Merge remote-tracking branch 'jmchilton/release_16.01' into dev

galaxyproject · Mar 5, 2016 · 3aa1023 · 3aa1023
2 parents 2e4f8f7 + 97793ab
commit 3aa1023
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Showing 7 changed files with 19 additions and 30 deletions.
diff --git a/config/tool_conf.xml.main b/config/tool_conf.xml.main
@@ -28,18 +28,18 @@
   </section>
   <section id="textutil" name="Text Manipulation">
     <tool file="filters/fixedValueColumn.xml" />
-    <tool file="filters/catWrapper.xml" />
+    <tool file="filters/catWrapper.xml" hidden="True" />
     <tool file="filters/condense_characters.xml" />
     <tool file="filters/convert_characters.xml" />
     <tool file="filters/mergeCols.xml" />
     <tool file="filters/CreateInterval.xml" />
-    <tool file="filters/cutWrapper.xml" />
+    <tool file="filters/cutWrapper.xml" hidden="True" />
     <tool file="filters/changeCase.xml" />
     <tool file="filters/pasteWrapper.xml" />
     <tool file="filters/remove_beginning.xml" />
     <tool file="filters/randomlines.xml" />
-    <tool file="filters/headWrapper.xml" />
-    <tool file="filters/tailWrapper.xml" />
+    <tool file="filters/headWrapper.xml" hidden="True" />
+    <tool file="filters/tailWrapper.xml" hidden="True" />
     <tool file="filters/trimmer.xml" />
     <tool file="filters/wc_gnu.xml" />
     <tool file="filters/secure_hash_message_digest.xml" />

diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py
@@ -1288,7 +1288,7 @@ def path_rewriter( path ):
                         dataset.extension = 'txt'
                 self.sa_session.add( dataset )
             if job.states.ERROR == final_job_state:
-                log.debug( "setting dataset state to ERROR" )
+                log.debug( "(%s) setting dataset %s state to ERROR", job.id, dataset_assoc.dataset.dataset.id )
                 # TODO: This is where the state is being set to error. Change it!
                 dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR
                 # Pause any dependent jobs (and those jobs' outputs)

diff --git a/lib/galaxy/tools/parameters/output_collect.py b/lib/galaxy/tools/parameters/output_collect.py
@@ -131,6 +131,13 @@ def populate_collection_elements( self, collection, root_collection_builder, out
                 filename=filename,
                 metadata_source_name=output_collection_def.metadata_source,
             )
+            log.debug(
+                "(%s) Created dynamic collection dataset for path [%s] with element identifier [%s] for output [%s].",
+                self.job.id,
+                filename,
+                designation,
+                output_collection_def.name,
+            )
             current_builder.add_dataset( element_identifiers[-1], dataset )
 
     def create_dataset(

diff --git a/manage_tools.sh b/manage_tools.sh
@@ -1,9 +1,11 @@
 #!/bin/sh
 
-if [ -d .venv ];
+: ${GALAXY_VIRTUAL_ENV:=.venv}
+
+if [ -d "$GALAXY_VIRTUAL_ENV" ];
 then
-    printf "Activating virtualenv at %s/.venv\n" $(pwd)
-    . .venv/bin/activate
+    printf "Activating virtualenv at $GALAXY_VIRTUAL_ENV\n"
+    . "$GALAXY_VIRTUAL_ENV/bin/activate"
 fi
 
 cd `dirname $0`

diff --git a/run_reports.sh b/run_reports.sh
@@ -11,21 +11,8 @@
 
 cd `dirname $0`
 
-# If there is a .venv/ directory, assume it contains a virtualenv that we
-# should run this instance in.
-if [ -d .venv ];
-then
-    . .venv/bin/activate
-fi
-
 ./scripts/common_startup.sh --skip-samples
 
-if [ -d .venv ];
-then
-    printf "Activating virtualenv at %s/.venv\n" $(pwd)
-    . .venv/bin/activate
-fi
-
 if [ -z "$GALAXY_REPORTS_CONFIG" ]; then
     if [ -f reports_wsgi.ini ]; then
         GALAXY_REPORTS_CONFIG=reports_wsgi.ini

diff --git a/run_tool_shed.sh b/run_tool_shed.sh
@@ -4,12 +4,6 @@ cd `dirname $0`
 
 ./scripts/common_startup.sh
 
-if [ -d .venv ];
-then
-    printf "Activating virtualenv at %s/.venv\n" $(pwd)
-    . .venv/bin/activate
-fi
-
 tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@`
 args=$@
 

diff --git a/templates/webapps/tool_shed/repository/view_repository.mako b/templates/webapps/tool_shed/repository/view_repository.mako
@@ -25,7 +25,7 @@
         tip_str = ''
         sharable_link_label = 'Link to this repository revision:'
         sharable_link_changeset_revision = changeset_revision
-    
+
     if heads:
         multiple_heads = len( heads ) > 1
     else:
@@ -119,8 +119,7 @@
         </div>
         %if repository.long_description:
             <div class="form-row">
-                <p>${repository.long_description|h}</p>
-                ## ${render_long_description( to_html_string( repository.long_description ) )}
+                ${render_long_description( to_html_string( repository.long_description ) )}
             </div>
         %endif
         %if repository.homepage_url: