arvados-cli 0.1.20140624171100 → 0.1.20140627084759

checksums.yaml

@@ -1,7 +1,7 @@
 ---
 SHA1:
-  metadata.gz: 93abeb0822dc61cb752c265e5759ecc0ac767093
-  data.tar.gz: 260099023bf2e48b27c097f704353d7b45d1edd7
+  metadata.gz: 06c70fbbfc1414385a57c4cebf5ad43f37d07cd1
+  data.tar.gz: 0f4d5a56998d20a5aad7226f378a65222491ae47
 SHA512:
-  metadata.gz: 81f11359d86207894e584c21fd0605d02eabd9ff03091f3d166571872e260af4954d8749deec720e8e5a3b4ce98026498863b3f47f3b31d4a032b5f549cc47cb
-  data.tar.gz: 6f354cd3cc7313058d816662bceb493ac0b1afedce810bc78b0bf960faca86e1a687ee80d387a4c99ed89e1546948b877dff9da04a5baad759683a69d23cdc97
+  metadata.gz: 0118d9b84ca1dacb0a3efed6ae994381afb79da89c7de816f0efc1d1f7bbf8ccc6c480236d3682324770dd4e264cb52fddd8b2a8a346beab1b35c011960a1875
+  data.tar.gz: 8ddd5031983ead996e4b7c2d77f4ebb3d46ca010c157ddd9612dae22420707ad5b8d7e8024e85531fe550b1bf48e8f501a1d435d54c975b176494db6ef6c491f

data/bin/arv

@@ -143,9 +143,14 @@ def check_subcommands client, arvados, subcommand, global_opts, remaining_opts
   end
 end
 
+def arv_edit_save_tmp tmp
+  FileUtils::cp tmp.path, tmp.path + ".saved"
+  puts "Saved contents to " + tmp.path + ".saved"
+end
+
 def arv_edit client, arvados, global_opts, remaining_opts
-  n = remaining_opts.shift
-  if n.nil? or n == "-h" or n == "--help"
+  uuid = remaining_opts.shift
+  if uuid.nil? or uuid == "-h" or uuid == "--help"
     puts head_banner
     puts "Usage: arv edit [uuid] [fields...]\n\n"
     puts "Fetch the specified Arvados object, select the specified fields, \n"
@@ -162,9 +167,9 @@ def arv_edit client, arvados, global_opts, remaining_opts
 
   # determine controller
 
-  m = /([a-z0-9]{5})-([a-z0-9]{5})-([a-z0-9]{15})/.match n
+  m = /([a-z0-9]{5})-([a-z0-9]{5})-([a-z0-9]{15})/.match uuid
   if !m
-    if /^[a-f0-9]{32}/.match n
+    if /^[a-f0-9]{32}/.match uuid
       abort "Arvados collections are not editable."
     else
       abort "#{n} does not appear to be an Arvados uuid"
@@ -187,7 +192,7 @@ def arv_edit client, arvados, global_opts, remaining_opts
   api_method = 'arvados.' + rsc + '.get'
 
   result = client.execute(:api_method => eval(api_method),
-                          :parameters => {"uuid" => n},
+                          :parameters => {"uuid" => uuid},
                           :authenticated => false,
                           :headers => {
                             authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
@@ -213,7 +218,7 @@ def arv_edit client, arvados, global_opts, remaining_opts
 
   require 'tempfile'
 
-  tmp = Tempfile.new([n, "." + global_opts[:format]])
+  tmp = Tempfile.new([uuid, "." + global_opts[:format]])
   tmp.write(content)
   tmp.close
 
@@ -251,9 +256,13 @@ def arv_edit client, arvados, global_opts, remaining_opts
           n += 1
         end
         puts "\nTry again (y/n)? "
-        yn = $stdin.read 1
+        yn = "X"
+        while not ["y", "Y", "n", "N"].include?(yn)
+          yn = $stdin.read 1
+        end
         if yn == 'n' or yn == 'N'
-          exit 1
+          arv_edit_save_tmp tmp
+          abort
         end
       end
     else
@@ -262,31 +271,45 @@ def arv_edit client, arvados, global_opts, remaining_opts
     end
   end
 
-  tmp.close(true)
-
-  if newobj != results
-    api_method = 'arvados.' + rsc + '.update'
-    dumped = Oj.dump(newobj)
-    result = client.execute(:api_method => eval(api_method),
-                            :parameters => {"uuid" => n, rsc.singularize => dumped},
-                            :authenticated => false,
-                            :headers => {
-                              authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
-                            })
-
-    begin
-      results = JSON.parse result.body
-    rescue JSON::ParserError => e
-      abort "Failed to parse server response:\n" + e.to_s
-    end
+  begin
+    if newobj != results
+      api_method = 'arvados.' + rsc + '.update'
+      dumped = Oj.dump(newobj)
 
-    if result.response.status != 200
-      puts "Update failed.  Server responded #{result.response.status}: #{results['errors']} "
-      puts "Update body was:"
-      puts dumped
+      begin
+        result = client.execute(:api_method => eval(api_method),
+                                :parameters => {"uuid" => uuid},
+                                :body => { rsc.singularize => dumped },
+                                :authenticated => false,
+                                :headers => {
+                                  authorization: 'OAuth2 '+ENV['ARVADOS_API_TOKEN']
+                                })
+      rescue Exception => e
+        puts "Error communicating with server, error was #{e}"
+        puts "Update body was:"
+        puts dumped
+        arv_edit_save_tmp tmp
+        abort
+      end
+
+      begin
+        results = JSON.parse result.body
+      rescue JSON::ParserError => e
+        abort "Failed to parse server response:\n" + e.to_s
+      end
+
+      if result.response.status != 200
+        puts "Update failed.  Server responded #{result.response.status}: #{results['errors']} "
+        puts "Update body was:"
+        puts dumped
+        arv_edit_save_tmp tmp
+        abort
+      end
+    else
+      puts "Object is unchanged, did not update."
     end
-  else
-    puts "Object is unchanged, did not update."
+  ensure
+    tmp.close(true)
   end
 
   exit 0

data/bin/arv-run-pipeline-instance

@@ -469,6 +469,7 @@ class WhRunPipelineInstance
             :repository => c[:repository],
             :nondeterministic => c[:nondeterministic],
             :output_is_persistent => c[:output_is_persistent] || false,
+            :runtime_constraints => c[:runtime_constraints],
             :owner_uuid => owner_uuid,
             # TODO: Delete the following three attributes when
             # supporting pre-20140418 API servers is no longer
@@ -591,7 +592,7 @@ class WhRunPipelineInstance
           ended += 1
           if c[:job][:success] == true
             succeeded += 1
-          elsif c[:job][:success] == false
+          elsif c[:job][:success] == false or c[:job][:cancelled_at]
             failed += 1
           end
         end

data/bin/crunch-job

@@ -639,6 +639,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     my $command =
 	"if [ -e $ENV{TASK_WORK} ]; then rm -rf $ENV{TASK_WORK}; fi; "
         ."mkdir -p $ENV{JOB_WORK} $ENV{CRUNCH_TMP} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} "
+        ."&& chmod og+wrx $ENV{TASK_WORK}"
 	."&& cd $ENV{CRUNCH_TMP} ";
     if ($build_script)
     {
@@ -657,22 +658,36 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       $command .=
           q{$(ip -o address show scope global |
               gawk 'match($4, /^([0-9\.:]+)\//, x){print "--dns", x[1]}') };
-      foreach my $env_key (qw(CRUNCH_SRC CRUNCH_TMP TASK_KEEPMOUNT))
-      {
-        $command .= "-v \Q$ENV{$env_key}:$ENV{$env_key}:rw\E ";
-      }
+      $command .= "-v \Q$ENV{TASK_WORK}:/tmp/crunch-job:rw\E ";
+      $command .= "-v \Q$ENV{CRUNCH_SRC}:/tmp/crunch-src:ro\E ";
+      $command .= "-v \Q$ENV{TASK_KEEPMOUNT}:/mnt:ro\E ";
       while (my ($env_key, $env_val) = each %ENV)
       {
         if ($env_key =~ /^(ARVADOS|JOB|TASK)_/) {
-          $command .= "-e \Q$env_key=$env_val\E ";
+          if ($env_key eq "TASK_WORK") {
+            $command .= "-e \QTASK_WORK=/tmp/crunch-job\E ";
+          }
+          elsif ($env_key eq "TASK_KEEPMOUNT") {
+            $command .= "-e \QTASK_KEEPMOUNT=/mnt\E ";
+          }
+          elsif ($env_key eq "CRUNCH_SRC") {
+            $command .= "-e \QCRUNCH_SRC=/tmp/crunch-src\E ";
+          }
+          else {
+            $command .= "-e \Q$env_key=$env_val\E ";
+          }
         }
       }
       $command .= "\Q$docker_hash\E ";
+      $command .= "stdbuf -o0 -e0 ";
+      $command .= "/tmp/crunch-src/crunch_scripts/" . $Job->{"script"};
     } else {
-      $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -poll=10000 "
+      # Non-docker run
+      $command .= "crunchstat -cgroup-root=/sys/fs/cgroup -poll=10000 ";
+      $command .= "stdbuf -o0 -e0 ";
+      $command .= "$ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
     }
-    $command .= "stdbuf -o0 -e0 ";
-    $command .= "$ENV{CRUNCH_SRC}/crunch_scripts/" . $Job->{"script"};
+
     my @execargs = ('bash', '-c', $command);
     srun (\@srunargs, \@execargs, undef, $build_script_to_send);
     exit (111);

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: arvados-cli
 version: !ruby/object:Gem::Version
-  version: 0.1.20140624171100
+  version: 0.1.20140627084759
 platform: ruby
 authors:
 - Arvados Authors
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2014-06-24 00:00:00.000000000 Z
+date: 2014-06-27 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: arvados
@@ -146,7 +146,7 @@ dependencies:
     - - "~>"
       - !ruby/object:Gem::Version
         version: '0.8'
-description: This is the Arvados SDK CLI gem, git revision bfc0b74c4f4e5b6485393827735ff9a875d4d8ac
+description: This is the Arvados SDK CLI gem, git revision 377b4f345a5ba45bb96497a6be2b571604a695a1
 email: gem-dev@curoverse.com
 executables:
 - arv