arvados-cli 0.1.20140826202602 → 0.1.20140827170424

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: bd9ebb9dddabe78ad6456c8b5c23279b368b5305
-  data.tar.gz: 2c834b9059f65215ef592b2af0e7d8a9aebe4ef8
+  metadata.gz: 90cc9aaaf46a6cf3ec9bf6061312ccdceb0f48bf
+  data.tar.gz: 8f9cbaf8c21301b8e1d3a9caf7937447bc64b757
 SHA512:
-  metadata.gz: cfe2966a72aa3e109bf42d00fac24309aacebb07557190db14a94c7bfd4579ebe535c2a8be68fcde68f5f818de20252b00771b2385fdecdc05b7b1043c744d7d
-  data.tar.gz: c8e032348584d3b812e75be31371773b783c918a3a6d4c82c1d562d3979f2bc1aaf75dbd4f6331f4aa1c58b09510babed4df61a740b25d7bd316839604cb6ea8
+  metadata.gz: 858b280278788af73c75afd2b67a3b16ccc76d461c116e7884736b008ae8f734df529286e8fc273a248a3ca1e7af77ddd627d090d19f42de4a2492bae104a990
+  data.tar.gz: 3ad8893233125003588dc393245703b76debe28b79a6fd73faaf4c094625ecf5c174c6de253a23ea64bb6178e70ef4d9656e9fc85d1676a6ca8b05ea007af1df

data/bin/arv-run-pipeline-instance

@@ -518,7 +518,6 @@ class WhRunPipelineInstance
             :script_version => c[:script_version],
             :repository => c[:repository],
             :nondeterministic => c[:nondeterministic],
-            :output_is_persistent => c[:output_is_persistent] || false,
             :runtime_constraints => c[:runtime_constraints],
             :owner_uuid => owner_uuid,
           }, {
@@ -562,37 +561,34 @@ class WhRunPipelineInstance
               # This is my first time discovering that the job
               # succeeded. (At the top of this loop, I was still
               # waiting for it to finish.)
-              if c[:output_is_persistent]
-                # I need to make sure a resources/wants link is in
-                # place to protect the output from garbage
-                # collection. (Normally Crunch does this for me, but
-                # here I might be reusing the output of someone else's
-                # job and I need to make sure it's understood that the
-                # output is valuable to me, too.)
-                wanted = c[:job][:output]
-                debuglog "checking for existing persistence link for #{wanted}"
-                @my_user_uuid ||= $arv.user.current[:uuid]
-                links = $arv.link.list(limit: 1,
-                                       filters:
-                                       [%w(link_class = resources),
-                                        %w(name = wants),
-                                        %w(tail_uuid =) + [@my_user_uuid],
-                                        %w(head_uuid =) + [wanted]
-                                       ])[:items]
-                if links.any?
-                  debuglog "link already exists, uuid #{links.first[:uuid]}"
-                else
-                  newlink = $arv.link.create link: \
-                  {
-                    link_class: 'resources',
-                    name: 'wants',
-                    tail_kind: 'arvados#user',
-                    tail_uuid: @my_user_uuid,
-                    head_kind: 'arvados#collection',
-                    head_uuid: wanted,
-                    owner_uuid: owner_uuid
+
+              debuglog "names: #{@instance[:name]} #{@template[:name]}", 0
+              if (not @instance[:name].nil?) and (not @instance[:name].empty?)
+                pipeline_name = @instance[:name]
+              else
+                fetch_template(@instance[:pipeline_template_uuid])
+                pipeline_name = @template[:name]
+              end
+              if c[:output_name] != false
+                output_name = c[:output_name] || "Output of #{cname} of #{pipeline_name}"
+                # Create a collection located in the same project as the pipeline with the contents of the output.
+                portable_data_hash = c[:job][:output]
+                collections = $arv.collection.list(limit: 1,
+                                                   filters: [['portable_data_hash', '=', portable_data_hash]],
+                                                   select: ["portable_data_hash", "manifest_text"]
+                                                   )[:items]
+                if collections.any?
+                  newcollection = {
+                    owner_uuid: owner_uuid,
+                    name: "#{output_name} at #{c[:job][:finished_at]}",
+                    portable_data_hash: collections.first[:portable_data_hash],
+                    manifest_text: collections.first[:manifest_text]
                   }
-                  debuglog "added link, uuid #{newlink[:uuid]}"
+                  debuglog "Creating collection #{newcollection}", 0
+                  newcollection_actual = $arv.collection.create collection: newcollection
+                  c[:output_uuid] = newcollection_actual[:uuid]
+                else
+                  debuglog "Could not find a collection with portable data hash #{portable_data_hash}", 0
                 end
               end
             end

data/bin/crunch-job

@@ -853,37 +853,15 @@ else {
   eval {
     open(my $orig_manifest, '-|', 'arv-get', $collated_output)
         or die "failed to get collated manifest: $!";
-    # Read the original manifest, and strip permission hints from it,
-    # so we can put the result in a Collection.
-    my @stripped_manifest_lines = ();
     my $orig_manifest_text = '';
     while (my $manifest_line = <$orig_manifest>) {
       $orig_manifest_text .= $manifest_line;
-      my @words = split(/ /, $manifest_line, -1);
-      foreach my $ii (0..$#words) {
-        if ($words[$ii] =~ /^[0-9a-f]{32}\+/) {
-          $words[$ii] =~ s/\+A[0-9a-f]{40}@[0-9a-f]{8}\b//;
-        }
-      }
-      push(@stripped_manifest_lines, join(" ", @words));
     }
-    my $stripped_manifest_text = join("", @stripped_manifest_lines);
     my $output = $arv->{'collections'}->{'create'}->execute('collection' => {
-      'uuid' => md5_hex($stripped_manifest_text),
       'manifest_text' => $orig_manifest_text,
     });
-    Log(undef, "output " . $output->{uuid});
-    $Job->update_attributes('output' => $output->{uuid}) if $job_has_uuid;
-    if ($Job->{'output_is_persistent'}) {
-      $arv->{'links'}->{'create'}->execute('link' => {
-        'tail_kind' => 'arvados#user',
-        'tail_uuid' => $User->{'uuid'},
-        'head_kind' => 'arvados#collection',
-        'head_uuid' => $Job->{'output'},
-        'link_class' => 'resources',
-        'name' => 'wants',
-      });
-    }
+    Log(undef, "output " . $output->{portable_data_hash});
+    $Job->update_attributes('output' => $output->{portable_data_hash}) if $job_has_uuid;
   };
   if ($@) {
     Log (undef, "Failed to register output manifest: $@");

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: arvados-cli
 version: !ruby/object:Gem::Version
-  version: 0.1.20140826202602
+  version: 0.1.20140827170424
 platform: ruby
 authors:
 - Arvados Authors
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-08-26 00:00:00.000000000 Z
+date: 2014-08-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: arvados
@@ -166,7 +166,7 @@ dependencies:
     - - "<"
       - !ruby/object:Gem::Version
         version: 1.0.0
-description: This is the Arvados SDK CLI gem, git revision 63330000144108862a4e2b02a7a8fa124d01163e
+description: This is the Arvados SDK CLI gem, git revision 0042e4b42d9f4d3900aefc68617cb28c5a61a522
 email: gem-dev@curoverse.com
 executables:
 - arv