1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/fbb7d4250604/
changeset: fbb7d4250604
user: dannon
date: 2012-04-18 22:30:11
summary: Fix missing sanitize_html import.
affected #: 1 file
diff -r fd33b522ceebbd0866f060b7309b14f9571ae06e -r fbb7d4250604ddd0ed2c2006ab6601e6e973bd72 lib/galaxy/datatypes/data.py
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -3,6 +3,7 @@
from galaxy.util.odict import odict
from galaxy.util.bunch import Bunch
from galaxy.util import inflector
+from galaxy.util.sanitize_html import sanitize_html
from cgi import escape
import metadata
import zipfile
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/45bd2e0fe8d0/
changeset: 45bd2e0fe8d0
user: jgoecks
date: 2012-04-18 21:09:36
summary: Fix decode issues with library datasets in Trackster.
affected #: 1 file
diff -r 9e9f489c6488e63a5d8b86ae64a81c9b4ddd306d -r 45bd2e0fe8d0eae68a82d3a141ebfc20d0ae7b2e lib/galaxy/web/base/controller.py
--- a/lib/galaxy/web/base/controller.py
+++ b/lib/galaxy/web/base/controller.py
@@ -322,7 +322,7 @@
if hda_ldda == "hda":
dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True )
else:
- dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id(dataset_id) )
+ dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( dataset_id )
try:
prefs = track_dict['prefs']
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/9e9f489c6488/
changeset: 9e9f489c6488
user: greg
date: 2012-04-18 20:29:01
summary: Fix for functinal tests when GALAXY_TEST_DBURI is not set in os.environ.
affected #: 1 file
diff -r 66c3172dff142cef1bdcecc257db797adc6e4584 -r 9e9f489c6488e63a5d8b86ae64a81c9b4ddd306d lib/galaxy/tool_shed/migrate/check.py
--- a/lib/galaxy/tool_shed/migrate/check.py
+++ b/lib/galaxy/tool_shed/migrate/check.py
@@ -21,6 +21,7 @@
def verify_tools( app, url, galaxy_config_file, engine_options={} ):
# Check the value in the migrate_tools.version database table column to verify that the number is in
# sync with the number of version scripts in ~/lib/galaxy/tools/migrate/versions.
+ running_functional_tests = galaxy_config_file.endswith( '.sample' )
dialect = ( url.split( ':', 1 ) )[0]
try:
egg = dialect_to_egg[ dialect ]
@@ -54,51 +55,52 @@
config_arg = ''
if os.path.abspath( os.path.join( os.getcwd(), 'universe_wsgi.ini' ) ) != galaxy_config_file:
config_arg = ' -c %s' % galaxy_config_file.replace( os.path.abspath( os.getcwd() ), '.' )
- # Automatically update the value of the migrate_tools.version database table column.
- cmd = 'sh manage_tools.sh%s upgrade' % config_arg
- proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
- return_code = proc.wait()
- output = proc.stdout.read( 32768 )
- if return_code != 0:
- raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output )
- elif missing_tool_configs:
- if len( tool_panel_configs ) == 1:
- plural = ''
- tool_panel_config_file_names = tool_panel_configs[ 0 ]
- else:
- plural = 's'
- tool_panel_config_file_names = ', '.join( tool_panel_configs )
- msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>"
- msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n"
- msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n"
- msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n"
- msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n"
- msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n"
- msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names )
- msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n"
- msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n"
- msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n'
- msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n"
- msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n"
- msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n"
- msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n"
- msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n"
- msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n"
- msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n"
- msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n"
- msg += output
- msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n"
- msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n"
- msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n"
- msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names )
- for i, missing_tool_config in enumerate( missing_tool_configs ):
- msg += "%s\n" % missing_tool_config
- # Should we do the following?
- #if i > 10:
- # msg += "\n...and %d more tools...\n" % ( len( missing_tool_configs ) - ( i + 1 ) )
- # break
- msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n"
- raise Exception( msg )
+ if not running_functional_tests:
+ # Automatically update the value of the migrate_tools.version database table column.
+ cmd = 'sh manage_tools.sh%s upgrade' % config_arg
+ proc = subprocess.Popen( args=cmd, shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT )
+ return_code = proc.wait()
+ output = proc.stdout.read( 32768 )
+ if return_code != 0:
+ raise Exception( "Error attempting to update the value of migrate_tools.version: %s" % output )
+ elif missing_tool_configs:
+ if len( tool_panel_configs ) == 1:
+ plural = ''
+ tool_panel_config_file_names = tool_panel_configs[ 0 ]
+ else:
+ plural = 's'
+ tool_panel_config_file_names = ', '.join( tool_panel_configs )
+ msg = "\n>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>"
+ msg += "\n\nThe list of files at the end of this message refers to tools that are configured to load into the tool panel for\n"
+ msg += "this Galaxy instance, but have been removed from the Galaxy distribution. These tools can be automatically installed\n"
+ msg += "from the Galaxy tool shed at http://toolshed.g2.bx.psu.edu.\n\n"
+ msg += "To skip this process, attempt to start your Galaxy server again (e.g., sh run.sh or whatever you use). If you do this,\n"
+ msg += "be aware that these tools will no longer be available in your Galaxy tool panel, and entries for each of them should\n"
+ msg += "be removed from your file%s named %s.\n\n" % ( plural, tool_panel_config_file_names )
+ msg += "CRITICAL NOTE IF YOU PLAN TO INSTALL\n"
+ msg += "The location in which the tool repositories will be installed is the value of the 'tool_path' attribute in the <tool>\n"
+ msg += 'tag of the file named ./migrated_tool_conf.xml (i.e., <toolbox tool_path="../shed_tools">). The default location\n'
+ msg += "setting is '../shed_tools', which may be problematic for some cluster environments, so make sure to change it before\n"
+ msg += "you execute the installation process if appropriate. The configured location must be outside of the Galaxy installation\n"
+ msg += "directory or it must be in a sub-directory protected by a properly configured .hgignore file if the directory is within\n"
+ msg += "the Galaxy installation directory hierarchy. This is because tool shed repositories will be installed using mercurial's\n"
+ msg += "clone feature, which creates .hg directories and associated mercurial repository files. Not having .hgignore properly\n"
+ msg += "configured could result in undesired behavior when modifying or updating your local Galaxy instance or the tool shed\n"
+ msg += "repositories if they are in directories that pose conflicts. See mercurial's .hgignore documentation at the following\n"
+ msg += "URL for details.\n\nhttp://mercurial.selenic.com/wiki/.hgignore\n\n"
+ msg += output
+ msg += "After the installation process finishes, you can start your Galaxy server. As part of this installation process,\n"
+ msg += "entries for each of the following tool config files will be added to the file named ./migrated_tool_conf.xml, so these\n"
+ msg += "tools will continue to be loaded into your tool panel. Because of this, existing entries for these files should be\n"
+ msg += "removed from your file%s named %s, but only after the installation process finishes.\n\n" % ( plural, tool_panel_config_file_names )
+ for i, missing_tool_config in enumerate( missing_tool_configs ):
+ msg += "%s\n" % missing_tool_config
+ # Should we do the following?
+ #if i > 10:
+ # msg += "\n...and %d more tools...\n" % ( len( missing_tool_configs ) - ( i + 1 ) )
+ # break
+ msg += "<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<<\n"
+ raise Exception( msg )
else:
log.info( "At migrate_tools version %d" % db_schema.version )
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/66c3172dff14/
changeset: 66c3172dff14
user: natefoo
date: 2012-04-18 20:15:52
summary: Handle errors in the job handler caused by idata.hid being None.
affected #: 1 file
diff -r d087c9f23f9bbf81176a253830b88cca15c458a7 -r 66c3172dff142cef1bdcecc257db797adc6e4584 lib/galaxy/jobs/handler.py
--- a/lib/galaxy/jobs/handler.py
+++ b/lib/galaxy/jobs/handler.py
@@ -207,14 +207,14 @@
continue
# don't run jobs for which the input dataset was deleted
if idata.deleted:
- JobWrapper( job, self ).fail( "input data %d (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) )
+ JobWrapper( job, self ).fail( "input data %s (file: %s) was deleted before the job started" % ( idata.hid, idata.file_name ) )
return JOB_INPUT_DELETED
# an error in the input data causes us to bail immediately
elif idata.state == idata.states.ERROR:
- JobWrapper( job, self ).fail( "input data %d is in error state" % ( idata.hid ) )
+ JobWrapper( job, self ).fail( "input data %s is in error state" % ( idata.hid ) )
return JOB_INPUT_ERROR
elif idata.state == idata.states.FAILED_METADATA:
- JobWrapper( job, self ).fail( "input data %d failed to properly set metadata" % ( idata.hid ) )
+ JobWrapper( job, self ).fail( "input data %s failed to properly set metadata" % ( idata.hid ) )
return JOB_INPUT_ERROR
elif idata.state != idata.states.OK and not ( idata.state == idata.states.SETTING_METADATA and job.tool_id is not None and job.tool_id == self.app.datatypes_registry.set_external_metadata_tool.id ):
# need to requeue
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/d087c9f23f9b/
changeset: d087c9f23f9b
user: dan
date: 2012-04-18 18:54:01
summary: Fix for LibraryDatasetDatasetAssociation.templates_dict when a content value is not set.
affected #: 1 file
diff -r 609b820ba1ea1ed753179b9228ca918b11969acf -r d087c9f23f9bbf81176a253830b88cca15c458a7 lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -1555,7 +1555,7 @@
name = field[ 'name' ]
else:
name = field[ 'label' ]
- tmp_dict[ name ] = content[ field[ 'name' ] ]
+ tmp_dict[ name ] = content.get( field[ 'name' ] )
template_data[template.name] = tmp_dict
return template_data
def templates_json( self, use_name=False ):
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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