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Merge branch 'release_15.03' into dev

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Dannon Baker
2015-03-12 10:34:17 -04:00
parent d4e37db5d9 dfd08b3aee
commit a75cc52c9e
2 changed files with 18 additions and 16 deletions
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lib/galaxy/tools/__init__.py
+17 -15
View File
@@ -2587,11 +2587,9 @@ class Tool( object, Dictifiable ):
hda_source_dict = {} # Mapping from HDA in history to source HDAs.
for hda in history.datasets:
source_hda = hda.copied_from_history_dataset_association
while source_hda:#should this check library datasets as well?
#FIXME: could be multiple copies of a hda in a single history, this does a better job of matching on cloned histories,
#but is still less than perfect when eg individual datasets are copied between histories
if source_hda not in hda_source_dict or source_hda.hid == hda.hid:
hda_source_dict[ source_hda ] = hda
while source_hda:
if source_hda.dataset.id not in hda_source_dict or source_hda.hid == hda.hid:
hda_source_dict[ source_hda.dataset.id ] = hda
source_hda = source_hda.copied_from_history_dataset_association
# Ditto for dataset collections.
@@ -2599,8 +2597,8 @@ class Tool( object, Dictifiable ):
for hdca in history.dataset_collections:
source_hdca = hdca.copied_from_history_dataset_collection_association
while source_hdca:
if source_hdca not in hdca_source_dict or source_hdca.hid == hdca.hid:
hdca_source_dict[ source_hdca ] = hdca
if source_hdca.collection.id not in hdca_source_dict or source_hdca.hid == hdca.hid:
hdca_source_dict[ source_hdca.collection.id ] = hdca
source_hdca = source_hdca.copied_from_history_dataset_collection_association
# Unpack unvalidated values to strings, they'll be validated when the
@@ -2619,17 +2617,21 @@ class Tool( object, Dictifiable ):
if isinstance(value,list):
values = []
for val in value:
if is_hashable( val ):
if val in history.datasets:
if isinstance(val, trans.app.model.HistoryDatasetAssociation):
if val.dataset.id in hda_source_dict:
values.append( hda_source_dict[ val.dataset.id ] )
else:
values.append( val )
elif val in hda_source_dict:
values.append( hda_source_dict[ val ])
return values
if is_hashable( value ) and value not in history.datasets and value in hda_source_dict:
return hda_source_dict[ value ]
if isinstance(value, trans.app.model.HistoryDatasetAssociation):
if value.dataset.id in hda_source_dict:
return hda_source_dict[ value.dataset.id ]
if isinstance(value, trans.app.model.HistoryDatasetCollectionAssociation):
if value.collection.id in hdca_source_dict:
return hdca_source_dict[ value.collection.id ]
elif isinstance( input, DataCollectionToolParameter ):
if is_hashable( value ) and value not in history.dataset_collections and value in hdca_source_dict:
return hdca_source_dict[ value ]
if value.collection.id in hdca_source_dict:
return hdca_source_dict[ value.collection.id ]
visit_input_values( tool_inputs, params, rerun_callback )
def _compare_tool_version( self, trans, job ):
templates/webapps/galaxy/workflow/run.mako
+1 -1
View File
@@ -513,7 +513,7 @@ if wf_parms:
<div class="metadataFormTitle">Workflow Parameters</div>
<div class="metadataFormBody">
%for parm in wf_parms:
<div class='form-row'><label style='width:100px;'>${parm}<input style="border:2px solid ${wf_parms[parm]};border-left-width:8px;" type="text" class='wf_parm_input ptag_${parm}' name="wf_parm|${parm}" value=""/></label></div>
<div class='form-row'><label>${parm}<br/><input size=40 style="border:2px solid ${wf_parms[parm]};border-left-width:8px;" type="text" class='wf_parm_input ptag_${parm}' name="wf_parm|${parm}" value=""/></label></div>
%endfor
</div>
</div>