June 2012 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Fix the DataTableManager to handle directories other than ~/tool-data.
by Bitbucket 14 Jun '12

14 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b761471d7590/ changeset: b761471d7590 user: greg date: 2012-06-14 20:33:21 summary: Fix the DataTableManager to handle directories other than ~/tool-data. affected #: 4 files diff -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e -r b761471d759097f03c0fb904e9543f02ed5096c9 lib/galaxy/jobs/deferred/genome_transfer.py --- a/lib/galaxy/jobs/deferred/genome_transfer.py +++ b/lib/galaxy/jobs/deferred/genome_transfer.py @@ -34,7 +34,7 @@ self.tool = app.toolbox.tools_by_id['__GENOME_INDEX__'] self.sa_session = app.model.context.current tdtman = ToolDataTableManager() - xmltree = tdtman.load_from_config_file(app.config.tool_data_table_config_path) + xmltree = tdtman.load_from_config_file( app.config.tool_data_table_config_path, app.config.tool_data_path ) for node in xmltree: table = node.get('name') location = node.findall('file')[0].get('path') diff -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e -r b761471d759097f03c0fb904e9543f02ed5096c9 lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -24,7 +24,7 @@ return self.data_tables.__getitem__( key ) def __contains__( self, key ): return self.data_tables.__contains__( key ) - def load_from_config_file( self, config_filename ): + def load_from_config_file( self, config_filename, tool_data_path ): tree = util.parse_xml( config_filename ) root = tree.getroot() table_elems = [] @@ -36,12 +36,12 @@ if table_elem_name and table_elem_name not in self.data_table_elem_names: self.data_table_elem_names.append( table_elem_name ) self.data_table_elems.append( table_elem ) - table = tool_data_table_types[ type ]( table_elem ) + table = tool_data_table_types[ type ]( table_elem, tool_data_path ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table log.debug( "Loaded tool data table '%s'", table.name ) return table_elems - def add_new_entries_from_config_file( self, config_filename, tool_data_table_config_path, persist=False ): + def add_new_entries_from_config_file( self, config_filename, tool_data_path, tool_data_table_config_path, persist=False ): """ This method is called when a tool shed repository that includes a tool_data_table_conf.xml.sample file is being installed into a local galaxy instance. We have 2 cases to handle, files whose root tag is <tables>, for example: @@ -64,7 +64,7 @@ # Make a copy of the current list of data_table_elem_names so we can persist later if changes to the config file are necessary. original_data_table_elem_names = [ name for name in self.data_table_elem_names ] if root.tag == 'tables': - table_elems = self.load_from_config_file( config_filename ) + table_elems = self.load_from_config_file( config_filename, tool_data_path ) else: table_elems = [] type = root.get( 'type', 'tabular' ) @@ -74,7 +74,7 @@ if table_elem_name and table_elem_name not in self.data_table_elem_names: self.data_table_elem_names.append( table_elem_name ) self.data_table_elems.append( root ) - table = tool_data_table_types[ type ]( root ) + table = tool_data_table_types[ type ]( root, tool_data_path ) if table.name not in self.data_tables: self.data_tables[ table.name ] = table log.debug( "Added new tool data table '%s'", table.name ) @@ -97,8 +97,9 @@ os.chmod( full_path, 0644 ) class ToolDataTable( object ): - def __init__( self, config_element ): + def __init__( self, config_element, tool_data_path ): self.name = config_element.get( 'name' ) + self.tool_data_path = tool_data_path self.missing_index_file = None class TabularToolDataTable( ToolDataTable ): @@ -115,8 +116,8 @@ type_key = 'tabular' - def __init__( self, config_element ): - super( TabularToolDataTable, self ).__init__( config_element ) + def __init__( self, config_element, tool_data_path ): + super( TabularToolDataTable, self ).__init__( config_element, tool_data_path ) self.configure_and_load( config_element ) def configure_and_load( self, config_element ): """ @@ -128,11 +129,24 @@ self.parse_column_spec( config_element ) # Read every file all_rows = [] + found = False for file_element in config_element.findall( 'file' ): filename = file_element.get( 'path' ) if os.path.exists( filename ): + found = True all_rows.extend( self.parse_file_fields( open( filename ) ) ) else: + # Since the path attribute can include a hard-coded path to a specific directory + # (e.g., <file path="tool-data/cg_crr_files.loc" />) which may not be the same value + # as self.tool_data_path, we'll parse the path to get the filename and see if it is + # in self.tool_data_path. + file_path, file_name = os.path.split( filename ) + if file_path and file_path != self.tool_data_path: + corrected_filename = os.path.join( self.tool_data_path, file_name ) + if os.path.exists( corrected_filename ): + found = True + all_rows.extend( self.parse_file_fields( open( corrected_filename ) ) ) + if not found: self.missing_index_file = filename log.warn( "Cannot find index file '%s' for tool data table '%s'" % ( filename, self.name ) ) self.data = all_rows diff -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e -r b761471d759097f03c0fb904e9543f02ed5096c9 lib/galaxy/tools/genome_index/__init__.py --- a/lib/galaxy/tools/genome_index/__init__.py +++ b/lib/galaxy/tools/genome_index/__init__.py @@ -67,7 +67,7 @@ if gitd: destination = None tdtman = ToolDataTableManager() - xmltree = tdtman.load_from_config_file(app.config.tool_data_table_config_path) + xmltree = tdtman.load_from_config_file( app.config.tool_data_table_config_path, app.config.tool_data_path ) for node in xmltree: table = node.get('name') location = node.findall('file')[0].get('path') diff -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e -r b761471d759097f03c0fb904e9543f02ed5096c9 lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -427,12 +427,12 @@ if datatypes_config: metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) sample_files, deleted_sample_files = get_list_of_copied_sample_files( repo, ctx, dir=work_dir ) + if sample_files: + trans.app.config.tool_data_path = work_dir # Handle the tool_data_table_conf.xml.sample file if it is included in the repository. if 'tool_data_table_conf.xml.sample' in sample_files: tool_data_table_config = copy_file_from_manifest( repo, ctx, 'tool_data_table_conf.xml.sample', work_dir ) error, correction_msg = handle_sample_tool_data_table_conf_file( trans.app, tool_data_table_config ) - if sample_files: - trans.app.config.tool_data_path = work_dir for filename in ctx: # Find all tool configs. ctx_file_name = strip_path( filename ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add the ability to browse the installation directory of tool dependencies for installed tool shed repositories.
by Bitbucket 14 Jun '12

14 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/bef69fd3fcc1/ changeset: bef69fd3fcc1 user: greg date: 2012-06-14 16:00:51 summary: Add the ability to browse the installation directory of tool dependencies for installed tool shed repositories. affected #: 10 files diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2740,7 +2740,13 @@ self.version = version self.type = type self.uninstalled = uninstalled - + def installation_directory( self, app ): + return os.path.join( app.config.tool_dependency_dir, + self.name, + self.version, + self.tool_shed_repository.owner, + self.tool_shed_repository.name, + self.installed_changeset_revision ) class ToolVersion( object ): def __init__( self, id=None, create_time=None, tool_id=None, tool_shed_repository=None ): self.id = id diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/tool_shed/tool_dependencies/install_util.py --- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py +++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py @@ -41,7 +41,7 @@ sa_session.add( tool_dependency ) sa_session.flush() return tool_dependency -def get_install_dir( app, repository, installed_changeset_revision, package_name, package_version ): +def get_tool_dependency_install_dir( app, repository, installed_changeset_revision, package_name, package_version ): return os.path.abspath( os.path.join( app.config.tool_dependency_dir, package_name, package_version, diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/tools/deps/__init__.py --- a/lib/galaxy/tools/deps/__init__.py +++ b/lib/galaxy/tools/deps/__init__.py @@ -46,7 +46,7 @@ if installed_tool_dependencies: for installed_dependency in installed_tool_dependencies: if not installed_dependency.uninstalled: - if installed_dependency.name == name and installed_dependency.version == version and installed_dependency.type == type: + if installed_dependency.name==name and installed_dependency.version==version and installed_dependency.type==type: break for base_path in self.base_paths: if installed_dependency: diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -956,6 +956,9 @@ file_name = strip_path( shed_tool_conf_dict[ 'config_filename' ] ) if shed_tool_conf == file_name: return index, shed_tool_conf_dict +def get_tool_dependency( trans, id ): + """Get a tool_dependency from the database via id""" + return trans.sa_session.query( trans.model.ToolDependency ).get( trans.security.decode_id( id ) ) def get_tool_panel_config_tool_path_install_dir( app, repository ): # Return shed-related tool panel config, the tool_path configured in it, and the relative path to the directory where the # repository is installed. This method assumes all repository tools are defined in a single shed-related tool panel config. diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -2,7 +2,7 @@ from galaxy.web.controllers.admin import * from galaxy.util.json import from_json_string, to_json_string from galaxy.util.shed_util import * -from galaxy.tool_shed.tool_dependencies.install_util import get_install_dir, not_installed +from galaxy.tool_shed.tool_dependencies.install_util import get_tool_dependency_install_dir, not_installed from galaxy.tool_shed.encoding_util import * from galaxy import eggs, tools @@ -148,6 +148,19 @@ return self.repository_list_grid( trans, **kwd ) @web.expose @web.require_admin + def browse_tool_dependency( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + tool_dependency = get_tool_dependency( trans, kwd[ 'id' ] ) + repository = get_repository( trans, kwd[ 'repository_id' ] ) + return trans.fill_template( '/admin/tool_shed_repository/browse_tool_dependency.mako', + repository=repository, + tool_dependency=tool_dependency, + message=message, + status=status ) + @web.expose + @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd[ 'tool_shed_url' ] galaxy_url = url_for( '/', qualified=True ) @@ -256,6 +269,7 @@ url = '%srepository/find_workflows?galaxy_url=%s&webapp=galaxy&no_reset=true' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) @web.json + @web.require_admin def get_file_contents( self, trans, file_path ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' @@ -341,7 +355,7 @@ for dependency_key, requirements_dict in tool_dependencies.items(): name = requirements_dict[ 'name' ] version = requirements_dict[ 'version' ] - install_dir = get_install_dir( trans.app, repository, repository.changeset_revision, name, version ) + install_dir = get_tool_dependency_install_dir( trans.app, repository, repository.changeset_revision, name, version ) if not_installed( install_dir ): filtered_tool_dependencies[ dependency_key ] = requirements_dict tool_dependencies = filtered_tool_dependencies @@ -585,6 +599,7 @@ message=message, status=status ) @web.json + @web.require_admin def open_folder( self, trans, folder_path ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/browse_repository.mako --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -10,7 +10,7 @@ <%def name="javascripts()"> ${parent.javascripts()} ${h.js( "ui.core", "jquery.dynatree" )} - ${common_javascripts(repository)} + ${common_javascripts(repository.name, repository.repo_files_directory(trans.app))} </%def><br/><br/> diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/browse_tool_dependency.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/browse_tool_dependency.mako @@ -0,0 +1,62 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/admin/tool_shed_repository/common.mako" import="*" /> + +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "dynatree_skin/ui.dynatree" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "ui.core", "jquery.dynatree" )} + ${common_javascripts(tool_dependency.name, tool_dependency.installation_directory( trans.app ))} +</%def> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="tool_dependency-${tool_dependency.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="tool_dependency-${tool_dependency.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a> + %if repository.tool_dependencies: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a> + %endif + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Browse tool dependency ${tool_dependency.name} installation directory</div> + <div class="toolFormBody"> + <div class="form-row" > + <label>Tool shed repository:</label> + ${repository.name} + <div style="clear: both"></div> + </div> + <div class="form-row" > + <label>Tool shed repository changeset revision:</label> + ${repository.changeset_revision} + <div style="clear: both"></div> + </div> + <div class="form-row" > + <label>Tool dependency installation directory:</label> + ${tool_dependency.installation_directory( trans.app )} + <div style="clear: both"></div> + </div> + <div class="form-row" > + <label>Contents:</label> + <div id="tree" > + Loading... + </div> + <div style="clear: both"></div> + </div> + <div class="form-row"> + <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> + </div> + </div> +</div> diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -1,4 +1,4 @@ -<%def name="common_javascripts(repository)"> +<%def name="common_javascripts(title_text, directory_path)"><script type="text/javascript"> $(function(){ $("#tree").ajaxComplete(function(event, XMLHttpRequest, ajaxOptions) { @@ -6,7 +6,7 @@ }); // --- Initialize sample trees $("#tree").dynatree({ - title: "${repository.name}", + title: "${title_text}", rootVisible: true, minExpandLevel: 0, // 1: root node is not collapsible persist: false, @@ -22,7 +22,7 @@ // initAjax is hard to fake, so we pass the children as object array: initAjax: {url: "${h.url_for( controller='admin_toolshed', action='open_folder' )}", dataType: "json", - data: { folder_path: "${repository.repo_files_directory(trans.app)}" }, + data: { folder_path: "${directory_path}" }, }, onLazyRead: function(dtnode){ dtnode.appendAjax({ @@ -43,7 +43,7 @@ var cell = $("#file_contents"); var selected_value; if (dtnode.data.key == 'root') { - selected_value = "${repository.repo_files_directory(trans.app)}/"; + selected_value = "${directory_path}/"; } else { selected_value = dtnode.data.key; }; @@ -66,221 +66,3 @@ }); </script></%def> - -<%def name="render_repository_contents( repository, can_reset_metadata=False )"> - <div class="toolForm"> - <div class="toolFormTitle">${repository.name}</div> - <div class="toolFormBody"> - <% - metadata = repository.metadata - missing_tool_dependencies = repository.missing_tool_dependencies - installed_tool_dependencies = repository.installed_tool_dependencies - %> - %if missing_tool_dependencies: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Missing tool dependencies</i></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>type</b></td> - <td><b>version</b></td> - </tr> - %for name, requirements_dict in missing_tool_dependencies.items(): - <tr> - <td>${requirements_dict[ 'name' ]}</td> - <td>${requirements_dict[ 'type' ]}</td> - <td>${requirements_dict[ 'version' ]}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if installed_tool_dependencies: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Installed tool dependencies</i></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>type</b></td> - <td><b>version</b></td> - </tr> - %for installed_tool_dependency in installed_tool_dependencies: - <tr> - <td>${installed_tool_dependency.name}</td> - <td>${installed_tool_dependency.type}</td> - <td>${installed_tool_dependency.version}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'tools' in metadata: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Tools</b><i> - click the name to view information about the tool</i></td> - </tr> - </table> - </div> - <div class="form-row"> - <% tool_dicts = metadata[ 'tools' ] %> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>description</b></td> - <td><b>version</b></td> - <td><b>requirements</b></td> - </tr> - %for tool_dict in tool_dicts: - <tr> - <td> - <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=tool_dict[ 'id' ] )}"> - ${tool_dict[ 'name' ]} - </a> - </td> - <td>${tool_dict[ 'description' ]}</td> - <td>${tool_dict[ 'version' ]}</td> - <td> - <% - if 'requirements' in tool_dict: - requirements = tool_dict[ 'requirements' ] - else: - requirements = None - %> - %if requirements: - <% - requirements_str = '' - for requirement_dict in tool_dict[ 'requirements' ]: - requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) - requirements_str = requirements_str.rstrip( ', ' ) - %> - ${requirements_str} - %else: - none - %endif - </td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'workflows' in metadata: - ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is - ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Workflows</b><i> - click the name to import</i></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <% workflow_tups = metadata[ 'workflows' ] %> - <table class="grid"> - <tr> - <td><b>name</b></td> - <td><b>steps</b></td> - <td><b>format-version</b></td> - <td><b>annotation</b></td> - </tr> - <% index = 0 %> - %for workflow_tup in workflow_tups: - <% - import os.path - relative_path = workflow_tup[ 0 ] - full_path = os.path.abspath( relative_path ) - workflow_dict = workflow_tup[ 1 ] - workflow_name = workflow_dict[ 'name' ] - ## Initially steps were not stored in the metadata record. - steps = workflow_dict.get( 'steps', [] ) - format_version = workflow_dict[ 'format-version' ] - annotation = workflow_dict[ 'annotation' ] - %> - <tr> - <td> - <div class="menubutton" style="float: left;" id="workflow-${index}-popup"> - ${workflow_name} - <div popupmenu="workflow-${index}-popup"> - <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a> - </div> - </div> - </td> - <td> - %if steps: - ${len( steps )} - %else: - unknown - %endif - </td> - <td>${format_version}</td> - <td>${annotation}</td> - </tr> - <% index += 1 %> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'datatypes' in metadata: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Data types</b></td> - </tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <% datatypes_dicts = metadata[ 'datatypes' ] %> - <table class="grid"> - <tr> - <td><b>extension</b></td> - <td><b>type</b></td> - <td><b>mimetype</b></td> - <td><b>subclass</b></td> - </tr> - %for datatypes_dict in datatypes_dicts: - <tr> - <td>${datatypes_dict.get( 'extension', ' ' )}</td> - <td>${datatypes_dict.get( 'dtype', ' ' )}</td> - <td>${datatypes_dict.get( 'mimetype', ' ' )}</td> - <td>${datatypes_dict.get( 'subclass', ' ' )}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if can_reset_metadata: - <form name="set_metadata" action="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post"> - <div class="form-row"> - <div style="float: left; width: 250px; margin-right: 10px;"> - <input type="submit" name="set_metadata_button" value="Reset metadata"/> - </div> - <div class="toolParamHelp" style="clear: both;"> - Inspect the repository and reset the above attributes. - </div> - </div> - </form> - %endif - </div> - </div> -</%def> diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -64,5 +64,223 @@ </div></div><p/> -${render_repository_contents( repository, can_reset_metadata=True )} +<div class="toolForm"> + <div class="toolFormTitle">${repository.name}</div> + <div class="toolFormBody"> + <% + metadata = repository.metadata + missing_tool_dependencies = repository.missing_tool_dependencies + installed_tool_dependencies = repository.installed_tool_dependencies + %> + %if missing_tool_dependencies: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Missing tool dependencies</i></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>type</b></td> + <td><b>version</b></td> + </tr> + %for name, requirements_dict in missing_tool_dependencies.items(): + <tr> + <td>${requirements_dict[ 'name' ]}</td> + <td>${requirements_dict[ 'type' ]}</td> + <td>${requirements_dict[ 'version' ]}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if installed_tool_dependencies: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Installed tool dependencies<i> - click the name to browse the dependency installation directory</i></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>type</b></td> + <td><b>version</b></td> + </tr> + %for installed_tool_dependency in installed_tool_dependencies: + <tr> + <td> + <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( installed_tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}"> + ${installed_tool_dependency.name} + </a> + </td> + <td>${installed_tool_dependency.type}</td> + <td>${installed_tool_dependency.version}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if 'tools' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Tools</b><i> - click the name to view information about the tool</i></td> + </tr> + </table> + </div> + <div class="form-row"> + <% tool_dicts = metadata[ 'tools' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> + %for tool_dict in tool_dicts: + <tr> + <td> + <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=tool_dict[ 'id' ] )}"> + ${tool_dict[ 'name' ]} + </a> + </td> + <td>${tool_dict[ 'description' ]}</td> + <td>${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: + <% + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) + %> + ${requirements_str} + %else: + none + %endif + </td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if 'workflows' in metadata: + ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is + ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Workflows</b><i> - click the name to import</i></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% workflow_tups = metadata[ 'workflows' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>steps</b></td> + <td><b>format-version</b></td> + <td><b>annotation</b></td> + </tr> + <% index = 0 %> + %for workflow_tup in workflow_tups: + <% + import os.path + relative_path = workflow_tup[ 0 ] + full_path = os.path.abspath( relative_path ) + workflow_dict = workflow_tup[ 1 ] + workflow_name = workflow_dict[ 'name' ] + ## Initially steps were not stored in the metadata record. + steps = workflow_dict.get( 'steps', [] ) + format_version = workflow_dict[ 'format-version' ] + annotation = workflow_dict[ 'annotation' ] + %> + <tr> + <td> + <div class="menubutton" style="float: left;" id="workflow-${index}-popup"> + ${workflow_name} + <div popupmenu="workflow-${index}-popup"> + <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a> + </div> + </div> + </td> + <td> + %if steps: + ${len( steps )} + %else: + unknown + %endif + </td> + <td>${format_version}</td> + <td>${annotation}</td> + </tr> + <% index += 1 %> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if 'datatypes' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Data types</b></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% datatypes_dicts = metadata[ 'datatypes' ] %> + <table class="grid"> + <tr> + <td><b>extension</b></td> + <td><b>type</b></td> + <td><b>mimetype</b></td> + <td><b>subclass</b></td> + </tr> + %for datatypes_dict in datatypes_dicts: + <tr> + <td>${datatypes_dict.get( 'extension', ' ' )}</td> + <td>${datatypes_dict.get( 'dtype', ' ' )}</td> + <td>${datatypes_dict.get( 'mimetype', ' ' )}</td> + <td>${datatypes_dict.get( 'subclass', ' ' )}</td> + </tr> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if can_reset_metadata: + <form name="set_metadata" action="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post"> + <div class="form-row"> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="submit" name="set_metadata_button" value="Reset metadata"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Inspect the repository and reset the above attributes. + </div> + </div> + </form> + %endif + </div> +</div><p/> diff -r b1f35669f93c4163cf803d64beb37a1cb0d5381c -r bef69fd3fcc191b9a9a4d140876a6ee932e9fc3e templates/admin/tool_shed_repository/manage_tool_dependencies.mako --- a/templates/admin/tool_shed_repository/manage_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/manage_tool_dependencies.mako @@ -24,7 +24,7 @@ %endif <div class="toolForm"> - <div class="toolFormTitle">${repository.name} repository's installed tool dependencies</div> + <div class="toolFormTitle">${repository.name} repository's tool dependencies</div><div class="toolFormBody"><div class="form-row"><table class="grid"> @@ -45,7 +45,18 @@ <tr><td bgcolor="#D8D8D8"><b>Name</b></td><td bgcolor="#D8D8D8">${name}</td></tr><tr><th>Version</th><td>${version}</td></tr><tr><th>Type</th><td>${type}</td></tr> - <tr><th>Install directory</th><td>${install_dir}</td></tr> + <tr> + <th>Install directory</th> + <td> + %if uninstalled: + This dependency is not currently installed + %else: + <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='browse_tool_dependency', id=trans.security.encode_id( tool_dependency.id ), repository_id=trans.security.encode_id( repository.id ) )}"> + ${install_dir} + </a> + %endif + </td> + </tr><tr><th>Installed changeset revision</th><td>${installed_changeset_revision}</td></tr><tr><th>Uninstalled</th><td>${uninstalled}</td></tr> %endfor Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add baseline support for managin dependencies for tools included in installed tool shed repositories, enhance installed repository browsing to enable browsing files, and a bit of code cleanup.
by Bitbucket 13 Jun '12

13 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/b1f35669f93c/ changeset: b1f35669f93c user: greg date: 2012-06-13 22:40:22 summary: Add baseline support for managin dependencies for tools included in installed tool shed repositories, enhance installed repository browsing to enable browsing files, and a bit of code cleanup. affected #: 12 files diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2665,7 +2665,12 @@ self.deleted = deleted self.uninstalled = uninstalled self.dist_to_shed = dist_to_shed - def repo_path( self, app ): + def repo_files_directory( self, app ): + repo_path = self.repo_path( app ) + if repo_path: + return os.path.join( app.config.root, repo_path, self.name ) + return None + def repo_path( self, app ): tool_shed_url = self.tool_shed if tool_shed_url.find( ':' ) > 0: # Eliminate the port, if any, since it will result in an invalid directory name. @@ -2673,7 +2678,7 @@ tool_shed = tool_shed_url.rstrip( '/' ) for index, shed_tool_conf_dict in enumerate( app.toolbox.shed_tool_confs ): tool_path = shed_tool_conf_dict[ 'tool_path' ] - relative_path = os.path.join( tool_path, tool_shed, 'repos', self.owner, self.name, self.installed_changeset_revision ) + relative_path = os.path.join( app.config.root, tool_path, tool_shed, 'repos', self.owner, self.name, self.installed_changeset_revision ) if os.path.exists( relative_path ): return relative_path return None @@ -2686,6 +2691,46 @@ @property def includes_workflows( self ): return self.metadata and 'workflows' in self.metadata + @property + def installed_tool_dependencies( self ): + """Return the repository's tool dependencies that are currently installed.""" + installed_dependencies = [] + for tool_dependency in self.tool_dependencies: + if not tool_dependency.uninstalled: + installed_dependencies.append( tool_dependency ) + return installed_dependencies + @property + def missing_tool_dependencies( self ): + """Return the repository's tool dependencies that are not currently installed.""" + def add_missing_dependency( missing_dependencies_dict, name, version, type, installed_changeset_revision=None ): + missing_dependencies_dict[ name ] = dict( version=version, + type=type, + installed_changeset_revision=installed_changeset_revision ) + return missing_dependencies_dict + missing_dependencies = {} + # Get the dependency information from the metadata for comparison against the installed tool dependencies. + tool_dependencies = self.metadata.get( 'tool_dependencies', None ) + if tool_dependencies: + for dependency_key, requirements_dict in tool_dependencies.items(): + name = requirements_dict[ 'name' ] + version = requirements_dict[ 'version' ] + type = requirements_dict[ 'type' ] + if self.tool_dependencies: + found = False + for installed_dependency in self.tool_dependencies: + if installed_dependency.name==name and installed_dependency.version==version and installed_dependency.type==type: + found = True + if installed_dependency.uninstalled: + missing_dependencies = add_missing_dependency( missing_dependencies, + installed_dependency.name, + installed_dependency.version, + installed_dependency.type, + installed_dependency.installed_changeset_revision ) + break + if not found: + missing_dependencies = add_missing_dependency( missing_dependencies, name, version, type ) + return missing_dependencies + return None class ToolDependency( object ): def __init__( self, tool_shed_repository_id=None, installed_changeset_revision=None, name=None, version=None, type=None, uninstalled=False ): diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -795,19 +795,15 @@ return tool_version.get_version_ids( self.app ) return [] @property - def installed_tool_dependencies( self ): - # If this tool is included in an installed tool shed repository and tool dependencies were installed along with the - # tool shed repository, then this method will return the repository's ToolDependency records. - if self.app.config.use_tool_dependencies: - if self.tool_shed: - tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_changeset_revision( self.app, - self.tool_shed, - self.repository_name, - self.repository_owner, - self.installed_changeset_revision ) - if tool_shed_repository: - return tool_shed_repository.tool_dependencies - return None + def tool_shed_repository( self ): + # If this tool is included in an installed tool shed repository, return it. + if self.tool_shed: + return get_tool_shed_repository_by_shed_name_owner_changeset_revision( self.app, + self.tool_shed, + self.repository_name, + self.repository_owner, + self.installed_changeset_revision ) + return None def __get_job_run_config( self, run_configs, key, job_params=None ): # Look through runners/handlers to find one with matching parameters. available_configs = [] @@ -2333,6 +2329,10 @@ environment to include this tools requirements. """ commands = [] + if self.tool_shed_repository: + installed_tool_dependencies = self.tool_shed_repository.tool_dependencies + else: + installed_tool_dependencies = None for requirement in self.requirements: # TODO: currently only supporting requirements of type package, # need to implement some mechanism for mapping other types @@ -2342,7 +2342,7 @@ script_file, base_path, version = self.app.toolbox.dependency_manager.find_dep( name=requirement.name, version=requirement.version, type=requirement.type, - installed_tool_dependencies=self.installed_tool_dependencies ) + installed_tool_dependencies=installed_tool_dependencies ) if script_file is None and base_path is None: log.warn( "Failed to resolve dependency on '%s', ignoring", requirement.name ) elif script_file is None: diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -29,6 +29,7 @@ '"' : '"', '&' : '&', '\'' : ''' } +MAX_CONTENT_SIZE = 32768 VALID_CHARS = set( string.letters + string.digits + "'\"-=_.()/+*^,:?!#[]%\\$@;{}" ) NOT_TOOL_CONFIGS = [ 'datatypes_conf.xml', 'tool_dependencies.xml' ] @@ -881,6 +882,37 @@ fh.close() return tmp_filename return None +def get_repository_file_contents( file_path ): + if is_gzip( file_path ): + to_html = to_html_str( '\ngzip compressed file\n' ) + elif is_bz2( file_path ): + to_html = to_html_str( '\nbz2 compressed file\n' ) + elif check_zip( file_path ): + to_html = to_html_str( '\nzip compressed file\n' ) + elif check_binary( file_path ): + to_html = to_html_str( '\nBinary file\n' ) + else: + to_html = '' + for i, line in enumerate( open( file_path ) ): + to_html = '%s%s' % ( to_html, to_html_str( line ) ) + if len( to_html ) > MAX_CONTENT_SIZE: + large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) + to_html = '%s%s' % ( to_html, to_html_str( large_str ) ) + break + return to_html +def get_repository_files( trans, folder_path ): + contents = [] + for item in os.listdir( folder_path ): + # Skip .hg directories + if str( item ).startswith( '.hg' ): + continue + if os.path.isdir( os.path.join( folder_path, item ) ): + # Append a '/' character so that our jquery dynatree will function properly. + item = '%s/' % item + contents.append( item ) + if contents: + contents.sort() + return contents def get_repository_owner( cleaned_repository_url ): items = cleaned_repository_url.split( 'repos' ) repo_path = items[ 1 ] @@ -1313,6 +1345,27 @@ if not os.path.exists( work_dir ): os.makedirs( work_dir ) return work_dir +def open_repository_files_folder( trans, folder_path ): + try: + files_list = get_repository_files( trans, folder_path ) + except OSError, e: + if str( e ).find( 'No such file or directory' ) >= 0: + # We have a repository with no contents. + return [] + folder_contents = [] + for filename in files_list: + is_folder = False + if filename and filename[-1] == os.sep: + is_folder = True + if filename: + full_path = os.path.join( folder_path, filename ) + node = { "title": filename, + "isFolder": is_folder, + "isLazy": is_folder, + "tooltip": full_path, + "key": full_path } + folder_contents.append( node ) + return folder_contents def panel_entry_per_tool( tool_section_dict ): # Return True if tool_section_dict looks like this. # {<Tool guid> : [{ tool_config : <tool_config_file>, id: <ToolSection id>, version : <ToolSection version>, name : <TooSection name>}]} diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c lib/galaxy/web/controllers/admin_toolshed.py --- a/lib/galaxy/web/controllers/admin_toolshed.py +++ b/lib/galaxy/web/controllers/admin_toolshed.py @@ -174,40 +174,6 @@ return trans.response.send_redirect( url ) @web.expose @web.require_admin - def check_installed_tool_dependencies( self, trans, repository_id, relative_install_dir ): - """See if any tool dependencies need to be installed.""" - tool_dependencies_missing = False - repository = get_repository( trans, repository_id ) - if repository.includes_tool_dependencies: - # Get the tool_dependencies.xml file from the repository. - work_dir = make_tmp_directory() - tool_dependencies_config = get_config_from_repository( trans.app, - 'tool_dependencies.xml', - repository, - repository.changeset_revision, - work_dir, - install_dir=relative_install_dir ) - # Parse the tool_dependencies.xml config. - tree = ElementTree.parse( tool_dependencies_config ) - root = tree.getroot() - ElementInclude.include( root ) - fabric_version_checked = False - for elem in root: - if elem.tag == 'package': - package_name = elem.get( 'name', None ) - package_version = elem.get( 'version', None ) - if package_name and package_version: - install_dir = get_install_dir( trans.app, repository, repository.installed_changeset_revision, package_name, package_version ) - if not_installed( install_dir ): - tool_dependencies_missing = True - break - try: - shutil.rmtree( work_dir ) - except: - pass - return tool_dependencies_missing - @web.expose - @web.require_admin def deactivate_or_uninstall_repository( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -289,6 +255,12 @@ galaxy_url = url_for( '/', qualified=True ) url = '%srepository/find_workflows?galaxy_url=%s&webapp=galaxy&no_reset=true' % ( tool_shed_url, galaxy_url ) return trans.response.send_redirect( url ) + @web.json + def get_file_contents( self, trans, file_path ): + # Avoid caching + trans.response.headers['Pragma'] = 'no-cache' + trans.response.headers['Expires'] = '0' + return get_repository_file_contents( file_path ) @web.expose @web.require_admin def install_tool_dependencies( self, trans, **kwd ): @@ -594,16 +566,32 @@ trans.sa_session.add( repository ) trans.sa_session.flush() message = "Repository metadata has been reset." - tool_dependencies_missing = self.check_installed_tool_dependencies( trans, repository_id, relative_install_dir ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=description, repo_files_dir=repo_files_dir, - tool_dependencies_missing=tool_dependencies_missing, message=message, status=status ) @web.expose @web.require_admin + def manage_tool_dependencies( self, trans, **kwd ): + params = util.Params( kwd ) + message = util.restore_text( params.get( 'message', '' ) ) + status = params.get( 'status', 'done' ) + repository_id = kwd[ 'id' ] + repository = get_repository( trans, repository_id ) + return trans.fill_template( '/admin/tool_shed_repository/manage_tool_dependencies.mako', + repository=repository, + message=message, + status=status ) + @web.json + def open_folder( self, trans, folder_path ): + # Avoid caching + trans.response.headers['Pragma'] = 'no-cache' + trans.response.headers['Expires'] = '0' + return open_repository_files_folder( trans, folder_path ) + @web.expose + @web.require_admin def reinstall_repository( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) @@ -709,6 +697,8 @@ trans.sa_session.flush() if install_tool_dependencies: dependency_str = ' along with tool dependencies' + if error_message: + dependency_str += ', but with some errors installing the dependencies' else: dependency_str = ' without tool dependencies' message += 'The <b>%s</b> repository has been reinstalled%s. ' % ( repository.name, dependency_str ) @@ -822,8 +812,7 @@ message = "The installed repository named '%s' has been updated to change set revision '%s'. " % ( name, latest_changeset_revision ) # See if any tool dependencies can be installed. shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) - tool_dependencies_missing = self.check_installed_tool_dependencies( trans, trans.security.encode_id( repository.id ), relative_install_dir ) - if tool_dependencies_missing: + if repository.missing_tool_dependencies: message += "Select <b>Install tool dependencies</b> from the repository's pop-up menu to install tool dependencies." else: message = "The directory containing the installed repository named '%s' cannot be found. " % name diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -2,7 +2,6 @@ from time import strftime from datetime import date, datetime from galaxy import util -from galaxy.datatypes.checkers import * from galaxy.web.base.controller import * from galaxy.web.form_builder import CheckboxField from galaxy.webapps.community import model @@ -10,7 +9,8 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy.util.json import from_json_string, to_json_string from galaxy.model.orm import * -from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, make_tmp_directory, NOT_TOOL_CONFIGS, strip_path +from galaxy.util.shed_util import get_changectx_for_changeset, get_configured_ui, get_repository_file_contents, make_tmp_directory, NOT_TOOL_CONFIGS +from galaxy.util.shed_util import open_repository_files_folder, strip_path from galaxy.tool_shed.encoding_util import * from common import * @@ -20,7 +20,6 @@ log = logging.getLogger( __name__ ) -MAX_CONTENT_SIZE = 32768 VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) README_FILES = [ 'readme', 'read_me', 'install' ] @@ -496,12 +495,10 @@ commit_message = util.restore_text( params.get( 'commit_message', 'Deleted selected files' ) ) repository = get_repository( trans, id ) repo = hg.repository( get_configured_ui(), repository.repo_path ) - current_working_dir = os.getcwd() # Update repository files for browsing. update_repository( repo ) is_malicious = changeset_is_malicious( trans, id, repository.tip ) return trans.fill_template( '/webapps/community/repository/browse_repository.mako', - repo=repo, repository=repository, commit_message=commit_message, is_malicious=is_malicious, @@ -1016,37 +1013,7 @@ # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - if is_gzip( file_path ): - to_html = to_html_str( '\ngzip compressed file\n' ) - elif is_bz2( file_path ): - to_html = to_html_str( '\nbz2 compressed file\n' ) - elif check_zip( file_path ): - to_html = to_html_str( '\nzip compressed file\n' ) - elif check_binary( file_path ): - to_html = to_html_str( '\nBinary file\n' ) - else: - to_html = '' - for i, line in enumerate( open( file_path ) ): - to_html = '%s%s' % ( to_html, to_html_str( line ) ) - if len( to_html ) > MAX_CONTENT_SIZE: - large_str = '\nFile contents truncated because file size is larger than maximum viewing size of %s\n' % util.nice_size( MAX_CONTENT_SIZE ) - to_html = '%s%s' % ( to_html, to_html_str( large_str ) ) - break - return to_html - def __get_files( self, trans, folder_path ): - contents = [] - for item in os.listdir( folder_path ): - # Skip .hg directories - if str( item ).startswith( '.hg' ): - continue - if os.path.isdir( os.path.join( folder_path, item ) ): - # Append a '/' character so that our jquery dynatree will - # function properly. - item = '%s/' % item - contents.append( item ) - if contents: - contents.sort() - return contents + return get_repository_file_contents( file_path ) @web.expose def get_readme( self, trans, **kwd ): """If the received changeset_revision includes a file named readme (case ignored), return it's contents.""" @@ -1558,34 +1525,13 @@ state.inputs = {} return state @web.json - def open_folder( self, trans, repository_id, key ): + def open_folder( self, trans, folder_path ): # The tool shed includes a repository source file browser, which currently depends upon # copies of the hg repository file store in the repo_path for browsing. # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' - repository = trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( repository_id ) ) - folder_path = key - try: - files_list = self.__get_files( trans, folder_path ) - except OSError, e: - if str( e ).find( 'No such file or directory' ) >= 0: - # We have a repository with no contents. - return [] - folder_contents = [] - for filename in files_list: - is_folder = False - if filename and filename[-1] == os.sep: - is_folder = True - if filename: - full_path = os.path.join( folder_path, filename ) - node = { "title": filename, - "isFolder": is_folder, - "isLazy": is_folder, - "tooltip": full_path, - "key": full_path } - folder_contents.append( node ) - return folder_contents + return open_repository_files_folder( trans, folder_path ) @web.expose def preview_tools_in_changeset( self, trans, repository_id, **kwd ): params = util.Params( kwd ) @@ -1769,7 +1715,6 @@ if params.get( 'select_files_to_delete_button', False ): if selected_files_to_delete: selected_files_to_delete = selected_files_to_delete.split( ',' ) - current_working_dir = os.getcwd() # Get the current repository tip. tip = repository.tip for selected_file in selected_files_to_delete: diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c templates/admin/tool_shed_repository/browse_repository.mako --- a/templates/admin/tool_shed_repository/browse_repository.mako +++ b/templates/admin/tool_shed_repository/browse_repository.mako @@ -2,6 +2,17 @@ <%namespace file="/message.mako" import="render_msg" /><%namespace file="/admin/tool_shed_repository/common.mako" import="*" /> +<%def name="stylesheets()"> + ${parent.stylesheets()} + ${h.css( "dynatree_skin/ui.dynatree" )} +</%def> + +<%def name="javascripts()"> + ${parent.javascripts()} + ${h.js( "ui.core", "jquery.dynatree" )} + ${common_javascripts(repository)} +</%def> + <br/><br/><ul class="manage-table-actions"><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> @@ -9,6 +20,9 @@ <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a> + %if repository.tool_dependencies: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a> + %endif </div></ul> @@ -16,4 +30,17 @@ ${render_msg( message, status )} %endif -${render_metadata( repository, can_reset_metadata=False )} +<div class="toolForm"> + <div class="toolFormTitle">Browse ${repository.name} revision ${repository.changeset_revision} files</div> + <div class="toolFormBody"> + <div class="form-row" > + <label>Contents:</label> + <div id="tree" > + Loading... + </div> + </div> + <div class="form-row"> + <div id="file_contents" class="toolParamHelp" style="clear: both;background-color:#FAFAFA;"></div> + </div> + </div> +</div> diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c templates/admin/tool_shed_repository/common.mako --- a/templates/admin/tool_shed_repository/common.mako +++ b/templates/admin/tool_shed_repository/common.mako @@ -1,154 +1,273 @@ -<%def name="render_metadata( repository, can_reset_metadata=False )"> +<%def name="common_javascripts(repository)"> + <script type="text/javascript"> + $(function(){ + $("#tree").ajaxComplete(function(event, XMLHttpRequest, ajaxOptions) { + _log("debug", "ajaxComplete: %o", this); // dom element listening + }); + // --- Initialize sample trees + $("#tree").dynatree({ + title: "${repository.name}", + rootVisible: true, + minExpandLevel: 0, // 1: root node is not collapsible + persist: false, + checkbox: true, + selectMode: 3, + onPostInit: function(isReloading, isError) { + //alert("reloading: "+isReloading+", error:"+isError); + logMsg("onPostInit(%o, %o) - %o", isReloading, isError, this); + // Re-fire onActivate, so the text is updated + this.reactivate(); + }, + fx: { height: "toggle", duration: 200 }, + // initAjax is hard to fake, so we pass the children as object array: + initAjax: {url: "${h.url_for( controller='admin_toolshed', action='open_folder' )}", + dataType: "json", + data: { folder_path: "${repository.repo_files_directory(trans.app)}" }, + }, + onLazyRead: function(dtnode){ + dtnode.appendAjax({ + url: "${h.url_for( controller='admin_toolshed', action='open_folder' )}", + dataType: "json", + data: { folder_path: dtnode.data.key }, + }); + }, + onSelect: function(select, dtnode) { + // Display list of selected nodes + var selNodes = dtnode.tree.getSelectedNodes(); + // convert to title/key array + var selKeys = $.map(selNodes, function(node) { + return node.data.key; + }); + }, + onActivate: function(dtnode) { + var cell = $("#file_contents"); + var selected_value; + if (dtnode.data.key == 'root') { + selected_value = "${repository.repo_files_directory(trans.app)}/"; + } else { + selected_value = dtnode.data.key; + }; + if (selected_value.charAt(selected_value.length-1) != '/') { + // Make ajax call + $.ajax( { + type: "POST", + url: "${h.url_for( controller='admin_toolshed', action='get_file_contents' )}", + dataType: "json", + data: { file_path: selected_value }, + success : function ( data ) { + cell.html( '<label>'+data+'</label>' ) + } + }); + } else { + cell.html( '' ); + }; + }, + }); + }); + </script> +</%def> + +<%def name="render_repository_contents( repository, can_reset_metadata=False )"><div class="toolForm"> - <div class="toolFormTitle">Repository contents</div> + <div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"> - <% metadata = repository.metadata %> - %if metadata: - %if 'tools' in metadata: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Tools</b><i> - click the name to view tool related information</i></td> + <% + metadata = repository.metadata + missing_tool_dependencies = repository.missing_tool_dependencies + installed_tool_dependencies = repository.installed_tool_dependencies + %> + %if missing_tool_dependencies: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Missing tool dependencies</i></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>type</b></td> + <td><b>version</b></td> + </tr> + %for name, requirements_dict in missing_tool_dependencies.items(): + <tr> + <td>${requirements_dict[ 'name' ]}</td> + <td>${requirements_dict[ 'type' ]}</td> + <td>${requirements_dict[ 'version' ]}</td></tr> - </table> - </div> - <div class="form-row"> - <% tool_dicts = metadata[ 'tools' ] %> - <table class="grid"> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if installed_tool_dependencies: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Installed tool dependencies</i></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>type</b></td> + <td><b>version</b></td> + </tr> + %for installed_tool_dependency in installed_tool_dependencies: <tr> - <td><b>name</b></td> - <td><b>description</b></td> - <td><b>version</b></td> - <td><b>requirements</b></td> + <td>${installed_tool_dependency.name}</td> + <td>${installed_tool_dependency.type}</td> + <td>${installed_tool_dependency.version}</td></tr> - %for tool_dict in tool_dicts: - <tr> - <td> - <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=tool_dict[ 'id' ] )}"> - ${tool_dict[ 'name' ]} - </a> - </td> - <td>${tool_dict[ 'description' ]}</td> - <td>${tool_dict[ 'version' ]}</td> - <td> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if 'tools' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Tools</b><i> - click the name to view information about the tool</i></td> + </tr> + </table> + </div> + <div class="form-row"> + <% tool_dicts = metadata[ 'tools' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>description</b></td> + <td><b>version</b></td> + <td><b>requirements</b></td> + </tr> + %for tool_dict in tool_dicts: + <tr> + <td> + <a class="view-info" href="${h.url_for( controller='admin_toolshed', action='view_tool_metadata', repository_id=trans.security.encode_id( repository.id ), tool_id=tool_dict[ 'id' ] )}"> + ${tool_dict[ 'name' ]} + </a> + </td> + <td>${tool_dict[ 'description' ]}</td> + <td>${tool_dict[ 'version' ]}</td> + <td> + <% + if 'requirements' in tool_dict: + requirements = tool_dict[ 'requirements' ] + else: + requirements = None + %> + %if requirements: <% - if 'requirements' in tool_dict: - requirements = tool_dict[ 'requirements' ] - else: - requirements = None + requirements_str = '' + for requirement_dict in tool_dict[ 'requirements' ]: + requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) + requirements_str = requirements_str.rstrip( ', ' ) %> - %if requirements: - <% - requirements_str = '' - for requirement_dict in tool_dict[ 'requirements' ]: - requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) - requirements_str = requirements_str.rstrip( ', ' ) - %> - ${requirements_str} - %else: - none - %endif - </td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'workflows' in metadata: - ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is - ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Workflows</b><i> - click the name to import</i></td> + ${requirements_str} + %else: + none + %endif + </td></tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <% workflow_tups = metadata[ 'workflows' ] %> - <table class="grid"> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if 'workflows' in metadata: + ## metadata[ 'workflows' ] is a list of tuples where each contained tuple is + ## [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Workflows</b><i> - click the name to import</i></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% workflow_tups = metadata[ 'workflows' ] %> + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>steps</b></td> + <td><b>format-version</b></td> + <td><b>annotation</b></td> + </tr> + <% index = 0 %> + %for workflow_tup in workflow_tups: + <% + import os.path + relative_path = workflow_tup[ 0 ] + full_path = os.path.abspath( relative_path ) + workflow_dict = workflow_tup[ 1 ] + workflow_name = workflow_dict[ 'name' ] + ## Initially steps were not stored in the metadata record. + steps = workflow_dict.get( 'steps', [] ) + format_version = workflow_dict[ 'format-version' ] + annotation = workflow_dict[ 'annotation' ] + %><tr> - <td><b>name</b></td> - <td><b>steps</b></td> - <td><b>format-version</b></td> - <td><b>annotation</b></td> + <td> + <div class="menubutton" style="float: left;" id="workflow-${index}-popup"> + ${workflow_name} + <div popupmenu="workflow-${index}-popup"> + <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a> + </div> + </div> + </td> + <td> + %if steps: + ${len( steps )} + %else: + unknown + %endif + </td> + <td>${format_version}</td> + <td>${annotation}</td></tr> - <% index = 0 %> - %for workflow_tup in workflow_tups: - <% - import os.path - relative_path = workflow_tup[ 0 ] - full_path = os.path.abspath( relative_path ) - workflow_dict = workflow_tup[ 1 ] - workflow_name = workflow_dict[ 'name' ] - ## Initially steps were not stored in the metadata record. - steps = workflow_dict.get( 'steps', [] ) - format_version = workflow_dict[ 'format-version' ] - annotation = workflow_dict[ 'annotation' ] - %> - <tr> - <td> - <div class="menubutton" style="float: left;" id="workflow-${index}-popup"> - ${workflow_name} - <div popupmenu="workflow-${index}-popup"> - <a class="action-button" href="${h.url_for( controller='workflow', action='import_workflow', installed_repository_file=full_path, repository_id=trans.security.encode_id( repository.id ) )}">Import to Galaxy</a> - </div> - </div> - </td> - <td> - %if steps: - ${len( steps )} - %else: - unknown - %endif - </td> - <td>${format_version}</td> - <td>${annotation}</td> - </tr> - <% index += 1 %> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif - %if 'datatypes' in metadata: - <div class="form-row"> - <table width="100%"> - <tr bgcolor="#D8D8D8" width="100%"> - <td><b>Data types</b></td> + <% index += 1 %> + %endfor + </table> + </div> + <div style="clear: both"></div> + %endif + %if 'datatypes' in metadata: + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"> + <td><b>Data types</b></td> + </tr> + </table> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <% datatypes_dicts = metadata[ 'datatypes' ] %> + <table class="grid"> + <tr> + <td><b>extension</b></td> + <td><b>type</b></td> + <td><b>mimetype</b></td> + <td><b>subclass</b></td> + </tr> + %for datatypes_dict in datatypes_dicts: + <tr> + <td>${datatypes_dict.get( 'extension', ' ' )}</td> + <td>${datatypes_dict.get( 'dtype', ' ' )}</td> + <td>${datatypes_dict.get( 'mimetype', ' ' )}</td> + <td>${datatypes_dict.get( 'subclass', ' ' )}</td></tr> - </table> - </div> - <div style="clear: both"></div> - <div class="form-row"> - <% datatypes_dicts = metadata[ 'datatypes' ] %> - <table class="grid"> - <tr> - <td><b>extension</b></td> - <td><b>type</b></td> - <td><b>mimetype</b></td> - <td><b>subclass</b></td> - </tr> - %for datatypes_dict in datatypes_dicts: - <% - extension = datatypes_dict.get( 'extension', ' ' ) - dtype = datatypes_dict.get( 'dtype', ' ' ) - mimetype = datatypes_dict.get( 'mimetype', ' ' ) - subclass = datatypes_dict.get( 'subclass', ' ' ) - %> - <tr> - <td>${extension}</td> - <td>${dtype}</td> - <td>${mimetype}</td> - <td>${subclass}</td> - </tr> - %endfor - </table> - </div> - <div style="clear: both"></div> - %endif + %endfor + </table> + </div> + <div style="clear: both"></div> %endif %if can_reset_metadata: <form name="set_metadata" action="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}" method="post"> diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -6,9 +6,12 @@ <ul class="manage-table-actions"><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + %if repository.tool_dependencies: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a> + %endif </div></ul> diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -6,13 +6,13 @@ <ul class="manage-table-actions"><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> %if repository.includes_tools: <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a> %endif - %if tool_dependencies_missing: - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='install_missing_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Install tool dependencies</a> + %if repository.tool_dependencies: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a> %endif <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a></div> @@ -64,5 +64,5 @@ </div></div><p/> -${render_metadata( repository, can_reset_metadata=True )} +${render_repository_contents( repository, can_reset_metadata=True )} <p/> diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c templates/admin/tool_shed_repository/manage_tool_dependencies.mako --- /dev/null +++ b/templates/admin/tool_shed_repository/manage_tool_dependencies.mako @@ -0,0 +1,56 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + +<% import os %> + +<br/><br/> +<ul class="manage-table-actions"> + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + %if repository.includes_tools: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='set_tool_versions', id=trans.security.encode_id( repository.id ) )}">Set tool versions</a> + %endif + %if repository.missing_tool_dependencies: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='install_missing_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Install missing tool dependencies</a> + %endif + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a> + </div> +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">${repository.name} repository's installed tool dependencies</div> + <div class="toolFormBody"> + <div class="form-row"> + <table class="grid"> + %for tool_dependency in repository.tool_dependencies: + <% + name = tool_dependency.name + version = tool_dependency.version + type = tool_dependency.type + installed_changeset_revision = tool_dependency.installed_changeset_revision + uninstalled = tool_dependency.uninstalled + install_dir = os.path.abspath( os.path.join( trans.app.config.tool_dependency_dir, + name, + version, + repository.owner, + repository.name, + installed_changeset_revision ) ) + %> + <tr><td bgcolor="#D8D8D8"><b>Name</b></td><td bgcolor="#D8D8D8">${name}</td></tr> + <tr><th>Version</th><td>${version}</td></tr> + <tr><th>Type</th><td>${type}</td></tr> + <tr><th>Install directory</th><td>${install_dir}</td></tr> + <tr><th>Installed changeset revision</th><td>${installed_changeset_revision}</td></tr> + <tr><th>Uninstalled</th><td>${uninstalled}</td></tr> + %endfor + </table> + <div style="clear: both"></div> + </div> + </div> +</div> diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c templates/admin/tool_shed_repository/view_tool_metadata.mako --- a/templates/admin/tool_shed_repository/view_tool_metadata.mako +++ b/templates/admin/tool_shed_repository/view_tool_metadata.mako @@ -5,9 +5,12 @@ <ul class="manage-table-actions"><li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li><div popupmenu="repository-${repository.id}-popup"> - <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository</a> + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='browse_repository', id=trans.security.encode_id( repository.id ) )}">Browse repository files</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ) )}">Manage repository</a><a class="action-button" href="${h.url_for( controller='admin_toolshed', action='check_for_updates', id=trans.security.encode_id( repository.id ) )}">Get updates</a> + %if repository.tool_dependencies: + <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='manage_tool_dependencies', id=trans.security.encode_id( repository.id ) )}">Manage tool dependencies</a> + %endif <a class="action-button" href="${h.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) )}">Deactivate or Uninstall</a></div></ul> @@ -95,15 +98,27 @@ requirements = None %> %if requirements: - <% - requirements_str = '' - for requirement_dict in metadata[ 'requirements' ]: - requirements_str += '%s (%s), ' % ( requirement_dict[ 'name' ], requirement_dict[ 'type' ] ) - requirements_str = requirements_str.rstrip( ', ' ) - %><div class="form-row"><label>Requirements:</label> - ${requirements_str} + <table class="grid"> + <tr> + <td><b>name</b></td> + <td><b>version</b></td> + <td><b>type</b></td> + </tr> + %for requirement_dict in requirements: + <% + requirement_name = requirement_dict[ 'name' ] or 'not provided' + requirement_version = requirement_dict[ 'version' ] or 'not provided' + requirement_type = requirement_dict[ 'type' ] or 'not provided' + %> + <tr> + <td>${requirement_name}</td> + <td>${requirement_version}</td> + <td>${requirement_type}</td> + </tr> + %endfor + </table><div style="clear: both"></div></div> %endif diff -r 599e16b18e34267a9563f47b1acaa234165482ea -r b1f35669f93c4163cf803d64beb37a1cb0d5381c templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -22,13 +22,13 @@ // initAjax is hard to fake, so we pass the children as object array: initAjax: {url: "${h.url_for( controller='repository', action='open_folder' )}", dataType: "json", - data: { repository_id: "${trans.security.encode_id( repository.id )}", key: "${repository.repo_path}" }, + data: { folder_path: "${repository.repo_path}" }, }, onLazyRead: function(dtnode){ dtnode.appendAjax({ url: "${h.url_for( controller='repository', action='open_folder' )}", dataType: "json", - data: { repository_id: "${trans.security.encode_id( repository.id )}", key: dtnode.data.key }, + data: { folder_path: dtnode.data.key }, }); }, onSelect: function(select, dtnode) { Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Make migration script compatible with MySQL.
by Bitbucket 13 Jun '12

13 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/599e16b18e34/ changeset: 599e16b18e34 user: jgoecks date: 2012-06-13 21:41:52 summary: Make migration script compatible with MySQL. affected #: 1 file diff -r ebd30e5e9120181833621fc9710c1066ad3f9aa7 -r 599e16b18e34267a9563f47b1acaa234165482ea lib/galaxy/model/migrate/versions/0095_hda_subsets.py --- a/lib/galaxy/model/migrate/versions/0095_hda_subsets.py +++ b/lib/galaxy/model/migrate/versions/0095_hda_subsets.py @@ -17,8 +17,8 @@ HistoryDatasetAssociationSubset_table = Table( "history_dataset_association_subset", metadata, Column( "id", Integer, primary_key=True ), - Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), - Column( "history_dataset_association_subset_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), + Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ) ), + Column( "history_dataset_association_subset_id", Integer, ForeignKey( "history_dataset_association.id" ) ), Column( "location", Unicode(255), index=True) ) @@ -32,6 +32,16 @@ except Exception, e: print str(e) log.debug( "Creating history_dataset_association_subset table failed: %s" % str( e ) ) + + # Manually create indexes because they are too long for MySQL databases. + i1 = Index( "ix_hda_id", HistoryDatasetAssociationSubset_table.c.history_dataset_association_id ) + i2 = Index( "ix_hda_subset_id", HistoryDatasetAssociationSubset_table.c.history_dataset_association_subset_id ) + try: + i1.create() + i2.create() + except Exception, e: + print str(e) + log.debug( "Adding indices to table 'history_dataset_association_subset' table failed: %s" % str( e ) ) def downgrade(): metadata.reflect() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Improve dataset fetching in visualizations.
by Bitbucket 13 Jun '12

13 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ebd30e5e9120/ changeset: ebd30e5e9120 user: jgoecks date: 2012-06-13 18:57:41 summary: Improve dataset fetching in visualizations. affected #: 3 files diff -r 5a3c60aca201a3cefc1baef1f945043afc52a3be -r ebd30e5e9120181833621fc9710c1066ad3f9aa7 lib/galaxy/visualization/tracks/data_providers.py --- a/lib/galaxy/visualization/tracks/data_providers.py +++ b/lib/galaxy/visualization/tracks/data_providers.py @@ -965,7 +965,7 @@ f = open( self.original_dataset.file_name ) return f, BigBedFile(file=f) -class BigWigDataProvider (BBIDataProvider ): +class BigWigDataProvider ( BBIDataProvider ): def _get_dataset( self ): if self.converted_dataset is not None: f = open( self.converted_dataset.file_name ) diff -r 5a3c60aca201a3cefc1baef1f945043afc52a3be -r ebd30e5e9120181833621fc9710c1066ad3f9aa7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -468,10 +468,7 @@ def pack_track( track_dict ): dataset_id = track_dict['dataset_id'] hda_ldda = track_dict.get('hda_ldda', 'hda') - if hda_ldda == "hda": - dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - else: - dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( dataset_id ) + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) try: prefs = track_dict['prefs'] @@ -545,6 +542,13 @@ return config + def get_hda_or_ldda( self, trans, hda_ldda, dataset_id ): + """ Returns either HDA or LDDA for hda/ldda and id combination. """ + if hda_ldda == "hda": + return self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) + else: + return trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) + # -- Helper functions -- def _create_visualization( self, trans, title, type, dbkey, slug=None, annotation=None ): diff -r 5a3c60aca201a3cefc1baef1f945043afc52a3be -r ebd30e5e9120181833621fc9710c1066ad3f9aa7 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -177,17 +177,22 @@ @web.json def add_track_async(self, trans, hda_id=None, ldda_id=None): + # Get dataset. if hda_id: hda_ldda = "hda" - dataset = self.get_dataset( trans, hda_id, check_ownership=False, check_accessible=True ) + dataset_id = hda_id elif ldda_id: hda_ldda = "ldda" - dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) + dataset_id = ldda_id + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + + # Get data provider. track_type, _ = dataset.datatype.get_track_type() track_data_provider_class = get_data_provider( original_dataset=dataset ) track_data_provider = track_data_provider_class( original_dataset=dataset ) - track = { + # Get track definition. + return { "track_type": track_type, "name": dataset.name, "hda_ldda": hda_ldda, @@ -197,16 +202,17 @@ "tool": get_tool_def( trans, dataset ), "tool_state": {} } - return track @web.json def bookmarks_from_dataset( self, trans, hda_id=None, ldda_id=None ): if hda_id: hda_ldda = "hda" - dataset = self.get_dataset( trans, hda_id, check_ownership=False, check_accessible=True ) + dataset_id = hda_id elif ldda_id: hda_ldda = "ldda" - dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( ldda_id ) ) + dataset_id = ldda_id + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) + rows = [] if isinstance( dataset.datatype, Bed ): data = RawBedDataProvider( original_dataset=dataset ).get_iterator() @@ -482,7 +488,7 @@ @web.require_login( "use Galaxy visualizations", use_panels=True ) def paramamonster( self, trans, hda_ldda, dataset_id ): # Get dataset. - dataset = self._get_dataset( trans, hda_ldda, dataset_id ) + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) return trans.fill_template_mako( "visualization/paramamonster.mako", dataset=dataset, tool=self.app.toolbox.tools_by_id[ 'cufflinks' ].to_dict( trans, for_display=True ) ) @@ -491,7 +497,7 @@ @web.require_login( "use Galaxy visualizations", use_panels=True ) def circster( self, trans, hda_ldda, dataset_id ): # Get dataset. - dataset = self._get_dataset( trans, hda_ldda, dataset_id ) + dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) # Get genome info. dbkey = dataset.dbkey @@ -535,11 +541,4 @@ # Store msg. data_sources_dict[ source_type ] = { "name" : data_source, "message": msg } - return data_sources_dict - - def _get_dataset( self, trans, hda_ldda, dataset_id ): - """ Returns either HDA or LDDA for hda/ldda and id combination. """ - if hda_ldda == "hda": - return self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - else: - return trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) \ No newline at end of file + return data_sources_dict \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Updates to trackster to work with f93ecd917348 and 4fbd05095ca7.
by Bitbucket 13 Jun '12

13 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/5a3c60aca201/ changeset: 5a3c60aca201 user: jgoecks date: 2012-06-13 18:29:20 summary: Updates to trackster to work with f93ecd917348 and 4fbd05095ca7. affected #: 3 files diff -r f93ecd917348aeef6332a6d441300ab505daad73 -r 5a3c60aca201a3cefc1baef1f945043afc52a3be lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -327,7 +327,7 @@ # Get datasources and check for messages. data_sources = self._get_datasources( trans, dataset ) messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] - msg = _get_highest_priority_msg( messages_list ) + msg = get_highest_priority_msg( messages_list ) if msg: return msg @@ -375,7 +375,7 @@ # Get datasources and check for messages. data_sources = self._get_datasources( trans, dataset ) messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] - return_message = _get_highest_priority_msg( messages_list ) + return_message = get_highest_priority_msg( messages_list ) if return_message: return return_message diff -r f93ecd917348aeef6332a6d441300ab505daad73 -r 5a3c60aca201a3cefc1baef1f945043afc52a3be templates/tracks/browser.mako --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -42,22 +42,21 @@ <script type='text/javascript' src="${h.url_for('/static/scripts/excanvas.js')}"></script><![endif]--> -${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.event.hover","jquery.mousewheel", "jquery.autocomplete", "viz/visualization", "viz/trackster", "viz/trackster_ui", "jquery.ui.sortable.slider", "farbtastic" )} +${h.js( "galaxy.base", "galaxy.panels", "json2", "jquery", "jstorage", "jquery.event.drag", "jquery.event.hover","jquery.mousewheel", "jquery.autocomplete", "mvc/data", "viz/visualization", "viz/trackster", "viz/trackster_ui", "jquery.ui.sortable.slider", "farbtastic" )} <script type="text/javascript"> // // Place URLs here so that url_for can be used to generate them. // galaxy_paths.set({ - visualization_url: "${h.url_for( action='save' )}" + visualization_url: "${h.url_for( action='save' )}", + run_tool_url: "${h.url_for( controller='/api/tools' )}" }); var add_track_async_url = "${h.url_for( action='add_track_async' )}", add_datasets_url = "${h.url_for( action='list_current_history_datasets' )}", default_data_url = "${h.url_for( action='data' )}", - raw_data_url = "${h.url_for( action='raw_data' )}", - run_tool_url = "${h.url_for( action='run_tool' )}", - rerun_tool_url = "${h.url_for( action='rerun_tool' )}", + raw_data_url = "${h.url_for( action='raw_data' )}", reference_url = "${h.url_for( action='reference' )}", chrom_url = "${h.url_for( action='chroms' )}", dataset_state_url = "${h.url_for( action='dataset_state' )}", diff -r f93ecd917348aeef6332a6d441300ab505daad73 -r 5a3c60aca201a3cefc1baef1f945043afc52a3be templates/visualization/paramamonster.mako --- a/templates/visualization/paramamonster.mako +++ b/templates/visualization/paramamonster.mako @@ -35,18 +35,42 @@ ${parent.javascripts()} ${h.templates( "tool_link", "panel_section", "tool_search" )} - ${h.js( "libs/d3", "viz/visualization", "viz/paramamonster", "mvc/tools" )} + ${h.js( "libs/d3", "mvc/data", "mvc/tools", "viz/visualization", "viz/paramamonster" )} <script type="text/javascript"> + var tool; $(function() { // -- Viz set up. -- - var tool = new Tool(JSON.parse('${ h.to_json_string( tool ) }')), - tool_param_tree = new ToolParameterTree({ tool: tool }), - tool_param_tree_view = new ToolParameterTreeView({ model: tool_param_tree }); + tool = new Tool(JSON.parse('${ h.to_json_string( tool ) }')); + // HACK: need to replace \ with \\ due to simplejson bug. + var dataset = new Dataset(JSON.parse('${ h.to_json_string( dataset.get_api_value() ).replace('\\', '\\\\' ) }')), + paramamonster_viz = new ParamaMonsterVisualization({ + tool: tool, + dataset: dataset + }); + viz_view = new ParamaMonsterVisualizationView({ model: paramamonster_viz }); - tool_param_tree_view.render(); - $('#param-tree').append(tool_param_tree_view.$el); + viz_view.render(); + $('.unified-panel-body').append(viz_view.$el); + + // Tool testing. + var regions = [ + new GenomeRegion({ + chrom: 'chr19', + start: '10000', + end: '26000' + }), + new GenomeRegion({ + chrom: 'chr19', + start: '30000', + end: '36000' + }) + ]; + + $.when(tool.rerun(dataset, regions)).then(function(outputs) { + console.log(outputs); + }); }); </script></%def> @@ -59,7 +83,5 @@ <div style="clear: both"></div></div><div class="unified-panel-body"> - <div id="param-tree"></div> - <div id="tile-view"></div></div></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Viz framework: (a) JavaScript support for running tools and enhancements to parameter viz.
by Bitbucket 13 Jun '12

13 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/f93ecd917348/ changeset: f93ecd917348 user: jgoecks date: 2012-06-13 18:10:54 summary: Viz framework: (a) JavaScript support for running tools and enhancements to parameter viz. affected #: 5 files diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 static/scripts/mvc/data.js --- /dev/null +++ b/static/scripts/mvc/data.js @@ -0,0 +1,16 @@ +/** + * A dataset. In Galaxy, datasets are associated with a history, so + * this object is also known as a HistoryDatasetAssociation. + */ +var Dataset = Backbone.Model.extend({ + defaults: { + id: "", + type: "", + name: "", + hda_ldda: "" + } +}); + +var DatasetCollection = Backbone.Collection.extend({ + model: Dataset +}); \ No newline at end of file diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 static/scripts/mvc/tools.js --- a/static/scripts/mvc/tools.js +++ b/static/scripts/mvc/tools.js @@ -51,11 +51,78 @@ } ], - urlRoot: galaxy_paths.attributes.root_path + 'api/tools', + urlRoot: galaxy_paths.get('tool_url'), apply_search_results: function(results) { ( _.indexOf(results, this.attributes.id) !== -1 ? this.show() : this.hide() ); return this.is_visible(); + }, + + /** + * Set a tool input's value. + */ + set_input_value: function(name, value) { + this.get('inputs').find(function(input) { + return input.get('name') === name; + }).set('value', value); + }, + + /** + * Run tool; returns a Deferred that resolves to the tool's output(s). + */ + run: function() { + return this._run() + }, + + /** + * Rerun tool using regions and a target dataset. + */ + rerun: function(target_dataset, regions) { + return this._run({ + action: 'rerun', + target_dataset_id: target_dataset.id, + regions: JSON.stringify(regions) + }); + }, + + /** + * Run tool; returns a Deferred that resolves to the tool's output(s). + * NOTE: this method is a helper method and should not be called directly. + */ + _run: function(additional_params) { + // Create payload. + var payload = _.extend({ + tool_id: this.id + }, additional_params), + input_dict = {}; + this.get('inputs').each(function(input) { + input_dict[input.get('name')] = input.get('value'); + }); + payload.inputs = input_dict; + + // Because job may require indexing datasets, use server-side + // deferred to ensure that job is run. Also use deferred that + // resolves to outputs from tool. + var run_deferred = $.Deferred(), + ss_deferred = new ServerStateDeferred({ + ajax_settings: { + url: this.urlRoot, + data: JSON.stringify(payload), + dataType: "json", + contentType: 'application/json', + type: "POST" + }, + interval: 2000, + success_fn: function(response) { + return response !== "pending"; + } + }); + + // Run job and resolve run_deferred to tool outputs. + $.when(ss_deferred.go()).then(function(result) { + run_deferred.resolve(new DatasetCollection().reset(result)); + }); + return run_deferred; } }); @@ -65,7 +132,9 @@ var ToolInput = Backbone.RelationalModel.extend({ defaults: { name: null, - type: null + label: null, + type: null, + value: null, }, initialize: function() { diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 static/scripts/viz/paramamonster.js --- a/static/scripts/viz/paramamonster.js +++ b/static/scripts/viz/paramamonster.js @@ -38,15 +38,16 @@ var param_samples = params_samples[index], param = param_samples.get('param'), - param_name = param.get('name'), + param_label = param.get('label'), settings = param_samples.get('samples'); // Create leaves when last parameter setting is reached. if (params_samples.length - 1 === index) { return _.map(settings, function(setting) { return { - name: param_name + '=' + setting, - param: param + name: param_label + '=' + setting, + param: param, + value: setting } }); } @@ -54,8 +55,9 @@ // Recurse to handle other parameters. return _.map(settings, function(setting) { return { - name: param_name + '=' + setting, + name: param_label + '=' + setting, param: param, + value: setting, children: create_tree_data(filtered_params_samples, index + 1) } }); @@ -94,104 +96,17 @@ }); /** - * A track in a genome browser. + * ParamaMonster visualization model. */ -var Track = Backbone.Model.extend({ - defaults: { - dataset: null - } -}); - -var FeatureTrack = Track.extend({ - defaults: { - track: null - }, +var ParamaMonsterVisualization = Visualization.extend({ + defaults: _.extend({}, Visualization.prototype.defaults, { + tool: null, + parameter_tree: null, + regions: null + }), - /** - * Draw FeatureTrack tile. - * @param result result from server - * @param cxt canvas context to draw on - * @param mode mode to draw in - * @param resolution view resolution - * @param region region to draw - * @param w_scale pixels per base - * @param ref_seq reference sequence data - */ - draw_tile: function(result, ctx, mode, resolution, region, w_scale, ref_seq) { - var track = this, - canvas = ctx.canvas, - tile_low = region.get('start'), - tile_high = region.get('end'), - min_height = 25, - left_offset = this.left_offset; - - // Drawing the summary tree (feature coverage histogram) - if (mode === "summary_tree" || mode === "Histogram") { - // Get summary tree data if necessary and set max if there is one. - if (result.dataset_type !== "summary_tree") { - var st_data = this.get_summary_tree_data(result.data, tile_low, tile_high, 200); - if (result.max) { - st_data.max = result.max; - } - result = st_data; - } - // Paint summary tree into canvas - var painter = new painters.SummaryTreePainter(result, tile_low, tile_high, this.prefs); - painter.draw(ctx, canvas.width, canvas.height, w_scale); - return new SummaryTreeTile(track, tile_index, resolution, canvas, result.data, result.max); - } - - // Handle row-by-row tracks - - // Preprocessing: filter features and determine whether all unfiltered features have been slotted. - var - filtered = [], - slots = this.slotters[w_scale].slots; - all_slotted = true; - if ( result.data ) { - var filters = this.filters_manager.filters; - for (var i = 0, len = result.data.length; i < len; i++) { - var feature = result.data[i]; - var hide_feature = false; - var filter; - for (var f = 0, flen = filters.length; f < flen; f++) { - filter = filters[f]; - filter.update_attrs(feature); - if (!filter.keep(feature)) { - hide_feature = true; - break; - } - } - if (!hide_feature) { - // Feature visible. - filtered.push(feature); - // Set flag if not slotted. - if ( !(feature[0] in slots) ) { - all_slotted = false; - } - } - } - } - - // Create painter. - var filter_alpha_scaler = (this.filters_manager.alpha_filter ? new FilterScaler(this.filters_manager.alpha_filter) : null); - var filter_height_scaler = (this.filters_manager.height_filter ? new FilterScaler(this.filters_manager.height_filter) : null); - // HACK: ref_seq will only be defined for ReadTracks, and only the ReadPainter accepts that argument - var painter = new (this.painter)(filtered, tile_low, tile_high, this.prefs, mode, filter_alpha_scaler, filter_height_scaler, ref_seq); - var feature_mapper = null; - - // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); - ctx.fillStyle = this.prefs.block_color; - ctx.font = ctx.canvas.manager.default_font; - ctx.textAlign = "right"; - - if (result.data) { - // Draw features. - feature_mapper = painter.draw(ctx, canvas.width, canvas.height, w_scale, slots); - feature_mapper.translation = -left_offset; - } - - return new FeatureTrackTile(track, tile_index, resolution, canvas, result.data, w_scale, mode, result.message, all_slotted, feature_mapper); + initialize: function(options) { + this.set('parameter_tree', new ToolParameterTree({ tool: this.get('tool') })); } }); @@ -207,7 +122,6 @@ className: 'tool-parameter-tree', initialize: function(options) { - this.model = options.model; }, render: function() { @@ -244,7 +158,32 @@ .attr("class", "node") .attr("transform", function(d) { return "translate(" + d.y + "," + d.x + ")"; }); - // Set up behavior when node is clicked. + node.append("circle") + .attr("r", 4.5); + + node.append("text") + .attr("dx", function(d) { return d.children ? -8 : 8; }) + .attr("dy", 3) + .attr("text-anchor", function(d) { return d.children ? "end" : "start"; }) + .text(function(d) { return d.name; }); + } +}); + +var ParamaMonsterVisualizationView = Backbone.View.extend({ + className: 'paramamonster', + + initialize: function(options) { + + }, + + render: function() { + // Set up tool parameter tree. + var tool_param_tree_view = new ToolParameterTreeView({ model: this.model.get('parameter_tree') }); + tool_param_tree_view.render(); + this.$el.append(tool_param_tree_view.$el); + + // When node clicked in tree, run tool and show tiles. + var node = d3.select(tool_param_tree_view.$el[0]).selectAll("g.node") node.on("click", function(d, i) { console.log(d, i); @@ -256,14 +195,6 @@ // Display tiles for region(s) of interest. }); - - node.append("circle") - .attr("r", 4.5); - - node.append("text") - .attr("dx", function(d) { return d.children ? -8 : 8; }) - .attr("dy", 3) - .attr("text-anchor", function(d) { return d.children ? "end" : "start"; }) - .text(function(d) { return d.name; }); - } + + }, }); \ No newline at end of file diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -11,11 +11,10 @@ /** * Implementation of a server-state based deferred. Server is repeatedly polled, and when * condition is met, deferred is resolved. - */ + */ var ServerStateDeferred = Backbone.Model.extend({ defaults: { - url: null, - url_params: {}, + ajax_settings: {}, interval: 1000, success_fn: function(result) { return true; } }, @@ -26,10 +25,11 @@ go: function() { var deferred = $.Deferred(), self = this, + ajax_settings = self.get('ajax_settings'), success_fn = self.get('success_fn'), interval = self.get('interval'), _go = function() { - $.getJSON(self.get('url'), self.get('url_params'), function(result) { + $.ajax(ajax_settings).success(function(result) { if (success_fn(result)) { // Result is good, so resolve. deferred.resolve(result); @@ -372,6 +372,14 @@ return this.get('chrom') + ":" + this.get('start') + "-" + this.get('end'); }, + toJSON: function() { + return { + chrom: this.get('chrom'), + start: this.get('start'), + end: this.get('end') + } + }, + /** * Compute the type of overlap between this region and another region. The overlap is computed relative to the given/second region; * hence, OVERLAP_START indicates that the first region overlaps the start (but not the end) of the second region. @@ -495,19 +503,6 @@ }); /** - * A dataset. In Galaxy, datasets are associated with a history, so - * this object is also known as a HistoryDatasetAssociation. - */ -var Dataset = Backbone.Model.extend({ - defaults: { - id: "", - type: "", - name: "", - hda_ldda: "" - } -}); - -/** * A histogram dataset. */ var HistogramDataset = Backbone.Model.extend({ diff -r 7387d416d655e086ad3b792058069ea82ce23a3c -r f93ecd917348aeef6332a6d441300ab505daad73 templates/base_panels.mako --- a/templates/base_panels.mako +++ b/templates/base_panels.mako @@ -52,7 +52,8 @@ // Set up needed paths. var galaxy_paths = new GalaxyPaths({ root_path: '${h.url_for( "/" )}', - image_path: '${h.url_for( "/static/images" )}' + image_path: '${h.url_for( "/static/images" )}', + tool_url: '${h.url_for( controller="/api/tools" )}' }); </script></%def> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Remove debugging statement.
by Bitbucket 13 Jun '12

13 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7387d416d655/ changeset: 7387d416d655 user: jgoecks date: 2012-06-13 17:35:25 summary: Remove debugging statement. affected #: 1 file diff -r 7705869d2c7798dbd31b30d6a229cbc3b9ab3e87 -r 7387d416d655e086ad3b792058069ea82ce23a3c lib/galaxy/web/api/tools.py --- a/lib/galaxy/web/api/tools.py +++ b/lib/galaxy/web/api/tools.py @@ -135,7 +135,6 @@ # Run tool on region if region is specificied. run_on_regions = False regions = from_json_string( payload.get( 'regions', None ) ) - print regions, payload if regions: if isinstance( regions, dict ): # Regions is a single region. Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Method name updates related to 4fbd05095ca7
by Bitbucket 13 Jun '12

13 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/7705869d2c77/ changeset: 7705869d2c77 user: jgoecks date: 2012-06-13 17:34:09 summary: Method name updates related to 4fbd05095ca7 affected #: 1 file diff -r 77ceb114bf57172579310a0b4347da0f5f46dec6 -r 7705869d2c7798dbd31b30d6a229cbc3b9ab3e87 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py +++ b/lib/galaxy/web/controllers/tracks.py @@ -273,7 +273,7 @@ # Dataset check. dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - msg = self._check_dataset_state( trans, dataset ) + msg = self.check_dataset_state( trans, dataset ) if msg: return msg @@ -301,7 +301,7 @@ # Dataset check. dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) - msg = self._check_dataset_state( trans, dataset ) + msg = self.check_dataset_state( trans, dataset ) if not msg: msg = messages.DATA @@ -320,7 +320,7 @@ dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) - msg = self._check_dataset_state( trans, dataset ) + msg = self.check_dataset_state( trans, dataset ) if msg: return msg @@ -368,7 +368,7 @@ dataset = self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: dataset = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( trans.security.decode_id( dataset_id ) ) - msg = self._check_dataset_state( trans, dataset ) + msg = self.check_dataset_state( trans, dataset ) if msg: return msg @@ -530,7 +530,7 @@ msg = None else: # Convert. - msg = self._convert_dataset( trans, dataset, data_source ) + msg = self.convert_dataset( trans, dataset, data_source ) # Store msg. data_sources_dict[ source_type ] = { "name" : data_source, "message": msg } 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: dannon: Initial commit of Galaxy Documentation.
by Bitbucket 13 Jun '12

13 Jun '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/77ceb114bf57/ changeset: 77ceb114bf57 user: dannon date: 2012-06-13 17:31:00 summary: Initial commit of Galaxy Documentation. affected #: 75 files diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/Makefile --- /dev/null +++ b/doc/Makefile @@ -0,0 +1,153 @@ +# Makefile for Sphinx documentation +# + +# You can set these variables from the command line. +SPHINXOPTS = +SPHINXBUILD = sphinx-build +PAPER = +BUILDDIR = build + +# Internal variables. +PAPEROPT_a4 = -D latex_paper_size=a4 +PAPEROPT_letter = -D latex_paper_size=letter +ALLSPHINXOPTS = -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source +# the i18n builder cannot share the environment and doctrees with the others +I18NSPHINXOPTS = $(PAPEROPT_$(PAPER)) $(SPHINXOPTS) source + +.PHONY: help clean html dirhtml singlehtml pickle json htmlhelp qthelp devhelp epub latex latexpdf text man changes linkcheck doctest gettext + +help: + @echo "Please use \`make <target>' where <target> is one of" + @echo " html to make standalone HTML files" + @echo " dirhtml to make HTML files named index.html in directories" + @echo " singlehtml to make a single large HTML file" + @echo " pickle to make pickle files" + @echo " json to make JSON files" + @echo " htmlhelp to make HTML files and a HTML help project" + @echo " qthelp to make HTML files and a qthelp project" + @echo " devhelp to make HTML files and a Devhelp project" + @echo " epub to make an epub" + @echo " latex to make LaTeX files, you can set PAPER=a4 or PAPER=letter" + @echo " latexpdf to make LaTeX files and run them through pdflatex" + @echo " text to make text files" + @echo " man to make manual pages" + @echo " texinfo to make Texinfo files" + @echo " info to make Texinfo files and run them through makeinfo" + @echo " gettext to make PO message catalogs" + @echo " changes to make an overview of all changed/added/deprecated items" + @echo " linkcheck to check all external links for integrity" + @echo " doctest to run all doctests embedded in the documentation (if enabled)" + +clean: + -rm -rf $(BUILDDIR)/* + +html: + $(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/html." + +dirhtml: + $(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml + @echo + @echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml." + +singlehtml: + $(SPHINXBUILD) -b singlehtml $(ALLSPHINXOPTS) $(BUILDDIR)/singlehtml + @echo + @echo "Build finished. The HTML page is in $(BUILDDIR)/singlehtml." + +pickle: + $(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle + @echo + @echo "Build finished; now you can process the pickle files." + +json: + $(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json + @echo + @echo "Build finished; now you can process the JSON files." + +htmlhelp: + $(SPHINXBUILD) -b htmlhelp $(ALLSPHINXOPTS) $(BUILDDIR)/htmlhelp + @echo + @echo "Build finished; now you can run HTML Help Workshop with the" \ + ".hhp project file in $(BUILDDIR)/htmlhelp." + +qthelp: + $(SPHINXBUILD) -b qthelp $(ALLSPHINXOPTS) $(BUILDDIR)/qthelp + @echo + @echo "Build finished; now you can run "qcollectiongenerator" with the" \ + ".qhcp project file in $(BUILDDIR)/qthelp, like this:" + @echo "# qcollectiongenerator $(BUILDDIR)/qthelp/Galaxy.qhcp" + @echo "To view the help file:" + @echo "# assistant -collectionFile $(BUILDDIR)/qthelp/Galaxy.qhc" + +devhelp: + $(SPHINXBUILD) -b devhelp $(ALLSPHINXOPTS) $(BUILDDIR)/devhelp + @echo + @echo "Build finished." + @echo "To view the help file:" + @echo "# mkdir -p $$HOME/.local/share/devhelp/Galaxy" + @echo "# ln -s $(BUILDDIR)/devhelp $$HOME/.local/share/devhelp/Galaxy" + @echo "# devhelp" + +epub: + $(SPHINXBUILD) -b epub $(ALLSPHINXOPTS) $(BUILDDIR)/epub + @echo + @echo "Build finished. The epub file is in $(BUILDDIR)/epub." + +latex: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo + @echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex." + @echo "Run \`make' in that directory to run these through (pdf)latex" \ + "(use \`make latexpdf' here to do that automatically)." + +latexpdf: + $(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex + @echo "Running LaTeX files through pdflatex..." + $(MAKE) -C $(BUILDDIR)/latex all-pdf + @echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex." + +text: + $(SPHINXBUILD) -b text $(ALLSPHINXOPTS) $(BUILDDIR)/text + @echo + @echo "Build finished. The text files are in $(BUILDDIR)/text." + +man: + $(SPHINXBUILD) -b man $(ALLSPHINXOPTS) $(BUILDDIR)/man + @echo + @echo "Build finished. The manual pages are in $(BUILDDIR)/man." + +texinfo: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo + @echo "Build finished. The Texinfo files are in $(BUILDDIR)/texinfo." + @echo "Run \`make' in that directory to run these through makeinfo" \ + "(use \`make info' here to do that automatically)." + +info: + $(SPHINXBUILD) -b texinfo $(ALLSPHINXOPTS) $(BUILDDIR)/texinfo + @echo "Running Texinfo files through makeinfo..." + make -C $(BUILDDIR)/texinfo info + @echo "makeinfo finished; the Info files are in $(BUILDDIR)/texinfo." + +gettext: + $(SPHINXBUILD) -b gettext $(I18NSPHINXOPTS) $(BUILDDIR)/locale + @echo + @echo "Build finished. The message catalogs are in $(BUILDDIR)/locale." + +changes: + $(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes + @echo + @echo "The overview file is in $(BUILDDIR)/changes." + +linkcheck: + $(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck + @echo + @echo "Link check complete; look for any errors in the above output " \ + "or in $(BUILDDIR)/linkcheck/output.txt." + +doctest: + $(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest + @echo "Testing of doctests in the sources finished, look at the " \ + "results in $(BUILDDIR)/doctest/output.txt." diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/conf.py --- /dev/null +++ b/doc/source/conf.py @@ -0,0 +1,254 @@ +# -*- coding: utf-8 -*- +# +# Galaxy documentation build configuration file, created by +# sphinx-quickstart on Tue Mar 6 10:44:44 2012. +# +# This file is execfile()d with the current directory set to its containing dir. +# +# Note that not all possible configuration values are present in this +# autogenerated file. +# +# All configuration values have a default; values that are commented out +# serve to show the default. + +import sys, os + + +####### REQUIRED GALAXY INCLUDES + +sys.path.append(os.path.join(os.getcwd(), '../../lib')) +import galaxy +from galaxy import eggs + +####### + +# If extensions (or modules to document with autodoc) are in another directory, +# add these directories to sys.path here. If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. +#sys.path.insert(0, os.path.abspath('.')) + +# -- General configuration ----------------------------------------------------- + +# If your documentation needs a minimal Sphinx version, state it here. +#needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be extensions +# coming with Sphinx (named 'sphinx.ext.*') or your custom ones. +extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.viewcode'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +#configure default autodoc's action +autodoc_default_flags = ['members', 'undoc-members'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +#source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'Galaxy' +copyright = u'2012, Galaxy Team' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +# version = '1' +# The full version, including alpha/beta/rc tags. +# release = '1' + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +#language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +#today = '' +# Else, today_fmt is used as the format for a strftime call. +#today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. +exclude_patterns = [] + +# The reST default role (used for this markup: `text`) to use for all documents. +#default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +#add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +#show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +#modindex_common_prefix = [] + + +# -- Options for HTML output --------------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. +html_theme = 'default' + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +#html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +#html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# "<project> v<release> documentation". +#html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +#html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +#html_logo = None + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +#html_favicon = None + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +#html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +#html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +#html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +#html_additional_pages = {} + +# If false, no module index is generated. +#html_domain_indices = True + +# If false, no index is generated. +#html_use_index = True + +# If true, the index is split into individual pages for each letter. +#html_split_index = False + +# If true, links to the reST sources are added to the pages. +#html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +#html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +#html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a <link> tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +#html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +#html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'Galaxydoc' + + +# -- Options for LaTeX output -------------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +#'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, author, documentclass [howto/manual]). +latex_documents = [ + ('index', 'Galaxy.tex', u'Galaxy Documentation', + u'Galaxy Team', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output -------------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', 'galaxy', u'Galaxy Documentation', + [u'Galaxy Team'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------------ + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', 'Galaxy', u'Galaxy Documentation', + u'Galaxy Team', 'Galaxy', 'Data intensive biology for everyone.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +#texinfo_appendices = [] + +# If false, no module index is generated. +#texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +#texinfo_show_urls = 'footnote' diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/index.rst --- /dev/null +++ b/doc/source/index.rst @@ -0,0 +1,29 @@ +Galaxy Documentation +******************** + +Galaxy is an open, web-based platform for accessible, reproducible, and +transparent computational biomedical research. + - Accessible: Users without programming experience can easily specify + parameters and run tools and workflows. + - Reproducible: Galaxy captures information so that any user can repeat and + understand a complete computational analysis. + - Transparent: Users share and publish analyses via the web and create + Pages, interactive, web-based documents that describe a complete + analysis. + +Contents +======== +.. toctree:: + :maxdepth: 4 + + API Documentation <lib/galaxy.web.api> + + Application Documentation <lib/galaxy> + +Indices and tables +================== + +* :ref:`genindex` +* :ref:`modindex` +* :ref:`search` + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/fpconst.rst --- /dev/null +++ b/doc/source/lib/fpconst.rst @@ -0,0 +1,7 @@ +fpconst Module +============== + +.. automodule:: fpconst + :members: + :undoc-members: + :show-inheritance: diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.actions.rst --- /dev/null +++ b/doc/source/lib/galaxy.actions.rst @@ -0,0 +1,11 @@ +actions Package +=============== + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.actions.admin + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.datatypes.converters.rst --- /dev/null +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -0,0 +1,251 @@ +converters Package +================== + +:mod:`bed_to_genetrack_converter` Module +---------------------------------------- + +.. automodule:: galaxy.datatypes.converters.bed_to_genetrack_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`bed_to_gff_converter` Module +---------------------------------- + +.. automodule:: galaxy.datatypes.converters.bed_to_gff_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`bedgraph_to_array_tree_converter` Module +---------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.bedgraph_to_array_tree_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`bgzip` Module +------------------- + +.. automodule:: galaxy.datatypes.converters.bgzip + :members: + :undoc-members: + :show-inheritance: + +:mod:`fasta_to_len` Module +-------------------------- + +.. automodule:: galaxy.datatypes.converters.fasta_to_len + :members: + :undoc-members: + :show-inheritance: + +:mod:`fasta_to_tabular_converter` Module +---------------------------------------- + +.. automodule:: galaxy.datatypes.converters.fasta_to_tabular_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`fastq_to_fqtoc` Module +---------------------------- + +.. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc + :members: + :undoc-members: + :show-inheritance: + +:mod:`fastqsolexa_to_fasta_converter` Module +-------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_fasta_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`fastqsolexa_to_qual_converter` Module +------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.fastqsolexa_to_qual_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`gff_to_bed_converter` Module +---------------------------------- + +.. automodule:: galaxy.datatypes.converters.gff_to_bed_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`gff_to_interval_index_converter` Module +--------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.gff_to_interval_index_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`interval_to_bed_converter` Module +--------------------------------------- + +.. automodule:: galaxy.datatypes.converters.interval_to_bed_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`interval_to_bedstrict_converter` Module +--------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.interval_to_bedstrict_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`interval_to_coverage` Module +---------------------------------- + +.. automodule:: galaxy.datatypes.converters.interval_to_coverage + :members: + :undoc-members: + :show-inheritance: + +:mod:`interval_to_interval_index_converter` Module +-------------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.interval_to_interval_index_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`interval_to_summary_tree_converter` Module +------------------------------------------------ + +.. automodule:: galaxy.datatypes.converters.interval_to_summary_tree_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`interval_to_tabix_converter` Module +----------------------------------------- + +.. automodule:: galaxy.datatypes.converters.interval_to_tabix_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`lped_to_fped_converter` Module +------------------------------------ + +.. automodule:: galaxy.datatypes.converters.lped_to_fped_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`lped_to_pbed_converter` Module +------------------------------------ + +.. automodule:: galaxy.datatypes.converters.lped_to_pbed_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`maf_to_fasta_converter` Module +------------------------------------ + +.. automodule:: galaxy.datatypes.converters.maf_to_fasta_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`maf_to_interval_converter` Module +--------------------------------------- + +.. automodule:: galaxy.datatypes.converters.maf_to_interval_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`pbed_ldreduced_converter` Module +-------------------------------------- + +.. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`pbed_to_lped_converter` Module +------------------------------------ + +.. automodule:: galaxy.datatypes.converters.pbed_to_lped_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`picard_interval_list_to_bed6_converter` Module +---------------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.picard_interval_list_to_bed6_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`sam_or_bam_to_summary_tree_converter` Module +-------------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.sam_or_bam_to_summary_tree_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`sam_to_bam` Module +------------------------ + +.. automodule:: galaxy.datatypes.converters.sam_to_bam + :members: + :undoc-members: + :show-inheritance: + +:mod:`vcf_to_interval_index_converter` Module +--------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.vcf_to_interval_index_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`vcf_to_summary_tree_converter` Module +------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.vcf_to_summary_tree_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`vcf_to_vcf_bgzip` Module +------------------------------ + +.. automodule:: galaxy.datatypes.converters.vcf_to_vcf_bgzip + :members: + :undoc-members: + :show-inheritance: + +:mod:`wiggle_to_array_tree_converter` Module +-------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.wiggle_to_array_tree_converter + :members: + :undoc-members: + :show-inheritance: + +:mod:`wiggle_to_simple_converter` Module +---------------------------------------- + +.. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.datatypes.display_applications.rst --- /dev/null +++ b/doc/source/lib/galaxy.datatypes.display_applications.rst @@ -0,0 +1,27 @@ +display_applications Package +============================ + +:mod:`application` Module +------------------------- + +.. automodule:: galaxy.datatypes.display_applications.application + :members: + :undoc-members: + :show-inheritance: + +:mod:`parameters` Module +------------------------ + +.. automodule:: galaxy.datatypes.display_applications.parameters + :members: + :undoc-members: + :show-inheritance: + +:mod:`util` Module +------------------ + +.. automodule:: galaxy.datatypes.display_applications.util + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.datatypes.rst --- /dev/null +++ b/doc/source/lib/galaxy.datatypes.rst @@ -0,0 +1,156 @@ +datatypes Package +================= + +:mod:`assembly` Module +---------------------- + +.. automodule:: galaxy.datatypes.assembly + :members: + :undoc-members: + :show-inheritance: + +:mod:`binary` Module +-------------------- + +.. automodule:: galaxy.datatypes.binary + :members: + :undoc-members: + :show-inheritance: + +:mod:`checkers` Module +---------------------- + +.. automodule:: galaxy.datatypes.checkers + :members: + :undoc-members: + :show-inheritance: + +:mod:`chrominfo` Module +----------------------- + +.. automodule:: galaxy.datatypes.chrominfo + :members: + :undoc-members: + :show-inheritance: + +:mod:`coverage` Module +---------------------- + +.. automodule:: galaxy.datatypes.coverage + :members: + :undoc-members: + :show-inheritance: + +:mod:`data` Module +------------------ + +.. automodule:: galaxy.datatypes.data + :members: + :undoc-members: + :show-inheritance: + +:mod:`genetics` Module +---------------------- + +.. automodule:: galaxy.datatypes.genetics + :members: + :undoc-members: + :show-inheritance: + +:mod:`images` Module +-------------------- + +.. automodule:: galaxy.datatypes.images + :members: + :undoc-members: + :show-inheritance: + +:mod:`interval` Module +---------------------- + +.. automodule:: galaxy.datatypes.interval + :members: + :undoc-members: + :show-inheritance: + +:mod:`metadata` Module +---------------------- + +.. automodule:: galaxy.datatypes.metadata + :members: + :undoc-members: + :show-inheritance: + +:mod:`ngsindex` Module +---------------------- + +.. automodule:: galaxy.datatypes.ngsindex + :members: + :undoc-members: + :show-inheritance: + +:mod:`qualityscore` Module +-------------------------- + +.. automodule:: galaxy.datatypes.qualityscore + :members: + :undoc-members: + :show-inheritance: + +:mod:`registry` Module +---------------------- + +.. automodule:: galaxy.datatypes.registry + :members: + :undoc-members: + :show-inheritance: + +:mod:`sequence` Module +---------------------- + +.. automodule:: galaxy.datatypes.sequence + :members: + :undoc-members: + :show-inheritance: + +:mod:`sniff` Module +------------------- + +.. automodule:: galaxy.datatypes.sniff + :members: + :undoc-members: + :show-inheritance: + +:mod:`tabular` Module +--------------------- + +.. automodule:: galaxy.datatypes.tabular + :members: + :undoc-members: + :show-inheritance: + +:mod:`tracks` Module +-------------------- + +.. automodule:: galaxy.datatypes.tracks + :members: + :undoc-members: + :show-inheritance: + +:mod:`xml` Module +----------------- + +.. automodule:: galaxy.datatypes.xml + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.datatypes.converters + galaxy.datatypes.display_applications + galaxy.datatypes.util + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.datatypes.util.rst --- /dev/null +++ b/doc/source/lib/galaxy.datatypes.util.rst @@ -0,0 +1,27 @@ +util Package +============ + +:mod:`util` Package +------------------- + +.. automodule:: galaxy.datatypes.util + :members: + :undoc-members: + :show-inheritance: + +:mod:`gff_util` Module +---------------------- + +.. automodule:: galaxy.datatypes.util.gff_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`image_util` Module +------------------------ + +.. automodule:: galaxy.datatypes.util.image_util + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.eggs.rst --- /dev/null +++ b/doc/source/lib/galaxy.eggs.rst @@ -0,0 +1,27 @@ +eggs Package +============ + +:mod:`eggs` Package +------------------- + +.. automodule:: galaxy.eggs + :members: + :undoc-members: + :show-inheritance: + +:mod:`dist` Module +------------------ + +.. automodule:: galaxy.eggs.dist + :members: + :undoc-members: + :show-inheritance: + +:mod:`scramble` Module +---------------------- + +.. automodule:: galaxy.eggs.scramble + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.exceptions.rst --- /dev/null +++ b/doc/source/lib/galaxy.exceptions.rst @@ -0,0 +1,11 @@ +exceptions Package +================== + +:mod:`exceptions` Package +------------------------- + +.. automodule:: galaxy.exceptions + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.external_services.result_handlers.rst --- /dev/null +++ b/doc/source/lib/galaxy.external_services.result_handlers.rst @@ -0,0 +1,11 @@ +result_handlers Package +======================= + +:mod:`basic` Module +------------------- + +.. automodule:: galaxy.external_services.result_handlers.basic + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.external_services.rst --- /dev/null +++ b/doc/source/lib/galaxy.external_services.rst @@ -0,0 +1,34 @@ +external_services Package +========================= + +:mod:`actions` Module +--------------------- + +.. automodule:: galaxy.external_services.actions + :members: + :undoc-members: + :show-inheritance: + +:mod:`parameters` Module +------------------------ + +.. automodule:: galaxy.external_services.parameters + :members: + :undoc-members: + :show-inheritance: + +:mod:`service` Module +--------------------- + +.. automodule:: galaxy.external_services.service + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.external_services.result_handlers + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.forms.rst --- /dev/null +++ b/doc/source/lib/galaxy.forms.rst @@ -0,0 +1,11 @@ +forms Package +============= + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.forms.forms + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.actions.rst --- /dev/null +++ b/doc/source/lib/galaxy.jobs.actions.rst @@ -0,0 +1,19 @@ +actions Package +=============== + +:mod:`actions` Package +---------------------- + +.. automodule:: galaxy.jobs.actions + :members: + :undoc-members: + :show-inheritance: + +:mod:`post` Module +------------------ + +.. automodule:: galaxy.jobs.actions.post + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.deferred.rst --- /dev/null +++ b/doc/source/lib/galaxy.jobs.deferred.rst @@ -0,0 +1,51 @@ +deferred Package +================ + +:mod:`deferred` Package +----------------------- + +.. automodule:: galaxy.jobs.deferred + :members: + :undoc-members: + :show-inheritance: + +:mod:`data_transfer` Module +--------------------------- + +.. automodule:: galaxy.jobs.deferred.data_transfer + :members: + :undoc-members: + :show-inheritance: + +:mod:`genome_transfer` Module +----------------------------- + +.. automodule:: galaxy.jobs.deferred.genome_transfer + :members: + :undoc-members: + :show-inheritance: + +:mod:`liftover_transfer` Module +------------------------------- + +.. automodule:: galaxy.jobs.deferred.liftover_transfer + :members: + :undoc-members: + :show-inheritance: + +:mod:`manual_data_transfer` Module +---------------------------------- + +.. automodule:: galaxy.jobs.deferred.manual_data_transfer + :members: + :undoc-members: + :show-inheritance: + +:mod:`pacific_biosciences_smrt_portal` Module +--------------------------------------------- + +.. automodule:: galaxy.jobs.deferred.pacific_biosciences_smrt_portal + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.rst --- /dev/null +++ b/doc/source/lib/galaxy.jobs.rst @@ -0,0 +1,45 @@ +jobs Package +============ + +:mod:`jobs` Package +------------------- + +.. automodule:: galaxy.jobs + :members: + :undoc-members: + :show-inheritance: + +:mod:`handler` Module +--------------------- + +.. automodule:: galaxy.jobs.handler + :members: + :undoc-members: + :show-inheritance: + +:mod:`manager` Module +--------------------- + +.. automodule:: galaxy.jobs.manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`transfer_manager` Module +------------------------------ + +.. automodule:: galaxy.jobs.transfer_manager + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.jobs.actions + galaxy.jobs.deferred + galaxy.jobs.runners + galaxy.jobs.splitters + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.runners.rst --- /dev/null +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -0,0 +1,59 @@ +runners Package +=============== + +:mod:`runners` Package +---------------------- + +.. automodule:: galaxy.jobs.runners + :members: + :undoc-members: + :show-inheritance: + +:mod:`drmaa` Module +------------------- + +.. automodule:: galaxy.jobs.runners.drmaa + :members: + :undoc-members: + :show-inheritance: + +:mod:`local` Module +------------------- + +.. automodule:: galaxy.jobs.runners.local + :members: + :undoc-members: + :show-inheritance: + +:mod:`lwr` Module +----------------- + +.. automodule:: galaxy.jobs.runners.lwr + :members: + :undoc-members: + :show-inheritance: + +:mod:`pbs` Module +----------------- + +.. automodule:: galaxy.jobs.runners.pbs + :members: + :undoc-members: + :show-inheritance: + +:mod:`sge` Module +----------------- + +.. automodule:: galaxy.jobs.runners.sge + :members: + :undoc-members: + :show-inheritance: + +:mod:`tasks` Module +------------------- + +.. automodule:: galaxy.jobs.runners.tasks + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.jobs.splitters.rst --- /dev/null +++ b/doc/source/lib/galaxy.jobs.splitters.rst @@ -0,0 +1,19 @@ +splitters Package +================= + +:mod:`basic` Module +------------------- + +.. automodule:: galaxy.jobs.splitters.basic + :members: + :undoc-members: + :show-inheritance: + +:mod:`multi` Module +------------------- + +.. automodule:: galaxy.jobs.splitters.multi + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.model.migrate.rst --- /dev/null +++ b/doc/source/lib/galaxy.model.migrate.rst @@ -0,0 +1,11 @@ +migrate Package +=============== + +:mod:`check` Module +------------------- + +.. automodule:: galaxy.model.migrate.check + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.model.orm.ext.rst --- /dev/null +++ b/doc/source/lib/galaxy.model.orm.ext.rst @@ -0,0 +1,19 @@ +ext Package +=========== + +:mod:`ext` Package +------------------ + +.. automodule:: galaxy.model.orm.ext + :members: + :undoc-members: + :show-inheritance: + +:mod:`assignmapper` Module +-------------------------- + +.. automodule:: galaxy.model.orm.ext.assignmapper + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.model.orm.rst --- /dev/null +++ b/doc/source/lib/galaxy.model.orm.rst @@ -0,0 +1,26 @@ +orm Package +=========== + +:mod:`orm` Package +------------------ + +.. automodule:: galaxy.model.orm + :members: + :undoc-members: + :show-inheritance: + +:mod:`logging_connection_proxy` Module +-------------------------------------- + +.. automodule:: galaxy.model.orm.logging_connection_proxy + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.model.orm.ext + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.model.rst --- /dev/null +++ b/doc/source/lib/galaxy.model.rst @@ -0,0 +1,51 @@ +model Package +============= + +:mod:`model` Package +-------------------- + +.. automodule:: galaxy.model + :members: + :undoc-members: + :show-inheritance: + +:mod:`custom_types` Module +-------------------------- + +.. automodule:: galaxy.model.custom_types + :members: + :undoc-members: + :show-inheritance: + +:mod:`item_attrs` Module +------------------------ + +.. automodule:: galaxy.model.item_attrs + :members: + :undoc-members: + :show-inheritance: + +:mod:`mapping` Module +--------------------- + +.. automodule:: galaxy.model.mapping + :members: + :undoc-members: + :show-inheritance: + +:mod:`mapping_tests` Module +--------------------------- + +.. automodule:: galaxy.model.mapping_tests + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.model.migrate + galaxy.model.orm + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.objectstore.rst --- /dev/null +++ b/doc/source/lib/galaxy.objectstore.rst @@ -0,0 +1,19 @@ +objectstore Package +=================== + +:mod:`objectstore` Package +-------------------------- + +.. automodule:: galaxy.objectstore + :members: + :undoc-members: + :show-inheritance: + +:mod:`s3_multipart_upload` Module +--------------------------------- + +.. automodule:: galaxy.objectstore.s3_multipart_upload + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.openid.rst --- /dev/null +++ b/doc/source/lib/galaxy.openid.rst @@ -0,0 +1,19 @@ +openid Package +============== + +:mod:`openid` Package +--------------------- + +.. automodule:: galaxy.openid + :members: + :undoc-members: + :show-inheritance: + +:mod:`providers` Module +----------------------- + +.. automodule:: galaxy.openid.providers + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.quota.rst --- /dev/null +++ b/doc/source/lib/galaxy.quota.rst @@ -0,0 +1,11 @@ +quota Package +============= + +:mod:`quota` Package +-------------------- + +.. automodule:: galaxy.quota + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.rst --- /dev/null +++ b/doc/source/lib/galaxy.rst @@ -0,0 +1,54 @@ +galaxy Package +============== + +:mod:`galaxy` Package +--------------------- + +.. automodule:: galaxy + :members: + :undoc-members: + :show-inheritance: + +:mod:`app` Module +----------------- + +.. automodule:: galaxy.app + :members: + :undoc-members: + :show-inheritance: + +:mod:`config` Module +-------------------- + +.. automodule:: galaxy.config + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.actions + galaxy.datatypes + galaxy.eggs + galaxy.exceptions + galaxy.external_services + galaxy.forms + galaxy.jobs + galaxy.model + galaxy.objectstore + galaxy.openid + galaxy.quota + galaxy.sample_tracking + galaxy.security + galaxy.tags + galaxy.tool_shed + galaxy.tools + galaxy.util + galaxy.visualization + galaxy.web + galaxy.webapps + galaxy.workflow + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.sample_tracking.rst --- /dev/null +++ b/doc/source/lib/galaxy.sample_tracking.rst @@ -0,0 +1,35 @@ +sample_tracking Package +======================= + +:mod:`data_transfer` Module +--------------------------- + +.. automodule:: galaxy.sample_tracking.data_transfer + :members: + :undoc-members: + :show-inheritance: + +:mod:`external_service_types` Module +------------------------------------ + +.. automodule:: galaxy.sample_tracking.external_service_types + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_types` Module +--------------------------- + +.. automodule:: galaxy.sample_tracking.request_types + :members: + :undoc-members: + :show-inheritance: + +:mod:`sample` Module +-------------------- + +.. automodule:: galaxy.sample_tracking.sample + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.security.rst --- /dev/null +++ b/doc/source/lib/galaxy.security.rst @@ -0,0 +1,19 @@ +security Package +================ + +:mod:`security` Package +----------------------- + +.. automodule:: galaxy.security + :members: + :undoc-members: + :show-inheritance: + +:mod:`validate_user_input` Module +--------------------------------- + +.. automodule:: galaxy.security.validate_user_input + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tags.rst --- /dev/null +++ b/doc/source/lib/galaxy.tags.rst @@ -0,0 +1,19 @@ +tags Package +============ + +:mod:`tags` Package +------------------- + +.. automodule:: galaxy.tags + :members: + :undoc-members: + :show-inheritance: + +:mod:`tag_handler` Module +------------------------- + +.. automodule:: galaxy.tags.tag_handler + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tool_shed.migrate.rst --- /dev/null +++ b/doc/source/lib/galaxy.tool_shed.migrate.rst @@ -0,0 +1,19 @@ +migrate Package +=============== + +:mod:`check` Module +------------------- + +.. automodule:: galaxy.tool_shed.migrate.check + :members: + :undoc-members: + :show-inheritance: + +:mod:`common` Module +-------------------- + +.. automodule:: galaxy.tool_shed.migrate.common + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tool_shed.rst --- /dev/null +++ b/doc/source/lib/galaxy.tool_shed.rst @@ -0,0 +1,51 @@ +tool_shed Package +================= + +:mod:`tool_shed` Package +------------------------ + +.. automodule:: galaxy.tool_shed + :members: + :undoc-members: + :show-inheritance: + +:mod:`encoding_util` Module +--------------------------- + +.. automodule:: galaxy.tool_shed.encoding_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`install_manager` Module +----------------------------- + +.. automodule:: galaxy.tool_shed.install_manager + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_shed_registry` Module +-------------------------------- + +.. automodule:: galaxy.tool_shed.tool_shed_registry + :members: + :undoc-members: + :show-inheritance: + +:mod:`update_manager` Module +---------------------------- + +.. automodule:: galaxy.tool_shed.update_manager + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tool_shed.migrate + galaxy.tool_shed.tool_dependencies + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tool_shed.tool_dependencies.rst --- /dev/null +++ b/doc/source/lib/galaxy.tool_shed.tool_dependencies.rst @@ -0,0 +1,27 @@ +tool_dependencies Package +========================= + +:mod:`common_util` Module +------------------------- + +.. automodule:: galaxy.tool_shed.tool_dependencies.common_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`fabric_util` Module +------------------------- + +.. automodule:: galaxy.tool_shed.tool_dependencies.fabric_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`install_util` Module +-------------------------- + +.. automodule:: galaxy.tool_shed.tool_dependencies.install_util + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.actions.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.actions.rst @@ -0,0 +1,51 @@ +actions Package +=============== + +:mod:`actions` Package +---------------------- + +.. automodule:: galaxy.tools.actions + :members: + :undoc-members: + :show-inheritance: + +:mod:`history_imp_exp` Module +----------------------------- + +.. automodule:: galaxy.tools.actions.history_imp_exp + :members: + :undoc-members: + :show-inheritance: + +:mod:`index_genome` Module +-------------------------- + +.. automodule:: galaxy.tools.actions.index_genome + :members: + :undoc-members: + :show-inheritance: + +:mod:`metadata` Module +---------------------- + +.. automodule:: galaxy.tools.actions.metadata + :members: + :undoc-members: + :show-inheritance: + +:mod:`upload` Module +-------------------- + +.. automodule:: galaxy.tools.actions.upload + :members: + :undoc-members: + :show-inheritance: + +:mod:`upload_common` Module +--------------------------- + +.. automodule:: galaxy.tools.actions.upload_common + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.data.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.data.rst @@ -0,0 +1,11 @@ +data Package +============ + +:mod:`data` Package +------------------- + +.. automodule:: galaxy.tools.data + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.deps.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.deps.rst @@ -0,0 +1,19 @@ +deps Package +============ + +:mod:`deps` Package +------------------- + +.. automodule:: galaxy.tools.deps + :members: + :undoc-members: + :show-inheritance: + +:mod:`tests` Module +------------------- + +.. automodule:: galaxy.tools.deps.tests + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.genome_index.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.genome_index.rst @@ -0,0 +1,19 @@ +genome_index Package +==================== + +:mod:`genome_index` Package +--------------------------- + +.. automodule:: galaxy.tools.genome_index + :members: + :undoc-members: + :show-inheritance: + +:mod:`index_genome` Module +-------------------------- + +.. automodule:: galaxy.tools.genome_index.index_genome + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.imp_exp.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.imp_exp.rst @@ -0,0 +1,27 @@ +imp_exp Package +=============== + +:mod:`imp_exp` Package +---------------------- + +.. automodule:: galaxy.tools.imp_exp + :members: + :undoc-members: + :show-inheritance: + +:mod:`export_history` Module +---------------------------- + +.. automodule:: galaxy.tools.imp_exp.export_history + :members: + :undoc-members: + :show-inheritance: + +:mod:`unpack_tar_gz_archive` Module +----------------------------------- + +.. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.parameters.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.parameters.rst @@ -0,0 +1,67 @@ +parameters Package +================== + +:mod:`parameters` Package +------------------------- + +.. automodule:: galaxy.tools.parameters + :members: + :undoc-members: + :show-inheritance: + +:mod:`basic` Module +------------------- + +.. automodule:: galaxy.tools.parameters.basic + :members: + :undoc-members: + :show-inheritance: + +:mod:`dynamic_options` Module +----------------------------- + +.. automodule:: galaxy.tools.parameters.dynamic_options + :members: + :undoc-members: + :show-inheritance: + +:mod:`grouping` Module +---------------------- + +.. automodule:: galaxy.tools.parameters.grouping + :members: + :undoc-members: + :show-inheritance: + +:mod:`input_translation` Module +------------------------------- + +.. automodule:: galaxy.tools.parameters.input_translation + :members: + :undoc-members: + :show-inheritance: + +:mod:`output` Module +-------------------- + +.. automodule:: galaxy.tools.parameters.output + :members: + :undoc-members: + :show-inheritance: + +:mod:`sanitize` Module +---------------------- + +.. automodule:: galaxy.tools.parameters.sanitize + :members: + :undoc-members: + :show-inheritance: + +:mod:`validation` Module +------------------------ + +.. automodule:: galaxy.tools.parameters.validation + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.rst @@ -0,0 +1,41 @@ +tools Package +============= + +:mod:`tools` Package +-------------------- + +.. automodule:: galaxy.tools + :members: + :undoc-members: + :show-inheritance: + +:mod:`exception_handling` Module +-------------------------------- + +.. automodule:: galaxy.tools.exception_handling + :members: + :undoc-members: + :show-inheritance: + +:mod:`test` Module +------------------ + +.. automodule:: galaxy.tools.test + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tools.actions + galaxy.tools.data + galaxy.tools.deps + galaxy.tools.genome_index + galaxy.tools.imp_exp + galaxy.tools.parameters + galaxy.tools.search + galaxy.tools.util + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.search.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.search.rst @@ -0,0 +1,11 @@ +search Package +============== + +:mod:`search` Package +--------------------- + +.. automodule:: galaxy.tools.search + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.util.galaxyops.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.util.galaxyops.rst @@ -0,0 +1,11 @@ +galaxyops Package +================= + +:mod:`galaxyops` Package +------------------------ + +.. automodule:: galaxy.tools.util.galaxyops + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.tools.util.rst --- /dev/null +++ b/doc/source/lib/galaxy.tools.util.rst @@ -0,0 +1,34 @@ +util Package +============ + +:mod:`util` Package +------------------- + +.. automodule:: galaxy.tools.util + :members: + :undoc-members: + :show-inheritance: + +:mod:`hyphy_util` Module +------------------------ + +.. automodule:: galaxy.tools.util.hyphy_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`maf_utilities` Module +--------------------------- + +.. automodule:: galaxy.tools.util.maf_utilities + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tools.util.galaxyops + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.util.rst --- /dev/null +++ b/doc/source/lib/galaxy.util.rst @@ -0,0 +1,139 @@ +util Package +============ + +:mod:`util` Package +------------------- + +.. automodule:: galaxy.util + :members: + :undoc-members: + :show-inheritance: + +:mod:`aliaspickler` Module +-------------------------- + +.. automodule:: galaxy.util.aliaspickler + :members: + :undoc-members: + :show-inheritance: + +:mod:`bunch` Module +------------------- + +.. automodule:: galaxy.util.bunch + :members: + :undoc-members: + :show-inheritance: + +:mod:`expressions` Module +------------------------- + +.. automodule:: galaxy.util.expressions + :members: + :undoc-members: + :show-inheritance: + +:mod:`hash_util` Module +----------------------- + +.. automodule:: galaxy.util.hash_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`heartbeat` Module +----------------------- + +.. automodule:: galaxy.util.heartbeat + :members: + :undoc-members: + :show-inheritance: + +:mod:`inflection` Module +------------------------ + +.. automodule:: galaxy.util.inflection + :members: + :undoc-members: + :show-inheritance: + +:mod:`json` Module +------------------ + +.. automodule:: galaxy.util.json + :members: + :undoc-members: + :show-inheritance: + +:mod:`lrucache` Module +---------------------- + +.. automodule:: galaxy.util.lrucache + :members: + :undoc-members: + :show-inheritance: + +:mod:`memdump` Module +--------------------- + +.. automodule:: galaxy.util.memdump + :members: + :undoc-members: + :show-inheritance: + +:mod:`none_like` Module +----------------------- + +.. automodule:: galaxy.util.none_like + :members: + :undoc-members: + :show-inheritance: + +:mod:`odict` Module +------------------- + +.. automodule:: galaxy.util.odict + :members: + :undoc-members: + :show-inheritance: + +:mod:`sanitize_html` Module +--------------------------- + +.. automodule:: galaxy.util.sanitize_html + :members: + :undoc-members: + :show-inheritance: + +:mod:`shed_util` Module +----------------------- + +.. automodule:: galaxy.util.shed_util + :members: + :undoc-members: + :show-inheritance: + +:mod:`streamball` Module +------------------------ + +.. automodule:: galaxy.util.streamball + :members: + :undoc-members: + :show-inheritance: + +:mod:`template` Module +---------------------- + +.. automodule:: galaxy.util.template + :members: + :undoc-members: + :show-inheritance: + +:mod:`topsort` Module +--------------------- + +.. automodule:: galaxy.util.topsort + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.visualization.rst --- /dev/null +++ b/doc/source/lib/galaxy.visualization.rst @@ -0,0 +1,26 @@ +visualization Package +===================== + +:mod:`visualization` Package +---------------------------- + +.. automodule:: galaxy.visualization + :members: + :undoc-members: + :show-inheritance: + +:mod:`genomes` Module +--------------------- + +.. automodule:: galaxy.visualization.genomes + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.visualization.tracks + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.visualization.tracks.rst --- /dev/null +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -0,0 +1,35 @@ +tracks Package +============== + +:mod:`tracks` Package +--------------------- + +.. automodule:: galaxy.visualization.tracks + :members: + :undoc-members: + :show-inheritance: + +:mod:`data_providers` Module +---------------------------- + +.. automodule:: galaxy.visualization.tracks.data_providers + :members: + :undoc-members: + :show-inheritance: + +:mod:`summary` Module +--------------------- + +.. automodule:: galaxy.visualization.tracks.summary + :members: + :undoc-members: + :show-inheritance: + +:mod:`visual_analytics` Module +------------------------------ + +.. automodule:: galaxy.visualization.tracks.visual_analytics + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.api.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.api.rst @@ -0,0 +1,352 @@ +Galaxy API Documentation +************************ + +Background +========== +In addition to being accessible through a web interface, Galaxy can now also be +accessed programmatically, through shell scripts and other programs. The web +interface is appropriate for things like exploratory analysis, visualization, +construction of workflows, and rerunning workflows on new datasets. + +The web interface is less suitable for things like + - Connecting a Galaxy instance directly to your sequencer and running + workflows whenever data is ready + - Running a workflow against multiple datasets (which can be done with the + web interface, but is tedious) + - When the analysis involves complex control, such as looping and + branching. + +The Galaxy API addresses these and other situations by exposing Galaxy +internals through an additional interface, known as an Application Programming +Interface, or API. + +Quickstart +========== + +Set the following option in universe_wsgi.ini and start the server:: + + enable_api = True + +Log in as your user, navigate to the API Keys page in the User menu, and +generate a new API key. Make a note of the API key, and then pull up a +terminal. Now we'll use the display.py script in your galaxy/scripts/api +directory for a short example:: + + % ./display.py my_key http://localhost:4096/api/histories + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc + name: Unnamed history + id: 8c49be448cfe29bc + #2: /api/histories/33b43b4e7093c91f + name: output test + id: 33b43b4e7093c91f + +The result is a Collection of the histories of the user specified by the API +key (you). To look at the details of a particular history, say #1 above, do +the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc + Member Information + ------------------ + state_details: {'ok': 1, 'failed_metadata': 0, 'upload': 0, 'discarded': 0, 'running': 0, 'setting_metadata': 0, 'error': 0, 'new': 0, 'queued': 0, 'empty': 0} + state: ok + contents_url: /api/histories/8c49be448cfe29bc/contents + id: 8c49be448cfe29bc + name: Unnamed history + +This gives detailed information about the specific member in question, in this +case the History. To view history contents, do the following:: + + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents + Collection Members + ------------------ + #1: /api/histories/8c49be448cfe29bc/contents/6f91353f3eb0fa4a + name: Pasted Entry + type: file + id: 6f91353f3eb0fa4a + +What we have here is another Collection of items containing all of the datasets +in this particular history. Finally, to view details of a particular dataset +in this collection, execute the following:: + + % ./display.py my_key http://localhost:4096/api/histories/8c49be448cfe29bc/contents/6f91353f3eb0f… + Member Information + ------------------ + misc_blurb: 1 line + name: Pasted Entry + data_type: txt + deleted: False + file_name: /Users/yoplait/work/galaxy-stock/database/files/000/dataset_82.dat + state: ok + download_url: /datasets/6f91353f3eb0fa4a/display?to_ext=txt + visible: True + genome_build: ? + model_class: HistoryDatasetAssociation + file_size: 17 + metadata_data_lines: 1 + id: 6f91353f3eb0fa4a + misc_info: uploaded txt file + metadata_dbkey: ? + +And now you've successfully used the API to request and select a history, +browse the contents of that history, and then look at detailed information +about a particular dataset. + +For a more comprehensive Data Library example, set the following option in your +universe_wsgi.ini as well, and restart galaxy again:: + + admin_users = you(a)example.org + library_import_dir = /path/to/some/directory + +In the directory you specified for 'library_import_dir', create some +subdirectories, and put (or symlink) files to import into Galaxy into those +subdirectories. + +In Galaxy, create an account that matches the address you put in 'admin_users', +then browse to that user's preferences and generate a new API Key. Copy the +key to your clipboard and then use these scripts:: + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + + 0 elements in collection + + % ./library_create_library.py my_key http://localhost:4096/api/libraries api_test 'API Test Library' + Response + -------- + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries + Collection Members + ------------------ + /api/libraries/f3f73e481f432006 + name: api_test + id: f3f73e481f432006 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006 + Member Information + ------------------ + synopsis: None + contents_url: /api/libraries/f3f73e481f432006/contents + description: API Test Library + name: api_test + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + + % ./library_create_folder.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591f61ddda595d2c3670 api_test_folder1 'API Test Folder 1' + Response + -------- + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: api_test_folder1 + id: 28202595c0d2591fa4f9089d2303fd89 + + % ./library_upload_from_import_dir.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents 28202595c0d2591fa4f9089d2303fd89 bed bed hg19 + Response + -------- + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: 2.bed + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: 3.bed + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents + Collection Members + ------------------ + /api/libraries/f3f73e481f432006/contents/28202595c0d2591f61ddda595d2c3670 + name: / + type: folder + id: 28202595c0d2591f61ddda595d2c3670 + /api/libraries/f3f73e481f432006/contents/28202595c0d2591fa4f9089d2303fd89 + name: /api_test_folder1 + type: folder + id: 28202595c0d2591fa4f9089d2303fd89 + /api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87d7b + name: /api_test_folder1/2.bed + type: file + id: e9ef7fdb2db87d7b + /api/libraries/f3f73e481f432006/contents/3b7f6a31f80a5018 + name: /api_test_folder1/3.bed + type: file + id: 3b7f6a31f80a5018 + + % ./display.py my_key http://localhost:4096/api/libraries/f3f73e481f432006/contents/e9ef7fdb2db87… + Member Information + ------------------ + misc_blurb: 68 regions + metadata_endCol: 3 + data_type: bed + metadata_columns: 6 + metadata_nameCol: 4 + uploaded_by: nate@... + metadata_strandCol: 6 + name: 2.bed + genome_build: hg19 + metadata_comment_lines: None + metadata_startCol: 2 + metadata_chromCol: 1 + file_size: 4272 + metadata_data_lines: 68 + message: + metadata_dbkey: hg19 + misc_info: uploaded bed file + date_uploaded: 2010-06-22T17:01:51.266119 + metadata_column_types: str, int, int, str, int, str + +Other parameters are valid when uploading, they are the same parameters as are +used in the web form, like 'link_data_only' and etc. + +The request and response format should be considered alpha and are subject to change. + + +API Controllers +=============== + +:mod:`datasets` Module +---------------------- + +.. automodule:: galaxy.web.api.datasets + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.web.api.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`genomes` Module +--------------------- + +.. automodule:: galaxy.web.api.genomes + :members: + :undoc-members: + :show-inheritance: + +:mod:`histories` Module +----------------------- + +.. automodule:: galaxy.web.api.histories + :members: + :undoc-members: + :show-inheritance: + +:mod:`history_contents` Module +------------------------------ + +.. automodule:: galaxy.web.api.history_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`libraries` Module +----------------------- + +.. automodule:: galaxy.web.api.libraries + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_contents` Module +------------------------------ + +.. automodule:: galaxy.web.api.library_contents + :members: + :undoc-members: + :show-inheritance: + +:mod:`permissions` Module +------------------------- + +.. automodule:: galaxy.web.api.permissions + :members: + :undoc-members: + :show-inheritance: + +:mod:`quotas` Module +-------------------- + +.. automodule:: galaxy.web.api.quotas + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_types` Module +--------------------------- + +.. automodule:: galaxy.web.api.request_types + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.web.api.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`roles` Module +------------------- + +.. automodule:: galaxy.web.api.roles + :members: + :undoc-members: + :show-inheritance: + +:mod:`samples` Module +--------------------- + +.. automodule:: galaxy.web.api.samples + :members: + :undoc-members: + :show-inheritance: + +:mod:`tools` Module +------------------- + +.. automodule:: galaxy.web.api.tools + :members: + :undoc-members: + :show-inheritance: + +:mod:`users` Module +------------------- + +.. automodule:: galaxy.web.api.users + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualizations` Module +---------------------------- + +.. automodule:: galaxy.web.api.visualizations + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflows` Module +----------------------- + +.. automodule:: galaxy.web.api.workflows + :members: + :undoc-members: + :show-inheritance: + + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.base.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.base.rst @@ -0,0 +1,11 @@ +base Package +============ + +:mod:`controller` Module +------------------------ + +.. automodule:: galaxy.web.base.controller + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.controllers.rst @@ -0,0 +1,235 @@ +controllers Package +=================== + +:mod:`controllers` Package +-------------------------- + +.. automodule:: galaxy.web.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.web.controllers.admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin_toolshed` Module +---------------------------- + +.. automodule:: galaxy.web.controllers.admin_toolshed + :members: + :undoc-members: + :show-inheritance: + +:mod:`async` Module +------------------- + +.. automodule:: galaxy.web.controllers.async + :members: + :undoc-members: + :show-inheritance: + +:mod:`cloud` Module +------------------- + +.. automodule:: galaxy.web.controllers.cloud + :members: + :undoc-members: + :show-inheritance: + +:mod:`data_admin` Module +------------------------ + +.. automodule:: galaxy.web.controllers.data_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`dataset` Module +--------------------- + +.. automodule:: galaxy.web.controllers.dataset + :members: + :undoc-members: + :show-inheritance: + +:mod:`error` Module +------------------- + +.. automodule:: galaxy.web.controllers.error + :members: + :undoc-members: + :show-inheritance: + +:mod:`external_service` Module +------------------------------ + +.. automodule:: galaxy.web.controllers.external_service + :members: + :undoc-members: + :show-inheritance: + +:mod:`external_services` Module +------------------------------- + +.. automodule:: galaxy.web.controllers.external_services + :members: + :undoc-members: + :show-inheritance: + +:mod:`forms` Module +------------------- + +.. automodule:: galaxy.web.controllers.forms + :members: + :undoc-members: + :show-inheritance: + +:mod:`history` Module +--------------------- + +.. automodule:: galaxy.web.controllers.history + :members: + :undoc-members: + :show-inheritance: + +:mod:`library` Module +--------------------- + +.. automodule:: galaxy.web.controllers.library + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_admin` Module +--------------------------- + +.. automodule:: galaxy.web.controllers.library_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`library_common` Module +---------------------------- + +.. automodule:: galaxy.web.controllers.library_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`mobile` Module +-------------------- + +.. automodule:: galaxy.web.controllers.mobile + :members: + :undoc-members: + :show-inheritance: + +:mod:`page` Module +------------------ + +.. automodule:: galaxy.web.controllers.page + :members: + :undoc-members: + :show-inheritance: + +:mod:`request_type` Module +-------------------------- + +.. automodule:: galaxy.web.controllers.request_type + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests` Module +---------------------- + +.. automodule:: galaxy.web.controllers.requests + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests_admin` Module +---------------------------- + +.. automodule:: galaxy.web.controllers.requests_admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`requests_common` Module +----------------------------- + +.. automodule:: galaxy.web.controllers.requests_common + :members: + :undoc-members: + :show-inheritance: + +:mod:`root` Module +------------------ + +.. automodule:: galaxy.web.controllers.root + :members: + :undoc-members: + :show-inheritance: + +:mod:`tag` Module +----------------- + +.. automodule:: galaxy.web.controllers.tag + :members: + :undoc-members: + :show-inheritance: + +:mod:`tool_runner` Module +------------------------- + +.. automodule:: galaxy.web.controllers.tool_runner + :members: + :undoc-members: + :show-inheritance: + +:mod:`tracks` Module +-------------------- + +.. automodule:: galaxy.web.controllers.tracks + :members: + :undoc-members: + :show-inheritance: + +:mod:`ucsc_proxy` Module +------------------------ + +.. automodule:: galaxy.web.controllers.ucsc_proxy + :members: + :undoc-members: + :show-inheritance: + +:mod:`user` Module +------------------ + +.. automodule:: galaxy.web.controllers.user + :members: + :undoc-members: + :show-inheritance: + +:mod:`visualization` Module +--------------------------- + +.. automodule:: galaxy.web.controllers.visualization + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflow` Module +---------------------- + +.. automodule:: galaxy.web.controllers.workflow + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.framework.helpers.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.framework.helpers.rst @@ -0,0 +1,19 @@ +helpers Package +=============== + +:mod:`helpers` Package +---------------------- + +.. automodule:: galaxy.web.framework.helpers + :members: + :undoc-members: + :show-inheritance: + +:mod:`grids` Module +------------------- + +.. automodule:: galaxy.web.framework.helpers.grids + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.framework.middleware.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -0,0 +1,51 @@ +middleware Package +================== + +:mod:`middleware` Package +------------------------- + +.. automodule:: galaxy.web.framework.middleware + :members: + :undoc-members: + :show-inheritance: + +:mod:`profile` Module +--------------------- + +.. automodule:: galaxy.web.framework.middleware.profile + :members: + :undoc-members: + :show-inheritance: + +:mod:`remoteuser` Module +------------------------ + +.. automodule:: galaxy.web.framework.middleware.remoteuser + :members: + :undoc-members: + :show-inheritance: + +:mod:`static` Module +-------------------- + +.. automodule:: galaxy.web.framework.middleware.static + :members: + :undoc-members: + :show-inheritance: + +:mod:`translogger` Module +------------------------- + +.. automodule:: galaxy.web.framework.middleware.translogger + :members: + :undoc-members: + :show-inheritance: + +:mod:`xforwardedhost` Module +---------------------------- + +.. automodule:: galaxy.web.framework.middleware.xforwardedhost + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.framework.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.framework.rst @@ -0,0 +1,35 @@ +framework Package +================= + +:mod:`framework` Package +------------------------ + +.. automodule:: galaxy.web.framework + :members: + :undoc-members: + :show-inheritance: + +:mod:`base` Module +------------------ + +.. automodule:: galaxy.web.framework.base + :members: + :undoc-members: + :show-inheritance: + +:mod:`openid_manager` Module +---------------------------- + +.. automodule:: galaxy.web.framework.openid_manager + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.web.framework.helpers + galaxy.web.framework.middleware + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.rst @@ -0,0 +1,46 @@ +web Package +=========== + +:mod:`web` Package +------------------ + +.. automodule:: galaxy.web + :members: + :undoc-members: + :show-inheritance: + +:mod:`buildapp` Module +---------------------- + +.. automodule:: galaxy.web.buildapp + :members: + :undoc-members: + :show-inheritance: + +:mod:`form_builder` Module +-------------------------- + +.. automodule:: galaxy.web.form_builder + :members: + :undoc-members: + :show-inheritance: + +:mod:`params` Module +-------------------- + +.. automodule:: galaxy.web.params + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.web.api + galaxy.web.base + galaxy.web.controllers + galaxy.web.framework + galaxy.web.security + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.web.security.rst --- /dev/null +++ b/doc/source/lib/galaxy.web.security.rst @@ -0,0 +1,11 @@ +security Package +================ + +:mod:`security` Package +----------------------- + +.. automodule:: galaxy.web.security + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.community.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.community.controllers.rst @@ -0,0 +1,59 @@ +controllers Package +=================== + +:mod:`controllers` Package +-------------------------- + +.. automodule:: galaxy.webapps.community.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`admin` Module +------------------- + +.. automodule:: galaxy.webapps.community.controllers.admin + :members: + :undoc-members: + :show-inheritance: + +:mod:`common` Module +-------------------- + +.. automodule:: galaxy.webapps.community.controllers.common + :members: + :undoc-members: + :show-inheritance: + +:mod:`hg` Module +---------------- + +.. automodule:: galaxy.webapps.community.controllers.hg + :members: + :undoc-members: + :show-inheritance: + +:mod:`repository` Module +------------------------ + +.. automodule:: galaxy.webapps.community.controllers.repository + :members: + :undoc-members: + :show-inheritance: + +:mod:`upload` Module +-------------------- + +.. automodule:: galaxy.webapps.community.controllers.upload + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflow` Module +---------------------- + +.. automodule:: galaxy.webapps.community.controllers.workflow + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.community.framework.middleware.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.community.framework.middleware.rst @@ -0,0 +1,19 @@ +middleware Package +================== + +:mod:`middleware` Package +------------------------- + +.. automodule:: galaxy.webapps.community.framework.middleware + :members: + :undoc-members: + :show-inheritance: + +:mod:`hg` Module +---------------- + +.. automodule:: galaxy.webapps.community.framework.middleware.hg + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.community.framework.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.community.framework.rst @@ -0,0 +1,18 @@ +framework Package +================= + +:mod:`framework` Package +------------------------ + +.. automodule:: galaxy.webapps.community.framework + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.community.framework.middleware + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.community.model.migrate.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.community.model.migrate.rst @@ -0,0 +1,11 @@ +migrate Package +=============== + +:mod:`check` Module +------------------- + +.. automodule:: galaxy.webapps.community.model.migrate.check + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.community.model.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.community.model.rst @@ -0,0 +1,26 @@ +model Package +============= + +:mod:`model` Package +-------------------- + +.. automodule:: galaxy.webapps.community.model + :members: + :undoc-members: + :show-inheritance: + +:mod:`mapping` Module +--------------------- + +.. automodule:: galaxy.webapps.community.model.mapping + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.community.model.migrate + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.community.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.community.rst @@ -0,0 +1,45 @@ +community Package +================= + +:mod:`community` Package +------------------------ + +.. automodule:: galaxy.webapps.community + :members: + :undoc-members: + :show-inheritance: + +:mod:`app` Module +----------------- + +.. automodule:: galaxy.webapps.community.app + :members: + :undoc-members: + :show-inheritance: + +:mod:`buildapp` Module +---------------------- + +.. automodule:: galaxy.webapps.community.buildapp + :members: + :undoc-members: + :show-inheritance: + +:mod:`config` Module +-------------------- + +.. automodule:: galaxy.webapps.community.config + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.community.controllers + galaxy.webapps.community.framework + galaxy.webapps.community.model + galaxy.webapps.community.security + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.community.security.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.community.security.rst @@ -0,0 +1,11 @@ +security Package +================ + +:mod:`security` Package +----------------------- + +.. automodule:: galaxy.webapps.community.security + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.demo_sequencer.controllers.rst @@ -0,0 +1,19 @@ +controllers Package +=================== + +:mod:`controllers` Package +-------------------------- + +.. automodule:: galaxy.webapps.demo_sequencer.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`common` Module +-------------------- + +.. automodule:: galaxy.webapps.demo_sequencer.controllers.common + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.demo_sequencer.framework.rst @@ -0,0 +1,11 @@ +framework Package +================= + +:mod:`framework` Package +------------------------ + +.. automodule:: galaxy.webapps.demo_sequencer.framework + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.demo_sequencer.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.demo_sequencer.rst @@ -0,0 +1,51 @@ +demo_sequencer Package +====================== + +:mod:`demo_sequencer` Package +----------------------------- + +.. automodule:: galaxy.webapps.demo_sequencer + :members: + :undoc-members: + :show-inheritance: + +:mod:`app` Module +----------------- + +.. automodule:: galaxy.webapps.demo_sequencer.app + :members: + :undoc-members: + :show-inheritance: + +:mod:`buildapp` Module +---------------------- + +.. automodule:: galaxy.webapps.demo_sequencer.buildapp + :members: + :undoc-members: + :show-inheritance: + +:mod:`config` Module +-------------------- + +.. automodule:: galaxy.webapps.demo_sequencer.config + :members: + :undoc-members: + :show-inheritance: + +:mod:`registry` Module +---------------------- + +.. automodule:: galaxy.webapps.demo_sequencer.registry + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.demo_sequencer.controllers + galaxy.webapps.demo_sequencer.framework + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.reports.controllers.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst @@ -0,0 +1,59 @@ +controllers Package +=================== + +:mod:`controllers` Package +-------------------------- + +.. automodule:: galaxy.webapps.reports.controllers + :members: + :undoc-members: + :show-inheritance: + +:mod:`jobs` Module +------------------ + +.. automodule:: galaxy.webapps.reports.controllers.jobs + :members: + :undoc-members: + :show-inheritance: + +:mod:`root` Module +------------------ + +.. automodule:: galaxy.webapps.reports.controllers.root + :members: + :undoc-members: + :show-inheritance: + +:mod:`sample_tracking` Module +----------------------------- + +.. automodule:: galaxy.webapps.reports.controllers.sample_tracking + :members: + :undoc-members: + :show-inheritance: + +:mod:`system` Module +-------------------- + +.. automodule:: galaxy.webapps.reports.controllers.system + :members: + :undoc-members: + :show-inheritance: + +:mod:`users` Module +------------------- + +.. automodule:: galaxy.webapps.reports.controllers.users + :members: + :undoc-members: + :show-inheritance: + +:mod:`workflows` Module +----------------------- + +.. automodule:: galaxy.webapps.reports.controllers.workflows + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.reports.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.reports.rst @@ -0,0 +1,42 @@ +reports Package +=============== + +:mod:`reports` Package +---------------------- + +.. automodule:: galaxy.webapps.reports + :members: + :undoc-members: + :show-inheritance: + +:mod:`app` Module +----------------- + +.. automodule:: galaxy.webapps.reports.app + :members: + :undoc-members: + :show-inheritance: + +:mod:`buildapp` Module +---------------------- + +.. automodule:: galaxy.webapps.reports.buildapp + :members: + :undoc-members: + :show-inheritance: + +:mod:`config` Module +-------------------- + +.. automodule:: galaxy.webapps.reports.config + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.reports.controllers + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.webapps.rst --- /dev/null +++ b/doc/source/lib/galaxy.webapps.rst @@ -0,0 +1,20 @@ +webapps Package +=============== + +:mod:`webapps` Package +---------------------- + +.. automodule:: galaxy.webapps + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.webapps.community + galaxy.webapps.demo_sequencer + galaxy.webapps.reports + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy.workflow.rst --- /dev/null +++ b/doc/source/lib/galaxy.workflow.rst @@ -0,0 +1,11 @@ +workflow Package +================ + +:mod:`modules` Module +--------------------- + +.. automodule:: galaxy.workflow.modules + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy_utils.rst --- /dev/null +++ b/doc/source/lib/galaxy_utils.rst @@ -0,0 +1,10 @@ +galaxy_utils Package +==================== + +Subpackages +----------- + +.. toctree:: + + galaxy_utils.sequence + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/galaxy_utils.sequence.rst --- /dev/null +++ b/doc/source/lib/galaxy_utils.sequence.rst @@ -0,0 +1,43 @@ +sequence Package +================ + +:mod:`fasta` Module +------------------- + +.. automodule:: galaxy_utils.sequence.fasta + :members: + :undoc-members: + :show-inheritance: + +:mod:`fastq` Module +------------------- + +.. automodule:: galaxy_utils.sequence.fastq + :members: + :undoc-members: + :show-inheritance: + +:mod:`sequence` Module +---------------------- + +.. automodule:: galaxy_utils.sequence.sequence + :members: + :undoc-members: + :show-inheritance: + +:mod:`transform` Module +----------------------- + +.. automodule:: galaxy_utils.sequence.transform + :members: + :undoc-members: + :show-inheritance: + +:mod:`vcf` Module +----------------- + +.. automodule:: galaxy_utils.sequence.vcf + :members: + :undoc-members: + :show-inheritance: + diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/log_tempfile.rst --- /dev/null +++ b/doc/source/lib/log_tempfile.rst @@ -0,0 +1,7 @@ +log_tempfile Module +=================== + +.. automodule:: log_tempfile + :members: + :undoc-members: + :show-inheritance: diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/mimeparse.rst --- /dev/null +++ b/doc/source/lib/mimeparse.rst @@ -0,0 +1,7 @@ +mimeparse Module +================ + +.. automodule:: mimeparse + :members: + :undoc-members: + :show-inheritance: diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/modules.rst --- /dev/null +++ b/doc/source/lib/modules.rst @@ -0,0 +1,13 @@ +lib +=== + +.. toctree:: + :maxdepth: 4 + + fpconst + galaxy + galaxy_utils + log_tempfile + mimeparse + pkg_resources + psyco_full diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/pkg_resources.rst --- /dev/null +++ b/doc/source/lib/pkg_resources.rst @@ -0,0 +1,7 @@ +pkg_resources Module +==================== + +.. automodule:: pkg_resources + :members: + :undoc-members: + :show-inheritance: diff -r 4fbd05095ca70adf740ed635451c0ec876635f50 -r 77ceb114bf57172579310a0b4347da0f5f46dec6 doc/source/lib/psyco_full.rst --- /dev/null +++ b/doc/source/lib/psyco_full.rst @@ -0,0 +1,7 @@ +psyco_full Module +================= + +.. automodule:: psyco_full + :members: + :undoc-members: + :show-inheritance: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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