1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/93ca67adcc56/
changeset: r5290:93ca67adcc56
user: dannon
date: 2011-03-31 17:27:49
summary: workflows api: patch from Tobias Wohlfrom <twohlfrom(a)illumina.com>
Fixed label output in workflow API in order to map the input datasets.
affected #: 1 file (9 bytes)
--- a/lib/galaxy/web/api/workflows.py Thu Mar 31 10:16:40 2011 -0400
+++ b/lib/galaxy/web/api/workflows.py Thu Mar 31 11:27:49 2011 -0400
@@ -57,7 +57,7 @@
inputs = {}
for step in latest_workflow.steps:
if step.type == 'data_input':
- inputs[step.id] = {'label':"Input Dataset", 'value':""}
+ inputs[step.id] = {'label':step.tool_inputs['name'], 'value':""}
else:
pass
# Eventually, allow regular tool parameters to be inserted and modified at runtime.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/b453988dce62/
changeset: r5289:b453988dce62
user: dan
date: 2011-03-31 16:16:40
summary: Fix for wrapping input values for change_format and label tags when tool is using check_values="false". Fixes issue seen when e.g. using an output label in a data_source tool.
affected #: 1 file (309 bytes)
--- a/lib/galaxy/tools/actions/__init__.py Wed Mar 30 17:20:10 2011 -0400
+++ b/lib/galaxy/tools/actions/__init__.py Thu Mar 31 10:16:40 2011 -0400
@@ -133,16 +133,18 @@
else:
new_list.append( value )
return new_list
- def wrap_values( inputs, input_values ):
+ def wrap_values( inputs, input_values, skip_missing_values = False ):
# Wrap tool inputs as necessary
for input in inputs.itervalues():
+ if input.name not in input_values and skip_missing_values:
+ continue
if isinstance( input, Repeat ):
for d in input_values[ input.name ]:
- wrap_values( input.inputs, d )
+ wrap_values( input.inputs, d, skip_missing_values = skip_missing_values )
elif isinstance( input, Conditional ):
values = input_values[ input.name ]
current = values[ "__current_case__" ]
- wrap_values( input.cases[current].inputs, values )
+ wrap_values( input.cases[current].inputs, values, skip_missing_values = skip_missing_values )
elif isinstance( input, DataToolParameter ):
input_values[ input.name ] = \
galaxy.tools.DatasetFilenameWrapper( input_values[ input.name ],
@@ -254,7 +256,7 @@
if output.change_format:
if params is None:
params = make_dict_copy( incoming )
- wrap_values( tool.inputs, params )
+ wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values )
for change_elem in output.change_format:
for when_elem in change_elem.findall( 'when' ):
check = when_elem.get( 'input', None )
@@ -304,7 +306,7 @@
# <outputs>
# <data format="input" name="output" label="Blat on ${<input_param>.name}" />
# </outputs>
- wrap_values( tool.inputs, params )
+ wrap_values( tool.inputs, params, skip_missing_values = not tool.check_values )
#tool (only needing to be set once) and on_string (set differently for each label) are overwritten for each output dataset label being determined
params['tool'] = tool
params['on_string'] = on_text
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/81b332adf892/
changeset: r5288:81b332adf892
user: jgoecks
date: 2011-03-30 23:20:10
summary: Send visual analytics output datasets to user's current history rather than input datasets' history. This enables users not logged in to use visual analytics in shared visualizations.
affected #: 1 file (11 bytes)
--- a/lib/galaxy/web/controllers/tracks.py Wed Mar 30 11:44:08 2011 -0400
+++ b/lib/galaxy/web/controllers/tracks.py Wed Mar 30 17:20:10 2011 -0400
@@ -2,7 +2,7 @@
Support for constructing and viewing custom "track" browsers within Galaxy.
"""
-import re, time, pkg_resources
+import re, pkg_resources
pkg_resources.require( "bx-python" )
from bx.seq.twobit import TwoBitFile
@@ -13,7 +13,6 @@
from galaxy.web.framework import simplejson
from galaxy.web.framework.helpers import time_ago, grids
from galaxy.util.bunch import Bunch
-from galaxy import util
from galaxy.datatypes.interval import Gff
from galaxy.visualization.tracks.data_providers import *
@@ -703,7 +702,8 @@
# Set input datasets for tool. Input datasets are subsets of full
# datasets and are based on chrom, low, high.
#
- hda_permissions = trans.app.security_agent.history_get_default_permissions( original_dataset.history )
+ job_history = trans.get_history( create=True )
+ hda_permissions = trans.app.security_agent.history_get_default_permissions( job_history )
messages_list = []
for jida in original_job.input_datasets:
input_dataset = jida.dataset
@@ -721,7 +721,7 @@
name="Subset [%s:%i-%i] of data %i" % \
( chrom, low, high, input_dataset.hid ),
visible=False )
- input_dataset.history.add_dataset( subset_dataset )
+ job_history.add_dataset( subset_dataset )
trans.sa_session.add( subset_dataset )
trans.app.security_agent.set_all_dataset_permissions( subset_dataset.dataset, hda_permissions )
@@ -744,7 +744,7 @@
# Start tool and handle outputs.
#
try:
- subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=original_dataset.history )
+ subset_job, subset_job_outputs = tool.execute( trans, incoming=tool_params, history=job_history )
except Exception, e:
# Lots of things can go wrong when trying to execute tool.
return to_json_string( { "error" : True, "message" : e.__class__.__name__ + ": " + str(e) } )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/3844b6d684b6/
changeset: r5286:3844b6d684b6
user: dan
date: 2011-03-30 16:40:09
summary: Minor fix for 5283:41a416e61021.
affected #: 1 file (4 bytes)
--- a/lib/galaxy/datatypes/data.py Wed Mar 30 10:38:45 2011 -0400
+++ b/lib/galaxy/datatypes/data.py Wed Mar 30 10:40:09 2011 -0400
@@ -441,7 +441,7 @@
est_lines = self.estimate_file_lines(dataset)
dataset.blurb = "~%s %s" % ( util.commaify(util.roundify(str(est_lines))), inflector.cond_plural(est_lines, self.line_class) )
else:
- dataset.blurb = "%s %s" % util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class)
+ dataset.blurb = "%s %s" % ( util.commaify( str(line_count) ), inflector.cond_plural(line_count, self.line_class) )
else:
dataset.peek = 'file does not exist'
dataset.blurb = 'file purged from disk'
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.