1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0a9263af45ec/
Changeset: 0a9263af45ec
User: dannon
Date: 2014-03-18 16:04:55
Summary: Update boto to 2.27.0 -- thirequired update to support VPC support that worked incorrectly in previous versions.
Affected #: 1 file
diff -r 91aa1db362c9f5c76160b09bab52b8a77b0f30b0 -r 0a9263af45ec678bea82a6d128f49cf5372d370d eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -35,7 +35,7 @@
amqp = 1.4.3
anyjson = 0.3.3
Beaker = 1.4
-boto = 2.25.0
+boto = 2.27.0
decorator = 3.1.2
docutils = 0.7
drmaa = 0.6
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/91aa1db362c9/
Changeset: 91aa1db362c9
User: carlfeberhard
Date: 2014-03-18 14:48:47
Summary: Saved visualizations: fix to display by slug to render built-in visualizations using original display code
Affected #: 1 file
diff -r dea106a05af8597b66846bde6d28bfe97a8ea338 -r 91aa1db362c9f5c76160b09bab52b8a77b0f30b0 lib/galaxy/webapps/galaxy/controllers/visualization.py
--- a/lib/galaxy/webapps/galaxy/controllers/visualization.py
+++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py
@@ -584,7 +584,8 @@
ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, visualization )
# Display.
- if trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins:
+ if( ( trans.app.visualizations_registry and visualization.type in trans.app.visualizations_registry.plugins )
+ and ( visualization.type not in trans.app.visualizations_registry.BUILT_IN_VISUALIZATIONS ) ):
# if a registry visualization, load a version of display.mako that will load the vis into an iframe :(
#TODO: simplest path from A to B but not optimal - will be difficult to do reg visualizations any other way
#TODO: this will load the visualization twice (once above, once when the iframe src calls 'saved')
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6b4139f8f40c/
Changeset: 6b4139f8f40c
User: mike8115
Date: 2014-02-22 02:32:01
Summary: Trello Card #1437: Optional Input Datasets Not Compatible with Parallelism Tag
multi.py edited to check for input.data is None.
Affected #: 1 file
diff -r 2403d6f67500ec35b16ce604142d98766286b65a -r 6b4139f8f40cda2bc21230fd4b32444474bfea8d lib/galaxy/jobs/splitters/multi.py
--- a/lib/galaxy/jobs/splitters/multi.py
+++ b/lib/galaxy/jobs/splitters/multi.py
@@ -44,18 +44,26 @@
# For things like paired end alignment, we need two inputs to be split. Since all inputs to all
# derived subtasks need to be correlated, allow only one input type to be split
+ # If shared_inputs are not specified, we assume all non-split inputs are shared inputs.
+ # For any input we must consider if each input is None. With optional arguments, a data input could be set to optional
type_to_input_map = {}
for input in parent_job.input_datasets:
- if input.name in split_inputs:
- type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name)
- elif input.name in shared_inputs:
- pass # pass original file name
- elif auto_shared_inputs:
- shared_inputs.append(input.name)
+ if input.dataset is None:
+ if input.name in shared_inputs:
+ shared_inputs.remove(input.name)
+ else:
+ pass
else:
- log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name)
- log.exception(log_error)
- raise Exception(log_error)
+ if input.name in split_inputs:
+ type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name)
+ elif input.name in shared_inputs:
+ pass # pass original file name
+ elif auto_shared_inputs:
+ shared_inputs.append(input.name)
+ else:
+ log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name)
+ log.exception(log_error)
+ raise Exception(log_error)
if len(type_to_input_map) > 1:
log_error = "The multi splitter does not support splitting inputs of more than one type"
https://bitbucket.org/galaxy/galaxy-central/commits/dea106a05af8/
Changeset: dea106a05af8
User: dannon
Date: 2014-03-18 13:57:36
Summary: Merged in mike8115/galaxy-central (pull request #334)
Trello Card #1437: Optional Input Datasets Not Compatible with Parallelism Tag
Affected #: 1 file
diff -r c53fbb2655e2756c8977782df2381d883c5aa8af -r dea106a05af8597b66846bde6d28bfe97a8ea338 lib/galaxy/jobs/splitters/multi.py
--- a/lib/galaxy/jobs/splitters/multi.py
+++ b/lib/galaxy/jobs/splitters/multi.py
@@ -44,18 +44,26 @@
# For things like paired end alignment, we need two inputs to be split. Since all inputs to all
# derived subtasks need to be correlated, allow only one input type to be split
+ # If shared_inputs are not specified, we assume all non-split inputs are shared inputs.
+ # For any input we must consider if each input is None. With optional arguments, a data input could be set to optional
type_to_input_map = {}
for input in parent_job.input_datasets:
- if input.name in split_inputs:
- type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name)
- elif input.name in shared_inputs:
- pass # pass original file name
- elif auto_shared_inputs:
- shared_inputs.append(input.name)
+ if input.dataset is None:
+ if input.name in shared_inputs:
+ shared_inputs.remove(input.name)
+ else:
+ pass
else:
- log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name)
- log.exception(log_error)
- raise Exception(log_error)
+ if input.name in split_inputs:
+ type_to_input_map.setdefault(input.dataset.datatype, []).append(input.name)
+ elif input.name in shared_inputs:
+ pass # pass original file name
+ elif auto_shared_inputs:
+ shared_inputs.append(input.name)
+ else:
+ log_error = "The input '%s' does not define a method for implementing parallelism" % str(input.name)
+ log.exception(log_error)
+ raise Exception(log_error)
if len(type_to_input_map) > 1:
log_error = "The multi splitter does not support splitting inputs of more than one type"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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