1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e832e4664714/
Changeset: e832e4664714
User: jmchilton
Date: 2014-06-20 23:00:38
Summary: Fix for interpreter on version commands (when different from command interpreter).
Thanks to Will Holtz for tracking down the problem and Peter Cock for submitting the patch.
Affected #: 1 file
diff -r c972ce1e3e8840309dceaa40ac6858c3156fdff3 -r e832e466471403d54d788193c938f3c4d139142c lib/galaxy/tools/__init__.py
--- a/lib/galaxy/tools/__init__.py
+++ b/lib/galaxy/tools/__init__.py
@@ -1264,7 +1264,7 @@
executable = self.version_string_cmd.split()[0]
abs_executable = os.path.abspath(os.path.join(self.tool_dir, executable))
command_line = self.version_string_cmd.replace(executable, abs_executable, 1)
- self.version_string_cmd = self.interpreter + " " + command_line
+ self.version_string_cmd = version_cmd_interpreter + " " + command_line
# Parallelism for tasks, read from tool config.
parallelism = root.find("parallelism")
if parallelism is not None and parallelism.get("method"):
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/c972ce1e3e88/
Changeset: c972ce1e3e88
User: guerler
Date: 2014-06-20 09:37:10
Summary: Charts: Fix last change
Affected #: 1 file
diff -r bace76c0aa9b41aa32b793506794cb69e38cf44e -r c972ce1e3e8840309dceaa40ac6858c3156fdff3 config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
--- a/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
+++ b/config/plugins/visualizations/charts/static/charts/others/heatmap/heatmap-plugin.js
@@ -207,11 +207,11 @@
// add tooltip events
boxes.selectAll('rect')
.on('dblclick', function(d) {
- d3.event.stopPropagation();
- var xLabel = self.categories.array.x[d.x];
- var yLabel = self.categories.array.y[d.y];
var url = self.chart.settings.get('url_template').trim();
if (url) {
+ d3.event.stopPropagation();
+ var xLabel = self.categories.array.x[d.x];
+ var yLabel = self.categories.array.y[d.y];
window.open(url.replace('__LABEL__', xLabel));
window.open(url.replace('__LABEL__', yLabel));
}
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/cfa24d46767a/
Changeset: cfa24d46767a
User: jmchilton
Date: 2014-06-20 06:21:42
Summary: Add a few more comments about dataset path rewriting in the dataset wrapper.
Affected #: 1 file
diff -r d781366bc120787e201b73a4dd99b56282169d86 -r cfa24d46767a41afa9e83cbf703eef837b47f1e2 lib/galaxy/tools/wrappers.py
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -209,13 +209,21 @@
def __getattr__( self, key ):
if self.false_path is not None and key == 'file_name':
+ # Path to dataset was rewritten for this job.
return self.false_path
elif self.false_extra_files_path is not None and key == 'extra_files_path':
+ # Path to extra files was rewritten for this job.
return self.false_extra_files_path
elif key == 'extra_files_path':
try:
+ # Assume it is an output and that this wrapper
+ # will be set with correct "files_path" for this
+ # job.
return self.files_path
except AttributeError:
+ # Otherwise, we have an input - delegate to model and
+ # object store to find the static location of this
+ # directory.
try:
return self.dataset.extra_files_path
except exceptions.ObjectNotFound:
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d781366bc120/
Changeset: d781366bc120
User: jmchilton
Date: 2014-06-20 06:07:21
Summary: Improved (different at least) extra_files_path handling for dataset outputs.
$output.extra_files_path will now mimic $output.files_path behavior - writing these files to the working directory to have them copied over later. This is more correct when using outputs_to_working_directory, running jobs as the real user, running jobs through LWR/Pulsar, or when using the NestedObjectStore. This is less efficient the 90% of the time when none of these conditions hold.
There is still an open issue that for inputs - $input.extra_files_path returns a non-exist path for DiskObjectStores but throws an error for NestedObjectStores. This behavior could be synchronized by this patch (https://gist.github.com/jmchilton/d05bcf02874762cdb829) - though I do not know if this is the intended behavior of NestedObjectStores.
Affected #: 1 file
diff -r 4eba60282f9d06ce6123478ea1bfa1f9ec741f45 -r d781366bc120787e201b73a4dd99b56282169d86 lib/galaxy/tools/wrappers.py
--- a/lib/galaxy/tools/wrappers.py
+++ b/lib/galaxy/tools/wrappers.py
@@ -1,4 +1,5 @@
import pipes
+from galaxy import exceptions
from galaxy.util.none_like import NoneDataset
from galaxy.util import odict
@@ -211,6 +212,17 @@
return self.false_path
elif self.false_extra_files_path is not None and key == 'extra_files_path':
return self.false_extra_files_path
+ elif key == 'extra_files_path':
+ try:
+ return self.files_path
+ except AttributeError:
+ try:
+ return self.dataset.extra_files_path
+ except exceptions.ObjectNotFound:
+ # NestedObjectstore raises an error here
+ # instead of just returning a non-existent
+ # path like DiskObjectStore.
+ raise
else:
return getattr( self.dataset, key )
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/4eba60282f9d/
Changeset: 4eba60282f9d
User: greg
Date: 2014-06-19 23:46:04
Summary: Fix for handling complex repository dependency definitions that contain recipes that include <package> tag sets that define dependencies needed only for compiling the dependent package.
Affected #: 1 file
diff -r d64ce44b0d0dc5fcf9978f6047fe78ef946165dc -r 4eba60282f9d06ce6123478ea1bfa1f9ec741f45 lib/tool_shed/util/commit_util.py
--- a/lib/tool_shed/util/commit_util.py
+++ b/lib/tool_shed/util/commit_util.py
@@ -130,7 +130,6 @@
Populate or unpopulate the toolshed and changeset_revision attributes of a <repository> tag that defines
a complex repository dependency.
"""
- # The received sub_elem looks something like the following:
# <repository name="package_eigen_2_0" owner="test" prior_installation_required="True" />
revised, repository_elem, error_message = handle_repository_dependency_elem( app, sub_elem, unpopulate=unpopulate )
if error_message:
@@ -432,22 +431,24 @@
for last_actions_index, last_actions_elem in enumerate( actions_group_elem ):
last_actions_package_altered = False
if last_actions_elem.tag == 'package':
+ last_actions_elem_package_elem_altered = False
for last_actions_elem_package_index, last_actions_elem_package_elem in enumerate( last_actions_elem ):
if last_actions_elem_package_elem.tag == 'repository':
# We have a complex repository dependency.
- altered, last_actions_package_altered, last_actions_elem, message = \
+ last_actions_package_altered, last_actions_elem_package_elem_altered, last_actions_elem, message = \
handle_complex_repository_dependency_elem( app,
last_actions_elem,
last_actions_elem_package_index,
last_actions_elem_package_elem,
+ last_actions_elem_package_elem_altered,
last_actions_package_altered,
- altered,
unpopulate=unpopulate )
+ if not altered and last_actions_package_altered:
+ altered = True
if message:
error_message += message
- if last_actions_package_altered:
- last_actions_elem[ last_actions_elem_package_index ] = last_actions_elem_package_elem
- actions_group_elem[ last_actions_index ] = last_actions_elem
+ if last_actions_elem_package_elem_altered:
+ actions_group_elem[ last_actions_index ] = last_actions_elem
else:
# Inspect the sub elements of last_actions_elem to locate all <repository> tags and
# populate them with toolshed and changeset_revision attributes if necessary.
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/98acf7d104af/
Changeset: 98acf7d104af
User: jmchilton
Date: 2014-06-19 20:11:55
Summary: Another LWR client update - improved exception logging.
Affected #: 1 file
diff -r 5111c44e87f5fb22e6340cdbf3104e6aea83d54c -r 98acf7d104afb923cd538a09f49fc58828d17e1c lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
--- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
+++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py
@@ -53,9 +53,13 @@
self.__connect_ssl = connect_ssl
self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE)
self.__timeout = timeout
+ # Be sure to log message publishing failures.
+ if publish_kwds.get("retry", False):
+ if "retry_policy" not in publish_kwds:
+ publish_kwds["retry_policy"] = {}
+ if "errback" not in publish_kwds["retry_policy"]:
+ publish_kwds["retry_policy"]["errback"] = self.__publish_errback
self.__publish_kwds = publish_kwds
- if "retry_policy" in self.__publish_kwds:
- self.__publish_kwds["retry_policy"]["errback"] = self.__publish_errback
@property
def url(self):
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