February 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c4145b92bc2a/ Changeset: c4145b92bc2a Branch: trevorw/specify-thirdparty-cookies-must-not-be-b-1392909850239 User: trevorw Date: 2014-02-20 16:27:57 Summary: specify third-party cookies must not be blocked - repository.py third-party cookies are normally (and hopefully) disabled for privacy Affected #: 1 file diff -r eae95d5fa975e1eef4de219564cb976720f18440 -r c4145b92bc2a9e63778950aef4d53723bcd353ee 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 @@ -870,7 +870,7 @@ 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) else: - message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url return trans.show_error_message( message ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. @@ -2047,7 +2047,7 @@ return trans.response.send_redirect( url ) else: message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url - message += 'You may need to enable cookies in your browser. ' + message += 'You may need to enable third-party cookies in your browser. ' status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_valid_categories', https://bitbucket.org/galaxy/galaxy-central/commits/952558f0dc0b/ Changeset: 952558f0dc0b User: greg Date: 2014-02-20 17:14:38 Summary: Merged in trevorw/galaxy-central-2/trevorw/specify-thirdparty-cookies-must-not-be-b-1392909850239 (pull request #326) specify third-party cookies must not be blocked - repository.py Affected #: 1 file diff -r 3158b15d961f6bef5db25b26d4bc0593f1b58d57 -r 952558f0dc0ba52355e87ef2d0ccef37f7f51bec 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 @@ -870,7 +870,7 @@ 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) else: - message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url return trans.show_error_message( message ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. @@ -2047,7 +2047,7 @@ return trans.response.send_redirect( url ) else: message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url - message += 'You may need to enable cookies in your browser. ' + message += 'You may need to enable third-party cookies in your browser. ' status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_valid_categories', 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 ToolEvaluator with optional Dataset Input selected.
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3158b15d961f/ Changeset: 3158b15d961f User: dan Date: 2014-02-20 17:07:16 Summary: Fix for ToolEvaluator with optional Dataset Input selected. Affected #: 1 file diff -r 3789ce7ddf1ac171a10956989818b4425486c44d -r 3158b15d961f6bef5db25b26d4bc0593f1b58d57 lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -181,9 +181,11 @@ tool=self, name=input.name ) - real_path = dataset.file_name - if real_path in input_dataset_paths: - wrapper_kwds[ "dataset_path" ] = input_dataset_paths[ real_path ] + if dataset: + #A None dataset does not have a filename + real_path = dataset.file_name + if real_path in input_dataset_paths: + wrapper_kwds[ "dataset_path" ] = input_dataset_paths[ real_path ] input_values[ input.name ] = \ DatasetFilenameWrapper( dataset, **wrapper_kwds ) elif isinstance( input, SelectToolParameter ): 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: 4 new changesets
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c82a791e23a6/ Changeset: c82a791e23a6 User: natefoo Date: 2014-02-20 16:51:42 Summary: Remove obsolete DRMAA_python egg from eggs.ini. Affected #: 1 file diff -r 9c673e0ea8919fea6941f24fdf6936686840bb71 -r c82a791e23a62b0821ad0b0f1bccc49541eb3583 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -9,12 +9,11 @@ [general] repository = http://eggs.galaxyproject.org ; these eggs must be scrambled for your local environment -no_auto = pbs_python DRMAA_python +no_auto = pbs_python [eggs:platform] bx_python = 0.7.1 Cheetah = 2.2.2 -DRMAA_python = 0.2 MarkupSafe = 0.12 mercurial = 2.2.3 MySQL_python = 1.2.3c1 https://bitbucket.org/galaxy/galaxy-central/commits/59e325832026/ Changeset: 59e325832026 User: natefoo Date: 2014-02-20 16:52:19 Summary: Minor updates to comments/documentation in universe_wsgi.ini.sample Affected #: 1 file diff -r c82a791e23a62b0821ad0b0f1bccc49541eb3583 -r 59e325832026a2f3cbdb031eef02c8ef690c3f03 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -3,7 +3,7 @@ # environment. To tune the application for a multi-user production # environment, see the documentation at: # -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server +# http://usegalaxy.org/production # # Throughout this sample configuration file, except where stated otherwise, @@ -11,7 +11,7 @@ # values are set to the default value. # Examples of many of these options are explained in more detail in the wiki: # -# http://wiki.g2.bx.psu.edu/Admin/Config +# https://wiki.galaxyproject.org/Admin/Config # # Config hackers are encouraged to check there before asking for help. @@ -140,9 +140,12 @@ # Other tool config files must include the tool_path as an attribute in the <toolbox> tag. #tool_path = tools -# Path to the directory in which managed tool dependencies are placed. To use -# the dependency system, see the documentation at: -# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies +# Path to the directory in which tool dependencies are placed. This is used by +# the tool shed to install dependencies and can also be used by administrators +# to manually install or link to dependencies. For details, see: +# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies +# If this option is not set to a valid path, installing tools with dependencies +# from the Tool Shed will fail. #tool_dependency_dir = None # Enable automatic polling of relative tool sheds to see if any updates @@ -169,7 +172,7 @@ # Directory where data used by tools is located, see the samples in that # directory and the wiki for help: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration +# https://wiki.galaxyproject.org/Admin/DataIntegration #tool_data_path = tool-data # Directory where chrom len files are kept, currently mainly used by trackster @@ -196,6 +199,10 @@ # directory. #cluster_files_directory = database/pbs +# Mako templates are compiled as needed and cached for reuse, this directory is +# used for the cache +#template_cache_path = database/compiled_templates + # External service types config file, defines what types of external_services configurations # are available in Galaxy. #external_service_type_config_file = external_service_types_conf.xml @@ -532,7 +539,7 @@ # -- Data Libraries # These library upload options are described in much more detail in the wiki: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files +# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles # Add an option to the library upload form which allows administrators to # upload a directory of files. @@ -590,7 +597,7 @@ # User authentication can be delegated to an upstream proxy server (usually # Apache). The upstream proxy should set a REMOTE_USER header in the request. # Enabling remote user disables regular logins. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy +# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy #use_remote_user = False # If use_remote_user is enabled and your external authentication @@ -618,7 +625,7 @@ # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Interface +# https://wiki.galaxyproject.org/Admin/Interface #admin_users = None # Force everyone to log in (disable anonymous access). @@ -723,8 +730,8 @@ # separate Galaxy into multiple processes. There are more than one way to do # this, and they are explained in detail in the documentation: # -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal… -# +# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling + # By default, Galaxy manages and executes jobs from within a single process and # notifies itself of new jobs via in-memory queues. Jobs are run locally on # the system on which Galaxy is started. Advanced job running capabilities can https://bitbucket.org/galaxy/galaxy-central/commits/3789ce7ddf1a/ Changeset: 3789ce7ddf1a User: natefoo Date: 2014-02-20 16:52:31 Summary: Remove empty/renamed sections in tool_conf.xml.main Affected #: 1 file diff -r 59e325832026a2f3cbdb031eef02c8ef690c3f03 -r 3789ce7ddf1ac171a10956989818b4425486c44d tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -154,9 +154,6 @@ <tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section> - <section id="clustal" name="Multiple Alignments"> - <tool file="rgenetics/rgClustalw.xml" /> - </section><section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /> @@ -227,8 +224,4 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section></toolbox> https://bitbucket.org/galaxy/galaxy-central/commits/15e8a74a9521/ Changeset: 15e8a74a9521 Branch: stable User: natefoo Date: 2014-02-20 16:52:31 Summary: Remove empty/renamed sections in tool_conf.xml.main Affected #: 1 file diff -r a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21 -r 15e8a74a95215bf2cc775e9848ca4a5ecc7e945f tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -154,9 +154,6 @@ <tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section> - <section id="clustal" name="Multiple Alignments"> - <tool file="rgenetics/rgClustalw.xml" /> - </section><section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /> @@ -227,8 +224,4 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section></toolbox> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Update boto to 2.25.0 in anticipation of supporting VPC
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eae95d5fa975/ Changeset: eae95d5fa975 User: dannon Date: 2014-02-20 01:33:27 Summary: Update boto to 2.25.0 in anticipation of supporting VPC Affected #: 1 file diff -r 85c38536c31583ef06db42c1f54d6248b79f96a5 -r eae95d5fa975e1eef4de219564cb976720f18440 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -35,7 +35,7 @@ amqp = 1.4.3 anyjson = 0.3.3 Beaker = 1.4 -boto = 2.5.2 +boto = 2.25.0 decorator = 3.1.2 docutils = 0.7 drmaa = 0.6 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 19 Feb '14

19 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a89bbdfd4a71/ Changeset: a89bbdfd4a71 Branch: stable User: inithello Date: 2014-02-19 22:34:01 Summary: Ensure that symlinks are moved before regular files, since this can in some cases causes a 'No such file or directory' error when the symlink target is moved before the symlink itself. Affected #: 1 file diff -r 0770af01a257818ee82f11a191d4305880ea0b91 -r a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -303,9 +303,19 @@ destination_directory = os.path.join( destination_dir ) if not os.path.isdir( destination_directory ): os.makedirs( destination_directory ) + symlinks = [] + regular_files = [] for file_name in os.listdir( source_directory ): source_file = os.path.join( source_directory, file_name ) destination_file = os.path.join( destination_directory, file_name ) + files_tuple = ( source_file, destination_file ) + if os.path.islink( source_file ): + symlinks.append( files_tuple ) + else: + regular_files.append( files_tuple ) + for source_file, destination_file in symlinks: + shutil.move( source_file, destination_file ) + for source_file, destination_file in regular_files: shutil.move( source_file, destination_file ) def move_file( current_dir, source, destination, rename_to=None ): https://bitbucket.org/galaxy/galaxy-central/commits/85c38536c315/ Changeset: 85c38536c315 User: inithello Date: 2014-02-19 22:34:22 Summary: Merge with a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21 Affected #: 1 file diff -r ee315625cf4e394bca8a05f25c82e78c978ed50c -r 85c38536c31583ef06db42c1f54d6248b79f96a5 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -303,9 +303,19 @@ destination_directory = os.path.join( destination_dir ) if not os.path.isdir( destination_directory ): os.makedirs( destination_directory ) + symlinks = [] + regular_files = [] for file_name in os.listdir( source_directory ): source_file = os.path.join( source_directory, file_name ) destination_file = os.path.join( destination_directory, file_name ) + files_tuple = ( source_file, destination_file ) + if os.path.islink( source_file ): + symlinks.append( files_tuple ) + else: + regular_files.append( files_tuple ) + for source_file, destination_file in symlinks: + shutil.move( source_file, destination_file ) + for source_file, destination_file in regular_files: shutil.move( source_file, destination_file ) def move_file( current_dir, source, destination, rename_to=None ): 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 DatasetListWrapper with optional inputs.
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ee315625cf4e/ Changeset: ee315625cf4e User: dan Date: 2014-02-19 22:15:48 Summary: Fix for DatasetListWrapper with optional inputs. Affected #: 1 file diff -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b -r ee315625cf4e394bca8a05f25c82e78c978ed50c lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -206,10 +206,12 @@ datasets = [datasets] def to_wrapper( dataset ): - real_path = dataset.file_name wrapper_kwds = kwargs.copy() - if real_path in dataset_paths: - wrapper_kwds[ "dataset_path" ] = dataset_paths[ real_path ] + if dataset: + #A None dataset does not have a filename + real_path = dataset.file_name + if real_path in dataset_paths: + wrapper_kwds[ "dataset_path" ] = dataset_paths[ real_path ] return DatasetFilenameWrapper( dataset, **wrapper_kwds ) list.__init__( self, map( to_wrapper, datasets ) ) 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 19 Feb '14

19 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a94e57976adf/ Changeset: a94e57976adf User: inithello Date: 2014-02-19 21:21:12 Summary: Fix for situation where duplicate database records would be created if a repository was uninstalled and reinstalled after getting updates from the tool shed. Affected #: 2 files diff -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 -r a94e57976adf8cee859bbe14e8275b73b16206bc 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 @@ -1381,7 +1381,7 @@ repository_dependencies = repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans, tool_shed_repository ) repo_info_dict = repository_util.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, + changeset_revision=tool_shed_repository.installed_changeset_revision, ctx_rev=tool_shed_repository.ctx_rev, repository_owner=tool_shed_repository.owner, repository_name=tool_shed_repository.name, diff -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 -r a94e57976adf8cee859bbe14e8275b73b16206bc 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 @@ -1617,6 +1617,13 @@ except: pass +def __repository_query( app ): + if app.name == "galaxy": + query = app.install_model.context.query( app.install_model.ToolShedRepository ) + else: + query = app.model.context.query( app.model.Repository ) + return query + def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ): """ Find out if a repository is already installed into Galaxy - there are several scenarios where this @@ -1866,10 +1873,3 @@ for arg in args: parts.append( arg.strip( '/' ) ) return '/'.join( parts ) - -def __repository_query( app ): - if app.name == "galaxy": - query = app.install_model.context.query( app.install_model.ToolShedRepository ) - else: - query = app.model.context.query( app.model.Repository ) - return query https://bitbucket.org/galaxy/galaxy-central/commits/c38c0a6893e4/ Changeset: c38c0a6893e4 User: inithello Date: 2014-02-19 21:23:45 Summary: Situations where a migration warning would be incorrectly displayed, and tools with matching filenames would be removed from the tool_conf.xml after running a migration script. Affected #: 9 files diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -186,8 +186,7 @@ # Tools outside of sections. file_path = elem.get( 'file', None ) if file_path: - file_name = suc.strip_path( file_path ) - if file_name in tool_configs_to_filter: + if file_path in tool_configs_to_filter: root.remove( elem ) persist_required = True elif elem.tag == 'section': @@ -196,8 +195,7 @@ if section_elem.tag == 'tool': file_path = section_elem.get( 'file', None ) if file_path: - file_name = suc.strip_path( file_path ) - if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter: + if file_path in tool_configs_to_filter: elem.remove( section_elem ) persist_required = True if persist_required: @@ -221,8 +219,7 @@ if proprietary_tool_panel_elem.tag == 'tool': # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name or tool_config == proprietary_tool_config: + if tool_config == proprietary_tool_config: # The tool is loaded outside of any sections. tool_sections.append( None ) if not is_displayed: @@ -233,8 +230,7 @@ if section_elem.tag == 'tool': # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = section_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name or tool_config == proprietary_tool_config: + if tool_config == proprietary_tool_config: # The tool is loaded inside of the section_elem. tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) if not is_displayed: @@ -312,8 +308,7 @@ # Tools outside of sections. file_path = elem.get( 'file', None ) if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs or file_path in migrated_tool_configs: + if file_path in migrated_tool_configs: if elem not in tool_panel_elems: tool_panel_elems.append( elem ) elif elem.tag == 'section': @@ -322,8 +317,7 @@ if section_elem.tag == 'tool': file_path = section_elem.get( 'file', None ) if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs or file_path in migrated_tool_configs: + if file_path in migrated_tool_configs: # Append the section, not the tool. if elem not in tool_panel_elems: tool_panel_elems.append( elem ) @@ -361,10 +355,8 @@ for tool_panel_dict in v: # Keep track of tool config file names associated with entries that have been made to the # migrated_tools_conf.xml file so they can be eliminated from all non-shed-related tool panel configs. - tool_config_file = tool_panel_dict.get( 'tool_config', None ) - if tool_config_file: - if tool_config_file not in tool_configs_to_filter: - tool_configs_to_filter.append( tool_config_file ) + if tool_config not in tool_configs_to_filter: + tool_configs_to_filter.append( tool_config ) else: print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0002_tools.xml --- a/scripts/migrate_tools/0002_tools.xml +++ b/scripts/migrate_tools/0002_tools.xml @@ -2,112 +2,112 @@ <toolshed name="toolshed.g2.bx.psu.edu"><repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /><repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="7334f6d0ac17"> - <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> - <tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_backtranseq.xml" /> - <tool id="EMBOSS: banana3" version="5.0.0" file="emboss_banana.xml" /> - <tool id="EMBOSS: biosed4" version="5.0.0" file="emboss_biosed.xml" /> - <tool id="EMBOSS: btwisted5" version="5.0.0" file="emboss_btwisted.xml" /> - <tool id="EMBOSS: cai_custom6" version="5.0.0" file="emboss_cai_custom.xml" /> - <tool id="EMBOSS: cai6" version="5.0.0" file="emboss_cai.xml" /> - <tool id="EMBOSS: chaos7" version="5.0.0" file="emboss_chaos.xml" /> - <tool id="EMBOSS: charge8" version="5.0.0" file="emboss_charge.xml" /> - <tool id="EMBOSS: checktrans9" version="5.0.0" file="emboss_checktrans.xml" /> - <tool id="EMBOSS: chips10" version="5.0.0" file="emboss_chips.xml" /> - <tool id="EMBOSS: cirdna11" version="5.0.0" file="emboss_cirdna.xml" /> - <tool id="EMBOSS: codcmp12" version="5.0.0" file="emboss_codcmp.xml" /> - <tool id="EMBOSS: coderet13" version="5.0.0" file="emboss_coderet.xml" /> - <tool id="EMBOSS: compseq14" version="5.0.0" file="emboss_compseq.xml" /> - <tool id="EMBOSS: cpgplot15" version="5.0.0" file="emboss_cpgplot.xml" /> - <tool id="EMBOSS: cpgreport16" version="5.0.0" file="emboss_cpgreport.xml" /> - <tool id="EMBOSS: cusp17" version="5.0.0" file="emboss_cusp.xml" /> - <tool id="EMBOSS: cutseq18" version="5.0.0" file="emboss_cutseq.xml" /> - <tool id="EMBOSS: dan19" version="5.0.0" file="emboss_dan.xml" /> - <tool id="EMBOSS: degapseq20" version="5.0.0" file="emboss_degapseq.xml" /> - <tool id="EMBOSS: descseq21" version="5.0.0" file="emboss_descseq.xml" /> - <tool id="EMBOSS: diffseq22" version="5.0.0" file="emboss_diffseq.xml" /> - <tool id="EMBOSS: digest23" version="5.0.0" file="emboss_digest.xml" /> - <tool id="EMBOSS: dotmatcher24" version="5.0.0" file="emboss_dotmatcher.xml" /> - <tool id="EMBOSS: dotpath25" version="5.0.0" file="emboss_dotpath.xml" /> - <tool id="EMBOSS: dottup26" version="5.0.0" file="emboss_dottup.xml" /> - <tool id="EMBOSS: dreg27" version="5.0.0" file="emboss_dreg.xml" /> - <tool id="EMBOSS: einverted28" version="5.0.0" file="emboss_einverted.xml" /> - <tool id="EMBOSS: epestfind29" version="5.0.0" file="emboss_epestfind.xml" /> - <tool id="EMBOSS: equicktandem31" version="5.0.0" file="emboss_equicktandem.xml" /> - <tool id="EMBOSS: est2genome32" version="5.0.0" file="emboss_est2genome.xml" /> - <tool id="EMBOSS: etandem33" version="5.0.0" file="emboss_etandem.xml" /> - <tool id="EMBOSS: extractfeat34" version="5.0.0" file="emboss_extractfeat.xml" /> - <tool id="EMBOSS: extractseq35" version="5.0.0" file="emboss_extractseq.xml" /> - <tool id="EMBOSS: freak36" version="5.0.0" file="emboss_freak.xml" /> - <tool id="EMBOSS: fuzznuc37" version="5.0.0" file="emboss_fuzznuc.xml" /> - <tool id="EMBOSS: fuzzpro38" version="5.0.0" file="emboss_fuzzpro.xml" /> - <tool id="EMBOSS: fuzztran39" version="5.0.0" file="emboss_fuzztran.xml" /> - <tool id="EMBOSS: garnier40" version="5.0.0" file="emboss_garnier.xml" /> - <tool id="EMBOSS: geecee41" version="5.0.0" file="emboss_geecee.xml" /> - <tool id="EMBOSS: getorf42" version="5.0.0" file="emboss_getorf.xml" /> - <tool id="EMBOSS: helixturnhelix43" version="5.0.0" file="emboss_helixturnhelix.xml" /> - <tool id="EMBOSS: hmoment44" version="5.0.0" file="emboss_hmoment.xml" /> - <tool id="EMBOSS: iep45" version="5.0.0" file="emboss_iep.xml" /> - <tool id="EMBOSS: infoseq46" version="5.0.0" file="emboss_infoseq.xml" /> - <tool id="EMBOSS: isochore47" version="5.0.0" file="emboss_isochore.xml" /> - <tool id="EMBOSS: lindna48" version="5.0.0" file="emboss_lindna.xml" /> - <tool id="EMBOSS: marscan49" version="5.0.0" file="emboss_marscan.xml" /> - <tool id="EMBOSS: maskfeat50" version="5.0.0" file="emboss_maskfeat.xml" /> - <tool id="EMBOSS: maskseq51" version="5.0.0" file="emboss_maskseq.xml" /> - <tool id="EMBOSS: matcher52" version="5.0.0" file="emboss_matcher.xml" /> - <tool id="EMBOSS: megamerger53" version="5.0.0" file="emboss_megamerger.xml" /> - <tool id="EMBOSS: merger54" version="5.0.0" file="emboss_merger.xml" /> - <tool id="EMBOSS: msbar55" version="5.0.0" file="emboss_msbar.xml" /> - <tool id="EMBOSS: needle56" version="5.0.0" file="emboss_needle.xml" /> - <tool id="EMBOSS: newcpgreport57" version="5.0.0" file="emboss_newcpgreport.xml" /> - <tool id="EMBOSS: newcpgseek58" version="5.0.0" file="emboss_newcpgseek.xml" /> - <tool id="EMBOSS: newseq59" version="5.0.0" file="emboss_newseq.xml" /> - <tool id="EMBOSS: noreturn60" version="5.0.0" file="emboss_noreturn.xml" /> - <tool id="EMBOSS: notseq61" version="5.0.0" file="emboss_notseq.xml" /> - <tool id="EMBOSS: nthseq62" version="5.0.0" file="emboss_nthseq.xml" /> - <tool id="EMBOSS: octanol63" version="5.0.0" file="emboss_octanol.xml" /> - <tool id="EMBOSS: oddcomp64" version="5.0.0" file="emboss_oddcomp.xml" /> - <tool id="EMBOSS: palindrome65" version="5.0.0" file="emboss_palindrome.xml" /> - <tool id="EMBOSS: pasteseq66" version="5.0.0" file="emboss_pasteseq.xml" /> - <tool id="EMBOSS: patmatdb67" version="5.0.0" file="emboss_patmatdb.xml" /> - <tool id="EMBOSS: pepcoil68" version="5.0.0" file="emboss_pepcoil.xml" /> - <tool id="EMBOSS: pepinfo69" version="5.0.0" file="emboss_pepinfo.xml" /> - <tool id="EMBOSS: pepnet70" version="5.0.0" file="emboss_pepnet.xml" /> - <tool id="EMBOSS: pepstats71" version="5.0.0" file="emboss_pepstats.xml" /> - <tool id="EMBOSS: pepwheel72" version="5.0.0" file="emboss_pepwheel.xml" /> - <tool id="EMBOSS: pepwindow73" version="5.0.0" file="emboss_pepwindow.xml" /> - <tool id="EMBOSS: pepwindowall74" version="5.0.0" file="emboss_pepwindowall.xml" /> - <tool id="EMBOSS: plotcon75" version="5.0.0" file="emboss_plotcon.xml" /> - <tool id="EMBOSS: plotorf76" version="5.0.0" file="emboss_plotorf.xml" /> - <tool id="EMBOSS: polydot77" version="5.0.0" file="emboss_polydot.xml" /> - <tool id="EMBOSS: preg78" version="5.0.0" file="emboss_preg.xml" /> - <tool id="EMBOSS: prettyplot79" version="5.0.0" file="emboss_prettyplot.xml" /> - <tool id="EMBOSS: prettyseq80" version="5.0.0" file="emboss_prettyseq.xml" /> - <tool id="EMBOSS: primersearch81" version="5.0.0" file="emboss_primersearch.xml" /> - <tool id="EMBOSS: revseq82" version="5.0.0" file="emboss_revseq.xml" /> - <tool id="EMBOSS: seqmatchall83" version="5.0.0" file="emboss_seqmatchall.xml" /> - <tool id="EMBOSS: seqret84" version="5.0.0" file="emboss_seqret.xml" /> - <tool id="EMBOSS: showfeat85" version="5.0.0" file="emboss_showfeat.xml" /> - <tool id="EMBOSS: shuffleseq87" version="5.0.0" file="emboss_shuffleseq.xml" /> - <tool id="EMBOSS: sigcleave88" version="5.0.0" file="emboss_sigcleave.xml" /> - <tool id="EMBOSS: sirna89" version="5.0.0" file="emboss_sirna.xml" /> - <tool id="EMBOSS: sixpack90" version="5.0.0" file="emboss_sixpack.xml" /> - <tool id="EMBOSS: skipseq91" version="5.0.0" file="emboss_skipseq.xml" /> - <tool id="EMBOSS: splitter92" version="5.0.0" file="emboss_splitter.xml" /> - <tool id="EMBOSS: supermatcher95" version="5.0.0" file="emboss_supermatcher.xml" /> - <tool id="EMBOSS: syco96" version="5.0.0" file="emboss_syco.xml" /> - <tool id="EMBOSS: tcode97" version="5.0.0" file="emboss_tcode.xml" /> - <tool id="EMBOSS: textsearch98" version="5.0.0" file="emboss_textsearch.xml" /> - <tool id="EMBOSS: tmap99" version="5.0.0" file="emboss_tmap.xml" /> - <tool id="EMBOSS: tranalign100" version="5.0.0" file="emboss_tranalign.xml" /> - <tool id="EMBOSS: transeq101" version="5.0.0" file="emboss_transeq.xml" /> - <tool id="EMBOSS: trimest102" version="5.0.0" file="emboss_trimest.xml" /> - <tool id="EMBOSS: trimseq103" version="5.0.0" file="emboss_trimseq.xml" /> - <tool id="EMBOSS: twofeat104" version="5.0.0" file="emboss_twofeat.xml" /> - <tool id="EMBOSS: union105" version="5.0.0" file="emboss_union.xml" /> - <tool id="EMBOSS: vectorstrip106" version="5.0.0" file="emboss_vectorstrip.xml" /> - <tool id="EMBOSS: water107" version="5.0.0" file="emboss_water.xml" /> - <tool id="EMBOSS: wobble108" version="5.0.0" file="emboss_wobble.xml" /> - <tool id="EMBOSS: wordcount109" version="5.0.0" file="emboss_wordcount.xml" /> - <tool id="EMBOSS: wordmatch110" version="5.0.0" file="emboss_wordmatch.xml" /> + <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_5/emboss_antigenic.xml" /> + <tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_5/emboss_backtranseq.xml" /> + <tool id="EMBOSS: banana3" version="5.0.0" file="emboss_5/emboss_banana.xml" /> + <tool id="EMBOSS: biosed4" version="5.0.0" file="emboss_5/emboss_biosed.xml" /> + <tool id="EMBOSS: btwisted5" version="5.0.0" file="emboss_5/emboss_btwisted.xml" /> + <tool id="EMBOSS: cai_custom6" version="5.0.0" file="emboss_5/emboss_cai_custom.xml" /> + <tool id="EMBOSS: cai6" version="5.0.0" file="emboss_5/emboss_cai.xml" /> + <tool id="EMBOSS: chaos7" version="5.0.0" file="emboss_5/emboss_chaos.xml" /> + <tool id="EMBOSS: charge8" version="5.0.0" file="emboss_5/emboss_charge.xml" /> + <tool id="EMBOSS: checktrans9" version="5.0.0" file="emboss_5/emboss_checktrans.xml" /> + <tool id="EMBOSS: chips10" version="5.0.0" file="emboss_5/emboss_chips.xml" /> + <tool id="EMBOSS: cirdna11" version="5.0.0" file="emboss_5/emboss_cirdna.xml" /> + <tool id="EMBOSS: codcmp12" version="5.0.0" file="emboss_5/emboss_codcmp.xml" /> + <tool id="EMBOSS: coderet13" version="5.0.0" file="emboss_5/emboss_coderet.xml" /> + <tool id="EMBOSS: compseq14" version="5.0.0" file="emboss_5/emboss_compseq.xml" /> + <tool id="EMBOSS: cpgplot15" version="5.0.0" file="emboss_5/emboss_cpgplot.xml" /> + <tool id="EMBOSS: cpgreport16" version="5.0.0" file="emboss_5/emboss_cpgreport.xml" /> + <tool id="EMBOSS: cusp17" version="5.0.0" file="emboss_5/emboss_cusp.xml" /> + <tool id="EMBOSS: cutseq18" version="5.0.0" file="emboss_5/emboss_cutseq.xml" /> + <tool id="EMBOSS: dan19" version="5.0.0" file="emboss_5/emboss_dan.xml" /> + <tool id="EMBOSS: degapseq20" version="5.0.0" file="emboss_5/emboss_degapseq.xml" /> + <tool id="EMBOSS: descseq21" version="5.0.0" file="emboss_5/emboss_descseq.xml" /> + <tool id="EMBOSS: diffseq22" version="5.0.0" file="emboss_5/emboss_diffseq.xml" /> + <tool id="EMBOSS: digest23" version="5.0.0" file="emboss_5/emboss_digest.xml" /> + <tool id="EMBOSS: dotmatcher24" version="5.0.0" file="emboss_5/emboss_dotmatcher.xml" /> + <tool id="EMBOSS: dotpath25" version="5.0.0" file="emboss_5/emboss_dotpath.xml" /> + <tool id="EMBOSS: dottup26" version="5.0.0" file="emboss_5/emboss_dottup.xml" /> + <tool id="EMBOSS: dreg27" version="5.0.0" file="emboss_5/emboss_dreg.xml" /> + <tool id="EMBOSS: einverted28" version="5.0.0" file="emboss_5/emboss_einverted.xml" /> + <tool id="EMBOSS: epestfind29" version="5.0.0" file="emboss_5/emboss_epestfind.xml" /> + <tool id="EMBOSS: equicktandem31" version="5.0.0" file="emboss_5/emboss_equicktandem.xml" /> + <tool id="EMBOSS: est2genome32" version="5.0.0" file="emboss_5/emboss_est2genome.xml" /> + <tool id="EMBOSS: etandem33" version="5.0.0" file="emboss_5/emboss_etandem.xml" /> + <tool id="EMBOSS: extractfeat34" version="5.0.0" file="emboss_5/emboss_extractfeat.xml" /> + <tool id="EMBOSS: extractseq35" version="5.0.0" file="emboss_5/emboss_extractseq.xml" /> + <tool id="EMBOSS: freak36" version="5.0.0" file="emboss_5/emboss_freak.xml" /> + <tool id="EMBOSS: fuzznuc37" version="5.0.0" file="emboss_5/emboss_fuzznuc.xml" /> + <tool id="EMBOSS: fuzzpro38" version="5.0.0" file="emboss_5/emboss_fuzzpro.xml" /> + <tool id="EMBOSS: fuzztran39" version="5.0.0" file="emboss_5/emboss_fuzztran.xml" /> + <tool id="EMBOSS: garnier40" version="5.0.0" file="emboss_5/emboss_garnier.xml" /> + <tool id="EMBOSS: geecee41" version="5.0.0" file="emboss_5/emboss_geecee.xml" /> + <tool id="EMBOSS: getorf42" version="5.0.0" file="emboss_5/emboss_getorf.xml" /> + <tool id="EMBOSS: helixturnhelix43" version="5.0.0" file="emboss_5/emboss_helixturnhelix.xml" /> + <tool id="EMBOSS: hmoment44" version="5.0.0" file="emboss_5/emboss_hmoment.xml" /> + <tool id="EMBOSS: iep45" version="5.0.0" file="emboss_5/emboss_iep.xml" /> + <tool id="EMBOSS: infoseq46" version="5.0.0" file="emboss_5/emboss_infoseq.xml" /> + <tool id="EMBOSS: isochore47" version="5.0.0" file="emboss_5/emboss_isochore.xml" /> + <tool id="EMBOSS: lindna48" version="5.0.0" file="emboss_5/emboss_lindna.xml" /> + <tool id="EMBOSS: marscan49" version="5.0.0" file="emboss_5/emboss_marscan.xml" /> + <tool id="EMBOSS: maskfeat50" version="5.0.0" file="emboss_5/emboss_maskfeat.xml" /> + <tool id="EMBOSS: maskseq51" version="5.0.0" file="emboss_5/emboss_maskseq.xml" /> + <tool id="EMBOSS: matcher52" version="5.0.0" file="emboss_5/emboss_matcher.xml" /> + <tool id="EMBOSS: megamerger53" version="5.0.0" file="emboss_5/emboss_megamerger.xml" /> + <tool id="EMBOSS: merger54" version="5.0.0" file="emboss_5/emboss_merger.xml" /> + <tool id="EMBOSS: msbar55" version="5.0.0" file="emboss_5/emboss_msbar.xml" /> + <tool id="EMBOSS: needle56" version="5.0.0" file="emboss_5/emboss_needle.xml" /> + <tool id="EMBOSS: newcpgreport57" version="5.0.0" file="emboss_5/emboss_newcpgreport.xml" /> + <tool id="EMBOSS: newcpgseek58" version="5.0.0" file="emboss_5/emboss_newcpgseek.xml" /> + <tool id="EMBOSS: newseq59" version="5.0.0" file="emboss_5/emboss_newseq.xml" /> + <tool id="EMBOSS: noreturn60" version="5.0.0" file="emboss_5/emboss_noreturn.xml" /> + <tool id="EMBOSS: notseq61" version="5.0.0" file="emboss_5/emboss_notseq.xml" /> + <tool id="EMBOSS: nthseq62" version="5.0.0" file="emboss_5/emboss_nthseq.xml" /> + <tool id="EMBOSS: octanol63" version="5.0.0" file="emboss_5/emboss_octanol.xml" /> + <tool id="EMBOSS: oddcomp64" version="5.0.0" file="emboss_5/emboss_oddcomp.xml" /> + <tool id="EMBOSS: palindrome65" version="5.0.0" file="emboss_5/emboss_palindrome.xml" /> + <tool id="EMBOSS: pasteseq66" version="5.0.0" file="emboss_5/emboss_pasteseq.xml" /> + <tool id="EMBOSS: patmatdb67" version="5.0.0" file="emboss_5/emboss_patmatdb.xml" /> + <tool id="EMBOSS: pepcoil68" version="5.0.0" file="emboss_5/emboss_pepcoil.xml" /> + <tool id="EMBOSS: pepinfo69" version="5.0.0" file="emboss_5/emboss_pepinfo.xml" /> + <tool id="EMBOSS: pepnet70" version="5.0.0" file="emboss_5/emboss_pepnet.xml" /> + <tool id="EMBOSS: pepstats71" version="5.0.0" file="emboss_5/emboss_pepstats.xml" /> + <tool id="EMBOSS: pepwheel72" version="5.0.0" file="emboss_5/emboss_pepwheel.xml" /> + <tool id="EMBOSS: pepwindow73" version="5.0.0" file="emboss_5/emboss_pepwindow.xml" /> + <tool id="EMBOSS: pepwindowall74" version="5.0.0" file="emboss_5/emboss_pepwindowall.xml" /> + <tool id="EMBOSS: plotcon75" version="5.0.0" file="emboss_5/emboss_plotcon.xml" /> + <tool id="EMBOSS: plotorf76" version="5.0.0" file="emboss_5/emboss_plotorf.xml" /> + <tool id="EMBOSS: polydot77" version="5.0.0" file="emboss_5/emboss_polydot.xml" /> + <tool id="EMBOSS: preg78" version="5.0.0" file="emboss_5/emboss_preg.xml" /> + <tool id="EMBOSS: prettyplot79" version="5.0.0" file="emboss_5/emboss_prettyplot.xml" /> + <tool id="EMBOSS: prettyseq80" version="5.0.0" file="emboss_5/emboss_prettyseq.xml" /> + <tool id="EMBOSS: primersearch81" version="5.0.0" file="emboss_5/emboss_primersearch.xml" /> + <tool id="EMBOSS: revseq82" version="5.0.0" file="emboss_5/emboss_revseq.xml" /> + <tool id="EMBOSS: seqmatchall83" version="5.0.0" file="emboss_5/emboss_seqmatchall.xml" /> + <tool id="EMBOSS: seqret84" version="5.0.0" file="emboss_5/emboss_seqret.xml" /> + <tool id="EMBOSS: showfeat85" version="5.0.0" file="emboss_5/emboss_showfeat.xml" /> + <tool id="EMBOSS: shuffleseq87" version="5.0.0" file="emboss_5/emboss_shuffleseq.xml" /> + <tool id="EMBOSS: sigcleave88" version="5.0.0" file="emboss_5/emboss_sigcleave.xml" /> + <tool id="EMBOSS: sirna89" version="5.0.0" file="emboss_5/emboss_sirna.xml" /> + <tool id="EMBOSS: sixpack90" version="5.0.0" file="emboss_5/emboss_sixpack.xml" /> + <tool id="EMBOSS: skipseq91" version="5.0.0" file="emboss_5/emboss_skipseq.xml" /> + <tool id="EMBOSS: splitter92" version="5.0.0" file="emboss_5/emboss_splitter.xml" /> + <tool id="EMBOSS: supermatcher95" version="5.0.0" file="emboss_5/emboss_supermatcher.xml" /> + <tool id="EMBOSS: syco96" version="5.0.0" file="emboss_5/emboss_syco.xml" /> + <tool id="EMBOSS: tcode97" version="5.0.0" file="emboss_5/emboss_tcode.xml" /> + <tool id="EMBOSS: textsearch98" version="5.0.0" file="emboss_5/emboss_textsearch.xml" /> + <tool id="EMBOSS: tmap99" version="5.0.0" file="emboss_5/emboss_tmap.xml" /> + <tool id="EMBOSS: tranalign100" version="5.0.0" file="emboss_5/emboss_tranalign.xml" /> + <tool id="EMBOSS: transeq101" version="5.0.0" file="emboss_5/emboss_transeq.xml" /> + <tool id="EMBOSS: trimest102" version="5.0.0" file="emboss_5/emboss_trimest.xml" /> + <tool id="EMBOSS: trimseq103" version="5.0.0" file="emboss_5/emboss_trimseq.xml" /> + <tool id="EMBOSS: twofeat104" version="5.0.0" file="emboss_5/emboss_twofeat.xml" /> + <tool id="EMBOSS: union105" version="5.0.0" file="emboss_5/emboss_union.xml" /> + <tool id="EMBOSS: vectorstrip106" version="5.0.0" file="emboss_5/emboss_vectorstrip.xml" /> + <tool id="EMBOSS: water107" version="5.0.0" file="emboss_5/emboss_water.xml" /> + <tool id="EMBOSS: wobble108" version="5.0.0" file="emboss_5/emboss_wobble.xml" /> + <tool id="EMBOSS: wordcount109" version="5.0.0" file="emboss_5/emboss_wordcount.xml" /> + <tool id="EMBOSS: wordmatch110" version="5.0.0" file="emboss_5/emboss_wordmatch.xml" /></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0003_tools.xml --- a/scripts/migrate_tools/0003_tools.xml +++ b/scripts/migrate_tools/0003_tools.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="213a3d6b579a"> - <tool id="freebayes" version="0.0.2 " file="freebayes.xml" /> + <tool id="freebayes" version="0.0.2 " file="variant_detection/freebayes.xml" /></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0004_tools.xml --- a/scripts/migrate_tools/0004_tools.xml +++ b/scripts/migrate_tools/0004_tools.xml @@ -2,11 +2,11 @@ <toolshed name="toolshed.g2.bx.psu.edu"><repository name="blast_datatypes" description="Datatypes for BLAST" changeset_revision="e1c29f302301" /><repository name="ncbi_blast_plus" description="Galaxy wrappers for NCBI BLAST+" changeset_revision="d375502056f1"> - <tool id="blastxml_to_tabular" version="0.0.8" file="blastxml_to_tabular.xml"/> - <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blastn_wrapper.xml"/> - <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blastp_wrapper.xml"/> - <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blastx_wrapper.xml"/> - <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_tblastn_wrapper.xml"/> - <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_tblastx_wrapper.xml"/> + <tool id="blastxml_to_tabular" version="0.0.8" file="ncbi_blast_plus/blastxml_to_tabular.xml"/> + <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastn_wrapper.xml"/> + <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastp_wrapper.xml"/> + <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastx_wrapper.xml"/> + <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml"/> + <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml"/></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0005_tools.xml --- a/scripts/migrate_tools/0005_tools.xml +++ b/scripts/migrate_tools/0005_tools.xml @@ -1,7 +1,7 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="bwa_wrappers" description="Galaxy wrappers for the BWA short read aligner." changeset_revision="ffa8aaa14f7c"> - <tool id="bwa_wrapper" version="1.2.3" file="bwa_wrapper.xml"/> - <tool id="bwa_color_wrapper" version="1.0.2" file="bwa_color_wrapper.xml"/> + <tool id="bwa_wrapper" version="1.2.3" file="sr_mapping/bwa_wrapper.xml"/> + <tool id="bwa_color_wrapper" version="1.0.2" file="sr_mapping/bwa_color_wrapper.xml"/></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0006_tools.xml --- a/scripts/migrate_tools/0006_tools.xml +++ b/scripts/migrate_tools/0006_tools.xml @@ -1,18 +1,18 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><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" /> - <tool id="PicardASMetrics" version="1.56.0" file="rgPicardASMetrics.xml" /> - <tool id="PicardGCBiasMetrics" version="1.56.0" file="rgPicardGCBiasMetrics.xml" /> - <tool id="rgEstLibComp" version="1.56.0" file="rgPicardLibComplexity.xml" /> - <tool id="PicardInsertSize" version="1.56.0" file="rgPicardInsertSize.xml" /> - <tool id="PicardHsMetrics" version="1.56.0" file="rgPicardHsMetrics.xml" /> - <tool id="picard_ARRG" version="1.56.0" file="picard_AddOrReplaceReadGroups.xml" /> - <tool id="picard_ReorderSam" version="1.56.0" file="picard_ReorderSam.xml" /> - <tool id="picard_ReplaceSamHeader" version="1.56.0" file="picard_ReplaceSamHeader.xml" /> - <tool id="rgPicFixMate" version="1.56.0" file="rgPicardFixMate.xml" /> - <tool id="rgPicardMarkDups" version="1.56.0" file="rgPicardMarkDups.xml" /> + <tool id="picard_FastqToSam" version="1.56.0" file="picard/picard_FastqToSam.xml" /> + <tool id="picard_SamToFastq" version="1.56.1" file="picard/picard_SamToFastq.xml" /> + <tool id="picard_BamIndexStats" version="1.56.0" file="picard/picard_BamIndexStats.xml" /> + <tool id="PicardASMetrics" version="1.56.0" file="picard/rgPicardASMetrics.xml" /> + <tool id="PicardGCBiasMetrics" version="1.56.0" file="picard/rgPicardGCBiasMetrics.xml" /> + <tool id="rgEstLibComp" version="1.56.0" file="picard/rgPicardLibComplexity.xml" /> + <tool id="PicardInsertSize" version="1.56.0" file="picard/rgPicardInsertSize.xml" /> + <tool id="PicardHsMetrics" version="1.56.0" file="picard/rgPicardHsMetrics.xml" /> + <tool id="picard_ARRG" version="1.56.0" file="picard/picard_AddOrReplaceReadGroups.xml" /> + <tool id="picard_ReorderSam" version="1.56.0" file="picard/picard_ReorderSam.xml" /> + <tool id="picard_ReplaceSamHeader" version="1.56.0" file="picard/picard_ReplaceSamHeader.xml" /> + <tool id="rgPicFixMate" version="1.56.0" file="picard/rgPicardFixMate.xml" /> + <tool id="rgPicardMarkDups" version="1.56.0" file="picard/rgPicardMarkDups.xml" /></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0007_tools.xml --- a/scripts/migrate_tools/0007_tools.xml +++ b/scripts/migrate_tools/0007_tools.xml @@ -1,15 +1,15 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="bowtie_wrappers" description="Galaxy wrappers for the Bowtie short read mapping tools." changeset_revision="0c7e4eadfb3c"> - <tool id="bowtie_wrapper" version="1.1.2" file="bowtie_wrapper.xml" /> + <tool id="bowtie_wrapper" version="1.1.2" file="sr_mapping/bowtie_wrapper.xml" /></repository><repository name="bowtie_color_wrappers" description="Galaxy wrappers for the Bowtie short read mapping tools on color space reads" changeset_revision="fd0914e451c5"> - <tool id="bowtie_color_wrapper" version="1.1.2" file="bowtie_color_wrapper.xml" /> + <tool id="bowtie_color_wrapper" version="1.1.2" file="sr_mapping/bowtie_color_wrapper.xml" /></repository><repository name="lastz" description="Galaxy wrappers for the Lastz alignment tool" changeset_revision="0801f8207d30"> - <tool id="lastz_wrapper_2" version="1.1.2" file="lastz_wrapper.xml" /> + <tool id="lastz_wrapper_2" version="1.1.2" file="sr_mapping/lastz_wrapper.xml" /></repository><repository name="lastz_paired_reads" description="Galaxy wrapper for the Lastz alignment tool on paired reads" changeset_revision="96825cee5c25"> - <tool id="lastz_paired_reads_wrapper" version="1.1.1" file="lastz_paired_reads_wrapper.xml" /> + <tool id="lastz_paired_reads_wrapper" version="1.1.1" file="sr_mapping/lastz_paired_reads_wrapper.xml" /></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -1,147 +1,147 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository owner="devteam" changeset_revision="dc20f447c0e2" name="bam_to_sam" description="Galaxy wrappers for the tool BAM-to-SAM: converts BAM format to SAM format"> - <tool id="bam_to_sam" version="1.0.3" file="bam_to_sam.xml" /> + <tool id="bam_to_sam" version="1.0.3" file="samtools/bam_to_sam.xml" /></repository><repository owner="devteam" changeset_revision="586c1f0e1515" name="categorize_elements_satisfying_criteria" description="Galaxy wrappers for the tool Categorize Elements: satisfying criteria"> - <tool id="categorize_elements_satisfying_criteria" version="1.0.0" file="categorize_elements_satisfying_criteria.xml" /> + <tool id="categorize_elements_satisfying_criteria" version="1.0.0" file="regVariation/categorize_elements_satisfying_criteria.xml" /></repository><repository owner="devteam" changeset_revision="acc3dc5d26e3" name="compute_motif_frequencies_for_all_motifs" description="Galaxy wrappers for the tool Compute Motif Frequencies For All Motifs: motif by motif"> - <tool id="compute_motif_frequencies_for_all_motifs" version="1.0.0" file="compute_motif_frequencies_for_all_motifs.xml" /> + <tool id="compute_motif_frequencies_for_all_motifs" version="1.0.0" file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /></repository><repository owner="devteam" changeset_revision="46325357b948" name="compute_motifs_frequency" description="Galaxy wrappers for the tool Compute Motif Frequencies: in indel flanking regions"> - <tool id="compute_motifs_frequency" version="1.0.0" file="compute_motifs_frequency.xml" /> + <tool id="compute_motifs_frequency" version="1.0.0" file="regVariation/compute_motifs_frequency.xml" /></repository><repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes"> - <tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" /> + <tool id="ctdBatch_1" version="1.0.0" file="phenotype_association/ctd.xml" /></repository><repository owner="devteam" changeset_revision="9a3f7a890da6" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."> - <tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" /> + <tool id="cuffcompare" version="0.0.5" file="ngs_rna/cuffcompare_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool."> - <tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" /> + <tool id="cuffdiff" version="0.0.6" file="ngs_rna/cuffdiff_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="b01956f26c36" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."> - <tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" /> + <tool id="cufflinks" version="0.0.6" file="ngs_rna/cufflinks_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="fdc55fd74f78" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."> - <tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" /> + <tool id="cuffmerge" version="0.0.5" file="ngs_rna/cuffmerge_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file"> - <tool id="delete_overlapping_indels" version="1.0.0" file="delete_overlapping_indels.xml" /> + <tool id="delete_overlapping_indels" version="1.0.0" file="regVariation/delete_overlapping_indels.xml" /></repository><repository owner="devteam" changeset_revision="de839553d2a2" name="divide_pg_snp" description="Galaxy wrappers for the tool Separate pgSnp alleles: into columns"> - <tool id="dividePgSnp" version="1.0.0" file="dividePgSnpAlleles.xml" /> + <tool id="dividePgSnp" version="1.0.0" file="phenotype_association/dividePgSnpAlleles.xml" /></repository><repository owner="devteam" changeset_revision="063ecbe59faf" name="draw_stacked_barplots" description="Galaxy wrappers for the tool Draw Stacked Bar Plots: for different categories and different criteria"> - <tool id="draw_stacked_barplots" version="1.0.0" file="draw_stacked_barplots.xml" /> + <tool id="draw_stacked_barplots" version="1.0.0" file="regVariation/draw_stacked_barplots.xml" /></repository><repository owner="devteam" changeset_revision="f2ab5b44870d" name="fasta_clipping_histogram" description="Galaxy wrappers for the tool Length Distribution chart"> - <tool id="cshl_fasta_clipping_histogram" version="1.0.0" file="fasta_clipping_histogram.xml" /> + <tool id="cshl_fasta_clipping_histogram" version="1.0.0" file="fastx_toolkit/fasta_clipping_histogram.xml" /></repository><repository owner="devteam" changeset_revision="8f0ae92440b8" name="fasta_formatter" description="Galaxy wrappers for the tool FASTA Width: formatter"> - <tool id="cshl_fasta_formatter" version="1.0.0" file="fasta_formatter.xml" /> + <tool id="cshl_fasta_formatter" version="1.0.0" file="fastx_toolkit/fasta_formatter.xml" /></repository><repository owner="devteam" changeset_revision="4b41e3076a50" name="fasta_nucleotide_changer" description="Galaxy wrappers for the tool RNA/DNA: converter"> - <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" file="fasta_nucleotide_changer.xml" /> + <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" file="fastx_toolkit/fasta_nucleotide_changer.xml" /></repository><repository owner="devteam" changeset_revision="e359ce20fbd9" name="fastq_quality_boxplot" description="Galaxy wrappers for the tool Draw quality score boxplot"> - <tool id="cshl_fastq_quality_boxplot" version="1.0.0" file="fastq_quality_boxplot.xml" /> + <tool id="cshl_fastq_quality_boxplot" version="1.0.0" file="fastx_toolkit/fastq_quality_boxplot.xml" /></repository><repository owner="devteam" changeset_revision="b87c74b61d81" name="fastq_quality_converter" description="Galaxy wrappers for the tool Quality format converter: (ASCII-Numeric)"> - <tool id="cshl_fastq_quality_converter" version="1.0.0" file="fastq_quality_converter.xml" /> + <tool id="cshl_fastq_quality_converter" version="1.0.0" file="fastx_toolkit/fastq_quality_converter.xml" /></repository><repository owner="devteam" changeset_revision="b145b9b26648" name="fastq_quality_filter" description="Galaxy wrappers for the Filter by quality tool."> - <tool id="cshl_fastq_quality_filter" version="1.0.0" file="fastq_quality_filter.xml" /> + <tool id="cshl_fastq_quality_filter" version="1.0.0" file="fastx_toolkit/fastq_quality_filter.xml" /></repository><repository owner="devteam" changeset_revision="04614cf6ed39" name="fastq_to_fasta" description="Galaxy wrappers for the tool FASTQ to FASTA: converter"> - <tool id="cshl_fastq_to_fasta" version="1.0.0" file="fastq_to_fasta.xml" /> + <tool id="cshl_fastq_to_fasta" version="1.0.0" file="fastx_toolkit/fastq_to_fasta.xml" /></repository><repository owner="devteam" changeset_revision="7f9660a246c0" name="fastx_artifacts_filter" description="Galaxy wrappers for the Remove sequencing artifacts tool."> - <tool id="cshl_fastx_artifacts_filter" version="1.0.0" file="fastx_artifacts_filter.xml" /> + <tool id="cshl_fastx_artifacts_filter" version="1.0.0" file="fastx_toolkit/fastx_artifacts_filter.xml" /></repository><repository owner="devteam" changeset_revision="a12850d0559b" name="fastx_barcode_splitter" description="Galaxy wrappers for the Barcode Splitter tool."> - <tool id="cshl_fastx_barcode_splitter" version="1.0.0" file="fastx_barcode_splitter.xml" /> + <tool id="cshl_fastx_barcode_splitter" version="1.0.0" file="fastx_toolkit/fastx_barcode_splitter.xml" /></repository><repository owner="devteam" changeset_revision="2fe2d2b9e8e4" name="fastx_clipper" description="Galaxy wrappers for the tool Clip: adapter sequences"> - <tool id="cshl_fastx_clipper" version="1.0.1" file="fastx_clipper.xml" /> + <tool id="cshl_fastx_clipper" version="1.0.1" file="fastx_toolkit/fastx_clipper.xml" /></repository><repository owner="devteam" changeset_revision="e942fd3a76a5" name="fastx_collapser" description="Galaxy wrappers for the tool Collapse: sequences"> - <tool id="cshl_fastx_collapser" version="1.0.0" file="fastx_collapser.xml" /> + <tool id="cshl_fastx_collapser" version="1.0.0" file="fastx_toolkit/fastx_collapser.xml" /></repository><repository owner="devteam" changeset_revision="bcc5424a4a3c" name="fastx_nucleotides_distribution" description="Galaxy wrappers for the Draw nucleotides distribution chart tool."> - <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" file="fastx_nucleotides_distribution.xml" /> + <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" file="fastx_toolkit/fastx_nucleotides_distribution.xml" /></repository><repository owner="devteam" changeset_revision="45f077341b24" name="fastx_quality_statistics" description="Galaxy wrappers for the Compute quality statistics tool."> - <tool id="cshl_fastx_quality_statistics" version="1.0.0" file="fastx_quality_statistics.xml" /> + <tool id="cshl_fastx_quality_statistics" version="1.0.0" file="fastx_toolkit/fastx_quality_statistics.xml" /></repository><repository owner="devteam" changeset_revision="d7bce63e6e09" name="fastx_renamer" description="Galaxy wrappers for the Rename sequences tool."> - <tool id="cshl_fastx_renamer" version="0.0.11" file="fastx_renamer.xml" /> + <tool id="cshl_fastx_renamer" version="0.0.11" file="fastx_toolkit/fastx_renamer.xml" /></repository><repository owner="devteam" changeset_revision="c58871138668" name="fastx_reverse_complement" description="Galaxy wrappers for the Reverse-Complement tool."> - <tool id="cshl_fastx_reverse_complement" version="1.0.0" file="fastx_reverse_complement.xml" /> + <tool id="cshl_fastx_reverse_complement" version="1.0.0" file="fastx_toolkit/fastx_reverse_complement.xml" /></repository><repository owner="devteam" changeset_revision="9cb372481a71" name="fastx_trimmer" description="Galaxy wrappers for the Trim sequences tool."> - <tool id="cshl_fastx_trimmer" version="1.0.0" file="fastx_trimmer.xml" /> + <tool id="cshl_fastx_trimmer" version="1.0.0" file="fastx_toolkit/fastx_trimmer.xml" /></repository><repository owner="devteam" changeset_revision="64133669255f" name="hgv_fundo" description="Galaxy wrappers for the tool FunDO: human genes associated with disease terms"> - <tool id="hgv_funDo" version="1.0.0" file="funDo.xml" /> + <tool id="hgv_funDo" version="1.0.0" file="phenotype_association/funDo.xml" /></repository><repository owner="devteam" changeset_revision="0e80ffa5b7f7" name="hgv_hilbertvis" description="Galaxy wrappers for the tool HVIS: visualization of genomic data with the Hilbert curve"> - <tool id="hgv_hilbertvis" version="1.0.0" file="hilbertvis.xml" /> + <tool id="hgv_hilbertvis" version="1.0.0" file="phenotype_association/hilbertvis.xml" /></repository><repository owner="devteam" changeset_revision="5ad24b81dd10" name="indels_3way" description="Galaxy wrappers for the tool Fetch Indels: from 3-way alignments"> - <tool id="indels_3way" version="1.0.3" file="getIndels_3way.xml" /> + <tool id="indels_3way" version="1.0.3" file="regVariation/getIndels_3way.xml" /></repository><repository owner="devteam" changeset_revision="4e31fad3f08e" name="microsatellite_birthdeath" description="Galaxy wrappers for the tool Identify microsatellite births and deaths: and causal mutational mechanisms from previously identified orthologous microsatellite sets"> - <tool id="microsatellite_birthdeath" version="1.0.0" file="microsatellite_birthdeath.xml" /> + <tool id="microsatellite_birthdeath" version="1.0.0" file="regVariation/microsatellite_birthdeath.xml" /></repository><repository 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file="rgWebLogo3.xml" /> + <tool id="rgweblogo3" version="0.4" file="rgenetics/rgWebLogo3.xml" /></repository></toolshed> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Swap amqplib for amqp. This was mostly a drop-in replacement, since it's a currently-maintained fork of amqplib, with slight updates to work with amqp 0-9-1.
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/890e70b0fd27/ Changeset: 890e70b0fd27 User: dannon Date: 2014-02-19 20:27:10 Summary: Swap amqplib for amqp. This was mostly a drop-in replacement, since it's a currently-maintained fork of amqplib, with slight updates to work with amqp 0-9-1. Affected #: 6 files diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -33,7 +33,6 @@ [eggs:noplatform] amqp = 1.4.3 -amqplib = 0.6.1 anyjson = 0.3.3 Beaker = 1.4 boto = 2.5.2 diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -45,7 +45,7 @@ from sqlalchemy.orm.exc import NoResultFound eggs.require( "pexpect" ) -eggs.require( "amqplib" ) +eggs.require( "amqp" ) import logging log = logging.getLogger( __name__ ) diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 lib/galaxy/webapps/demo_sequencer/framework/__init__.py --- a/lib/galaxy/webapps/demo_sequencer/framework/__init__.py +++ b/lib/galaxy/webapps/demo_sequencer/framework/__init__.py @@ -31,7 +31,7 @@ import mako.runtime pkg_resources.require( "pexpect" ) -pkg_resources.require( "amqplib" ) +pkg_resources.require( "amqp" ) import logging log = logging.getLogger( __name__ ) diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 lib/galaxy/webapps/galaxy/controllers/requests_admin.py --- a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py @@ -6,7 +6,9 @@ from galaxy import model, util from galaxy.web.form_builder import * from .requests_common import RequestsGrid, invalid_id_redirect -from amqplib import client_0_8 as amqp +from galaxy import eggs +eggs.require("amqp") +import amqp import logging, os, pexpect, ConfigParser log = logging.getLogger( __name__ ) @@ -696,8 +698,7 @@ conn = amqp.Connection( host=trans.app.config.amqp[ 'host' ] + ":" + trans.app.config.amqp[ 'port' ], userid=trans.app.config.amqp[ 'userid' ], password=trans.app.config.amqp[ 'password' ], - virtual_host=trans.app.config.amqp[ 'virtual_host' ], - insist=False ) + virtual_host=trans.app.config.amqp[ 'virtual_host' ]) chan = conn.channel() msg = amqp.Message( rmq_msg, content_type='text/plain', diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 scripts/galaxy_messaging/client/amqp_publisher.py --- a/scripts/galaxy_messaging/client/amqp_publisher.py +++ b/scripts/galaxy_messaging/client/amqp_publisher.py @@ -1,18 +1,23 @@ ''' -This script gets barcode data from a barcode scanner using serial communication +This script gets barcode data from a barcode scanner using serial communication and sends the state representated by the barcode scanner & the barcode string -to the Galaxy LIMS RabbitMQ server. The message is sent in XML which has 2 tags, +to the Galaxy LIMS RabbitMQ server. The message is sent in XML which has 2 tags, barcode & state. The state of the scanner should be set in the galaxy_amq.ini -file as a configuration variable. +file as a configuration variable. ''' -from amqplib import client_0_8 as amqp +import array import ConfigParser -import sys, os +import optparse +import os import serial -import array +import sys import time -import optparse + +from galaxy import eggs +eggs.require("amqp") + +import amqp xml = \ @@ -31,14 +36,14 @@ print values data = xml % values print data - conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], - userid=amqp_config['userid'], - password=amqp_config['password'], - virtual_host=amqp_config['virtual_host'], - insist=False) + conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], + userid=amqp_config['userid'], + password=amqp_config['password'], + virtual_host=amqp_config['virtual_host'],) + chan = conn.channel() - msg = amqp.Message(data, - content_type='text/plain', + msg = amqp.Message(data, + content_type='text/plain', application_headers={'msg_type': 'sample_state_update'}) msg.properties["delivery_mode"] = 2 chan.basic_publish(msg, @@ -55,13 +60,13 @@ msg = s.read(bytes) print msg handle_scan(states, amqp_config, msg.strip()) - - + + def main(): parser = optparse.OptionParser() - parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', + parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', dest='config_file', action='store') - parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', + parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', dest='port', action='store') (opts, args) = parser.parse_args() config = ConfigParser.ConfigParser() @@ -81,7 +86,7 @@ states[config.get(section, 'prefix')] = config.get(section, 'state') count = count + 1 else: - break + break print amqp_config print states s = serial.Serial(int(opts.port)) @@ -90,6 +95,6 @@ s.close() print 'Port %s is open: %s' %( opts.port, s.isOpen()) - + if __name__ == '__main__': main() diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 scripts/galaxy_messaging/server/amqp_consumer.py --- a/scripts/galaxy_messaging/server/amqp_consumer.py +++ b/scripts/galaxy_messaging/server/amqp_consumer.py @@ -1,8 +1,8 @@ ''' Galaxy Messaging with AMQP (RabbitMQ) -Galaxy uses AMQ protocol to receive messages from external sources like +Galaxy uses AMQ protocol to receive messages from external sources like bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -For Galaxy to receive messages from a message queue the RabbitMQ server has +For Galaxy to receive messages from a message queue the RabbitMQ server has to be set up with a user account and other parameters listed in the [galaxy_amqp] section in the universe_wsgi.ini config file Once the RabbitMQ server has been setup and started with the given parameters, @@ -32,8 +32,8 @@ from galaxy import eggs from galaxy.web.api.requests import RequestsAPIController import pkg_resources -pkg_resources.require( "amqplib" ) -from amqplib import client_0_8 as amqp +pkg_resources.require( "amqp" ) +import amqp import logging log = logging.getLogger("GalaxyAMQP") @@ -45,7 +45,7 @@ log.addHandler(fh) # data transfer script -data_transfer_script = os.path.join( os.getcwd(), +data_transfer_script = os.path.join( os.getcwd(), "scripts/galaxy_messaging/server/data_transfer.py" ) global config global config_file_name @@ -54,13 +54,13 @@ def start_data_transfer( message ): # fork a new process to transfer datasets - cmd = '%s "%s" "%s" "%s"' % ( "python", - data_transfer_script, + cmd = '%s "%s" "%s" "%s"' % ( "python", + data_transfer_script, message.body, config_file_name ) # Galaxy config file name pid = subprocess.Popen(cmd, shell=True).pid log.debug('Started process (%i): %s' % (pid, str(cmd))) - + def update_sample_state( message ): dom = xml.dom.minidom.parseString(message.body) barcode = get_value(dom, 'barcode') @@ -69,7 +69,7 @@ log.debug('Barcode: ' + barcode) log.debug('State: ' + state) log.debug('API Key: ' + api_key) - # validate + # validate if not barcode or not state or not api_key: log.debug( 'Incomplete sample_state_update message received. Sample barcode, desired state and user API key is required.' ) return @@ -78,13 +78,13 @@ galaxydb = GalaxyDbInterface( dbconnstr ) sample_id = galaxydb.get_sample_id( field_name='bar_code', value=barcode ) if sample_id == -1: - log.debug( 'Invalid barcode.' ) + log.debug( 'Invalid barcode.' ) return galaxydb.change_state(sample_id, state) # after updating the sample state, update request status request_id = galaxydb.get_request_id(sample_id) update_request( api_key, request_id ) - + def update_request( api_key, request_id ): encoded_request_id = api.encode_id( config.get( "app:main", "id_secret" ), request_id ) data = dict( update_type=RequestsAPIController.update_types.REQUEST ) @@ -111,9 +111,9 @@ def main(): parser = optparse.OptionParser() - parser.add_option('-c', '--config-file', help='Galaxy configuration file', + parser.add_option('-c', '--config-file', help='Galaxy configuration file', dest='config_file', action='store') - parser.add_option('-s', '--http-server-section', help='Name of the HTTP server section in the Galaxy configuration file', + parser.add_option('-s', '--http-server-section', help='Name of the HTTP server section in the Galaxy configuration file', dest='http_server_section', action='store') (opts, args) = parser.parse_args() log.debug( "GALAXY LISTENER PID: " + str(os.getpid()) + " - " + str( opts ) ) @@ -129,33 +129,32 @@ for option in config.options("galaxy_amqp"): amqp_config[option] = config.get("galaxy_amqp", option) log.debug( str( amqp_config ) ) - # connect - conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], - userid=amqp_config['userid'], - password=amqp_config['password'], - virtual_host=amqp_config['virtual_host'], - insist=False) + # connect + conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], + userid=amqp_config['userid'], + password=amqp_config['password'], + virtual_host=amqp_config['virtual_host']) chan = conn.channel() - chan.queue_declare( queue=amqp_config['queue'], - durable=True, - exclusive=True, + chan.queue_declare( queue=amqp_config['queue'], + durable=True, + exclusive=True, auto_delete=False) - chan.exchange_declare( exchange=amqp_config['exchange'], - type="direct", - durable=True, - auto_delete=False,) - chan.queue_bind( queue=amqp_config['queue'], - exchange=amqp_config['exchange'], + chan.exchange_declare( exchange=amqp_config['exchange'], + type="direct", + durable=True, + auto_delete=False,) + chan.queue_bind( queue=amqp_config['queue'], + exchange=amqp_config['exchange'], routing_key=amqp_config['routing_key']) - chan.basic_consume( queue=amqp_config['queue'], - no_ack=True, - callback=recv_callback, + chan.basic_consume( queue=amqp_config['queue'], + no_ack=True, + callback=recv_callback, consumer_tag="testtag") log.debug('Connected to rabbitmq server - '+amqp_config['host']+":"+amqp_config['port']) while True: chan.wait() - chan.basic_cancel("testtag") + chan.basic_cancel("testtag") chan.close() conn.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: remove anonymous template
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dcca6c291a69/ Changeset: dcca6c291a69 User: carlfeberhard Date: 2014-02-19 19:54:55 Summary: History panel: remove anonymous template Affected #: 11 files diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/mvc/history/current-history-panel.js --- a/static/scripts/mvc/history/current-history-panel.js +++ b/static/scripts/mvc/history/current-history-panel.js @@ -272,12 +272,6 @@ } }); -//------------------------------------------------------------------------------ TEMPLATES -CurrentHistoryPanel.templates = { - historyPanel : Handlebars.templates[ 'template-history-historyPanel' ], - anonHistoryPanel : Handlebars.templates[ 'template-history-historyPanel-anon' ] -}; - //============================================================================== return { CurrentHistoryPanel : CurrentHistoryPanel diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -401,12 +401,6 @@ } }); -//------------------------------------------------------------------------------ TEMPLATES -HistoryPanel.templates = { - historyPanel : Handlebars.templates[ 'template-history-historyPanel' ], - anonHistoryPanel : Handlebars.templates[ 'template-history-historyPanel-anon' ] -}; - //============================================================================== return { HistoryPanel : HistoryPanel diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/packed/mvc/history/current-history-panel.js --- a/static/scripts/packed/mvc/history/current-history-panel.js +++ b/static/scripts/packed/mvc/history/current-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-edit","mvc/history/history-panel"],function(b,e){var c=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});c.storageKey=function d(){return("history-panel")};var a=e.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left pane to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};this.preferences=new c(_.extend({id:c.storageKey()},_.pick(f,_.keys(c.prototype.defaults))));e.HistoryPanel.prototype.initialize.call(this,f);if(this.model){console.debug(this.model);this.model.checkForUpdates()}},loadCurrentHistory:function(g){var f=this;return this.loadHistoryWithHDADetails("current",g).then(function(i,h){f.trigger("current-history",f)})},switchToHistory:function(i,h){var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories/"+i+"/set_as_current")};return this.loadHistoryWithHDADetails(i,h,g).then(function(k,j){f.trigger("switched-history",f)})},createNewHistory:function(h){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,h,g).then(function(j,i){f.trigger("new-history",f)})},setModel:function(h,f,g){g=g||{};e.HistoryPanel.prototype.setModel.call(this,h,f,g);this.model.checkForUpdates();return this},_setUpModelEventHandlers:function(){e.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(g,h,f){if((!g.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[g.id])}},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children());f.renderBasedOnPrefs()}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},connectToQuotaMeter:function(f){if(!f){return this}this.listenTo(f,"quota:over",this.showQuotaMessage);this.listenTo(f,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(f&&f.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var f=this.$el.find(".quota-message");if(f.is(":hidden")){f.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var f=this.$el.find(".quota-message");if(!f.is(":hidden")){f.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(f){if(!f){return this}this.on("new-storage",function(h,g){if(f&&h){f.findItemByHtml(_l("Include Deleted Datasets")).checked=h.get("show_deleted");f.findItemByHtml(_l("Include Hidden Datasets")).checked=h.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});a.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{CurrentHistoryPanel:a}}); \ No newline at end of file +define(["mvc/dataset/hda-edit","mvc/history/history-panel"],function(b,e){var c=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});c.storageKey=function d(){return("history-panel")};var a=e.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left pane to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};this.preferences=new c(_.extend({id:c.storageKey()},_.pick(f,_.keys(c.prototype.defaults))));e.HistoryPanel.prototype.initialize.call(this,f);if(this.model){console.debug(this.model);this.model.checkForUpdates()}},loadCurrentHistory:function(g){var f=this;return this.loadHistoryWithHDADetails("current",g).then(function(i,h){f.trigger("current-history",f)})},switchToHistory:function(i,h){var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories/"+i+"/set_as_current")};return this.loadHistoryWithHDADetails(i,h,g).then(function(k,j){f.trigger("switched-history",f)})},createNewHistory:function(h){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,h,g).then(function(j,i){f.trigger("new-history",f)})},setModel:function(h,f,g){g=g||{};e.HistoryPanel.prototype.setModel.call(this,h,f,g);this.model.checkForUpdates();return this},_setUpModelEventHandlers:function(){e.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(g,h,f){if((!g.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[g.id])}},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children());f.renderBasedOnPrefs()}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},connectToQuotaMeter:function(f){if(!f){return this}this.listenTo(f,"quota:over",this.showQuotaMessage);this.listenTo(f,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(f&&f.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var f=this.$el.find(".quota-message");if(f.is(":hidden")){f.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var f=this.$el.find(".quota-message");if(!f.is(":hidden")){f.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(f){if(!f){return this}this.on("new-storage",function(h,g){if(f&&h){f.findItemByHtml(_l("Include Deleted Datasets")).checked=h.get("show_deleted");f.findItemByHtml(_l("Include Hidden Datasets")).checked=h.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.isHidden()),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.isHidden())});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:d}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.isHidden()),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.isHidden())});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:d}}); \ No newline at end of file diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/packed/templates/compiled/history-templates.js --- a/static/scripts/packed/templates/compiled/history-templates.js +++ b/static/scripts/packed/templates/compiled/history-templates.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-body"]=b(function(g,r,p,k,z){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);z=z||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';if(B=p.body){B=B.call(D,{hash:{},data:C})}else{B=D.body;B=typeof B===e?B.apply(D):B}if(B||B===0){A+=B}A+='\n </div>\n <div class="dataset-actions clear">\n <div class="left"></div>\n <div class="right"></div>\n </div>\n\n ';return A}function m(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';B=p["if"].call(D,D.misc_blurb,{hash:{},inverse:o.noop,fn:o.program(4,l,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.data_type,{hash:{},inverse:o.noop,fn:o.program(6,j,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.metadata_dbkey,{hash:{},inverse:o.noop,fn:o.program(9,f,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.misc_info,{hash:{},inverse:o.noop,fn:o.program(12,x,C),data:C});if(B||B===0){A+=B}A+='\n </div>\n\n <div class="dataset-actions clear">\n <div class="left"></div>\n <div class="right"></div>\n </div>\n\n ';B=p.unless.call(D,D.deleted,{hash:{},inverse:o.noop,fn:o.program(14,w,C),data:C});if(B||B===0){A+=B}A+="\n\n ";return A}function l(D,C){var A="",B;A+='\n <div class="dataset-blurb">\n <span class="value">';if(B=p.misc_blurb){B=B.call(D,{hash:{},data:C})}else{B=D.misc_blurb;B=typeof B===e?B.apply(D):B}A+=d(B)+"</span>\n </div>\n ";return A}function j(E,D){var A="",C,B;A+='\n <div class="dataset-datatype">\n <label class="prompt">';B={hash:{},inverse:o.noop,fn:o.program(7,i,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+='</label>\n <span class="value">';if(C=p.data_type){C=C.call(E,{hash:{},data:D})}else{C=E.data_type;C=typeof C===e?C.apply(E):C}A+=d(C)+"</span>\n </div>\n ";return A}function i(B,A){return"format"}function f(E,D){var A="",C,B;A+='\n <div class="dataset-dbkey">\n <label class="prompt">';B={hash:{},inverse:o.noop,fn:o.program(10,y,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+='</label>\n <span class="value">\n ';if(C=p.metadata_dbkey){C=C.call(E,{hash:{},data:D})}else{C=E.metadata_dbkey;C=typeof C===e?C.apply(E):C}A+=d(C)+"\n </span>\n </div>\n ";return A}function 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Click 'Get Data' on the left pane to start"}r+='<div class="history-controls">\n <div class="history-search-controls">\n <div class="history-search-input"></div>\n </div>\n\n <div class="history-title">\n ';i=q["if"].call(s,s.name,{hash:{},inverse:p.noop,fn:p.program(1,o,y),data:y});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=q["if"].call(s,s.nice_size,{hash:{},inverse:p.noop,fn:p.program(3,n,y),data:y});if(i||i===0){r+=i}r+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n ';i=q["if"].call(s,s.deleted,{hash:{},inverse:p.noop,fn:p.program(5,l,y),data:y});if(i||i===0){r+=i}r+='\n\n <div class="message-container">\n ';i=q["if"].call(s,s.message,{hash:{},inverse:p.noop,fn:p.program(8,h,y),data:y});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:p.noop,fn:p.program(10,x,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+=".\n ";f={hash:{},inverse:p.noop,fn:p.program(12,w,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='.\n </div>\n \n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="history-dataset-actions">\n <div class="btn-group">\n <button class="history-select-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:p.noop,fn:p.program(14,v,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='</button>\n <button class="history-deselect-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:p.noop,fn:p.program(16,u,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='</button>\n </div>\n <button class="history-dataset-action-popup-btn btn btn-default"\n >';f={hash:{},inverse:p.noop,fn:p.program(18,t,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='...</button>\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:p.noop,fn:p.program(20,j,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+="\n </div>";return r})})(); \ No newline at end of file diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/templates/compiled/history-templates.js --- a/static/scripts/templates/compiled/history-templates.js +++ b/static/scripts/templates/compiled/history-templates.js @@ -302,261 +302,6 @@ }); })();(function() { var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-hda-skeleton'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"errormessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":\n "; - options = {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n "; - return buffer; - } -function program2(depth0,data) { - - - return "There was an error getting the data for this dataset"; - } - -function program4(depth0,data) { - - var stack1; - if (stack1 = helpers.error) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.error; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - return escapeExpression(stack1); - } - -function program6(depth0,data) { - - var buffer = "", stack1; - buffer += "\n "; - stack1 = helpers['if'].call(depth0, depth0.purged, {hash:{},inverse:self.program(10, program10, data),fn:self.program(7, program7, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - return buffer; - } -function program7(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-purged-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n\n "; - return buffer; - } -function program8(depth0,data) { - - - return "This dataset has been deleted and removed from disk."; - } - -function program10(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-deleted-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program11(depth0,data) { - - - return "This dataset has been deleted."; - } - -function program13(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-hidden-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program14(depth0,data) { - - - return "This dataset has been hidden."; - } - - buffer += "<div class=\"dataset hda\">\n <div class=\"dataset-warnings\">\n "; - stack1 = helpers['if'].call(depth0, depth0.error, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers.unless.call(depth0, depth0.visible, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"dataset-selector\"><span class=\"fa fa-2x fa-square-o\"></span></div>\n <div class=\"dataset-primary-actions\"></div>\n " - + "\n <div class=\"dataset-title-bar clear\" tabindex=\"0\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">"; - if (stack1 = helpers.hid) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n <span class=\"dataset-name\">"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n </div>\n\n <div class=\"dataset-body\"></div>\n</div>"; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel-anon'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-name\">\n "; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </div>\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-size\">"; - if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program5(depth0,data) { - - var buffer = "", stack1; - buffer += "\n " - + "\n <div class=\""; - if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "message\">"; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program7(depth0,data) { - - - return "You are over your disk quota"; - } - -function program9(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program11(depth0,data) { - - - return "All"; - } - -function program13(depth0,data) { - - - return "None"; - } - -function program15(depth0,data) { - - - return "For all selected"; - } - -function program17(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n " - + "\n "; - stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; - stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n <div class=\"message-container\">\n "; - stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; - options = {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "...</button>\n </div>\n\n </div>" - + "\n\n " - + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>"; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { this.compilerInfo = [4,'>= 1.0.0']; helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; @@ -660,7 +405,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n "; + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div class=\"message-container\">\n "; diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/templates/compiled/template-history-historyPanel-anon.js --- a/static/scripts/templates/compiled/template-history-historyPanel-anon.js +++ /dev/null @@ -1,133 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel-anon'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-name\">\n "; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </div>\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-size\">"; - if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program5(depth0,data) { - - var buffer = "", stack1; - buffer += "\n " - + "\n <div class=\""; - if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "message\">"; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program7(depth0,data) { - - - return "You are over your disk quota"; - } - -function program9(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program11(depth0,data) { - - - return "All"; - } - -function program13(depth0,data) { - - - return "None"; - } - -function program15(depth0,data) { - - - return "For all selected"; - } - -function program17(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n " - + "\n "; - stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; - stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n <div class=\"message-container\">\n "; - stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; - options = {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "...</button>\n </div>\n\n </div>" - + "\n\n " - + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>"; - return buffer; - }); -})(); \ No newline at end of file diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -103,7 +103,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n "; + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div class=\"message-container\">\n "; diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -63,62 +63,3 @@ {{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} </div></script> - - - -<script type="text/template" class="template-history" id="template-history-historyPanel-anon"> - - <div class="history-controls"> - <div class="history-search-controls"> - <div class="history-search-input"></div> - </div> - - <div class="history-title"> - {{! wouldn't this always be 'unnamed history'? }} - {{#if name }} - <div class="history-name"> - {{name}} - </div> - {{/if}} - </div> - - <div class="history-subtitle clear"> - {{#if nice_size }} - <div class="history-size">{{nice_size}}</div> - {{/if}} - - <div class="history-secondary-actions"></div> - </div> - - <div class="message-container"> - {{#if message}} - {{! should already be localized }} - <div class="{{status}}message">{{message}}</div> - {{/if}} - </div> - - <div class="quota-message errormessage"> - {{#local}}You are over your disk quota{{/local}}. - {{#local}}Tool execution is on hold until your disk usage drops below your allocated quota{{/local}}. - </div> - - <div class="history-dataset-actions"> - <div class="btn-group"> - <button class="history-select-all-datasets-btn btn btn-default" - data-mode="select">{{#local}}All{{/local}}</button> - <button class="history-deselect-all-datasets-btn btn btn-default" - data-mode="select">{{#local}}None{{/local}}</button> - </div> - <button class="history-dataset-action-popup-btn btn btn-default" - >{{#local}}For all selected{{/local}}...</button> - </div> - - </div>{{! end history-controls }} - - {{! where the datasets/hdas are added }} - <div class="datasets-list"></div> - - <div class="empty-history-message infomessagesmall"> - {{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} - </div> -</script> 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: guerler: Grids: Fix negative page numbers
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b31e0927331b/ Changeset: b31e0927331b User: guerler Date: 2014-02-19 19:20:42 Summary: Grids: Fix negative page numbers Affected #: 2 files diff -r 057069969de059c08a6b6e8343b10bb7cfeea926 -r b31e0927331b7890590585bc9e2d7621b05bce88 static/scripts/mvc/grid/grid-template.js --- a/static/scripts/mvc/grid/grid-template.js +++ b/static/scripts/mvc/grid/grid-template.js @@ -246,7 +246,7 @@ var page_link_range = num_page_links / 2; var min_page = cur_page_num - page_link_range var min_offset = 0; - if (min_page == 0) { + if (min_page <= 0) { // Min page is too low. min_page = 1; min_offset = page_link_range - ( cur_page_num - min_page ); diff -r 057069969de059c08a6b6e8343b10bb7cfeea926 -r b31e0927331b7890590585bc9e2d7621b05bce88 static/scripts/packed/mvc/grid/grid-template.js --- a/static/scripts/packed/mvc/grid/grid-template.js +++ b/static/scripts/packed/mvc/grid/grid-template.js @@ -1,1 +1,1 @@ -define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g==0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}); \ No newline at end of file +define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g<=0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced 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