[ARVADOS] updated: 3c54f04e5509dc041f526c70f1a396617cfc8644

git at public.curoverse.com git at public.curoverse.com
Mon Aug 25 20:24:23 EDT 2014


Summary of changes:
 apps/workbench/app/helpers/application_helper.rb |  3 ++-
 apps/workbench/app/models/pipeline_instance.rb   |  6 +++++-
 sdk/cli/bin/crunch-job                           | 11 ++++++-----
 3 files changed, 13 insertions(+), 7 deletions(-)

       via  3c54f04e5509dc041f526c70f1a396617cfc8644 (commit)
       via  bd9ea502223067b31a4b2fbde469bd293f3fa358 (commit)
      from  da34478ce3e42df6d138c6e6e1db7c49d9d5902c (commit)

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commit 3c54f04e5509dc041f526c70f1a396617cfc8644
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Aug 25 20:24:12 2014 -0400

    Instead of munging TASK_WORK var, mkdir -p it (and therefore JOB_WORK)
    in setup script.
    
    Without this, scripts that write to arvados.current_job().tmpdir
    (i.e., JOB_WORK) fail.
    
    No issue #

diff --git a/sdk/cli/bin/crunch-job b/sdk/cli/bin/crunch-job
index 4b6632c..6eb9956 100755
--- a/sdk/cli/bin/crunch-job
+++ b/sdk/cli/bin/crunch-job
@@ -649,7 +649,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
     my $build_script_to_send = "";
     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}"
+        ."mkdir -p $ENV{CRUNCH_TMP} $ENV{JOB_WORK} $ENV{TASK_WORK} $ENV{TASK_KEEPMOUNT} "
 	."&& cd $ENV{CRUNCH_TMP} ";
     if ($build_script)
     {
@@ -674,10 +674,7 @@ for (my $todo_ptr = 0; $todo_ptr <= $#jobstep_todo; $todo_ptr ++)
       while (my ($env_key, $env_val) = each %ENV)
       {
         if ($env_key =~ /^(ARVADOS|JOB|TASK)_/) {
-          if ($env_key eq "TASK_WORK") {
-            $command .= "--env=\QTASK_WORK=/tmp/crunch-job\E ";
-          }
-          elsif ($env_key eq "TASK_KEEPMOUNT") {
+          if ($env_key eq "TASK_KEEPMOUNT") {
             $command .= "--env=\QTASK_KEEPMOUNT=/keep\E ";
           }
           else {
@@ -1500,10 +1497,14 @@ __DATA__
 # checkout-and-build
 
 use Fcntl ':flock';
+use File::Path qw( make_path );
 
 my $destdir = $ENV{"CRUNCH_SRC"};
 my $commit = $ENV{"CRUNCH_SRC_COMMIT"};
 my $repo = $ENV{"CRUNCH_SRC_URL"};
+my $task_work = $ENV{"TASK_WORK"};
+
+make_path $task_work or die "Failed to create temporary working directory ($task_work): $!";
 
 open L, ">", "$destdir.lock" or die "$destdir.lock: $!";
 flock L, LOCK_EX;

commit bd9ea502223067b31a4b2fbde469bd293f3fa358
Author: Tom Clegg <tom at curoverse.com>
Date:   Mon Aug 25 16:53:02 2014 -0400

    Do not blow up with pipeline has a plain value in a script_parameter. No issue #

diff --git a/apps/workbench/app/helpers/application_helper.rb b/apps/workbench/app/helpers/application_helper.rb
index e3f6fdc..1f0e5e2 100644
--- a/apps/workbench/app/helpers/application_helper.rb
+++ b/apps/workbench/app/helpers/application_helper.rb
@@ -233,6 +233,7 @@ module ApplicationHelper
       else
         attrvalue = ''
       end
+      preconfigured_search_str = value_info[:search_for]
     end
 
     if !object or
@@ -281,7 +282,7 @@ module ApplicationHelper
          action_name: 'OK',
          action_href: pipeline_instance_path(id: object.uuid),
          action_method: 'patch',
-         preconfigured_search_str: "#{value_info[:search_for]}",
+         preconfigured_search_str: (preconfigured_search_str || ""),
          action_data: {
            merge: true,
            selection_param: selection_param,
diff --git a/apps/workbench/app/models/pipeline_instance.rb b/apps/workbench/app/models/pipeline_instance.rb
index fa9fab6..df14f4e 100644
--- a/apps/workbench/app/models/pipeline_instance.rb
+++ b/apps/workbench/app/models/pipeline_instance.rb
@@ -46,7 +46,11 @@ class PipelineInstance < ArvadosBase
   def component_input_title(component_name, input_name)
     component = components[component_name]
     return nil if component.nil?
-    component[:script_parameters].andand[input_name.to_sym].andand[:title] ||
+    param_info = component[:script_parameters].andand[input_name.to_sym]
+    if param_info.is_a?(Hash) and param_info[:title]
+      param_info[:title]
+    else
       "\"#{input_name.to_s}\" parameter for #{component[:script]} script in #{component_name} component"
+    end
   end
 end

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