1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/96871214fe2f/
changeset: 96871214fe2f
user: dannon
date: 2012-09-19 16:32:19
summary: Prevent reflective XSS through message display.
affected #: 1 file
diff -r 70b60fd07d6a0ab6889c79a9518fd894e13f9c8d -r 96871214fe2f962004decde001de94d1ba827e94 templates/message.mako
--- a/templates/message.mako
+++ b/templates/message.mako
@@ -82,12 +82,12 @@
## Render large message.
<%def name="render_large_message( message, status )">
- <div class="${status}messagelarge" style="margin: 1em">${_(message)}</div>
+ <div class="${status}messagelarge" style="margin: 1em">${_(message) | h}</div></%def>
## Render a message
<%def name="render_msg( msg, status='done' )">
- <div class="${status}message">${_(msg)}</div>
+ <div class="${status}message">${_(msg) | h}</div><br/></%def>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/70b60fd07d6a/
changeset: 70b60fd07d6a
user: dannon
date: 2012-09-19 06:10:47
summary: Cloud Launch - Fix for rare instance udpate() that happens when (rarely) Amazon doesn't have the instance fully registered before update() is called.
affected #: 1 file
diff -r 572f0d4ed0ae934e1b2975a6a2940589fc593204 -r 70b60fd07d6a0ab6889c79a9518fd894e13f9c8d lib/galaxy/web/controllers/cloudlaunch.py
--- a/lib/galaxy/web/controllers/cloudlaunch.py
+++ b/lib/galaxy/web/controllers/cloudlaunch.py
@@ -22,7 +22,6 @@
from boto.exception import EC2ResponseError
from boto.s3.connection import OrdinaryCallingFormat, S3Connection
-
log = logging.getLogger(__name__)
PKEY_PREFIX = 'gxy_pkey'
@@ -98,7 +97,12 @@
while not instance.public_dns_name:
# Can take a second to have public dns name registered.
# DBTODO, push this into a page update, this is not ideal.
- instance.update()
+ try:
+ instance.update()
+ except EC2ResponseError:
+ #This can happen when update is invoked before the instance is fully registered. Prevent
+ #failure, wait it out.
+ pass
ct +=1
time.sleep(1)
if kp_material:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/572f0d4ed0ae/
changeset: 572f0d4ed0ae
user: jgoecks
date: 2012-09-19 04:33:49
summary: Fix bug in setting dbkey for new track browser.
affected #: 1 file
diff -r 8153e8d25009d71a523e0f2df24ed12922825d8f -r 572f0d4ed0ae934e1b2975a6a2940589fc593204 lib/galaxy/web/controllers/visualization.py
--- a/lib/galaxy/web/controllers/visualization.py
+++ b/lib/galaxy/web/controllers/visualization.py
@@ -696,11 +696,11 @@
Display browser for the visualization denoted by id and add the datasets listed in `dataset_ids`.
"""
- # Display new browser if no id provided.
+ # Set up new browser if no id provided.
if not id:
return trans.fill_template( "tracks/browser.mako", config={},
add_dataset=kwargs.get("dataset_id", None),
- default_dbkey=kwargs.get("default_dbkey", None) )
+ default_dbkey=kwargs.get("dbkey", None) )
# Display saved visualization.
vis = self.get_visualization( trans, id, check_ownership=False, check_accessible=True )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/8153e8d25009/
changeset: 8153e8d25009
user: dannon
date: 2012-09-19 02:49:29
summary: Fix create_all_fasta_loc to work when inspect_dir is not set.
affected #: 1 file
diff -r 05a1728683032985f7feccc007b25c083d263c9b -r 8153e8d25009d71a523e0f2df24ed12922825d8f scripts/loc_files/create_all_fasta_loc.py
--- a/scripts/loc_files/create_all_fasta_loc.py
+++ b/scripts/loc_files/create_all_fasta_loc.py
@@ -195,7 +195,7 @@
if options.inspect_dir:
paths_to_look_in = [ os.path.join( options.genome_dir, '%s', id ) for id in options.inspect_dir.split( ',' ) ]
else:
- paths_to_look_in = os.path.join( options.genome_dir, '%s' )
+ paths_to_look_in = [os.path.join( options.genome_dir, '%s' )]
# say what we're looking in
print '\nLooking in:\n\t%s' % '\n\t'.join( [ p % '<build_name>' for p in paths_to_look_in ] )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/05a172868303/
changeset: 05a172868303
user: jgoecks
date: 2012-09-18 23:11:18
summary: Tophat2 wrapper fixes. Thanks to Jim Johnson and Lance Parsons.
affected #: 1 file
diff -r 0cf3b64e80777c45425a57f4f69d806df839fcf4 -r 05a1728683032985f7feccc007b25c083d263c9b tools/ngs_rna/tophat2_wrapper.xml
--- a/tools/ngs_rna/tophat2_wrapper.xml
+++ b/tools/ngs_rna/tophat2_wrapper.xml
@@ -3,6 +3,8 @@
<description>Gapped-read mapper for RNA-seq data</description><version_command>tophat2 --version</version_command><requirements>
+ <requirement type="package">samtools</requirement>
+ <requirement type="package">bowtie2</requirement><requirement type="package">tophat2</requirement></requirements><command interpreter="python">
@@ -297,7 +299,7 @@
<outputs><data format="tabular" name="fusions" label="${tool.name} on ${on_string}: fusions" from_work_dir="tophat_out/fusions.out">
- <filter>(params['fusion_search']['do_search'] == 'Yes')</filter>
+ <filter>(params['settingsType'] == 'full' and params['fusion_search']['do_search'] == 'Yes')</filter></data><data format="bed" name="insertions" label="${tool.name} on ${on_string}: insertions" from_work_dir="tophat_out/insertions.bed"><actions>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/3f12146d6d81/
changeset: 3f12146d6d81
user: smcmanus
date: 2012-09-18 20:10:56
summary: Fixed call to check_tool_output for TaskWrapper.
affected #: 1 file
diff -r 23107188eab8aa8f0c5ed721af30ff13b19bd61c -r 3f12146d6d81e08f662ada2011a6973e4230512d lib/galaxy/jobs/__init__.py
--- a/lib/galaxy/jobs/__init__.py
+++ b/lib/galaxy/jobs/__init__.py
@@ -1048,7 +1048,7 @@
# Check what the tool returned. If the stdout or stderr matched
# regular expressions that indicate errors, then set an error.
# The same goes if the tool's exit code was in a given range.
- if ( self.check_tool_output( stdout, stderr, tool_exit_code ) ):
+ if ( self.check_tool_output( stdout, stderr, tool_exit_code, task ) ):
task.state = task.states.OK
else:
task.state = task.states.ERROR
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/23107188eab8/
changeset: 23107188eab8
user: greg
date: 2012-09-18 19:54:19
summary: Fix for getting updates for tool shed repositories installed into a local Galaxy instance.
affected #: 1 file
diff -r 2f655fb9e6a8873f1faff3b0fed4c0288a2e4c2b -r 23107188eab8aa8f0c5ed721af30ff13b19bd61c lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -795,19 +795,25 @@
changeset_hash = str( repo.changectx( changeset ) )
ctx = get_changectx_for_changeset( repo, changeset_hash )
if update_to_changeset_hash:
- if get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_hash ):
- # We found a RepositoryMetadata record.
- if changeset_hash == repository.tip:
- # The current ctx is the repository tip, so use it.
+ if changeset_hash == repository.tip:
+ update_to_ctx = get_changectx_for_changeset( repo, changeset_hash )
+ latest_changeset_revision = changeset_hash
+ break
+ else:
+ repository_metadata = get_repository_metadata_by_changeset_revision( trans,
+ trans.security.encode_id( repository.id ),
+ changeset_hash )
+ if repository_metadata:
+ # We found a RepositoryMetadata record.
update_to_ctx = get_changectx_for_changeset( repo, changeset_hash )
latest_changeset_revision = changeset_hash
+ break
else:
- update_to_ctx = get_changectx_for_changeset( repo, update_to_changeset_hash )
- latest_changeset_revision = update_to_changeset_hash
- break
- elif not update_to_changeset_hash and changeset_hash == changeset_revision:
- # We've found the changeset in the changelog for which we need to get the next update.
- update_to_changeset_hash = changeset_hash
+ update_to_changeset_hash = changeset_hash
+ else:
+ if changeset_hash == changeset_revision:
+ # We've found the changeset in the changelog for which we need to get the next update.
+ update_to_changeset_hash = changeset_hash
if from_update_manager:
if latest_changeset_revision == changeset_revision:
return no_update
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/aa1ad2112bb7/
changeset: aa1ad2112bb7
user: jgoecks
date: 2012-09-18 19:14:49
summary: Remove dubugging statement from last commit.
affected #: 2 files
diff -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be -r aa1ad2112bb7918987dc31250ac214e45ba75641 lib/galaxy/datatypes/tabular.py
--- a/lib/galaxy/datatypes/tabular.py
+++ b/lib/galaxy/datatypes/tabular.py
@@ -313,8 +313,6 @@
if col_type in [ 'int', 'float' ]:
num_numerical_cols += 1
- print dataset.name, num_numerical_cols
-
vizs = super( Tabular, self ).get_visualizations( dataset )
if num_numerical_cols >= 2:
vizs.append( 'scatterplot' )
diff -r aa0469dd0078fd792ff34db8cd8ee36ae0e9c9be -r aa1ad2112bb7918987dc31250ac214e45ba75641 templates/root/history_common.mako
--- a/templates/root/history_common.mako
+++ b/templates/root/history_common.mako
@@ -232,8 +232,8 @@
visualizations = data.get_visualizations()
## HACK: if there are visualizations, only provide trackster for now since others
## are not ready.
- if visualizations:
- visualizations = [ 'trackster' ]
+ #if visualizations:
+ # visualizations = [ 'trackster' ]
%>
%if visualizations:
<a href="${h.url_for( controller='visualization' )}"
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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