- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Include the galaxy_url param in the new request to the tool shed.
by commits-noreply＠bitbucket.org 12 May '13

12 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bc5cd95d042b/ Changeset: bc5cd95d042b User: greg Date: 2013-05-12 17:05:49 Summary: Include the galaxy_url param in the new request to the tool shed. Affected #: 1 file diff -r dc7d35578676935777d1f315693a4c15498919e8 -r bc5cd95d042bc062c688bee6b3e9cbf74d853fb1 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -299,8 +299,11 @@ fh.write( encoded_required_repository_str ) fh.close() encoded_tmp_file_name = encoding_util.tool_shed_encode( os.path.abspath( tmp_file_name ) ) + galaxy_url = web.url_for( '/', qualified=True ) # Send a request to the tool shed to enable it to read the temporary file. - url = suc.url_join( tool_shed_url, '/repository/get_required_repo_info_dict?encoded_tmp_file_name=%s' % encoded_tmp_file_name ) + url = suc.url_join( tool_shed_url, + '/repository/get_required_repo_info_dict?encoded_tmp_file_name=%s&galaxy_url=%s' % \ + ( encoded_tmp_file_name, galaxy_url ) ) else: encoded_tmp_file_name = None tmp_file_name = None @@ -311,7 +314,7 @@ message = 'The selected tool shed repositories cannot be installed until the tool shed at ' message += '%s and the Galaxy instance at %s ' % ( str( tool_shed_url ), str( trans.request.base ) ) message += 'are both updated to at least the June 3, 2013 Galaxy release. These upgrades ' - message += 'are necessary because the number of repositories you are attemping to install ' + message += 'are necessary because the number of repositories you are attempting to install ' message += 'generates an HTTP request that is longer than 8177 bytes which cannot be handled ' message += 'by tool shed or Galaxy instances older than this release.' log.debug( message ) 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 0

commit/galaxy-central: greg: Persist the encoded string resulting from the information needed to install tool shed repositories if the string generates an HTTP request longer than 8177 bytes and enhance the necessary tool shed and Galaxy methods to handle this scenario.
by commits-noreply＠bitbucket.org 12 May '13

12 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc7d35578676/ Changeset: dc7d35578676 User: greg Date: 2013-05-12 16:47:33 Summary: Persist the encoded string resulting from the information needed to install tool shed repositories if the string generates an HTTP request longer than 8177 bytes and enhance the necessary tool shed and Galaxy methods to handle this scenario. Affected #: 2 files diff -r d09a3531b3d35a3921fdaa52beed7481f0391ca8 -r dc7d35578676935777d1f315693a4c15498919e8 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -4,9 +4,11 @@ import re import string import tempfile +import urllib2 from time import gmtime from time import strftime -from datetime import date, datetime +from datetime import date +from datetime import datetime from galaxy import util from galaxy import web from galaxy.util.odict import odict @@ -1471,12 +1473,29 @@ repo_info_dicts=repo_info_dicts ) @web.json - def get_required_repo_info_dict( self, trans, encoded_str ): + def get_required_repo_info_dict( self, trans, encoded_str=None, **kwd ): """ Retrieve and return a dictionary that includes a list of dictionaries that each contain all of the information needed to install the list of repositories defined by the received encoded_str. """ - encoded_required_repository_str = encoding_util.tool_shed_decode( encoded_str ) + # In some cases the received encoded_str will be long. With apache, the default limit for the length of the request line is 8190 bytes + # (http://httpd.apache.org/docs/2.2/mod/core.html#limitrequestline) And if we subtract three bytes for the request method (i.e. GET), + # eight bytes for the version information (i.e. HTTP/1.0/HTTP/1.1) and two bytes for the separating space, we end up with 8177 bytes for + # the URI path plus query. The referer handles requests longer than this by persisting the encoded_str to a temporary file which we + # can read. + encoded_tmp_file_name = kwd.get( 'encoded_tmp_file_name', None ) + if encoded_str: + encoded_required_repository_str = encoding_util.tool_shed_decode( encoded_str ) + else: + # The request would have been longer than 8190 bytes if it included the encoded_str, so we'll send a request to the Galaxy instance to + # stream the string to us. + galaxy_url = suc.handle_galaxy_url( trans, **kwd ) + if galaxy_url and encoded_tmp_file_name: + url = suc.url_join( galaxy_url, '/common_install_util/stream_file_contents?encoded_tmp_file_name=%s' % encoded_tmp_file_name ) + response = urllib2.urlopen( url ) + encoded_required_repository_str = response.read() + else: + raise Exception( "Required galaxy_url or encoded_tmp_file_name request parameters missing." ) encoded_required_repository_tups = encoded_required_repository_str.split( encoding_util.encoding_sep2 ) decoded_required_repository_tups = [] for encoded_required_repository_tup in encoded_required_repository_tups: diff -r d09a3531b3d35a3921fdaa52beed7481f0391ca8 -r dc7d35578676935777d1f315693a4c15498919e8 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -1,5 +1,6 @@ import logging import os +import tempfile from galaxy import eggs from galaxy import util from galaxy.util import json @@ -285,7 +286,43 @@ encoded_required_repository_str = encoding_util.encoding_sep2.join( encoded_required_repository_tups ) encoded_required_repository_str = encoding_util.tool_shed_encode( encoded_required_repository_str ) url = suc.url_join( tool_shed_url, '/repository/get_required_repo_info_dict?encoded_str=%s' % encoded_required_repository_str ) - text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) + # In some cases the above URL will be long. With apache, the default limit for the length of the request line is 8190 bytes + # (http://httpd.apache.org/docs/2.2/mod/core.html#limitrequestline) And if we subtract three bytes for the request method + # (i.e. GET), eight bytes for the version information (i.e. HTTP/1.0/HTTP/1.1) and two bytes for the separating space, we end + # up with 8177 bytes for the URI path plus query. + if len( url ) >= 8177: + # Persist the encoded string to a temporary file. + fh = tempfile.NamedTemporaryFile( 'wb' ) + tmp_file_name = fh.name + fh.close() + fh = open( tmp_file_name, 'wb' ) + fh.write( encoded_required_repository_str ) + fh.close() + encoded_tmp_file_name = encoding_util.tool_shed_encode( os.path.abspath( tmp_file_name ) ) + # Send a request to the tool shed to enable it to read the temporary file. + url = suc.url_join( tool_shed_url, '/repository/get_required_repo_info_dict?encoded_tmp_file_name=%s' % encoded_tmp_file_name ) + else: + encoded_tmp_file_name = None + tmp_file_name = None + try: + text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) + except Exception, e: + if encoded_tmp_file_name: + message = 'The selected tool shed repositories cannot be installed until the tool shed at ' + message += '%s and the Galaxy instance at %s ' % ( str( tool_shed_url ), str( trans.request.base ) ) + message += 'are both updated to at least the June 3, 2013 Galaxy release. These upgrades ' + message += 'are necessary because the number of repositories you are attemping to install ' + message += 'generates an HTTP request that is longer than 8177 bytes which cannot be handled ' + message += 'by tool shed or Galaxy instances older than this release.' + log.debug( message ) + else: + log.exception() + text = None + if tmp_file_name: + try: + os.unlink( tmp_file_name ) + except: + pass if text: required_repo_info_dict = json.from_json_string( text ) required_repo_info_dicts = [] @@ -356,3 +393,7 @@ app.model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) return installed_tool_dependencies + +def stream_file_contents( trans, encoded_tmp_file_name ): + tmp_file_name = encoding_util.tool_shed_decode( encoded_tmp_file_name ) + return open( tmp_file_name ) 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 0

commit/galaxy-central: greg: Fix for updating metadata for a tool shed repository that defines complex repository dependencies.
by commits-noreply＠bitbucket.org 11 May '13

11 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d09a3531b3d3/ Changeset: d09a3531b3d3 User: greg Date: 2013-05-11 19:16:09 Summary: Fix for updating metadata for a tool shed repository that defines complex repository dependencies. Affected #: 3 files diff -r 7dc222a7163a5049cc407ad1a049dd091ac27b03 -r d09a3531b3d35a3921fdaa52beed7481f0391ca8 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -487,9 +487,9 @@ tool_shed_repository, trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed ) - url = suc.url_join( tool_shed_url, - '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % - ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) + url = suc.url_join( tool_shed_url, + '/repository/get_tool_versions?name=%s&owner=%s&changeset_revision=%s' % + ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.changeset_revision ) ) text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) if text: tool_version_dicts = json.from_json_string( text ) diff -r 7dc222a7163a5049cc407ad1a049dd091ac27b03 -r d09a3531b3d35a3921fdaa52beed7481f0391ca8 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1857,23 +1857,14 @@ else: tool_shed, name, owner, changeset_revision, prior_installation_required, error_message = repository_dependency_tup prior_installation_required = util.asbool( str( prior_installation_required ) ) - rd_key = container_util.generate_repository_dependencies_key_for_repository( toolshed_base_url=tool_shed, - repository_name=name, - repository_owner=owner, - changeset_revision=changeset_revision, - prior_installation_required=prior_installation_required ) if repository_dependencies_dict: - if rd_key in repository_dependencies_dict: - repository_dependencies = repository_dependencies_dict[ rd_key ] - for repository_dependency_tup in repository_dependency_tups: - if repository_dependency_tup not in repository_dependencies: - repository_dependencies.append( repository_dependency_tup ) - repository_dependencies_dict[ rd_key ] = repository_dependencies - else: - repository_dependencies_dict[ rd_key ] = repository_dependency_tups + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + for repository_dependency_tup in repository_dependency_tups: + if repository_dependency_tup not in repository_dependencies: + repository_dependencies.append( repository_dependency_tup ) + repository_dependencies_dict[ 'repository_dependencies' ] = repository_dependencies else: - repository_dependencies_dict = dict( root_key=rd_key, - description=description, + repository_dependencies_dict = dict( description=description, repository_dependencies=repository_dependency_tups ) if repository_dependencies_dict: if is_valid: diff -r 7dc222a7163a5049cc407ad1a049dd091ac27b03 -r d09a3531b3d35a3921fdaa52beed7481f0391ca8 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -198,7 +198,7 @@ def create_or_update_tool_shed_repository( app, name, description, installed_changeset_revision, ctx_rev, repository_clone_url, metadata_dict, status, current_changeset_revision=None, owner='', dist_to_shed=False ): """ - Update a tool shed repository record i the Galaxy database with the new information received. If a record defined by the received tool shed, repository name + Update a tool shed repository record in the Galaxy database with the new information received. If a record defined by the received tool shed, repository name and owner does not exists, create a new record with the received information. """ # The received value for dist_to_shed will be True if the InstallManager is installing a repository that contains tools or datatypes that used @@ -1052,6 +1052,10 @@ prior_installation_required = util.asbool( str( prior_installation_required ) ) return tool_shed, name, owner, changeset_revision, prior_installation_required +def pretty_print( dict=None ): + if dict: + return json.to_json_string( dict, sort_keys=True, indent=4 * ' ' ) + def remove_dir( dir ): """Attempt to remove a directory from disk.""" if os.path.exists( 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 0

commit/galaxy-central: jgoecks: Trackster: fix bug in variant track drawing.
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7dc222a7163a/ Changeset: 7dc222a7163a User: jgoecks Date: 2013-05-10 23:16:20 Summary: Trackster: fix bug in variant track drawing. Affected #: 1 file diff -r b4733e42a2c98c42401bca5e0643fc4d4dcf2db6 -r 7dc222a7163a5049cc407ad1a049dd091ac27b03 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4266,7 +4266,7 @@ draw_tile: function(result, ctx, mode, resolution, region, w_scale) { // Data could be coverage data or variant data. if (result.dataset_type === 'bigwig') { - return this._draw_line_track_tile(result, ctx, "Histogram", region, resolution, w_scale); + return this._draw_line_track_tile(result, ctx, "Histogram", resolution, region, w_scale); } else { // result.dataset_type === 'variant' var view = this.view, 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 0

commit/galaxy-central: Dave Bouvier: Add a new tool dependency action download_file to download a file without extracting it.
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b4733e42a2c9/ Changeset: b4733e42a2c9 User: Dave Bouvier Date: 2013-05-10 20:48:15 Summary: Add a new tool dependency action download_file to download a file without extracting it. Affected #: 3 files diff -r f72fd96d3fac5e17ec5c9aaece023b0ae74db696 -r b4733e42a2c98c42401bca5e0643fc4d4dcf2db6 lib/tool_shed/galaxy_install/tool_dependencies/common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/common_util.py @@ -151,6 +151,9 @@ def isgzip( file_path ): return checkers.is_gzip( file_path ) +def isjar( file_path ): + return iszip( file_path ) and file_path.endswith( '.jar' ) + def istar( file_path ): return tarfile.is_tarfile( file_path ) diff -r f72fd96d3fac5e17ec5c9aaece023b0ae74db696 -r b4733e42a2c98c42401bca5e0643fc4d4dcf2db6 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -71,6 +71,8 @@ # <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.18/samtools-0.1…</action> common_util.extract_tar( downloaded_file_path, work_dir ) dir = common_util.tar_extraction_directory( work_dir, downloaded_filename ) + elif common_util.isjar( downloaded_file_path ): + dir = os.path.curdir elif common_util.iszip( downloaded_file_path ): # <action type="download_by_url">http://downloads.sourceforge.net/project/picard/picard-tools/1.56/picard-to…</action> zip_archive_extracted = common_util.extract_zip( downloaded_file_path, work_dir ) @@ -85,6 +87,14 @@ if return_code: return dir = package_name + elif action_type == 'download_file': + # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> + # Download a single file to the working directory. + filtered_actions = actions[ 1: ] + url = action_dict[ 'url' ] + filename = url.split( '/' )[ -1 ] + common_util.url_download( work_dir, filename, url ) + dir = os.path.curdir else: # We're handling a complex repository dependency where we only have a set_environment tag set. # <action type="set_environment"> @@ -137,6 +147,11 @@ return_code = handle_command( app, tool_dependency, install_dir, cmd ) if return_code: return + elif action_type == 'download_file': + # Download a single file to the current directory. + url = action_dict[ 'url' ] + filename = url.split( '/' )[ -1 ] + common_util.url_download( current_dir, filename, url ) def log_results( command, fabric_AttributeString, file_path ): """ diff -r f72fd96d3fac5e17ec5c9aaece023b0ae74db696 -r b4733e42a2c98c42401bca5e0643fc4d4dcf2db6 lib/tool_shed/galaxy_install/tool_dependencies/install_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py @@ -341,6 +341,12 @@ action_dict[ 'target_filename' ] = action_elem.attrib[ 'target_filename' ] else: continue + elif action_type == 'download_file': + # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> + if action_elem.text: + action_dict[ 'url' ] = action_elem.text + else: + continue elif action_type == 'make_directory': # <action type="make_directory">$INSTALL_DIR/lib/python</action> if action_elem.text: 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 0

commit/galaxy-central: greg: Fixes for displaying README files associated with an uninstalled tool shed repository.
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f72fd96d3fac/ Changeset: f72fd96d3fac User: greg Date: 2013-05-10 20:24:19 Summary: Fixes for displaying README files associated with an uninstalled tool shed repository. Affected #: 2 files diff -r 43e37c4cc6cfbcdaba7e29a8bfac1b96dc5e7990 -r f72fd96d3fac5e17ec5c9aaece023b0ae74db696 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -1130,7 +1130,7 @@ """ Select or change the tool panel section to contain the tools included in the tool shed repository being reinstalled. If there are updates available for the repository in the tool shed, the tool_dependencies and repository_dependencies associated with the updated changeset revision - will have been retrieved from the tool shed and passed in the received kwd. In this case, the stored tool shed repository metqdata from the + will have been retrieved from the tool shed and passed in the received kwd. In this case, the stored tool shed repository metadata from the Galaxy database will not be used since it is outdated. """ message = '' @@ -1185,7 +1185,12 @@ includes_tool_dependencies = True if 'workflows' in metadata: includes_workflows = True - readme_files_dict = readme_util.build_readme_files_dict( metadata ) + # Since we're reinstalling, we need to send a request to the tool shed to get the README files. + url = suc.url_join( tool_shed_url, + 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \ + ( tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) ) + raw_text = common_util.tool_shed_get( trans.app, tool_shed_url, url ) + readme_files_dict = json.from_json_string( raw_text ) tool_dependencies = metadata.get( 'tool_dependencies', None ) repository_dependencies = self.get_repository_dependencies( trans=trans, repository_id=repository_id, diff -r 43e37c4cc6cfbcdaba7e29a8bfac1b96dc5e7990 -r f72fd96d3fac5e17ec5c9aaece023b0ae74db696 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1373,7 +1373,8 @@ invalid_tools = metadata.get( 'invalid_tools', None ) # Handle README files. if repository.has_readme_files: - if reinstalling: + if reinstalling or repository.status not in [ trans.model.ToolShedRepository.installation_status.DEACTIVATED, + trans.model.ToolShedRepository.installation_status.INSTALLED ]: # Since we're reinstalling, we need to send a request to the tool shed to get the README files. url = suc.url_join( tool_shed_url, 'repository/get_readme_files?name=%s&owner=%s&changeset_revision=%s' % \ 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 0

commit/galaxy-central: greg: For tool dependencies whose installation ended in an error, still display them when attempting to uninstall them.
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43e37c4cc6cf/ Changeset: 43e37c4cc6cf User: greg Date: 2013-05-10 19:52:28 Summary: For tool dependencies whose installation ended in an error, still display them when attempting to uninstall them. Affected #: 1 file diff -r 60fe1081baac6aa1e2e9d2e4f8e22945df102671 -r 43e37c4cc6cfbcdaba7e29a8bfac1b96dc5e7990 templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako @@ -51,15 +51,15 @@ tool_dependency.tool_shed_repository.owner, tool_dependency.tool_shed_repository.name, tool_dependency.tool_shed_repository.installed_changeset_revision ) + if not os.path.exists( install_dir ): + install_dir = "This dependency's installation directory does not exist, click <b>Uninstall</b> to reset for installation." %> - %if os.path.exists( install_dir ): - <tr> - <td>${tool_dependency.name}</td> - <td>${tool_dependency.version}</td> - <td>${tool_dependency.type}</td> - <td>${install_dir}</td> - </tr> - %endif + <tr> + <td>${tool_dependency.name}</td> + <td>${tool_dependency.version}</td> + <td>${tool_dependency.type}</td> + <td>${install_dir}</td> + </tr> %endfor </table><div style="clear: both"></div> 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 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/60fe1081baac/ Changeset: 60fe1081baac User: dan Date: 2013-05-10 17:55:40 Summary: use_panels fix for login.mako in toolshed. Affected #: 1 file diff -r c8762ac39f04cc41da1f59444fdcff655559f4d4 -r 60fe1081baac6aa1e2e9d2e4f8e22945df102671 templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -3,7 +3,7 @@ def inherit(context): if context.get('trans').webapp.name == 'galaxy' and context.get( 'use_panels', True ): return '/webapps/galaxy/base_panels.mako' - elif context.get('trans').webapp.name == 'tool_shed': + elif context.get('trans').webapp.name == 'tool_shed' and context.get( 'use_panels', True ): return '/webapps/tool_shed/base_panels.mako' else: return '/base.mako' https://bitbucket.org/galaxy/galaxy-central/commits/7cf2f256b3d9/ Changeset: 7cf2f256b3d9 Branch: stable User: dan Date: 2013-05-10 17:55:40 Summary: use_panels fix for login.mako in toolshed. Affected #: 1 file diff -r 429636bbc4ab4c5715dea09cee9ff546d94346de -r 7cf2f256b3d9c32f76567f49a0935b0ca9da9f7e templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -3,7 +3,7 @@ def inherit(context): if context.get('trans').webapp.name == 'galaxy' and context.get( 'use_panels', True ): return '/webapps/galaxy/base_panels.mako' - elif context.get('trans').webapp.name == 'tool_shed': + elif context.get('trans').webapp.name == 'tool_shed' and context.get( 'use_panels', True ): return '/webapps/tool_shed/base_panels.mako' else: return '/base.mako' 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 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c8762ac39f04/ Changeset: c8762ac39f04 User: dan Date: 2013-05-10 17:49:16 Summary: use_panels fix for login.mako. Affected #: 1 file diff -r 45c048c8756438ee829498aac0e8c1e29f85d661 -r c8762ac39f04cc41da1f59444fdcff655559f4d4 templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -1,7 +1,7 @@ <%! #This is a hack, we should restructure templates to avoid this. def inherit(context): - if context.get('trans').webapp.name == 'galaxy': + if context.get('trans').webapp.name == 'galaxy' and context.get( 'use_panels', True ): return '/webapps/galaxy/base_panels.mako' elif context.get('trans').webapp.name == 'tool_shed': return '/webapps/tool_shed/base_panels.mako' https://bitbucket.org/galaxy/galaxy-central/commits/429636bbc4ab/ Changeset: 429636bbc4ab Branch: stable User: dan Date: 2013-05-10 17:49:16 Summary: use_panels fix for login.mako. Affected #: 1 file diff -r 35b87dd34a79aa4b94c9c3dd8ff17b4143cd340c -r 429636bbc4ab4c5715dea09cee9ff546d94346de templates/user/login.mako --- a/templates/user/login.mako +++ b/templates/user/login.mako @@ -1,7 +1,7 @@ <%! #This is a hack, we should restructure templates to avoid this. def inherit(context): - if context.get('trans').webapp.name == 'galaxy': + if context.get('trans').webapp.name == 'galaxy' and context.get( 'use_panels', True ): return '/webapps/galaxy/base_panels.mako' elif context.get('trans').webapp.name == 'tool_shed': return '/webapps/tool_shed/base_panels.mako' 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 0

commit/galaxy-central: dan: Add openid_consumer_cache to .hgignore.
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/45c048c87564/ Changeset: 45c048c87564 User: dan Date: 2013-05-10 17:28:57 Summary: Add openid_consumer_cache to .hgignore. Affected #: 1 file diff -r f0da1c8355df9a68c3db5fecd27ed20def89a3ec -r 45c048c8756438ee829498aac0e8c1e29f85d661 .hgignore --- a/.hgignore +++ b/.hgignore @@ -20,6 +20,7 @@ database/pbs database/tmp database/*.sqlite +database/openid_consumer_cache # Python bytecode *.pyc 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 0