galaxy-commits May 2013

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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 11 May '13

11 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.

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commit/galaxy-central: greg: Fixes for displaying README files associated with an uninstalled tool shed repository.
by commits-noreply＠bitbucket.org 11 May '13

11 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.

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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 11 May '13

11 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.

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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.

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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.

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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.

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commit/galaxy-central: greg: Fix for defining the order for installing repositories from the tool shed where 1 or more repositories defines a repository dependency with prior_installation_required=True.
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f0da1c8355df/ Changeset: f0da1c8355df User: greg Date: 2013-05-10 17:06:35 Summary: Fix for defining the order for installing repositories from the tool shed where 1 or more repositories defines a repository dependency with prior_installation_required=True. Affected #: 2 files diff -r 72f47fad3d219d44988d672dc41f30748ba8d5ff -r f0da1c8355df9a68c3db5fecd27ed20def89a3ec lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -248,25 +248,31 @@ # Install the repositories, keeping track of each one for later display. for index, tsr_id in enumerate( ordered_tsr_ids ): tool_shed_repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) - repo_info_dict = ordered_repo_info_dicts[ index ] - tool_panel_section_key = ordered_tool_panel_section_keys[ index ] - repository_util.install_tool_shed_repository( trans, - tool_shed_repository, - repo_info_dict, - tool_panel_section_key, - shed_tool_conf, - tool_path, - install_tool_dependencies, - reinstalling=False ) - tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) ) - tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', - action='show', - id=trans.security.encode_id( tool_shed_repository.id ) ) - installed_tool_shed_repositories.append( tool_shed_repository_dict ) - else: + if tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, + trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: + + repo_info_dict = ordered_repo_info_dicts[ index ] + tool_panel_section_key = ordered_tool_panel_section_keys[ index ] + repository_util.install_tool_shed_repository( trans, + tool_shed_repository, + repo_info_dict, + tool_panel_section_key, + shed_tool_conf, + tool_path, + install_tool_dependencies, + reinstalling=False ) + tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=default_tool_shed_repository_value_mapper( trans, tool_shed_repository ) ) + tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', + action='show', + id=trans.security.encode_id( tool_shed_repository.id ) ) + installed_tool_shed_repositories.append( tool_shed_repository_dict ) + elif message: log.error( message, exc_info=True ) trans.response.status = 500 return dict( status='error', error=message ) + elif not created_or_updated_tool_shed_repositories and not message: + # We're attempting to install more than 1 repository, and all of them have already been installed. + return dict( status='error', error='All repositories that you are attempting to install have been previously installed.' ) # Display the list of installed repositories. return installed_tool_shed_repositories diff -r 72f47fad3d219d44988d672dc41f30748ba8d5ff -r f0da1c8355df9a68c3db5fecd27ed20def89a3ec 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 @@ -95,6 +95,34 @@ tool_dependencies ) return repo_info_dict +def get_next_prior_install_required_dict_entry( prior_install_required_dict, processed_tsr_ids ): + """ + The order in which the prior_install_required_dict is processed is critical in order to ensure that the ultimate repository installation order is correctly + defined. This method determines the next key / value pair from the received prior_install_required_dict that should be processed. + """ + # Return the first key / value pair that is not yet processed and whose value is an empty list. + for key, value in prior_install_required_dict.items(): + if key in processed_tsr_ids: + continue + if not value: + return key + # Return the first key / value pair that is not yet processed and whose ids in value are all included in processed_tsr_ids. + for key, value in prior_install_required_dict.items(): + if key in processed_tsr_ids: + continue + all_contained = True + for required_repository_id in value: + if required_repository_id not in processed_tsr_ids: + all_contained = False + break + if all_contained: + return key + # Return the first key / value pair that is not yet processed. Hopefully this is all that is necessary at this point. + for key, value in prior_install_required_dict.items(): + if key in processed_tsr_ids: + continue + return key + def get_prior_install_required_dict( trans, tsr_ids, repo_info_dicts ): """ Return a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is contained in the received list of tsr_ids @@ -591,10 +619,13 @@ # Create a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is contained in the received list of tsr_ids # and whose associated repository must be installed prior to the repository associated with the tsr_id key. prior_install_required_dict = get_prior_install_required_dict( trans, tsr_ids, repo_info_dicts ) - # Create the ordered_tsr_ids, the ordered_repo_info_dicts and the ordered_tool_panel_section_keys lists. - for tsr_id in tsr_ids: + processed_tsr_ids = [] + while len( processed_tsr_ids ) != len( prior_install_required_dict.keys() ): + tsr_id = get_next_prior_install_required_dict_entry( prior_install_required_dict, processed_tsr_ids ) + processed_tsr_ids.append( tsr_id ) + # Create the ordered_tsr_ids, the ordered_repo_info_dicts and the ordered_tool_panel_section_keys lists. if tsr_id not in ordered_tsr_ids: - prior_install_required_ids = prior_install_required_dict.get( tsr_id, [] ) + prior_install_required_ids = prior_install_required_dict[ tsr_id ] for prior_install_required_id in prior_install_required_ids: if prior_install_required_id not in ordered_tsr_ids: # Install the associated repository dependency first. 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.

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commit/galaxy-central: dan: Fix for generating password via pbkdf2_bin for Python < 2.6.8
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/72f47fad3d21/ Changeset: 72f47fad3d21 User: dan Date: 2013-05-10 16:14:49 Summary: Fix for generating password via pbkdf2_bin for Python < 2.6.8 Affected #: 1 file diff -r 41cbbcb908236c14818dfb2b3372ea545ece718b -r 72f47fad3d219d44988d672dc41f30748ba8d5ff lib/galaxy/security/passwords.py --- a/lib/galaxy/security/passwords.py +++ b/lib/galaxy/security/passwords.py @@ -70,7 +70,7 @@ rv = u = _pseudorandom(salt + _pack_int(block)) for i in xrange(iterations - 1): u = _pseudorandom(''.join(map(chr, u))) - rv = starmap(xor, izip(rv, u)) + rv = starmap( xor, zip( rv, u ) ) #Python < 2.6.8: starmap requires function inputs to be tuples, so we need to use zip instead of izip buf.extend(rv) return ''.join(map(chr, buf))[:keylen] 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.

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commit/galaxy-central: jgoecks: Select2 enhancements: (a) bump up z-index so that select2 works in modal dialogs; (b) add select2 to base_panels for pervasive access and remove from individual templates; and (c) use select2 in Trackster and discontinue use of custom jQuery combobox.
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/41cbbcb90823/ Changeset: 41cbbcb90823 User: jgoecks Date: 2013-05-10 15:38:51 Summary: Select2 enhancements: (a) bump up z-index so that select2 works in modal dialogs; (b) add select2 to base_panels for pervasive access and remove from individual templates; and (c) use select2 in Trackster and discontinue use of custom jQuery combobox. Affected #: 6 files diff -r 75a49f8d1bd38939a426660e379da8128631cbe2 -r 41cbbcb908236c14818dfb2b3372ea545ece718b static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -831,11 +831,11 @@ .select2-container .select2-choice span{margin-right:26px;display:block;overflow:hidden;white-space:nowrap;-o-text-overflow:ellipsis;-ms-text-overflow:ellipsis;text-overflow:ellipsis;} .select2-container .select2-choice abbr{display:block;position:absolute;right:26px;top:8px;width:12px;height:12px;font-size:1px;background:url('../images/select2.png') right top no-repeat;cursor:pointer;text-decoration:none;border:0;outline:0;} .select2-container .select2-choice abbr:hover{background-position:right -11px;cursor:pointer;} -.select2-drop{background:#fff;color:#000;border:1px solid #aaa;border-top:0;position:absolute;top:100%;-webkit-box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);-o-box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);z-index:9999;width:100%;margin-top:-1px;-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;} +.select2-drop{background:#fff;color:#000;border:1px solid #aaa;border-top:0;position:absolute;top:100%;-webkit-box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);-o-box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);box-shadow:0 4px 5px rgba(0, 0, 0, 0.15);z-index:24999;width:100%;margin-top:-1px;-webkit-border-radius:0 0 4px 4px;-moz-border-radius:0 0 4px 4px;border-radius:0 0 4px 4px;} .select2-drop.select2-drop-above{-webkit-border-radius:4px 4px 0px 0px;-moz-border-radius:4px 4px 0px 0px;border-radius:4px 4px 0px 0px;margin-top:1px;border-top:1px solid #aaa;border-bottom:0;-webkit-box-shadow:0 -4px 5px rgba(0, 0, 0, 0.15);-moz-box-shadow:0 -4px 5px rgba(0, 0, 0, 0.15);-o-box-shadow:0 -4px 5px rgba(0, 0, 0, 0.15);box-shadow:0 -4px 5px rgba(0, 0, 0, 0.15);} .select2-container .select2-choice div{-webkit-border-radius:0 4px 4px 0;-moz-border-radius:0 4px 4px 0;border-radius:0 4px 4px 0;-moz-background-clip:padding;-webkit-background-clip:padding-box;background-clip:padding-box;background:#ccc;background-image:-webkit-gradient(linear, left bottom, left top, color-stop(0, #cccccc), color-stop(0.6, #eeeeee));background-image:-webkit-linear-gradient(center bottom, #cccccc 0%, #eeeeee 60%);background-image:-moz-linear-gradient(center bottom, #cccccc 0%, #eeeeee 60%);background-image:-o-linear-gradient(bottom, #cccccc 0%, #eeeeee 60%);background-image:-ms-linear-gradient(top, #cccccc 0%, #eeeeee 60%);filter:progid:DXImageTransform.Microsoft.gradient(startColorstr='#cccccc', endColorstr='#eeeeee', GradientType=0);background-image:linear-gradient(top, #cccccc 0%, #eeeeee 60%);border-left:1px solid #aaa;position:absolute;right:0;top:0;display:block;height:100%;width:18px;} .select2-container .select2-choice div b{background:url('../images/select2.png') no-repeat 0 1px;display:block;width:100%;height:100%;} -.select2-search{display:inline-block;white-space:nowrap;z-index:10000;min-height:26px;width:100%;margin:0;padding-left:4px;padding-right:4px;} +.select2-search{display:inline-block;white-space:nowrap;z-index:25000;min-height:26px;width:100%;margin:0;padding-left:4px;padding-right:4px;} .select2-search-hidden{display:block;position:absolute;left:-10000px;} .select2-search input{background:#ffffff url('../images/select2.png') no-repeat 100% -22px;background:url('../images/select2.png') no-repeat 100% -22px,-webkit-gradient(linear, left bottom, left top, color-stop(0.85, #ffffff), color-stop(0.99, #eeeeee));background:url('../images/select2.png') no-repeat 100% -22px,-webkit-linear-gradient(center bottom, #ffffff 85%, #eeeeee 99%);background:url('../images/select2.png') no-repeat 100% -22px,-moz-linear-gradient(center bottom, #ffffff 85%, #eeeeee 99%);background:url('../images/select2.png') no-repeat 100% -22px,-o-linear-gradient(bottom, #ffffff 85%, #eeeeee 99%);background:url('../images/select2.png') no-repeat 100% -22px,-ms-linear-gradient(top, #ffffff 85%, #eeeeee 99%);background:url('../images/select2.png') no-repeat 100% -22px,linear-gradient(top, #ffffff 85%, #eeeeee 99%);padding:4px 20px 4px 5px;outline:0;border:1px solid #aaa;font-family:sans-serif;font-size:1em;width:100%;margin:0;height:auto !important;min-height:26px;-webkit-box-shadow:none;-moz-box-shadow:none;box-shadow:none;border-radius:0;-moz-border-radius:0;-webkit-border-radius:0;} .select2-drop.select2-drop-above .select2-search input{margin-top:4px;} diff -r 75a49f8d1bd38939a426660e379da8128631cbe2 -r 41cbbcb908236c14818dfb2b3372ea545ece718b static/style/select2.less --- a/static/style/select2.less +++ b/static/style/select2.less @@ -109,7 +109,7 @@ -moz-box-shadow: 0 4px 5px rgba(0, 0, 0, .15); -o-box-shadow: 0 4px 5px rgba(0, 0, 0, .15); box-shadow: 0 4px 5px rgba(0, 0, 0, .15); - z-index: 9999; + z-index: 24999; width:100%; margin-top:-1px; @@ -166,7 +166,7 @@ .select2-search { display: inline-block; white-space: nowrap; - z-index: 10000; + z-index: 25000; min-height: 26px; width: 100%; margin: 0; diff -r 75a49f8d1bd38939a426660e379da8128631cbe2 -r 41cbbcb908236c14818dfb2b3372ea545ece718b templates/base/base_panels.mako --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -52,6 +52,7 @@ ${h.js( 'libs/jquery/jquery', 'libs/json2', + 'libs/jquery/select2', 'libs/bootstrap', 'libs/underscore', 'libs/backbone/backbone', diff -r 75a49f8d1bd38939a426660e379da8128631cbe2 -r 41cbbcb908236c14818dfb2b3372ea545ece718b templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -13,7 +13,7 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "galaxy.panels", "libs/jquery/select2", "libs/jquery/jstorage" )} + ${h.js( "galaxy.panels", "libs/jquery/jstorage" )} <script type="text/javascript"> $(function() { $(window).bind("refresh_on_change", function() { diff -r 75a49f8d1bd38939a426660e379da8128631cbe2 -r 41cbbcb908236c14818dfb2b3372ea545ece718b templates/webapps/galaxy/tracks/browser.mako --- a/templates/webapps/galaxy/tracks/browser.mako +++ b/templates/webapps/galaxy/tracks/browser.mako @@ -105,10 +105,7 @@ "Create": function() { $(document).trigger("convert_to_values"); continue_fn(); } }); $("#new-title").focus(); - $("select[name='dbkey']").combobox({ - appendTo: $("#overlay"), - size: 40 - }); + $("select[name='dbkey']").select2({ width: 'resolve'}); // To support the large number of options for dbkey, enable scrolling in overlay. $("#overlay").css("overflow", "auto"); } diff -r 75a49f8d1bd38939a426660e379da8128631cbe2 -r 41cbbcb908236c14818dfb2b3372ea545ece718b templates/webapps/galaxy/workflow/run.mako --- a/templates/webapps/galaxy/workflow/run.mako +++ b/templates/webapps/galaxy/workflow/run.mako @@ -2,7 +2,6 @@ <%def name="javascripts()"> ${parent.javascripts()} - ${h.js( "libs/jquery/select2" )} <script type="text/javascript"> $( function() { function show_tool_body(title){ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 10 May '13

10 May '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/35b87dd34a79/ Changeset: 35b87dd34a79 Branch: stable User: Dave Bouvier Date: 2013-05-09 20:25:51 Summary: Only look for and process tool help image definitions if the tool XML defines a help block. Affected #: 1 file diff -r 7930e04adb535b8bf3c7973efc5cdce0fb384034 -r 35b87dd34a79aa4b94c9c3dd8ff17b4143cd340c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1357,23 +1357,23 @@ """ # TODO: Allow raw HTML or an external link. self.help = root.find("help") - # Handle tool shelp image display for tools that are contained in repositories that are in the lool shed or installed into Galaxy. - # When tool config files use the speical string $PATH_TO_IMAGES, the folloing code will replace that string with the path on disk. - if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0: - if self.app.name == 'galaxy': - repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) ) - if repository: - path_to_images = '/tool_runner/static/images/%s' % self.repository_id - self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) - elif self.app.name == 'tool_shed': - repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) ) - if repository: - path_to_images = '/repository/static/images/%s' % self.repository_id - self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) self.help_by_page = list() help_header = "" help_footer = "" if self.help is not None: + # Handle tool help image display for tools that are contained in repositories that are in the tool shed or installed into Galaxy. + # When tool config files use the special string $PATH_TO_IMAGES, the following code will replace that string with the path on disk. + if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0: + if self.app.name == 'galaxy': + repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) ) + if repository: + path_to_images = '/tool_runner/static/images/%s' % self.repository_id + self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) + elif self.app.name == 'tool_shed': + repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) ) + if repository: + path_to_images = '/repository/static/images/%s' % self.repository_id + self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) help_pages = self.help.findall( "page" ) help_header = self.help.text try: https://bitbucket.org/galaxy/galaxy-central/commits/d914458eb4f3/ Changeset: d914458eb4f3 User: Dave Bouvier Date: 2013-05-09 20:26:35 Summary: Merge in fixes from stable branch. Affected #: 4 files diff -r 6ba6f297b9694e29ff774a33e9b88b9f666ddee7 -r d914458eb4f31b39f175ccdbc31668b13072ea23 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1266,23 +1266,23 @@ """ # TODO: Allow raw HTML or an external link. self.help = root.find("help") - # Handle tool shelp image display for tools that are contained in repositories that are in the lool shed or installed into Galaxy. - # When tool config files use the speical string $PATH_TO_IMAGES, the folloing code will replace that string with the path on disk. - if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0: - if self.app.name == 'galaxy': - repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) ) - if repository: - path_to_images = '/tool_runner/static/images/%s' % self.repository_id - self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) - elif self.app.name == 'tool_shed': - repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) ) - if repository: - path_to_images = '/repository/static/images/%s' % self.repository_id - self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) self.help_by_page = list() help_header = "" help_footer = "" if self.help is not None: + # Handle tool help image display for tools that are contained in repositories that are in the tool shed or installed into Galaxy. + # When tool config files use the special string $PATH_TO_IMAGES, the following code will replace that string with the path on disk. + if self.repository_id and self.help.text.find( '$PATH_TO_IMAGES' ) >= 0: + if self.app.name == 'galaxy': + repository = self.sa_session.query( self.app.model.ToolShedRepository ).get( self.app.security.decode_id( self.repository_id ) ) + if repository: + path_to_images = '/tool_runner/static/images/%s' % self.repository_id + self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) + elif self.app.name == 'tool_shed': + repository = self.sa_session.query( self.app.model.Repository ).get( self.app.security.decode_id( self.repository_id ) ) + if repository: + path_to_images = '/repository/static/images/%s' % self.repository_id + self.help.text = self.help.text.replace( '$PATH_TO_IMAGES', path_to_images ) help_pages = self.help.findall( "page" ) help_header = self.help.text try: https://bitbucket.org/galaxy/galaxy-central/commits/7e72e623a2aa/ Changeset: 7e72e623a2aa User: Dave Bouvier Date: 2013-05-09 20:43:45 Summary: Merged. Affected #: 1 file diff -r d914458eb4f31b39f175ccdbc31668b13072ea23 -r 7e72e623a2aa71a7eaae78b9f7f03e3abff4fce6 templates/webapps/tool_shed/repository/common.mako --- a/templates/webapps/tool_shed/repository/common.mako +++ b/templates/webapps/tool_shed/repository/common.mako @@ -544,6 +544,7 @@ <%def name="render_repository_dependency( repository_dependency, pad, parent, row_counter, row_is_header=False )"><% + from galaxy.util import string_as_bool encoded_id = trans.security.encode_id( repository_dependency.id ) if trans.webapp.name == 'galaxy': if repository_dependency.tool_shed_repository_id: @@ -557,6 +558,7 @@ repository_name = str( repository_dependency.repository_name ) repository_owner = str( repository_dependency.repository_owner ) changeset_revision = str( repository_dependency.changeset_revision ) + prior_installation_required = string_as_bool( str( repository_dependency.prior_installation_required ) ) if prior_installation_required: prior_installation_required_str = " <i>(prior install required)</i>" else: @@ -676,6 +678,7 @@ <%def name="render_tool_dependency( tool_dependency, pad, parent, row_counter, row_is_header )"><% + from galaxy.util import string_as_bool encoded_id = trans.security.encode_id( tool_dependency.id ) is_missing = tool_dependency.installation_status not in [ 'Installed' ] if row_is_header: @@ -725,7 +728,17 @@ ${tool_dependency.install_dir | h} %endif %else: - ${tool_dependency.is_orphan | h} + %if row_is_header: + ${tool_dependency.is_orphan | h} + %else: + <% + if string_as_bool( str( tool_dependency.is_orphan ) ): + is_orpan = 'yes' + else: + is_orphan = 'no' + %> + ${is_orphan | h} + %endif %endif </${cell_type}></tr> https://bitbucket.org/galaxy/galaxy-central/commits/6905bc773595/ Changeset: 6905bc773595 User: Dave Bouvier Date: 2013-05-09 20:56:19 Summary: Fix Galaxy side user creation in tool shed functional tests. Affected #: 1 file diff -r 7e72e623a2aa71a7eaae78b9f7f03e3abff4fce6 -r 6905bc773595db5951247d6057e9c42b9c6e735f test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -312,12 +312,7 @@ def create_user_in_galaxy( self, cntrller='user', email='test(a)bx.psu.edu', password='testuser', username='admin-user', redirect='' ): self.visit_galaxy_url( "/user/create?cntrller=%s&use_panels=False" % cntrller ) - tc.fv( '1', 'email', email ) - tc.fv( '1', 'redirect', redirect ) - tc.fv( '1', 'password', password ) - tc.fv( '1', 'confirm', password ) - tc.fv( '1', 'username', username ) - tc.submit( 'create_user_button' ) + self.submit_form( '1', 'create_user_button', email=email, password=password, confirm=password, username=username, redirect=redirect ) previously_created = False username_taken = False invalid_username = False @@ -509,10 +504,7 @@ self.create_user_in_galaxy( email=email, password=password, username=username, redirect=redirect ) if previously_created: self.visit_galaxy_url( "/user/login?use_panels=False" ) - tc.fv( '1', 'email', email ) - tc.fv( '1', 'redirect', redirect ) - tc.fv( '1', 'password', password ) - tc.submit( 'login_button' ) + self.submit_form( '1', 'login_button', email=email, redirect=redirect, password=password ) def galaxy_logout( self ): self.home() https://bitbucket.org/galaxy/galaxy-central/commits/75a49f8d1bd3/ Changeset: 75a49f8d1bd3 User: Dave Bouvier Date: 2013-05-09 21:50:27 Summary: Merged again. Affected #: 1 file Diff not available. 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.

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galaxy-commits May 2013