1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/ecd131b136d0/
changeset: ecd131b136d0
user: james_taylor
date: 2012-10-26 22:23:01
summary: libraries: fix in query for 'datasets_are_public'
affected #: 1 file
diff -r 50b1d7a65bd2760699d9982d6e1ab60f2dbd665a -r ecd131b136d00d5753992061d12b12156be8b277 lib/galaxy/security/__init__.py
--- a/lib/galaxy/security/__init__.py
+++ b/lib/galaxy/security/__init__.py
@@ -879,7 +879,7 @@
# Now get all datasets which have DATASET_ACCESS actions:
access_data_perms = trans.sa_session.query( trans.app.model.DatasetPermissions ) \
- .filter( and_( trans.app.model.DatasetPermissions.dataset_id in dataset_ids,
+ .filter( and_( trans.app.model.DatasetPermissions.dataset_id.in_( dataset_ids ),
trans.app.model.DatasetPermissions.action == self.permitted_actions.DATASET_ACCESS.action ) ) \
.all()
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 commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/b2975e2fa684/
changeset: b2975e2fa684
user: natefoo
date: 2012-10-26 18:56:23
summary: Download eggs from Galaxy resources in EC2.
affected #: 1 file
diff -r bfbd456ebbbe7cff89ffda39091d37ffdbdf2d2a -r b2975e2fa6844b230ca4a656ecdb82f9e6612815 eggs.ini
--- a/eggs.ini
+++ b/eggs.ini
@@ -7,7 +7,7 @@
;
[general]
-repository = http://eggs.g2.bx.psu.edu
+repository = http://eggs.galaxyproject.org
; these eggs must be scrambled for your local environment
no_auto = pbs_python DRMAA_python
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 commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/bfbd456ebbbe/
changeset: bfbd456ebbbe
user: natefoo
date: 2012-10-26 16:55:46
summary: Log the underlying cause of job output collection failure in the drmaa runner.
affected #: 1 file
diff -r 720b4067ab5e5b617569278155ab21216c0de176 -r bfbd456ebbbe7cff89ffda39091d37ffdbdf2d2a lib/galaxy/jobs/runners/drmaa.py
--- a/lib/galaxy/jobs/runners/drmaa.py
+++ b/lib/galaxy/jobs/runners/drmaa.py
@@ -353,11 +353,11 @@
# The exit code should only be 8 bits, but read more anyway
exit_code_str = ecfh.read(32)
which_try = (self.app.config.retry_job_output_collection + 1)
- except:
+ except Exception, e:
if which_try == self.app.config.retry_job_output_collection:
stdout = ''
stderr = 'Job output not returned from cluster'
- log.debug( stderr )
+ log.warning( '%s: %s' % ( stderr, str( e ) ) )
else:
time.sleep(1)
which_try += 1
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 commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f156b9e14443/
changeset: f156b9e14443
user: greg
date: 2012-10-25 20:46:57
summary: Fix for determining the extraction directory for tool dependency tarballs when installing tool dependencies along with tool shed repositories.
affected #: 2 files
diff -r 42eedc24fdd62034ce039bf56b2bbb0b382c63e0 -r f156b9e144437e541127009c2a32efc1019af5c7 lib/galaxy/tool_shed/tool_dependencies/common_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/common_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/common_util.py
@@ -1,18 +1,6 @@
import os, shutil, tarfile, urllib2, zipfile
from galaxy.datatypes.checkers import *
-def zipfile_ok( path_to_archive ):
- """
- This function is a bit pedantic and not functionally necessary. It checks whether there is no file pointing outside of the extraction,
- because ZipFile.extractall() has some potential security holes. See python zipfile documentation for more details.
- """
- basename = os.path.realpath( os.path.dirname( path_to_archive ) )
- zip_archive = zipfile.ZipFile( path_to_archive )
- for member in zip_archive.namelist():
- member_path = os.path.realpath( os.path.join( basename, member ) )
- if not member_path.startswith( basename ):
- return False
- return True
def create_env_var_dict( elem, tool_dependency_install_dir=None, tool_shed_repository_install_dir=None ):
env_var_name = elem.get( 'name', 'PATH' )
env_var_action = elem.get( 'action', 'prepend_to' )
@@ -103,6 +91,7 @@
os.makedirs( destination_directory )
shutil.move( source_file, destination_directory )
def tar_extraction_directory( file_path, file_name ):
+ """Try to return the correct extraction directory."""
file_name = file_name.strip()
extensions = [ '.tar.gz', '.tgz', '.tar.bz2', '.zip' ]
for extension in extensions:
@@ -111,8 +100,8 @@
if os.path.exists( os.path.abspath( os.path.join( file_path, dir_name ) ) ):
return dir_name
if os.path.exists( os.path.abspath( os.path.join( file_path, file_name ) ) ):
- return os.path.abspath( os.path.join( file_path, file_name ) )
- raise ValueError( 'Could not find directory %s' % os.path.abspath( os.path.join( file_path, file_name[ :-len( extension ) ] ) ) )
+ return os.path.abspath( file_path )
+ raise ValueError( 'Could not find path to file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) )
def url_download( install_dir, downloaded_file_name, download_url ):
file_path = os.path.join( install_dir, downloaded_file_name )
src = None
@@ -138,3 +127,15 @@
if os.path.isdir( os.path.join( file_path, files[ 0 ] ) ):
return os.path.abspath( os.path.join( file_path, files[ 0 ] ) )
raise ValueError( 'Could not find directory for the extracted file %s' % os.path.abspath( os.path.join( file_path, file_name ) ) )
+def zipfile_ok( path_to_archive ):
+ """
+ This function is a bit pedantic and not functionally necessary. It checks whether there is no file pointing outside of the extraction,
+ because ZipFile.extractall() has some potential security holes. See python zipfile documentation for more details.
+ """
+ basename = os.path.realpath( os.path.dirname( path_to_archive ) )
+ zip_archive = zipfile.ZipFile( path_to_archive )
+ for member in zip_archive.namelist():
+ member_path = os.path.realpath( os.path.join( basename, member ) )
+ if not member_path.startswith( basename ):
+ return False
+ return True
diff -r 42eedc24fdd62034ce039bf56b2bbb0b382c63e0 -r f156b9e144437e541127009c2a32efc1019af5c7 lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
@@ -79,7 +79,7 @@
if not os.path.exists( dir ):
os.makedirs( dir )
# The package has been down-loaded, so we can now perform all of the actions defined for building it.
- with lcd( dir ):
+ with lcd( dir ):
for action_tup in actions[ 1: ]:
action_type, action_dict = action_tup
current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
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 commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/1136605c015d/
changeset: 1136605c015d
user: inithello
date: 2012-10-25 19:25:39
summary: Updated migration script to reference repository with correct use of tool dependency tag sets.
affected #: 1 file
diff -r b121409702081725920cec548eea991b1bbe6a6f -r 1136605c015d0e28ba42c9ad83f860652ee453a4 scripts/migrate_tools/0006_tools.xml
--- a/scripts/migrate_tools/0006_tools.xml
+++ b/scripts/migrate_tools/0006_tools.xml
@@ -1,6 +1,6 @@
<?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu">
- <repository name="picard" description="Galaxy wrappers for captain picard." changeset_revision="1cd7f3b42609">
+ <repository name="picard" description="Galaxy wrappers for the Picard SAM/BAM manipulation tools." changeset_revision="e0232cbac965"><tool id="picard_FastqToSam" version="1.56.0" file="picard_FastqToSam.xml" /><tool id="picard_SamToFastq" version="1.56.1" file="picard_SamToFastq.xml" /><tool id="picard_BamIndexStats" version="1.56.0" file="picard_BamIndexStats.xml" />
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.