("run-command {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
 
     rcode = subprocess.call(cmd, stdout=stdoutfile)
 
@@ -63,6 +63,12 @@ finally:
     for l in links:
         os.unlink(l)
 
+    print("run-command output:")
+
+    subprocess.call(["find", "."])
+
+    print("run-command writing to keep")
+
     out = arvados.CollectionWriter()
     out.write_directory_tree(".", max_manifest_depth=0)
     outuuid = out.finish()
@@ -77,5 +83,8 @@ if rcode == 0:
     os.chdir("..")
     shutil.rmtree("tmpdir")
     shutil.rmtree("output")
+    print("run-command success")
+else:
+    print("run-command failed")
 
 sys.exit(rcode)

commit 9cb30aa6a84d5b3c7a3ae0d4fc398d64cbd6c306
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jul 1 13:50:31 2014 -0400

    Improve error messages

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index aa50cde..39357d4 100755
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -50,12 +50,14 @@ try:
         stdoutname = subst.do_substitution(p, p["stdout"])
         stdoutfile = open(stdoutname, "wb")
 
-    print("Running command: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
+    print("run-command running: {}{}".format(' '.join(cmd), (" > " + stdoutname) if stdoutname != None else ""))
 
     rcode = subprocess.call(cmd, stdout=stdoutfile)
 
+    print("run-command completed with exit code %i" % rcode)
+
 except Exception as e:
-    print("Caught exception {}".format(e))
+    print("run-command exception: {}".format(e))
 
 finally:
     for l in links:

commit cb05caebb2978eb19a93e9156aafba71e9aaa82a
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jul 1 12:54:46 2014 -0400

    Set success/failed flag explicitly based on return code.

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index a0c7cfe..aa50cde 100755
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -56,7 +56,6 @@ try:
 
 except Exception as e:
     print("Caught exception {}".format(e))
-    rcode = 1
 
 finally:
     for l in links:
@@ -64,7 +63,13 @@ finally:
 
     out = arvados.CollectionWriter()
     out.write_directory_tree(".", max_manifest_depth=0)
-    arvados.current_task().set_output(out.finish())
+    outuuid = out.finish()
+    arvados.api('v1').job_tasks().update(uuid=arvados.current_task()['uuid'],
+                                         body={
+                                             'output':outuuid,
+                                             'success': (rcode == 0),
+                                             'progress':1.0
+                                         }).execute()
 
 if rcode == 0:
     os.chdir("..")

commit 2456d3322ba8397401d5033e6509cf0ffc59f98e
Author: Peter Amstutz <peter.amstutz at curoverse.com>
Date:   Tue Jul 1 10:23:09 2014 -0400

    Make sure set return code non-zero.

diff --git a/crunch_scripts/run-command b/crunch_scripts/run-command
index 528baab..a0c7cfe 100755
--- a/crunch_scripts/run-command
+++ b/crunch_scripts/run-command
@@ -56,6 +56,7 @@ try:
 
 except Exception as e:
     print("Caught exception {}".format(e))
+    rcode = 1
 
 finally:
     for l in links:

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