February 2013 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: greg: Handle all Galaxy utilitiy types when reinstalling an uninstalled tool shed repository. The shed-related config file can now be selected when reinstalling repositories with any contents so that a differnt "tool_path" location can be selected for the location of the reinstalled repository.
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/305680a482c3/ changeset: 305680a482c3 user: greg date: 2013-02-19 21:01:09 summary: Handle all Galaxy utilitiy types when reinstalling an uninstalled tool shed repository. The shed-related config file can now be selected when reinstalling repositories with any contents so that a differnt "tool_path" location can be selected for the location of the reinstalled repository. affected #: 5 files diff -r 32fc25b8900059f63b0d41d52aa582f06426928c -r 305680a482c3096b082daffa5ff665f5f60d1528 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -951,6 +951,7 @@ .first() def get_update_to_changeset_revision_and_ctx_rev( trans, repository ): """Return the changeset revision hash to which the repository can be updated.""" + changeset_revision_dict = {} tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) url = suc.url_join( tool_shed_url, 'repository/get_changeset_revision_and_ctx_rev?name=%s&owner=%s&changeset_revision=%s' % \ ( repository.name, repository.owner, repository.installed_changeset_revision ) ) @@ -959,18 +960,34 @@ encoded_update_dict = response.read() if encoded_update_dict: update_dict = encoding_util.tool_shed_decode( encoded_update_dict ) - changeset_revision = update_dict[ 'changeset_revision' ] - ctx_rev = update_dict[ 'ctx_rev' ] + includes_data_managers = update_dict.get( 'includes_data_managers', False ) + includes_datatypes = update_dict.get( 'includes_datatypes', False ) includes_tools = update_dict.get( 'includes_tools', False ) + includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False ) + includes_workflows = update_dict.get( 'includes_workflows', False ) has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False ) + changeset_revision = update_dict.get( 'changeset_revision', None ) + ctx_rev = update_dict.get( 'ctx_rev', None ) response.close() + changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers + changeset_revision_dict[ 'includes_datatypes' ] = includes_datatypes + changeset_revision_dict[ 'includes_tools' ] = includes_tools + changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies + changeset_revision_dict[ 'includes_workflows' ] = includes_workflows + changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies + changeset_revision_dict[ 'changeset_revision' ] = changeset_revision + changeset_revision_dict[ 'ctx_rev' ] = ctx_rev except Exception, e: log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) ) - includes_tools = False - has_repository_dependencies = False - changeset_revision = None - ctx_rev = None - return changeset_revision, ctx_rev, includes_tools, has_repository_dependencies + changeset_revision_dict[ 'includes_data_managers' ] = False + changeset_revision_dict[ 'includes_datatypes' ] = False + changeset_revision_dict[ 'includes_tools' ] = False + changeset_revision_dict[ 'includes_tool_dependencies' ] = False + changeset_revision_dict[ 'includes_workflows' ] = False + changeset_revision_dict[ 'has_repository_dependencies' ] = False + changeset_revision_dict[ 'changeset_revision' ] = None + changeset_revision_dict[ 'ctx_rev' ] = None + return changeset_revision_dict def handle_missing_data_table_entry( app, relative_install_dir, tool_path, repository_tools_tups ): """ Inspect each tool to see if any have input parameters that are dynamically generated select lists that require entries in the diff -r 32fc25b8900059f63b0d41d52aa582f06426928c -r 305680a482c3096b082daffa5ff665f5f60d1528 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1298,21 +1298,29 @@ @web.expose def get_changeset_revision_and_ctx_rev( self, trans, **kwd ): """Handle a request from a local Galaxy instance to retrieve the changeset revision hash to which an installed repository can be updated.""" - def has_tools_and_repository_dependencies( repository_metadata ): + def has_galaxy_utilities( repository_metadata ): + includes_data_managers = False + includes_datatypes = False includes_tools = False has_repository_dependencies = False + includes_tool_dependencies = False + includes_workflows = False if repository_metadata: metadata = repository_metadata.metadata if metadata: + if 'data_manager' in metadata: + includes_data_managers = True + if 'datatypes' in metadata: + includes_datatypes = True if 'tools' in metadata: includes_tools = True - else: - includes_tools = False + if 'tool_dependencies' in metadata: + includes_tool_dependencies = True if 'repository_dependencies' in metadata: has_repository_dependencies = True - else: - has_repository_dependencies = False - return includes_tools, has_repository_dependencies + if 'workflows' in metadata: + includes_workflows = True + return includes_data_managers, includes_datatypes, includes_tools, includes_tool_dependencies, has_repository_dependencies, includes_workflows params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) @@ -1324,7 +1332,8 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, trans.security.encode_id( repository.id ), changeset_revision ) - includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( repository_metadata ) + includes_data_managers, includes_datatypes, includes_tools, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \ + has_galaxy_utilities( repository_metadata ) repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) # Default to the received changeset revision and ctx_rev. @@ -1333,8 +1342,12 @@ latest_changeset_revision = changeset_revision update_dict = dict( changeset_revision=changeset_revision, ctx_rev=ctx_rev, + includes_data_managers=includes_data_managers, + includes_datatypes=includes_datatypes, includes_tools=includes_tools, - has_repository_dependencies=has_repository_dependencies ) + includes_tool_dependencies=includes_tool_dependencies, + has_repository_dependencies=has_repository_dependencies, + includes_workflows=includes_workflows ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. return encoding_util.tool_shed_encode( update_dict ) @@ -1356,7 +1369,8 @@ trans.security.encode_id( repository.id ), changeset_hash ) if update_to_repository_metadata: - includes_tools, has_repository_dependencies = has_tools_and_repository_dependencies( update_to_repository_metadata ) + includes_data_managers, includes_datatypes, includes_tools, includes_tool_dependencies, has_repository_dependencies, includes_workflows = \ + has_galaxy_utilities( update_to_repository_metadata ) # We found a RepositoryMetadata record. if changeset_hash == repository.tip( trans.app ): # The current ctx is the repository tip, so use it. @@ -1369,7 +1383,11 @@ elif not update_to_changeset_hash and changeset_hash == changeset_revision: # We've found the changeset in the changelog for which we need to get the next update. update_to_changeset_hash = changeset_hash + update_dict[ 'includes_data_managers' ] = includes_data_managers + update_dict[ 'includes_datatypes' ] = includes_datatypes update_dict[ 'includes_tools' ] = includes_tools + update_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies + update_dict[ 'includes_workflows' ] = includes_workflows update_dict[ 'has_repository_dependencies' ] = has_repository_dependencies update_dict[ 'changeset_revision' ] = str( latest_changeset_revision ) update_dict[ 'ctx_rev' ] = str( update_to_ctx.rev() ) @@ -1601,16 +1619,22 @@ repository_metadata=repository_metadata, tool_dependencies=None, repository_dependencies=None ) + includes_data_managers = False + includes_datatypes = False + includes_tools = False + includes_workflows = False + readme_files_dict = None metadata = repository_metadata.metadata if metadata: - readme_files_dict = suc.build_readme_files_dict( metadata ) + if 'data_manager' in metadata: + includes_data_managers = True + if 'datatypes' in metadata: + includes_datatypes = True if 'tools' in metadata: includes_tools = True - else: - includes_tools = False - else: - readme_files_dict = None - includes_tools = False + if 'workflows' in metadata: + includes_workflows = True + readme_files_dict = suc.build_readme_files_dict( metadata ) # See if the repo_info_dict was populated with repository_dependencies or tool_dependencies. for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = \ @@ -1623,9 +1647,12 @@ includes_tool_dependencies = True else: includes_tool_dependencies = False - return dict( includes_tools=includes_tools, + return dict( includes_data_managers=includes_data_managers, + includes_datatypes=includes_datatypes, + includes_tools=includes_tools, has_repository_dependencies=has_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, + includes_workflows=includes_workflows, readme_files_dict=readme_files_dict, repo_info_dict=repo_info_dict ) def get_versions_of_tool( self, trans, repository, repository_metadata, guid ): diff -r 32fc25b8900059f63b0d41d52aa582f06426928c -r 305680a482c3096b082daffa5ff665f5f60d1528 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -383,29 +383,23 @@ if repository.uninstalled: # Since we're reinstalling the repository we need to find the latest changeset revision to which it can be updated so that we # can reset the metadata if necessary. This will ensure that information about repository dependencies and tool dependencies - # will be current. Only allow selecting a different section in the tool panel if the repository was uninstalled. - current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \ - shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) - if current_ctx_rev == repository.ctx_rev: - # The uninstalled repository is current. - if repository.includes_tools or repository.has_repository_dependencies: + # will be current. Only allow selecting a different section in the tool panel if the repository was uninstalled. + changeset_revision_dict = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, repository ) + current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) + current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) + if current_changeset_revision and current_ctx_rev: + if current_ctx_rev == repository.ctx_rev: + # The uninstalled repository is current. return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reselect_tool_panel_section', **kwd ) ) else: - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='reinstall_repository', - **kwd ) ) - else: - # The uninstalled repository has updates available in the tool shed. - updated_repo_info_dict = self.get_updated_repository_information( trans=trans, - repository_id=trans.security.encode_id( repository.id ), - repository_name=repository.name, - repository_owner=repository.owner, - changeset_revision=current_changeset_revision ) - has_repository_dependencies = updated_repo_info_dict.get( 'has_repository_dependencies', False ) - includes_tool_dependencies = updated_repo_info_dict.get( 'includes_tool_dependencies', False ) - if has_repository_dependencies or includes_tool_dependencies: + # The uninstalled repository has updates available in the tool shed. + updated_repo_info_dict = self.get_updated_repository_information( trans=trans, + repository_id=trans.security.encode_id( repository.id ), + repository_name=repository.name, + repository_owner=repository.owner, + changeset_revision=current_changeset_revision ) json_repo_info_dict = json.to_json_string( updated_repo_info_dict ) encoded_repo_info_dict = encoding_util.tool_shed_encode( json_repo_info_dict ) kwd[ 'latest_changeset_revision' ] = current_changeset_revision @@ -414,10 +408,14 @@ return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reselect_tool_panel_section', **kwd ) ) - else: - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='reinstall_repository', - **kwd ) ) + else: + message = "Unable to get latest revision for repository <b>%s</b> from the tool shed, so repository " % str( repository.name ) + message += "reinstallation is not possible at this time." + status = "error" + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='browse_repositories', + message=message, + status=status ) ) else: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='activate_repository', @@ -903,8 +901,9 @@ if cloned_ok: if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. - current_changeset_revision, current_ctx_rev, includes_tools, has_repository_dependencies = \ - shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) + changeset_revision_dict = shed_util.get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) + current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) + current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) if current_ctx_rev != ctx_rev: repo = hg.repository( suc.get_configured_ui(), path=os.path.abspath( install_dir ) ) shed_util.pull_repository( repo, repository_clone_url, current_changeset_revision ) @@ -1367,7 +1366,7 @@ containers_dicts.append( containers_dict ) # Merge all containers into a single container. containers_dict = shed_util.merge_containers_dicts_for_new_install( containers_dicts ) - # Handle tool dependencies chack box. + # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: message = "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " @@ -1566,6 +1565,7 @@ Galaxy database will not be used since it is outdated. """ message = '' + status = 'done' repository_id = kwd.get( 'id', None ) latest_changeset_revision = kwd.get( 'latest_changeset_revision', None ) latest_ctx_rev = kwd.get( 'latest_ctx_rev', None ) @@ -1580,19 +1580,36 @@ encoded_updated_repo_info_dict = kwd.get( 'updated_repo_info_dict', None ) updated_repo_info_dict = encoding_util.tool_shed_decode( encoded_updated_repo_info_dict ) readme_files_dict = updated_repo_info_dict.get( 'readme_files_dict', None ) + includes_data_managers = updated_repo_info_dict.get( 'includes_data_managers', False ) + includes_datatypes = updated_repo_info_dict.get( 'includes_datatypes', False ) includes_tools = updated_repo_info_dict.get( 'includes_tools', False ) + includes_workflows = updated_repo_info_dict.get( 'includes_workflows', False ) has_repository_dependencies = updated_repo_info_dict.get( 'has_repository_dependencies', False ) includes_tool_dependencies = updated_repo_info_dict.get( 'includes_tool_dependencies', False ) repo_info_dict = updated_repo_info_dict[ 'repo_info_dict' ] else: # There are no updates available from the tool shed for the repository, so use it's locally stored metadata. + has_repository_dependencies = False + includes_data_managers = False + includes_datatypes = False + includes_tool_dependencies = False + includes_tools = False + includes_workflows = False + readme_files_dict = None + tool_dependencies = None if metadata: + if 'data_manager' in metadata: + includes_data_managers = True + if 'datatypes' in metadata: + includes_datatypes = True + if 'tools' in metadata: + includes_tools = True + if 'tool_dependencies' in metadata: + includes_tool_dependencies = True + if 'workflows' in metadata: + includes_workflows = True readme_files_dict = suc.build_readme_files_dict( metadata ) tool_dependencies = metadata.get( 'tool_dependencies', None ) - else: - readme_files_dict = None - tool_dependencies = None - includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies repository_dependencies = self.get_repository_dependencies( trans=trans, repository_id=repository_id, repository_name=tool_shed_repository.name, @@ -1615,33 +1632,39 @@ has_repository_dependencies = True else: has_repository_dependencies = False - # Get the location in the tool panel in which the tool was originally loaded. - if 'tool_panel_section' in metadata: - tool_panel_dict = metadata[ 'tool_panel_section' ] - if tool_panel_dict: - if shed_util.panel_entry_per_tool( tool_panel_dict ): - # The following forces everything to be loaded into 1 section (or no section) in the tool panel. - tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] - tool_section_dict = tool_section_dicts[ 0 ] - original_section_name = tool_section_dict[ 'name' ] + if includes_tools: + # Get the location in the tool panel in which the tools were originally loaded. + if 'tool_panel_section' in metadata: + tool_panel_dict = metadata[ 'tool_panel_section' ] + if tool_panel_dict: + if shed_util.panel_entry_per_tool( tool_panel_dict ): + # The following forces everything to be loaded into 1 section (or no section) in the tool panel. + tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] + tool_section_dict = tool_section_dicts[ 0 ] + original_section_name = tool_section_dict[ 'name' ] + else: + original_section_name = tool_panel_dict[ 'name' ] else: - original_section_name = tool_panel_dict[ 'name' ] + original_section_name = '' else: original_section_name = '' + tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) + no_changes_check_box = CheckboxField( 'no_changes', checked=True ) + if original_section_name: + message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ + % ( tool_shed_repository.name, original_section_name ) + message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " + message += "different section in the tool panel. " + status = 'warning' + else: + message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name + message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " + status = 'warning' else: + no_changes_check_box = None original_section_name = '' - tool_panel_section_select_field = build_tool_panel_section_select_field( trans ) - no_changes_check_box = CheckboxField( 'no_changes', checked=True ) - if original_section_name: - message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ - % ( tool_shed_repository.name, original_section_name ) - message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " - message += "different section in the tool panel. " - status = 'warning' - else: - message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % tool_shed_repository.name - message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " - status = 'warning' + tool_panel_section_select_field = None + shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans ) containers_dict = shed_util.populate_containers_dict_for_new_install( trans=trans, tool_shed_url=tool_shed_url, tool_path=tool_path, @@ -1669,12 +1692,17 @@ repository=tool_shed_repository, no_changes_check_box=no_changes_check_box, original_section_name=original_section_name, + includes_data_managers=includes_data_managers, + includes_datatypes=includes_datatypes, + includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies, + includes_workflows=includes_workflows, has_repository_dependencies=has_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, install_tool_dependencies_check_box=install_tool_dependencies_check_box, containers_dict=containers_dict, tool_panel_section_select_field=tool_panel_section_select_field, + shed_tool_conf_select_field=shed_tool_conf_select_field, encoded_repo_info_dict=encoding_util.tool_shed_encode( repo_info_dict ), repo_info_dict=repo_info_dict, message=message, diff -r 32fc25b8900059f63b0d41d52aa582f06426928c -r 305680a482c3096b082daffa5ff665f5f60d1528 templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -41,28 +41,55 @@ </div> ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )} %endif - <div style="clear: both"></div> - <div class="form-row"> - ${no_changes_check_box.get_html()} - <label style="display: inline;">No changes</label> - <div class="toolParamHelp" style="clear: both;"> - Uncheck and select a different tool panel section to load the tools into a different section in the tool panel. + %if shed_tool_conf_select_field: + <div class="form-row"> + <table class="colored" width="100%"> + <th bgcolor="#EBD9B2">Choose the configuration file whose tool_path setting will be used for installing repositories</th> + </table></div> - </div> - <div class="form-row"> - <label>Add new tool panel section:</label> - <input name="new_tool_panel_section" type="textfield" value="" size="40"/> - <div class="toolParamHelp" style="clear: both;"> - Add a new tool panel section to contain the installed tools (optional). + <% + if len( shed_tool_conf_select_field.options ) == 1: + select_help = "Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be " + select_help += "installed using it's <b>tool_path</b> setting." + else: + select_help = "Your Galaxy instance is configured with %d shed-related tool configuration files, " % len( shed_tool_conf_select_field.options ) + select_help += "so select the file whose <b>tool_path</b> setting you want used for installing repositories." + %> + <div class="form-row"> + <label>Shed tool configuration file:</label> + ${shed_tool_conf_select_field.get_html()} + <div class="toolParamHelp" style="clear: both;"> + ${select_help} + </div></div> - </div> - <div class="form-row"> - <label>Select existing tool panel section:</label> - ${tool_panel_section_select_field.get_html()} - <div class="toolParamHelp" style="clear: both;"> - Choose an existing section in your tool panel to contain the installed tools (optional). + <div style="clear: both"></div> + %else: + <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf}"/> + %endif + %if includes_tools: + <div style="clear: both"></div> + <div class="form-row"> + ${no_changes_check_box.get_html()} + <label style="display: inline;">No changes</label> + <div class="toolParamHelp" style="clear: both;"> + Uncheck and select a different tool panel section to load the tools into a different section in the tool panel. + </div></div> - </div> + <div class="form-row"> + <label>Add new tool panel section:</label> + <input name="new_tool_panel_section" type="textfield" value="" size="40"/> + <div class="toolParamHelp" style="clear: both;"> + Add a new tool panel section to contain the installed tools (optional). + </div> + </div> + <div class="form-row"> + <label>Select existing tool panel section:</label> + ${tool_panel_section_select_field.get_html()} + <div class="toolParamHelp" style="clear: both;"> + Choose an existing section in your tool panel to contain the installed tools (optional). + </div> + </div> + %endif <div class="form-row"><input type="submit" name="select_tool_panel_section_button" value="Install"/></div> diff -r 32fc25b8900059f63b0d41d52aa582f06426928c -r 305680a482c3096b082daffa5ff665f5f60d1528 templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -81,12 +81,12 @@ ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )} <div style="clear: both"></div> %endif - <div class="form-row"> - <table class="colored" width="100%"> - <th bgcolor="#EBD9B2">Choose the tool panel section to contain the installed tools (optional)</th> - </table> - </div> %if shed_tool_conf_select_field: + <div class="form-row"> + <table class="colored" width="100%"> + <th bgcolor="#EBD9B2">Choose the tool panel section to contain the installed tools (optional)</th> + </table> + </div><% if len( shed_tool_conf_select_field.options ) == 1: select_help = "Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be " 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: carlfeberhard: functional_tests.py: add debugging statement for app config
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/32fc25b89000/ changeset: 32fc25b89000 user: carlfeberhard date: 2013-02-19 20:31:56 summary: functional_tests.py: add debugging statement for app config affected #: 1 file diff -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 -r 32fc25b8900059f63b0d41d52aa582f06426928c scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -84,7 +84,6 @@ global_conf.update( get_static_settings() ) return global_conf - def parse_tool_panel_config( config, shed_tools_dict ): """ Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed. @@ -293,6 +292,7 @@ kwargs[ 'object_store' ] = 'distributed' kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample' # Build the Universe Application + log.debug( 'app.kwargs:\n%s', pprint.pformat( kwargs ) ) app = UniverseApplication( job_queue_workers = 5, id_secret = 'changethisinproductiontoo', template_path = "templates", 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: carlfeberhard: browser tests: refactor framework into modules; add history panel tests, anon-user history panel tests
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/973b8d73409f/ changeset: 973b8d73409f user: carlfeberhard date: 2013-02-19 20:04:41 summary: browser tests: refactor framework into modules; add history panel tests, anon-user history panel tests affected #: 10 files diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/anon-history-tests.js --- /dev/null +++ b/test/casperjs/anon-history-tests.js @@ -0,0 +1,181 @@ +// have to handle errors here - or phantom/casper won't bail but _HANG_ +try { + var utils = require( 'utils' ), + xpath = require( 'casper' ).selectXPath, + format = utils.format, + + //...if there's a better way - please let me know, universe + scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + + spaceghost.start(); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} + + +// ------------------------------------------------------------------- +/* TODO: + run a tool + +*/ +// =================================================================== globals and helpers +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} + +var galaxyCookieName = 'galaxysession', + + nameSelector = 'div#history-name', + unnamedName = 'Unnamed history', + subtitleSelector = 'div#history-subtitle-area', + initialSizeStr = '0 bytes', + tagIconSelector = '#history-tag.icon-button', + annoIconSelector = '#history-annotate.icon-button', + //emptyMsgSelector = '#emptyHistoryMessage'; + emptyMsgSelector = '.infomessagesmall', + emptyMsgStr = "Your history is empty. Click 'Get Data' on the left pane to start", + + tooltipSelector = '.bs-tooltip', + anonNameTooltip = 'You must be logged in to edit your history name', + + editableTextClass = 'editable-text', + editableTextInputSelector = 'input#renaming-active'; + +var historyFrameInfo = {}, + testUploadInfo = {}; + + +// =================================================================== TESTS +// ------------------------------------------------------------------- anonymous new, history +// open galaxy - ensure not logged in +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + var loggedInAs = spaceghost.user.loggedInAs(); + this.debug( 'loggedInAs: ' + loggedInAs ); + if( loggedInAs ){ this.logout(); } +}); + +// ------------------------------------------------------------------- check anon cookies +spaceghost.then( function testAnonCookies(){ + this.test.comment( 'session cookie for anon-user should be present and well formed' ); + var cookies = this.page.cookies; + this.debug( this.jsonStr( this.page.cookies ) ); + //??: what are 'well formed' values? + this.test.assert( cookies.length === 1, "Has one cookie" ); + var galaxyCookie = cookies[0]; + this.test.assert( galaxyCookie.name === galaxyCookieName, "Cookie named: " + galaxyCookieName ); + this.test.assert( !galaxyCookie.secure, "Cookie.secure is false" ); +}); + +// ------------------------------------------------------------------- check the empty history for well formedness +// grab the history frame bounds for mouse later tests +spaceghost.then( function(){ + historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); + //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); +}); + +spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ + this.test.comment( 'history panel for anonymous user, new history' ); + this.withFrame( this.selectors.frames.history, function(){ + this.test.comment( "frame should have proper url and title: 'History'" ); + this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); + this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); + + this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); + this.test.assertExists( nameSelector, nameSelector + ' exists' ); + this.test.assertVisible( nameSelector, 'History name is visible' ); + this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); + + this.test.comment( "history subtitle should display size and size should be 0 bytes" ); + this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); + this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); + this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, + 'History subtitle has "' + initialSizeStr + '"' ); + + this.test.comment( "NO tags or annotations icons should be available for an anonymous user" ); + this.test.assertDoesntExist( tagIconSelector, 'Tag icon button not found' ); + this.test.assertDoesntExist( annoIconSelector, 'Annotation icon button not found' ); + + this.test.comment( "A message about the current history being empty should be displayed" ); + this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); + this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); + this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, + 'Message contains "' + emptyMsgStr + '"' ); + + this.test.comment( 'name should have a tooltip with info on anon-user name editing' ); + // mouse over to find tooltip + //NOTE!!: bounds are returned relative to containing frame - need to adjust using historyFrameInfo + //TODO: into conv. fn + var nameInfo = this.getElementInfo( nameSelector ); + //this.debug( 'nameInfo:' + this.jsonStr( nameInfo ) ); + this.page.sendEvent( 'mousemove', + historyFrameInfo.x + nameInfo.x + 1, historyFrameInfo.y + nameInfo.y + 1 ); + this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); + this.test.assertSelectorHasText( tooltipSelector, anonNameTooltip ); + + this.test.comment( 'name should NOT be editable when clicked by anon-user' ); + this.test.assert( nameInfo.attributes[ 'class' ].indexOf( editableTextClass ) === -1, + "Name field is not class for editable text" ); + this.click( nameSelector ); + this.test.assertDoesntExist( editableTextInputSelector, "Clicking on name does not create an input" ); + }); +}); + +// ------------------------------------------------------------------- anon user can upload file +spaceghost.then( function testAnonUpload(){ + this.test.comment( 'anon-user should be able to upload files' ); + spaceghost.tools.uploadFile( '../../test-data/1.txt', function uploadCallback( _uploadInfo ){ + this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); + var hasHda = _uploadInfo.hdaElement, + hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], + hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'historyItem-ok' ) !== -1; + this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); + uploadInfo = _uploadInfo; + }); +}); +spaceghost.then( function testAnonUpload(){ + this.test.comment( "empty should be NO LONGER be displayed" ); + this.test.assertNotVisible( emptyMsgSelector, 'Empty history message is not visible' ); +}); + + +// ------------------------------------------------------------------- anon user can run tool on file + +// ------------------------------------------------------------------- anon user registers/logs in -> same history +spaceghost.user.loginOrRegisterUser( email, password ); +//??: why is a reload needed here? If we don't, loggedInAs === '' ... +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + + this.test.comment( 'anon-user should login and be associated with previous history' ); + var loggedInAs = spaceghost.user.loggedInAs(); + this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); + + this.withFrame( this.selectors.frames.history, function(){ + var hdaInfo = this.historypanel.hdaElementInfoByTitle( uploadInfo.name, uploadInfo.hid ); + this.test.assert( hdaInfo !== null, "After logging in - found a matching hda by name and hid" ); + if( hdaInfo ){ + this.test.assert( uploadInfo.hdaElement.attributes.id === hdaInfo.attributes.id, + "After logging in - found a matching hda by hda view id: " + hdaInfo.attributes.id ); + } + }); +}); + + +// =================================================================== +spaceghost.run( function(){ + this.test.done(); +}); diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/casperjs_runner.py --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -95,6 +95,8 @@ stderr_msg = process.stderr.readline() stderr_msg = self.strip_escape_codes( stderr_msg.strip() ) log.debug( '(%s): %s', rel_script_path, stderr_msg ) + # HACK: this is the last string displayed using the debug settings - afterwards it hangs + # so: bail on this string if stderr_msg.startswith( self.casper_done_str ): break @@ -117,7 +119,7 @@ self.exec_path, self.casper_info ) raise - self.handle_js_results( stdout_output ) + return self.handle_js_results( stdout_output ) def build_command_line( self, rel_script_path, *args, **kwargs ): """Build the headless browser command line list for subprocess. @@ -284,35 +286,61 @@ log.debug( '\n--------------- tearing down module' ) +test_user = { + 'email': 'test1(a)test.test', + 'password': '123456' +} + # ==================================================================== TESTCASE EXAMPLE -# these could be broken out into other files - shouldn't be necc. ATM -class UserTests( CasperJSTestCase ): +# these could be broken out into other py files - shouldn't be necc. ATM +class Test_01_User( CasperJSTestCase ): """TestCase that uses javascript and a headless browser to test dynamic pages. """ + #debug = True def test_10_registration( self ): """User registration tests: register new user, logout, attempt bad registrations. """ # all keywords will be compiled into a single JSON obj and passed to the server - self.run_js_script( 'registration-tests.js', self.env.url, - testuser={ 'email': 'test1(a)test.test', 'password': '123456' }) + self.run_js_script( 'registration-tests.js', + testuser=test_user ) + #TODO:?? could theoretically do db cleanup, checks here with SQLALX #TODO: have run_js_script return other persistant fixture data (uploaded files, etc.) def test_20_login( self ): """User log in tests. """ - self.run_js_script( 'login-tests.js', self.env.url, - testuser={ 'email': 'test1(a)test.test', 'password': '123456' }) + self.run_js_script( 'login-tests.js', + testuser=test_user ) -class ToolTests( CasperJSTestCase ): +class Test_02_Tools( CasperJSTestCase ): """(Minimal) casperjs tests for tools. """ #debug = True def test_10_upload( self ): """Tests uploading files """ - self.run_js_script( 'upload-tests.js' ) + self.run_js_script( 'upload-tests.js', + testuser=test_user ) + + +class Test_03_HistoryPanel( CasperJSTestCase ): + """(Minimal) casperjs tests for tools. + """ + #debug = True + def test_00_history_panel( self ): + """Test history panel basics (controls, structure, refresh, history options menu, etc.). + """ + self.run_js_script( 'history-panel-tests.js', + testuser=test_user ) + + def test_10_anonymous_histories( self ): + """Test history panel basics with an anonymous user. + """ + self.run_js_script( 'anon-history-tests.js', + testuser=test_user ) + # ==================================================================== MAIN diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/history-panel-tests.js --- /dev/null +++ b/test/casperjs/history-panel-tests.js @@ -0,0 +1,252 @@ +// have to handle errors here - or phantom/casper won't bail but _HANG_ +try { + var utils = require( 'utils' ), + xpath = require( 'casper' ).selectXPath, + format = utils.format, + + //...if there's a better way - please let me know, universe + scriptDir = require( 'system' ).args[3] + // remove the script filename + .replace( /[\w|\.|\-|_]*$/, '' ) + // if given rel. path, prepend the curr dir + .replace( /^(?!\/)/, './' ), + spaceghost = require( scriptDir + 'spaceghost' ).create({ + // script options here (can be overridden by CLI) + //verbose: true, + //logLevel: debug, + scriptDir: scriptDir + }); + + spaceghost.start(); + +} catch( error ){ + console.debug( error ); + phantom.exit( 1 ); +} + + +// =================================================================== +/* TODO: +*/ +// =================================================================== globals and helpers +var email = spaceghost.user.getRandomEmail(), + password = '123456'; +if( spaceghost.fixtureData.testUser ){ + email = spaceghost.fixtureData.testUser.email; + password = spaceghost.fixtureData.testUser.password; +} +var newHistoryName = "Test History"; + +var nameSelector = 'div#history-name', + unnamedName = 'Unnamed history', + subtitleSelector = 'div#history-subtitle-area', + initialSizeStr = '0 bytes', + tagIconSelector = '#history-tag.icon-button', + annoIconSelector = '#history-annotate.icon-button', + //emptyMsgSelector = '#emptyHistoryMessage'; + emptyMsgSelector = '.infomessagesmall', + emptyMsgStr = "Your history is empty. Click 'Get Data' on the left pane to start", + + tooltipSelector = '.bs-tooltip', + nameTooltip = 'Click to rename history', + + editableTextClass = 'editable-text', + editableTextInputSelector = 'input#renaming-active'; + +var historyFrameInfo = {}, + testUploadInfo = {}; + + +// =================================================================== TESTS +// ------------------------------------------------------------------- start a new user +spaceghost.user.loginOrRegisterUser( email, password ); +//??: why is a reload needed here? If we don't, loggedInAs === '' ... +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + var loggedInAs = spaceghost.user.loggedInAs(); + this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); +}); + +// ------------------------------------------------------------------- check structure of empty history +// grab the history frame bounds for mouse later tests +spaceghost.then( function(){ + historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); + //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); +}); + +spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ + this.test.comment( 'history panel, new history' ); + this.withFrame( this.selectors.frames.history, function(){ + this.test.comment( "frame should have proper url and title: 'History'" ); + this.test.assertMatch( this.getCurrentUrl(), /\/history/, 'Found history frame url' ); + this.test.assertTitle( this.getTitle(), 'History', 'Found history frame title' ); + + this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); + this.test.assertExists( nameSelector, nameSelector + ' exists' ); + this.test.assertVisible( nameSelector, 'History name is visible' ); + this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); + + this.test.comment( "history subtitle should display size and size should be 0 bytes" ); + this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); + this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); + this.test.assertSelectorHasText( subtitleSelector, initialSizeStr, + 'History subtitle has "' + initialSizeStr + '"' ); + + this.test.comment( "tags and annotation icons should be available" ); + this.test.assertExists( tagIconSelector, 'Tag icon button found' ); + this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); + + this.test.comment( "A message about the current history being empty should be displayed" ); + this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); + this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); + this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, + 'Message contains "' + emptyMsgStr + '"' ); + + }); +}); + +// ------------------------------------------------------------------- name editing +spaceghost.then( function(){ + this.test.comment( 'history panel, editing the history name' ); + this.withFrame( this.selectors.frames.history, function(){ + this.test.comment( 'name should have a tooltip with proper info on name editing' ); + var nameInfo = this.getElementInfo( nameSelector ); + this.page.sendEvent( 'mousemove', + historyFrameInfo.x + nameInfo.x + 1, historyFrameInfo.y + nameInfo.y + 1 ); + this.test.assertExists( tooltipSelector, "Found tooltip after name hover" ); + this.test.assertSelectorHasText( tooltipSelector, nameTooltip ); + + this.test.comment( 'name should be create an input when clicked' ); + this.test.assert( nameInfo.attributes[ 'class' ].indexOf( editableTextClass ) !== -1, + "Name field classed for editable text" ); + this.click( nameSelector ); + this.test.assertExists( editableTextInputSelector, "Clicking on name creates an input" ); + + this.test.comment( 'name should be editable by entering keys and pressing enter' ); + //NOTE: casperjs.sendKeys adds a click before and a selector.blur after sending - won't work here + //TODO: to conv. fn + this.page.sendEvent( 'keypress', newHistoryName ); + this.page.sendEvent( 'keypress', this.page.event.key.Enter ); + this.wait( 1000, function(){ + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); + this.test.assertDoesntExist( editableTextInputSelector, "Input disappears after pressing enter" ); + }); + }); +}); +spaceghost.then( function(){ + this.withFrame( this.selectors.frames.history, function(){ + this.test.comment( 'name should revert if user clicks away while editing' ); + this.click( nameSelector ); + this.page.sendEvent( 'keypress', "Woodchipper metagenomics, Fargo, ND" ); + + // click above the name input element + var inputInfo = this.getElementInfo( editableTextInputSelector ); + this.page.sendEvent( 'mousedown', + historyFrameInfo.x + inputInfo.x + 1, historyFrameInfo.y + inputInfo.y - 5 ); + + this.wait( 1000, function(){ + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); + this.test.assertDoesntExist( editableTextInputSelector, "Input disappears after clicking away" ); + }); + }); +}); +spaceghost.then( function(){ + this.withFrame( this.selectors.frames.history, function(){ + this.test.comment( 'name should revert if user hits ESC while editing' ); + this.click( nameSelector ); + this.page.sendEvent( 'keypress', "Arsenic Bacteria" ); + + this.page.sendEvent( 'keypress', this.page.event.key.Escape ); + this.wait( 1000, function(){ + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is STILL ' + newHistoryName ); + this.test.assertDoesntExist( editableTextInputSelector, "Input disappears after hitting ESC" ); + }); + }); +}); + + +// ------------------------------------------------------------------- check structure of NON empty history +/* +// upload file: 1.txt +spaceghost.then( function upload(){ + this.test.comment( 'anon-user should be able to upload files' ); + spaceghost.uploadFile( '../../test-data/1.txt', function uploadCallback( _uploadInfo ){ + this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); + var hasHda = _uploadInfo.hdaElement, + hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], + hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'historyItem-ok' ) !== -1; + this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); + uploadInfo = _uploadInfo; + }); +}); + +//TODO: for each uploaded file: 1 file per (standard) datatype (or some subset) +// txt, tabular, sam, bam, fasta, fastq, bed, gff, +*/ + +// ------------------------------------------------------------------- +//history panel + // structure of empty + // upload file + // structure of not empty + // tags + // annotation + // history refresh + // history options + // structure + + // deleted + + // hidden + + // persistant expansion (or in hdaView?) + +//hdaView +// with hpanel: + // (we assume hda is in the ok state) + // with collapsed hda: + // can we see the hid? + // can we see the title? + // three primary action buttons: + // they exist? + // Do they have good hrefs, targets? + // Are they enabled? + // do they have proper tooltips? + // display + // edit + // delete + //??: click through? + + // with expaned hda: + // can we see the hid, title, and primary display buttons? + + // misc info: no dbkey specified - is there a '?' link leading to edit attr? + // misc info: uploaded sam file + // misc info: format: sam + + // secondary actions: + // download + // info + // rerun + // visualizations + + // tags and annotations + //TODO: to their own file? tested elsewhere? + + // peek: + // proper headers? + // lines? + // scrollbar? + + // can re-collapse? + + + + + + + + +// =================================================================== +spaceghost.run( function(){ + this.test.done(); +}); diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/login-tests.js --- a/test/casperjs/login-tests.js +++ b/test/casperjs/login-tests.js @@ -32,7 +32,7 @@ */ // =================================================================== globals and helpers -var email = spaceghost.getRandomEmail(), +var email = spaceghost.user.getRandomEmail(), password = '123456'; if( spaceghost.fixtureData.testUser ){ email = spaceghost.fixtureData.testUser.email; @@ -40,51 +40,38 @@ } // =================================================================== TESTS +// register a user (again...) spaceghost.thenOpen( spaceghost.baseUrl, function(){ - this.test.comment( 'loading galaxy homepage' ); - // can we load galaxy? - this.test.assertTitle( 'Galaxy' ); + this.test.comment( 'registering: ' + email ); + spaceghost.user.registerUser( email, password ); }); -// ------------------------------------------------------------------- should work - -// register a user (again...) -spaceghost.then( function(){ - this.test.comment( 'registering: ' + email ); - spaceghost.registerUser( email, password ); -}); -// capture a sshot -//spaceghost.then( function(){ -// this.clickLabel( 'User' ); -// this.capture( 'register.png' ); -//}); - // log them out - check for empty logged in text spaceghost.then( function(){ this.test.comment( 'logging out: ' + email ); - spaceghost.logout(); + spaceghost.user.logout(); }); spaceghost.then( function(){ this.test.assertSelectorDoesntHaveText( xpath( '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' ), /\w/ ); - this.test.assert( spaceghost.loggedInAs() === '', 'loggedInAs() is empty string' ); + this.test.assert( spaceghost.user.loggedInAs() === '', 'loggedInAs() is empty string' ); }); // log them back in - check for email in logged in text spaceghost.then( function(){ this.test.comment( 'logging back in: ' + email ); - spaceghost._submitLogin( email, password ); //No such user + spaceghost.user._submitLogin( email, password ); //No such user }); -spaceghost.then( function(){ +spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.test.assertSelectorHasText( xpath( '//a[contains(text(),"Logged in as")]/span["id=#user-email"]' ), email ); - this.test.assert( spaceghost.loggedInAs() === email, 'loggedInAs() matches email' ); + this.test.assert( spaceghost.user.loggedInAs() === email, 'loggedInAs() matches email' ); }); // finally log back out for next tests spaceghost.then( function(){ this.test.comment( 'logging out: ' + email ); - spaceghost.logout(); + spaceghost.user.logout(); }); // ------------------------------------------------------------------- shouldn't work @@ -93,7 +80,7 @@ spaceghost.each( badEmails, function( self, badEmail ){ self.then( function(){ this.test.comment( 'attempting bad email: ' + badEmail ); - this._submitLogin( badEmail, password ); + this.user._submitLogin( badEmail, password ); }); self.then(function(){ this.assertErrorMessage( 'No such user' ); @@ -105,7 +92,7 @@ spaceghost.each( badPasswords, function( self, badPassword ){ self.then( function(){ this.test.comment( 'attempting bad password: ' + badPassword ); - this._submitLogin( email, badPassword ); + this.user._submitLogin( email, badPassword ); }); self.then(function(){ this.assertErrorMessage( 'Invalid password' ); @@ -118,7 +105,7 @@ this.assertStepsRaise( 'GalaxyError: LoginError', function(){ this.then( function(){ this.test.comment( 'testing (js) error thrown on bad email' ); - this.login( 'nihilist', '1234' ); + this.user.login( 'nihilist', '1234' ); }); }); }); @@ -127,15 +114,16 @@ this.assertStepsRaise( 'GalaxyError: LoginError', function(){ this.then( function(){ this.test.comment( 'testing (js) error thrown on bad password' ); - this.login( email, '1234' ); + this.user.login( email, '1234' ); }); }); }); spaceghost.then( function(){ - this.logout(); + this.user.logout(); }); - +/* +*/ // =================================================================== spaceghost.run( function(){ this.test.done(); diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/modules/historypanel.js --- /dev/null +++ b/test/casperjs/modules/historypanel.js @@ -0,0 +1,118 @@ +// =================================================================== module object, exports +/** Creates a new tools module object. + * @exported + */ +exports.create = function createHistoryPanel( spaceghost ){ + return new HistoryPanel( spaceghost ); +}; + +/** HistoryPanel object constructor. + * @param {SpaceGhost} spaceghost a spaceghost instance + */ +var HistoryPanel = function HistoryPanel( spaceghost ){ + this.options = { + progressIntervalDelay : 500 + }; + //??: circ ref? + this.spaceghost = spaceghost; +}; +exports.HistoryPanel = HistoryPanel; + +HistoryPanel.prototype.toString = function toString(){ + return this.spaceghost + '.HistoryPanel'; +}; + +// ------------------------------------------------------------------- +/* TODO: + run a tool + +*/ +// =================================================================== INTERNAL + +// =================================================================== API (external) +//TODO: to history module +/** Find the casper element info of the hda wrapper given the hda title and hid. + * NOTE: if more than one is found, will return the first found. + * precondition: you should wrap this with withFrame( 'galaxy_history' ) :( + * @param {String} title the title of the hda + * @param {Int} hid (optional) the hid of the hda to look for + * @returns {Object|null} ElementInfo of the historyItemWrapper found, null if not found + */ +HistoryPanel.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title, hid ){ + var spaceghost = this.spaceghost, + titleContains = ( hid !== undefined )?( hid + ': ' + title ):( title ), + wrapperInfo = null; + + //NOTE: depends on jquery + wrapperInfo = spaceghost.evaluate( function( titleContains ){ + // find the title, then the wrapper (2 containers up) + var $title = $( '.historyItemTitle:contains(' + titleContains + ')' ); + var $wrapper = $title.parent().parent(); + return (( $wrapper.attr( 'id' ) )?( __utils__.getElementInfo( '#' + $wrapper.attr( 'id' ) )):( null )); + }, titleContains ); + + return wrapperInfo; +}; + +/** Wait for the hda with given id to move into the given state. + * whenInStateFn and timeoutFn will be passed the hda element info (see Casper#getElementInfo) + * @param {String} hdaSelector selector for hda (should be historyItemWrapper) + * @param {String} finalState hda state to wait for (e.g. 'ok', 'error', 'running', 'queued', etc.) + * @param {Function} whenInStateFn called when hda goes into finalState + * @param {Function} timeoutFn called when maxWaitMs have passed without the desired state + * @param {Int} maxWaitMs number of milliseconds to wait before timing out (defaults to options.waitTimeout) + */ +HistoryPanel.prototype.waitForHdaState = function waitForHdaState( hdaSelector, finalState, + whenInStateFn, timeoutFn, maxWaitMs ){ + //TODO:?? explicitly a historyWrapper id? + // we need a larger timeout for these - it can take a bit + maxWaitMs = maxWaitMs || this.spaceghost.options.waitTimeout; + var spaceghost = this.spaceghost, + finalStateClass = '.historyItem-' + finalState; + + spaceghost.then( function(){ + spaceghost.withFrame( spaceghost.selectors.frames.history, function(){ + + // save the old time out + var oldWaitTimeout = spaceghost.options.waitTimeout, + + // output some progress indicator within the test (debug) + progressIntervalId = setInterval( function progress(){ + // get the state from the hda wrapper's class + var state = spaceghost.evaluate( function( hdaSelector ){ + if( !$( hdaSelector )[0] ){ return '(no hda found)'; } + var $wrapperClasses = $( hdaSelector ).attr( 'class' ); + //TODO: remove magic string/regex + return $wrapperClasses.match( /historyItem\-(\w+)/ )[1]; + }, hdaSelector ); + spaceghost.debug( hdaSelector + ': ' + state ); + }, spaceghost.historypanel.options.progressIntervalDelay ), + + // when done, close down the progress reporter and reset the wait timeout to what it was + finallyFn = function(){ + spaceghost.options.waitTimeout = oldWaitTimeout; + clearInterval( progressIntervalId ); + }; + + spaceghost.options.waitTimeout = maxWaitMs; + spaceghost.waitForSelector( hdaSelector + finalStateClass, + + // if the hda state became 'ok', call the whenInStateFn and close up + function _whenInState(){ + var hdaInfo = spaceghost.elementInfoOrNull( hdaSelector ); + spaceghost.debug( 'HDA now in state ' + finalState ); + //spaceghost.debug( 'HDA:\n' + hdaInfo ); + whenInStateFn.call( spaceghost, hdaInfo ); + finallyFn(); + + // if we've timed out, call the timeoutFn and close up + }, function timeout(){ + var hdaInfo = spaceghost.elementInfoOrNull( hdaSelector ); + spaceghost.debug( 'HDA timed out. HDA = ' + spaceghost.jsonStr( hdaInfo ) ); + timeoutFn.call( spaceghost, hdaInfo ); + finallyFn(); + } + ); + }); + }); +}; diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/modules/tools.js --- /dev/null +++ b/test/casperjs/modules/tools.js @@ -0,0 +1,221 @@ +// =================================================================== module object, exports +/** Creates a new tools module object. + * @exported + */ +exports.create = function createTools( spaceghost ){ + return new Tools( spaceghost ); +}; + +/** Tools object constructor. + * @param {SpaceGhost} spaceghost a spaceghost instance + */ +var Tools = function Tools( spaceghost ){ + //??: circ ref? + this.options = { + defaultUploadWait : ( 30 * 1000 ) + }; + this.spaceghost = spaceghost; +}; +exports.Tools = Tools; + +Tools.prototype.toString = function toString(){ + return this.spaceghost + '.Tools'; +}; + + +// =================================================================== INTERNAL +/** Tests uploading a file. + * NOTE: this version does NOT throw an error on a bad upload. + * It is meant for testing the upload functionality and, therefore, is marked as private. + * Other tests should use uploadFile + * @param {String} filepath the local filesystem path of the file to upload (absolute (?)) + */ +Tools.prototype._uploadFile = function _uploadFile( filepath ){ + var spaceghost = this.spaceghost, + uploadInfo = {}; + //TODO: check file exists using phantom.fs + //TODO: pull from test data + uploadInfo[ spaceghost.selectors.tools.upload.fileInput ] = filepath; + spaceghost.debug( 'uploading file: ' + filepath ); + + spaceghost.then( function(){ + spaceghost.withFrame( spaceghost.selectors.frames.tools, function(){ + spaceghost.clickLabel( spaceghost.labels.tools.upload.panelLabel ); + }); + }); + + spaceghost.then( function beginUpload(){ + spaceghost.withFrame( spaceghost.selectors.frames.main, function(){ + spaceghost.fill( spaceghost.selectors.tools.general.form, uploadInfo, false ); + + // the following throws: + // [error] [remote] Failed dispatching clickmouse event on xpath selector: //input[@value="Execute"]: + // PageError: TypeError: 'undefined' is not a function (evaluating '$(spaceghost).formSerialize()') + // ...and yet the upload still seems to work + spaceghost.click( xpath( spaceghost.selectors.tools.general.executeButton_xpath ) ); + }); + }); + + // debugging + spaceghost.withFrame( spaceghost.selectors.frames.main, function afterUpload(){ + var messageInfo = spaceghost.elementInfoOrNull( spaceghost.selectors.messages.all ); + spaceghost.debug( 'post upload message:\n' + spaceghost.jsonStr( messageInfo ) ); + }); +}; + +/** Uploads a file. + * @param {String} filepath the local filesystem path of the file to upload (absolute (?)) + */ +//Tools.prototype.uploadFile = function uploadFile( filepath ){ +// this._uploadFile( filepath ); +// this.then( function(){ +// this.withFrame( this.selectors.frames.main, function mainAfterUpload(){ +// var messageInfo = this.elementInfoOrNull( this.selectors.messages.all ); +// if( ( !messageInfo ) +// || ( messageInfo.attributes[ 'class' ] !== 'donemessagelarge' ) +// || ( messageInfo.text.indexOf( this.text.upload.success ) === -1 ) ){ +// throw new GalaxyError( 'UploadError: ' + this.jsonStr( messageInfo ) ); +// } +// }); +// }); +// return this; +//}; + +/** Parses the hid and name of a newly uploaded file from the tool execution donemessagelarge + * @param {String} doneMsgText the text extracted from the donemessagelarge after a tool execution + */ +Tools.prototype._parseDoneMessageForTool = function parseDoneMessageForTool( doneMsgText ){ + //TODO: test on non-upload + var executionInfo = {}; + var textMatch = doneMsgText.match( /added to the queue:\n\n(\d+)\: (.*)\n/m ); + if( textMatch ){ + if( textMatch.length > 1 ){ + executionInfo.hid = parseInt( textMatch[1], 10 ); + } + if( textMatch.length > 2 ){ + executionInfo.name = textMatch[2]; + } + executionInfo.name = textMatch[2]; + } + return executionInfo; +}; + +// ------------------------------------------------------------------- get avail. tools +// list available tools +//spaceghost.then( function(){ +// spaceghost.withFrame( 'galaxy_tools', function(){ +// //var availableTools = this.fetchText( 'a.tool-link' ); +// +// var availableTools = this.evaluate( function(){ +// //var toolTitles = __utils__.findAll( 'div.toolTitle' ); +// //return Array.prototype.map.call( toolTitles, function( e ){ +// // //return e.innerHtml; +// // return e.textContent || e.innerText; +// //}).join( '\n' ); +// +// var toolLinks = __utils__.findAll( 'a.tool-link' ); +// return Array.prototype.map.call( toolLinks, function( e ){ +// //return e.innerHtml; +// return e.textContent || e.innerText; +// }).join( '\n' ); +// }); +// this.debug( 'availableTools: ' + availableTools ); +// }); +//}); + +// =================================================================== API (external) +/** get filename from filepath + * @param {String} filepath (POSIX) filepath + * @returns {String} filename part of filepath + */ +Tools.prototype.filenameFromFilepath = function filenameFromFilepath( filepath ){ + var lastSepIndex = filepath.lastIndexOf( '/' ); + if( lastSepIndex !== -1 ){ + return filepath.slice( lastSepIndex + 1 ); + } + return filepath; +}; + +/** Wait for the hda with given id to move into the given state. + * callback function will be passed an uploadInfo object in the form: + * filepath: the filepath of the uploaded file + * filename: the filename of the uploaded file + * hid: the hid of the uploaded file hda in the current history + * name: the name of the uploaded file hda + * hdaElement: the hda DOM (casperjs form) element info object (see Casper#getElementInfo) + * @param {String} filepath (POSIX) filepath + * @param {Function} callback callback function called after hda moves into ok state (will be passed uploadInfo) + * @param {Integer} timeoutAfterMs milliseconds to wait before timing out (defaults to options.defaultUploadWait) + */ +Tools.prototype.uploadFile = function uploadFile( filepath, callback, timeoutAfterMs ){ + timeoutAfterMs = timeoutAfterMs || this.options.defaultUploadWait; + var spaceghost = this.spaceghost, + filename = this.filenameFromFilepath( filepath ), + uploadInfo = {}; + + // precondition: filepath is relative to scriptDir + filepath = spaceghost.options.scriptDir + '/' + filepath; + + // upload the file erroring if a done message is not displayed, aggregate info about upload + spaceghost.info( 'uploading file: ' + filepath + ' (timeout after ' + timeoutAfterMs + ')' ); + this._uploadFile( filepath ); + spaceghost.withFrame( spaceghost.selectors.frames.main, function toolExecuted(){ + spaceghost.debug( 'checking for done message' ); + var doneElementInfo = spaceghost.elementInfoOrNull( spaceghost.selectors.messages.donelarge ); + if( !doneElementInfo ){ + throw new spaceghost.GalaxyError( 'Upload Error: no done message uploading "' + filepath + '"' ); + } + spaceghost.debug( 'doneElementInfo: ' + spaceghost.jsonStr( doneElementInfo ) ); + // grab the hid and uploaded hda name from the done message + uploadInfo = spaceghost.tools._parseDoneMessageForTool( doneElementInfo.text ); + uploadInfo.filename = filename; + uploadInfo.filepath = filepath; + spaceghost.debug( 'uploadInfo: ' + spaceghost.jsonStr( uploadInfo ) ); + }); + + // the hpanel should refresh and display the uploading file, wait for that to go into the ok state + // throw if uploaded HDA doesn't appear, or it doesn't move to 'ok' after allotted time + spaceghost.then( function getNewHda(){ + spaceghost.debug( 'beginning wait for upload file\'s ok state' ); + // get the hda view DOM element from the upload name and hid + spaceghost.withFrame( spaceghost.selectors.frames.history, function(){ + var hdaInfo = spaceghost.historypanel.hdaElementInfoByTitle( uploadInfo.name, uploadInfo.hid ); + if( !hdaInfo ){ + throw new spaceghost.GalaxyError( 'Upload Error: uploaded file HDA not found: ' + + uploadInfo.hid + ', ' + uploadInfo.name ); + } + spaceghost.debug( 'hdaInfo: ' + spaceghost.jsonStr( hdaInfo ) ); + uploadInfo.hdaElement = hdaInfo; + // uploadInfo now has filepath, filename, name, hid, and hdaElement + }); + + spaceghost.then( function waitForOk(){ + spaceghost.debug( 'beginning wait for upload file\'s ok state' ); + + // currently best way to get hda state is using the historyItem-<state> class of the historyItemWrapper + var hdaStateClass = uploadInfo.hdaElement.attributes[ 'class' ].match( /historyItem\-(\w+)/ )[0]; + if( hdaStateClass !== 'historyItem-ok' ){ + + spaceghost.historypanel.waitForHdaState( '#' + uploadInfo.hdaElement.attributes.id, 'ok', + function whenInStateFn( hdaInfo ){ + // refresh hdaElement info + uploadInfo.hdaElement = hdaInfo; + callback.call( spaceghost, uploadInfo ); + + }, function timeoutFn( hdaInfo ){ + var finalClass = (( hdaInfo )?( hdaInfo.attributes[ 'class' ] ):( undefined )); + spaceghost.debug( 'final classes: ' + finalClass ); + throw new spaceghost.GalaxyError( 'Upload Error: timeout waiting for ok state: ' + + '"' + uploadInfo.hid + ': ' + uploadInfo.name + '"' + + ' (waited ' + timeoutAfterMs + ' ms)' ); + + }, timeoutAfterMs ); + } + }); + }); + return spaceghost; +}; +//TODO: upload via url +//TODO: upload by textarea + + diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/modules/user.js --- /dev/null +++ b/test/casperjs/modules/user.js @@ -0,0 +1,209 @@ +// =================================================================== module object, exports +/** Creates a new user module object. + * @exported + */ +exports.create = function createUser( spaceghost ){ + return new User( spaceghost ); +}; + +/** User object constructor. + * @param {SpaceGhost} spaceghost a spaceghost instance + */ +var User = function User( spaceghost ){ + //??: circ ref? + this.spaceghost = spaceghost; +}; +exports.User = User; + +User.prototype.toString = function toString(){ + return this.spaceghost + '.User'; +}; + + +// =================================================================== INTERNAL +/** Tests registering a new user on the Galaxy instance by submitting the registration form. + * NOTE: this version does NOT throw an error on a bad registration. + * It is meant for testing the registration functionality and, therefore, is marked as private. + * Other tests should use registerUser + * @param {String} email the users email address + * @param {String} password the users password + * @param {String} username the users ...username! (optional: will use 1st part of email) + * @param {String} confirm password confirmation (optional: defaults to password) + */ +User.prototype._submitRegistration = function _submitRegistration( email, password, username, confirm ){ + var spaceghost = this.spaceghost, + userInfo = { + email : email, + password: password, + // default username to first part of email + username:( !username && email.match( /^\w*/ ) )?( email.match( /^\w*/ ) ):( username ), + // default confirm: duplicate of password + confirm : ( confirm !== undefined )?( confirm ):( password ) + }; + + spaceghost.debug( 'registering user:\n' + spaceghost.jsonStr( userInfo ) ); + spaceghost.thenOpen( spaceghost.baseUrl, function(){ + spaceghost.clickLabel( spaceghost.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.labels.masthead.userMenu.register ); + + spaceghost.withFrame( spaceghost.selectors.frames.main, function mainBeforeRegister(){ + spaceghost.debug( 'submitting registration... ' + spaceghost.getCurrentUrl() ); + spaceghost.fill( spaceghost.selectors.registrationPage.form, userInfo, false ); + // need manual submit (not a normal html form) + spaceghost.click( xpath( spaceghost.selectors.registrationPage.submit_xpath ) ); + }); + + //// debugging + //spaceghost.withFrame( spaceghost.selectors.frames.main, function mainAfterRegister(){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.selectors.messages.all ); + // spaceghost.debug( 'post registration message:\n' + spaceghost.jsonStr( messageInfo ) ); + //}); + }); +}; + +/** Tests logging in a user on the Galaxy instance by submitting the login form. + * NOTE: this version does NOT throw an error on a bad login. + * It is meant for testing the login functionality and, therefore, is marked as private. + * Other tests should use login + * @param {String} email the users email address + * @param {String} password the users password + */ +User.prototype._submitLogin = function logoutUser( email, password ){ + var spaceghost = this.spaceghost, + loginInfo = { + //NOTE: keys are used as name selectors in the fill fn - must match the names of the inputs + email: email, + password: password + }; + + spaceghost.thenOpen( spaceghost.baseUrl, function(){ + + spaceghost.clickLabel( spaceghost.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.labels.masthead.userMenu.login ); + + spaceghost.withFrame( spaceghost.selectors.frames.main, function mainBeforeLogin(){ + spaceghost.debug( '(' + spaceghost.getCurrentUrl() + ') logging in user:\n' + + spaceghost.jsonStr( loginInfo ) ); + spaceghost.fill( spaceghost.selectors.loginPage.form, loginInfo, false ); + spaceghost.click( xpath( spaceghost.selectors.loginPage.submit_xpath ) ); + }); + + //// debugging + //spaceghost.withFrame( spaceghost.selectors.frames.main, function mainAfterLogin(){ + // //TODO: prob. could use a more generalized form of this for url breakdown/checking + // if( spaceghost.getCurrentUrl().search( spaceghost.selectors.loginPage.url_regex ) != -1 ){ + // var messageInfo = spaceghost.getElementInfo( spaceghost.selectors.messages.all ); + // spaceghost.debug( 'post login message:\n' + spaceghost.jsonStr( messageInfo ) ); + // } + //}); + }); +}; + + +// =================================================================== API (external) +/** Register a new user on the Galaxy instance. + * @param {String} email the users email address + * @param {String} password the users password + * @param {String} username the users ...username! (optional: will use 1st part of email) + * @returns {SpaceGhost} the spaceghost instance (for chaining) + */ +User.prototype.registerUser = function registerUser( email, password, username ){ + var spaceghost = this.spaceghost; + this._submitRegistration( email, password, username ); + spaceghost.then( function(){ + spaceghost.withFrame( spaceghost.selectors.frames.main, function mainAfterRegister(){ + var messageInfo = spaceghost.getElementInfo( spaceghost.selectors.messages.all ); + spaceghost.debug( 'post registration message:\n' + this.jsonStr( messageInfo ) ); + + if( messageInfo.attributes[ 'class' ] === 'errormessage' ){ + throw new spaceghost.GalaxyError( 'RegistrationError: ' + messageInfo.html ); + } + }); + }); + return spaceghost; +}; + +/** Logs in a user. Throws error on bad log in. + * @param {String} email the users email address + * @param {String} password the users password + * @returns {SpaceGhost} the spaceghost instance (for chaining) + */ +User.prototype.login = function login( email, password ){ + var spaceghost = this.spaceghost; + this._submitLogin( email, password ); + spaceghost.then( function(){ + spaceghost.withFrame( spaceghost.selectors.frames.main, function mainAfterLogin(){ + if( spaceghost.getCurrentUrl().search( spaceghost.selectors.loginPage.url_regex ) != -1 ){ + var messageInfo = spaceghost.getElementInfo( spaceghost.selectors.messages.all ); + if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ + throw new spaceghost.GalaxyError( 'LoginError: ' + messageInfo.html ); + } + } + }); + if( spaceghost.user.loggedInAs() === email ){ + spaceghost.debug( 'logged in as ' + email ); + } + }); + return spaceghost; +}; + +/** Fetch the email of the currently logged in user (or '' if not logged in) + * @returns {String} email of currently logged in user or '' if no one logged in + */ +User.prototype.loggedInAs = function loggedInAs(){ + var spaceghost = this.spaceghost, + userEmail = ''; + try { + var loggedInInfo = spaceghost.getElementInfo( xpath( spaceghost.selectors.masthead.userMenu.userEmail_xpath ) ); + userEmail = loggedInInfo.text; + } catch( err ){ + spaceghost.error( err ); + } + //console.debug( 'loggedInInfo:', spaceghost.jsonStr( loggedInInfo ) ); + return userEmail; +}; + +/** Log out the current user + * @returns {SpaceGhost} the spaceghost instance (for chaining) + */ +User.prototype.logout = function logoutUser(){ + var spaceghost = this.spaceghost; + spaceghost.thenOpen( spaceghost.baseUrl, function(){ + //TODO: handle already logged out + spaceghost.clickLabel( spaceghost.labels.masthead.menus.user ); + spaceghost.clickLabel( spaceghost.labels.masthead.userMenu.logout ); + }); + return spaceghost; +}; + +/** Attempts to login a user - if that raises an error (LoginError), register the user + * @param {String} email the users email address + * @param {String} password the users password + * @param {String} username the users ...username! (optional: will use 1st part of email) + * @returns {SpaceGhost} the spaceghost instance (for chaining) + */ +User.prototype.loginOrRegisterUser = function loginOrRegisterUser( email, password, username ){ + var spaceghost = this.spaceghost; + // attempt a login, if that fails - register + spaceghost.tryStepsCatch( function tryToLogin(){ + spaceghost.open( spaceghost.baseUrl ).user.login( email, password ); + + }, function failedLoginRegister(){ + spaceghost.open( spaceghost.baseUrl ).user.registerUser( email, password, username ); + }); + return spaceghost; +}; + +/** Gets a psuedo-random (unique?) email based on the time stamp. + * Helpful for testing registration. + * @param {String} username email user (defaults to 'test') + * @param {String} domain email domain (defaults to 'test.test') + * @returns {String} new email as string + */ +User.prototype.getRandomEmail = function getRandomEmail( username, domain ){ + username = username || 'test'; + domain = domain || 'test.test'; + return username + Date.now() + '@' + domain; +}; + + diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/registration-tests.js --- a/test/casperjs/registration-tests.js +++ b/test/casperjs/registration-tests.js @@ -24,7 +24,6 @@ phantom.exit( 1 ); } - // =================================================================== /* TODO: move selectors and assertText strings into global object for easier editing @@ -33,7 +32,7 @@ */ // =================================================================== globals and helpers -var email = spaceghost.getRandomEmail(), +var email = spaceghost.user.getRandomEmail(), password = '123456', confirm = password, username = 'test' + Date.now(); @@ -60,29 +59,27 @@ // ------------------------------------------------------------------- register a new user spaceghost.then( function(){ this.test.comment( 'registering user: ' + email ); - this._submitUserRegistration( email, password, username, confirm ); + this.user._submitRegistration( email, password, username, confirm ); }); spaceghost.thenOpen( spaceghost.baseUrl, function(){ this.clickLabel( 'User' ); this.test.assertSelectorHasText( 'a #user-email', email, '#user-email === ' + email ); }); - // ------------------------------------------------------------------- log out that user spaceghost.then( function(){ this.test.comment( 'logging out user: ' + email ); - this.logout(); + this.user.logout(); }); spaceghost.then( function(){ this.debug( 'email:' + this.getElementInfo( 'a #user-email' ).html ); this.test.assert( !this.getElementInfo( 'a #user-email' ).html, '#user-email is empty' ); }); - // ------------------------------------------------------------------- bad user registrations spaceghost.then( function(){ this.test.comment( 'attempting to re-register user: ' + email ); - this._submitUserRegistration( email, password, username, confirm ); + this.user._submitRegistration( email, password, username, confirm ); }); spaceghost.then(function(){ this.assertErrorMessage( 'User with that email already exists' ); @@ -93,7 +90,7 @@ spaceghost.each( badEmails, function( self, badEmail ){ self.then( function(){ this.test.comment( 'attempting bad email: ' + badEmail ); - this._submitUserRegistration( badEmail, password, username, confirm ); + this.user._submitRegistration( badEmail, password, username, confirm ); }); self.then(function(){ this.assertErrorMessage( 'Enter a real email address' ); @@ -105,7 +102,7 @@ spaceghost.each( badPasswords, function( self, badPassword ){ self.then( function(){ this.test.comment( 'attempting bad password: ' + badPassword ); - this._submitUserRegistration( spaceghost.getRandomEmail(), badPassword, username, confirm ); + this.user._submitRegistration( spaceghost.user.getRandomEmail(), badPassword, username, confirm ); }); self.then(function(){ this.assertErrorMessage( 'Use a password of at least 6 characters' ); @@ -117,7 +114,7 @@ spaceghost.each( badConfirms, function( self, badConfirm ){ self.then( function(){ this.test.comment( 'attempting bad password confirmation: ' + badConfirm ); - this._submitUserRegistration( spaceghost.getRandomEmail(), password, username, badConfirm ); + this.user._submitRegistration( spaceghost.user.getRandomEmail(), password, username, badConfirm ); }); self.then(function(){ this.assertErrorMessage( 'Passwords do not match' ); @@ -128,10 +125,10 @@ //NOTE: that short username errors only show AFTER checking for existing/valid emails // so: we need to generate new emails for each one spaceghost.then( function(){ - var newEmail = spaceghost.getRandomEmail(), + var newEmail = spaceghost.user.getRandomEmail(), badUsername = 'bob'; this.test.comment( 'attempting short username: ' + badUsername ); - this._submitUserRegistration( newEmail, password, badUsername, confirm ); + this.user._submitRegistration( newEmail, password, badUsername, confirm ); }); spaceghost.then(function(){ this.assertErrorMessage( 'Public name must be at least 4 characters in length' ); @@ -141,9 +138,9 @@ var badUsernames = [ 'BOBERT', 'Robert Paulson', 'bobert!', 'bob_dobbs' ]; spaceghost.each( badUsernames, function( self, badUsername ){ self.then( function(){ - var newEmail = spaceghost.getRandomEmail(); + var newEmail = spaceghost.user.getRandomEmail(); this.test.comment( 'attempting bad username: ' + badUsername ); - this._submitUserRegistration( newEmail, password, badUsername, confirm ); + this.user._submitRegistration( newEmail, password, badUsername, confirm ); }); self.then(function(){ this.assertErrorMessage( "Public name must contain only lower-case letters, numbers and '-'" ); @@ -152,28 +149,29 @@ // ...and the name can't be used already spaceghost.then( function(){ - var newEmail = spaceghost.getRandomEmail(); + var newEmail = spaceghost.user.getRandomEmail(); this.test.comment( 'attempting previously used username with new user: ' + newEmail ); - this._submitUserRegistration( newEmail, password, username, confirm ); + this.user._submitRegistration( newEmail, password, username, confirm ); }); spaceghost.then(function(){ this.assertErrorMessage( 'Public name is taken; please choose another' ); }); -// ------------------------------------------------------------------- test the tests +// ------------------------------------------------------------------- test the convenience fns // these versions are for conv. use in other tests, they should throw errors if used improperly spaceghost.then( function(){ this.assertStepsRaise( 'GalaxyError: RegistrationError', function(){ this.then( function(){ this.test.comment( 'testing (js) error thrown on bad email' ); - this.registerUser( '@internet', '123456', 'ignobel' ); + this.user.registerUser( '@internet', '123456', 'ignobel' ); }); }); }); spaceghost.then( function(){ - this.logout(); + //??: necessary? + this.user.logout(); }); // =================================================================== diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -72,6 +72,14 @@ //console.debug( 'CasperError:' + CasperError ); +// ------------------------------------------------------------------- included libs +//??: can we require underscore, etc. from the ../../static/scripts/lib? +// yep! +//var _ = require( '../../static/scripts/libs/underscore' ); +//var stooges = [{name : 'moe', age : 40}, {name : 'larry', age : 50}, {name : 'curly', age : 60}]; +//console.debug( JSON.stringify( _.pluck(stooges, 'name') ) ); +//exports._ = _; + // ------------------------------------------------------------------- error types PageError.prototype = new CasperError(); PageError.prototype.constructor = CasperError; @@ -79,6 +87,7 @@ CasperError.apply( this, arguments ); this.name = "PageError"; } +SpaceGhost.prototype.PageError = PageError; GalaxyError.prototype = new CasperError(); GalaxyError.prototype.constructor = CasperError; @@ -86,6 +95,7 @@ CasperError.apply( this, arguments ); this.name = "GalaxyError"; } +SpaceGhost.prototype.GalaxyError = GalaxyError; AlertError.prototype = new CasperError(); AlertError.prototype.constructor = CasperError; @@ -93,11 +103,12 @@ CasperError.apply( this, arguments ); this.name = "AlertError"; } +SpaceGhost.prototype.AlertError = AlertError; // =================================================================== METHODS / OVERRIDES // ------------------------------------------------------------------- set up /** More initialization: cli, event handlers, etc. - * @param {Object} options option hash + * @param {Object} options option hash */ SpaceGhost.prototype.init = function init( options ){ //console.debug( 'init, options:', JSON.stringify( options, null, 2 ) ); @@ -122,6 +133,8 @@ ].concat( this.options.clientScripts ); this.debug( 'clientScripts:\n' + this.jsonStr( this.options.clientScripts ) ); + this._loadModules(); + }; /** Allow CLI arguments to set options if the proper option name is used. @@ -371,7 +384,16 @@ }; -// ------------------------------------------------------------------- page control +// ------------------------------------------------------------------- sub modules +/** Load sub modules (similar to casperjs.test) + */ +SpaceGhost.prototype._loadModules = function _loadModules(){ + this.user = require( this.options.scriptDir + 'modules/user' ).create( this ); + this.tools = require( this.options.scriptDir + 'modules/tools' ).create( this ); + this.historypanel = require( this.options.scriptDir + 'modules/historypanel' ).create( this ); +}; + +// =================================================================== PAGE CONTROL /** An override of casper.open specifically for Galaxy. * (Currently only used to change language headers) */ @@ -530,327 +552,8 @@ }; + // =================================================================== GALAXY CONVENIENCE -/** Gets a psuedo-random (unique?) email based on the time stamp. - * Helpful for testing registration. - * @param {String} username email user (defaults to 'test') - * @param {String} domain email domain (defaults to 'test.test') - */ -SpaceGhost.prototype.getRandomEmail = function getRandomEmail( username, domain ){ - username = username || 'test'; - domain = domain || 'test.test'; - return username + Date.now() + '@' + domain; -}; - - -/** Tests registering a new user on the Galaxy instance by submitting the registration form. - * NOTE: this version does NOT throw an error on a bad registration. - * It is meant for testing the registration functionality and, therefore, is marked as private. - * Other tests should use registerUser - * @param {String} email the users email address - * @param {String} password the users password - * @param {String} username the users ...username! (optional: will use 1st part of email) - * @param {String} confirm password confirmation (optional: defaults to password) - */ -SpaceGhost.prototype._submitUserRegistration = function _submitUserRegistration( email, password, username, confirm ){ - var userInfo = { - email : email, - password: password, - // default username to first part of email - username:( !username && email.match( /^\w*/ ) )?( email.match( /^\w*/ ) ):( username ), - // default confirm duplicate of password - confirm : ( confirm !== undefined )?( confirm ):( password ) - }; - this.debug( 'registering user:\n' + this.jsonStr( userInfo ) ); - - this.thenOpen( this.baseUrl, function(){ - - this.clickLabel( this.labels.masthead.menus.user ); - this.clickLabel( this.labels.masthead.userMenu.register ); - - this.withFrame( this.selectors.frames.main, function mainBeforeRegister(){ - this.debug( 'submitting registration... ' + this.getCurrentUrl() ); - this.fill( this.selectors.registrationPage.form, userInfo, false ); - // need manual up - this.click( xpath( this.selectors.registrationPage.submit_xpath ) ); - }); - - this.withFrame( this.selectors.frames.main, function mainAfterRegister(){ - var messageInfo = this.getElementInfo( this.selectors.messages.all ); - this.debug( 'post registration message:\n' + this.jsonStr( messageInfo ) ); - }); - }); -}; - -/** Register a new user on the Galaxy instance. - * @param {String} email the users email address - * @param {String} password the users password - * @param {String} username the users ...username! (optional: will use 1st part of email) - */ -SpaceGhost.prototype.registerUser = function registerUser( email, password, username ){ - this._submitUserRegistration( email, password, username ); - this.then( function(){ - this.withFrame( this.selectors.frames.main, function mainAfterRegister(){ - var messageInfo = this.getElementInfo( this.selectors.messages.all ); - this.debug( 'post registration message:\n' + this.jsonStr( messageInfo ) ); - - if( messageInfo.attributes[ 'class' ] === 'errormessage' ){ - throw new GalaxyError( 'RegistrationError: ' + messageInfo.html ); - } - }); - }); - return this; -}; - -/** Log out the current user - */ -SpaceGhost.prototype.logout = function logoutUser(){ - this.clickLabel( this.labels.masthead.menus.user ); - this.clickLabel( this.labels.masthead.userMenu.login ); - this.thenOpen( this.baseUrl, function(){ - //TODO: handle already logged out - this.clickLabel( this.labels.masthead.menus.user ); - this.clickLabel( this.labels.masthead.userMenu.logout ); - }); -}; - -/** Tests logging in a user on the Galaxy instance by submitting the login form. - * NOTE: this version does NOT throw an error on a bad login. - * It is meant for testing the login functionality and, therefore, is marked as private. - * Other tests should use login - * @param {String} email the users email address - * @param {String} password the users password - */ -SpaceGhost.prototype._submitLogin = function logoutUser( email, password ){ - var loginInfo = { - //NOTE: keys are used as name selectors in the fill fn - must match the names of the inputs - email: email, - password: password - }; - - this.thenOpen( this.baseUrl, function(){ - - this.clickLabel( this.labels.masthead.menus.user ); - this.clickLabel( this.labels.masthead.userMenu.login ); - - this.withFrame( this.selectors.frames.main, function mainBeforeLogin(){ - this.debug( '(' + this.getCurrentUrl() + ') logging in user:\n' + this.jsonStr( loginInfo ) ); - this.fill( this.selectors.loginPage.form, loginInfo, false ); - this.click( xpath( this.selectors.loginPage.submit_xpath ) ); - }); - this.withFrame( this.selectors.frames.main, function mainAfterLogin(){ - //TODO: prob. could use a more generalized form of this for url breakdown/checking - if( this.getCurrentUrl().search( this.selectors.loginPage.url_regex ) != -1 ){ - var messageInfo = this.getElementInfo( this.selectors.messages.all ); - this.debug( 'post login message:\n' + this.jsonStr( messageInfo ) ); - } - }); - }); -}; - -/** Logs in a user. Throws error on bad log in. - * @param {String} email the users email address - * @param {String} password the users password - */ -SpaceGhost.prototype.login = function login( email, password ){ - this._submitLogin( email, password ); - this.then( function(){ - this.withFrame( this.selectors.frames.main, function mainAfterLogin(){ - if( this.getCurrentUrl().search( this.selectors.loginPage.url_regex ) != -1 ){ - var messageInfo = this.getElementInfo( this.selectors.messages.all ); - if( messageInfo && messageInfo.attributes[ 'class' ] === 'errormessage' ){ - throw new GalaxyError( 'LoginError: ' + messageInfo.html ); - } - } - }); - if( this.loggedInAs() === email ){ - this.debug( 'logged in as ' + email ); - } - }); - return this; -}; - -/** Fetch the email of the currently logged in user (or '' if not logged in) - * @returns {String} email of currently logged in user or '' if no one logged in - */ -SpaceGhost.prototype.loggedInAs = function loggedInAs(){ - var userEmail = ''; - try { - var loggedInInfo = this.getElementInfo( xpath( this.selectors.masthead.userMenu.userEmail_xpath ) ); - userEmail = loggedInInfo.text; - } catch( err ){ - this.error( err ); - } - //console.debug( 'loggedInInfo:', this.jsonStr( loggedInInfo ) ); - return userEmail; -}; - -/** Attempts to login a user - if that raises an error (LoginError), register the user - * @param {String} email the users email address - * @param {String} password the users password - * @param {String} username the users ...username! (optional: will use 1st part of email) - */ -SpaceGhost.prototype.loginOrRegisterUser = function loginOrRegisterUser( email, password, username ){ - // attempt a login, if that fails - register - this.tryStepsCatch( function tryToLogin(){ - this.open( this.baseUrl ).login( email, password ); - - }, function failedLoginRegister(){ - this.open( this.baseUrl ).registerUser( email, password, username ); - }); - return this; -}; - -/** Tests uploading a file. - * NOTE: this version does NOT throw an error on a bad upload. - * It is meant for testing the upload functionality and, therefore, is marked as private. - * Other tests should use uploadFile - * @param {String} filepath the local filesystem path of the file to upload (absolute (?)) - */ -SpaceGhost.prototype._uploadFile = function _uploadFile( filepath ){ - var uploadInfo = {}; - //TODO: check file exists using phantom.fs - //TODO: pull from test data - uploadInfo[ this.tools.upload.fileInput ] = filepath; - this.debug( 'uploading file: ' + filepath ); - - spaceghost.then( function(){ - spaceghost.withFrame( this.selectors.frames.tools, function(){ - this.clickLabel( this.tools.upload.panelLabel ); - }); - }); - - this.then( function beginUpload(){ - spaceghost.withFrame( this.selectors.frames.main, function(){ - this.fill( this.tools.general.form, uploadInfo, false ); - - // the following throws: - // [error] [remote] Failed dispatching clickmouse event on xpath selector: //input[@value="Execute"]: - // PageError: TypeError: 'undefined' is not a function (evaluating '$(this).formSerialize()') - - // ...and yet the upload still seems to work - this.click( xpath( this.tools.general.executeButton_xpath ) ); - }); - }); - this.withFrame( this.selectors.frames.main, function afterUpload(){ - var messageInfo = this.elementInfoOrNull( this.selectors.messages.all ); - this.debug( 'post upload message:\n' + this.jsonStr( messageInfo ) ); - }); -}; - -/** Uploads a file. - * @param {String} filepath the local filesystem path of the file to upload (absolute (?)) - */ -SpaceGhost.prototype.uploadFile = function uploadFile( filepath ){ - this._uploadFile( filepath ); - this.then( function(){ - this.withFrame( this.selectors.frames.main, function mainAfterUpload(){ - var messageInfo = this.elementInfoOrNull( this.selectors.messages.all ); - if( ( !messageInfo ) - || ( messageInfo.attributes[ 'class' ] !== 'donemessagelarge' ) - || ( messageInfo.text.indexOf( this.text.upload.success ) === -1 ) ){ - throw new GalaxyError( 'UploadError: ' + this.jsonStr( messageInfo ) ); - } - }); - }); - return this; -}; - -/** Parses the hid and name of a newly uploaded file from the tool execution donemessagelarge - * @param {String} doneMsgText the text extracted from the donemessagelarge after a tool execution - */ -SpaceGhost.prototype.parseDoneMessageForTool = function parseDoneMessageForTool( doneMsgText ){ - //TODO: test on non-upload - var executionInfo = {}; - var textMatch = doneMsgText.match( /added to the queue:\n\n(\d+)\: (.*)\n/m ); - if( textMatch ){ - if( textMatch.length > 1 ){ - executionInfo.hid = parseInt( textMatch[1], 10 ); - } - if( textMatch.length > 2 ){ - executionInfo.name = textMatch[2]; - } - executionInfo.name = textMatch[2]; - } - return executionInfo; -}; - -/** Find the casper element info of the hda wrapper given the hda title and hid. - * NOTE: if more than one is found, will return the first found. - * precondition: you should wrap this with withFrame( 'galaxy_history' ) :( - * @param {String} title the title of the hda - * @param {Int} hid (optional) the hid of the hda to look for - * @returns {Object|null} ElementInfo of the historyItemWrapper found, null if not found - */ -SpaceGhost.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title, hid ){ - var spaceghost = this, - titleContains = ( hid !== undefined )?( hid + ': ' + title ):( title ), - wrapperInfo = null; - - wrapperInfo = spaceghost.evaluate( function( titleContains ){ - // find the title, then the wrapper (2 containers up) - var $title = $( '.historyItemTitle:contains(' + titleContains + ')' ); - var $wrapper = $title.parent().parent(); - return (( $wrapper.attr( 'id' ) )?( __utils__.getElementInfo( '#' + $wrapper.attr( 'id' ) )):( null )); - }, titleContains ); - - return wrapperInfo; -}; - -/** Wait for the hda with given id to move into the given state. - * @param {String} hdaSelector selector for hda (should be historyItemWrapper) - * @param {String} finalState hda state to wait for (e.g. 'ok', 'error', 'running', 'queued', etc.) - * @param {Function} whenInStateFn called when hda goes into finalState - * @param {Function} timeoutFn called when maxWaitMs have passed without the desired state - * @param {Int} maxWaitMs number of milliseconds to wait before timing out (defaults to options.waitTimeout) - */ -SpaceGhost.prototype.waitForHdaState = function waitForHdaState( hdaSelector, finalState, - whenInStateFn, timeoutFn, maxWaitMs ){ - //TODO:?? explicitly a historyWrapper id? - maxWaitMs = maxWaitMs || this.options.waitTimeout; - var finalStateClass = '.historyItem-' + finalState; - - this.then( function(){ - this.withFrame( this.selectors.frames.history, function(){ - // wait for state, preferrably debugging intermediate states - var spaceghost = this, - - // we need a larger timeout for these - it can take a bit - oldWaitTimeout = this.options.waitTimeout, - - // output some progress indicator within the test (debug) - progressIntervalId = setInterval( function progress(){ - var state = spaceghost.evaluate( function( hdaSelector ){ - var $wrapperClasses = $( hdaSelector ).attr( 'class' ); - return $wrapperClasses.match( /historyItem\-(\w+)/ )[1]; - }, hdaSelector ); - spaceghost.debug( hdaSelector + ': ' + state ); - }, 1000 ), - - // when done, close down the progress reporter and reset the wait timeout to what it was - finallyFn = function(){ - spaceghost.options.waitTimeout = oldWaitTimeout; - clearInterval( progressIntervalId ); - }; - - this.options.waitTimeout = maxWaitMs; - this.waitForSelector( hdaSelector + finalStateClass, function _whenInState(){ - this.debug( 'HDA now in state ' + finalState + ':\n' - + this.jsonStr( this.elementInfoOrNull( hdaSelector ) ) ); - whenInStateFn.call( this ); - finallyFn(); - - }, function timeout(){ - this.debug( 'timed out:\n' - + this.jsonStr( this.elementInfoOrNull( hdaSelector ) ) ); - timeoutFn.call( this ); - finallyFn(); - } - ); - }); - }); -}; - // =================================================================== MISCELAIN /** Send message to stderr */ @@ -958,9 +661,10 @@ history : 'galaxy_history' }, messages : { - all : '[class*="message"]', + all : '[class*="message"]', error : '.errormessage', - done : '.donemessage' + done : '.donemessage', + donelarge : '.donemessagelarge' }, loginPage : { form : 'form#login', @@ -970,6 +674,15 @@ registrationPage : { form : 'form#registration', submit_xpath : "//input[@value='Submit']" + }, + tools : { + general : { + form : 'form#tool_form', + executeButton_xpath : '//input[@value="Execute"]' + }, + upload : { + fileInput : 'files_0|file_data' // is this general? + } } }; @@ -983,17 +696,11 @@ login : 'Login', logout : 'Logout' } - } -}; - -SpaceGhost.prototype.tools = { - general : { - form : 'form#tool_form', - executeButton_xpath : '//input[@value="Execute"]' }, - upload : { - panelLabel : 'Upload File', - fileInput : 'files_0|file_data' // is this general? + tools : { + upload : { + panelLabel : 'Upload File' + } } }; @@ -1007,6 +714,12 @@ } }; +SpaceGhost.prototype.loadJSONFile = function loadJSONFile( filepath ){ + //precondition: filepath is relative to script dir + filepath = this.options.scriptDir + filepath; + return JSON.parse( require( 'fs' ).read( filepath ) ); +}; + // =================================================================== EXPORTS /** */ @@ -1021,10 +734,3 @@ return new SpaceGhost(options); }; -// ------------------------------------------------------------------- included libs -//??: can we require underscore, etc. from the ../../static/scripts/lib? -// yep! -//var _ = require( '../../static/scripts/libs/underscore' ); -//var stooges = [{name : 'moe', age : 40}, {name : 'larry', age : 50}, {name : 'curly', age : 60}]; -//console.debug( JSON.stringify( _.pluck(stooges, 'name') ) ); -//exports._ = _; diff -r e45b9ade65b1a27ded8d55a3003b153035551148 -r 973b8d73409ff4ebc33cc3ff6faf172417fb1978 test/casperjs/upload-tests.js --- a/test/casperjs/upload-tests.js +++ b/test/casperjs/upload-tests.js @@ -32,7 +32,7 @@ general tool execution */ // =================================================================== globals and helpers -var email = spaceghost.getRandomEmail(), +var email = spaceghost.user.getRandomEmail(), password = '123456'; if( spaceghost.fixtureData.testUser ){ email = spaceghost.fixtureData.testUser.email; @@ -42,44 +42,22 @@ // =================================================================== TESTS // ------------------------------------------------------------------- start a new user -spaceghost.loginOrRegisterUser( email, password ); +spaceghost.user.loginOrRegisterUser( email, password ); //??: why is a reload needed here? If we don't, loggedInAs === '' ... spaceghost.thenOpen( spaceghost.baseUrl, function(){ - var loggedInAs = spaceghost.loggedInAs(); + var loggedInAs = spaceghost.user.loggedInAs(); this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); }); -// ------------------------------------------------------------------- get avail. tools -// list available tools -//spaceghost.then( function(){ -// spaceghost.withFrame( 'galaxy_tools', function(){ -// //var availableTools = this.fetchText( 'a.tool-link' ); -// -// var availableTools = this.evaluate( function(){ -// //var toolTitles = __utils__.findAll( 'div.toolTitle' ); -// //return Array.prototype.map.call( toolTitles, function( e ){ -// // //return e.innerHtml; -// // return e.textContent || e.innerText; -// //}).join( '\n' ); -// -// var toolLinks = __utils__.findAll( 'a.tool-link' ); -// return Array.prototype.map.call( toolLinks, function( e ){ -// //return e.innerHtml; -// return e.textContent || e.innerText; -// }).join( '\n' ); -// }); -// this.debug( 'availableTools: ' + availableTools ); -// }); -//}); -// ------------------------------------------------------------------- upload from fs -// test uploading from the filesystem +// ------------------------------------------------------------------- long form +// upload a file from the filesystem var uploadInfo = {}; spaceghost.then( function(){ // strangely, this works with a non-existant file --> empty txt file var filename = '1.sam'; var filepath = this.options.scriptDir + '/../../test-data/' + filename; - this._uploadFile( filepath ); + this.tools._uploadFile( filepath ); // when an upload begins successfully... // 1. main should reload with a donemessagelarge @@ -90,7 +68,7 @@ this.test.assert( doneElementInfo !== null, "Found donemessagelarge after uploading file" ); - uploadInfo = this.parseDoneMessageForTool( doneElementInfo.text ); + uploadInfo = this.tools._parseDoneMessageForTool( doneElementInfo.text ); this.test.assert( uploadInfo.hid >= 0, 'Found sensible hid from upload donemessagelarge: ' + uploadInfo.hid ); this.test.assert( uploadInfo.name === filename, @@ -99,12 +77,12 @@ }); -// wait for upload to finish +// move to the history panel and wait for upload to finish spaceghost.then( function(){ var hdaInfo = null; this.withFrame( 'galaxy_history', function(){ - hdaInfo = this.hdaElementInfoByTitle( uploadInfo.name, uploadInfo.hid ); + hdaInfo = this.historypanel.hdaElementInfoByTitle( uploadInfo.name, uploadInfo.hid ); this.debug( 'hda:\n' + this.jsonStr( hdaInfo ) ); }); @@ -113,7 +91,7 @@ //precondition: needs class var hdaStateClass = hdaInfo.attributes[ 'class' ].match( /historyItem\-(\w+)/ )[0]; if( hdaStateClass !== 'historyItem-ok' ){ - this.waitForHdaState( '#' + hdaInfo.attributes.id, 'ok', + this.historypanel.waitForHdaState( '#' + hdaInfo.attributes.id, 'ok', function whenInStateFn(){ this.test.assert( true, 'Upload completed successfully for: ' + uploadInfo.name ); @@ -126,6 +104,34 @@ }); }); +spaceghost.then( function(){ + this.test.comment( 'testing convenience function' ); + spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ + this.test.assert( uploadInfo.hdaElement !== null, "Convenience function produced hda in ok state" ); + }); +}); + +/* +//??: this error's AND waitFor()s THREE times - something to do with assertStepsRaise + waitFor +spaceghost.then( function(){ + this.test.comment( 'testing convenience function timeout error' ); + this.assertStepsRaise( 'GalaxyError: Upload Error: timeout waiting', function(){ + spaceghost.then( function(){ + spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ + this.test.fail( "Convenience function did not timeout!" ); + }, 250 ); + }); + }); +}); + +// this correctly errors +spaceghost.then( function(){ + spaceghost.tools.uploadFile( '../../test-data/1.sam', function( uploadInfo ){ + this.test.fail( "Convenience function did not timeout!" ); + }, 250 ); +}); +*/ + // =================================================================== spaceghost.run( function(){ this.test.done(); Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 19 Feb '13

19 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d5896e8a60fa/ changeset: d5896e8a60fa branch: stable user: inithello date: 2013-02-19 18:29:29 summary: Fix for installing a repository that only contains a workflow, then importing that workflow to Galaxy. affected #: 1 file diff -r 8da37d3985ab9c489760e64d4e3eb707dfbeb4b8 -r d5896e8a60fa948f1713d4b5e30126a12a958679 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -740,8 +740,8 @@ repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) changeset_revision = repository.changeset_revision metadata = repository.metadata - workflows = metadata[ 'workflows' ] - tools_metadata = metadata[ 'tools' ] + workflows = metadata.get( 'workflows', [] ) + tools_metadata = metadata.get( 'tools', [] ) workflow_dict = None for workflow_data_tuple in workflows: # The value of workflow_data_tuple is ( relative_path_to_workflow_file, exported_workflow_dict ). https://bitbucket.org/galaxy/galaxy-central/commits/e45b9ade65b1/ changeset: e45b9ade65b1 user: inithello date: 2013-02-19 18:29:29 summary: Fix for installing a repository that only contains a workflow, then importing that workflow to Galaxy. affected #: 1 file diff -r 445b212b1c6d8159cb5b6f81300cf5dd3f1eebee -r e45b9ade65b1a27ded8d55a3003b153035551148 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -745,8 +745,8 @@ repository = suc.get_tool_shed_repository_by_id( trans, repository_id ) changeset_revision = repository.changeset_revision metadata = repository.metadata - workflows = metadata[ 'workflows' ] - tools_metadata = metadata[ 'tools' ] + workflows = metadata.get( 'workflows', [] ) + tools_metadata = metadata.get( 'tools', [] ) workflow_dict = None for workflow_data_tuple in workflows: # The value of workflow_data_tuple is ( relative_path_to_workflow_file, exported_workflow_dict ). 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: natefoo: Fix the manage jobs admin interface broken by the removal of the manager. This necessitated removing the job lock feature, although it should return in a future release when we have handler communication outside the database.
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/445b212b1c6d/ changeset: 445b212b1c6d user: natefoo date: 2013-02-19 17:30:29 summary: Fix the manage jobs admin interface broken by the removal of the manager. This necessitated removing the job lock feature, although it should return in a future release when we have handler communication outside the database. affected #: 4 files diff -r 9852dd712f5c628d1f635fe643f036eb2b930863 -r 445b212b1c6d8159cb5b6f81300cf5dd3f1eebee lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -1690,7 +1690,7 @@ """ Implements the JobQueue / JobStopQueue interface but does nothing """ - def put( self, *args ): + def put( self, *args, **kwargs ): return def put_stop( self, *args ): return diff -r 9852dd712f5c628d1f635fe643f036eb2b930863 -r 445b212b1c6d8159cb5b6f81300cf5dd3f1eebee lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -493,7 +493,7 @@ .filter( ( model.Job.state == model.Job.states.DELETED_NEW ) \ & ( model.Job.handler == self.app.config.server_name ) ).all() for job in newly_deleted_jobs: - jobs_to_check.append( ( job, None ) ) + jobs_to_check.append( ( job, job.stderr ) ) # Also pull from the queue (in the case of Administrative stopped jobs) try: while 1: diff -r 9852dd712f5c628d1f635fe643f036eb2b930863 -r 445b212b1c6d8159cb5b6f81300cf5dd3f1eebee lib/galaxy/web/base/controllers/admin.py --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -1016,8 +1016,6 @@ deleted = [] msg = None status = None - if self.app.config.job_manager != self.app.config.server_name: - return trans.show_error_message( 'This Galaxy instance (%s) is not the job manager (%s). If using multiple servers, please directly access the job manager instance to manage jobs.' % (self.app.config.server_name, self.app.config.job_manager) ) job_ids = util.listify( stop ) if job_ids and stop_msg in [ None, '' ]: msg = 'Please enter an error message to display to the user describing why the job was terminated' @@ -1026,7 +1024,15 @@ if stop_msg[-1] not in PUNCTUATION: stop_msg += '.' for job_id in job_ids: - trans.app.job_manager.job_stop_queue.put( job_id, error_msg="This job was stopped by an administrator: %s For more information or help" % stop_msg ) + error_msg = "This job was stopped by an administrator: %s <a href='%s' target='_blank'>Contact support</a> for additional help." \ + % ( stop_msg, self.app.config.get("support_url", "http://wiki.galaxyproject.org/Support" ) ) + if trans.app.config.track_jobs_in_database: + job = trans.app.model.Job.get( job_id ) + job.stderr = error_msg + job.state = trans.app.model.Job.states.DELETED_NEW + trans.sa_session.add( job ) + else: + trans.app.job_manager.job_stop_queue.put( job_id, error_msg=error_msg ) deleted.append( str( job_id ) ) if deleted: msg = 'Queued job' @@ -1035,11 +1041,7 @@ msg += ' for deletion: ' msg += ', '.join( deleted ) status = 'done' - if ajl_submit: - if job_lock == 'on': - trans.app.job_manager.job_queue.job_lock = True - else: - trans.app.job_manager.job_queue.job_lock = False + trans.sa_session.flush() cutoff_time = datetime.utcnow() - timedelta( seconds=int( cutoff ) ) jobs = trans.sa_session.query( trans.app.model.Job ) \ .filter( and_( trans.app.model.Job.table.c.update_time < cutoff_time, @@ -1060,8 +1062,7 @@ last_updated = last_updated, cutoff = cutoff, msg = msg, - status = status, - job_lock = trans.app.job_manager.job_queue.job_lock ) + status = status ) ## ---- Utility methods ------------------------------------------------------- diff -r 9852dd712f5c628d1f635fe643f036eb2b930863 -r 445b212b1c6d8159cb5b6f81300cf5dd3f1eebee templates/admin/jobs.mako --- a/templates/admin/jobs.mako +++ b/templates/admin/jobs.mako @@ -46,6 +46,7 @@ <td>Last Update</td><td>Tool</td><td>State</td> + <td>Inputs</td><td>Command Line</td><td>Job Runner</td><td>PID/Cluster ID</td> @@ -67,6 +68,13 @@ <td>${last_updated[job.id]} ago</td><td>${job.tool_id}</td><td>${job.state}</td> + <% + try: + inputs = ", ".join( [ '%s %s' % ( da.dataset.id, da.dataset.state ) for da in job.input_datasets ] ) + except: + inputs = 'Unable to determine inputs' + %> + <td>${inputs}</td><td>${job.command_line}</td><td>${job.job_runner_name}</td><td>${job.job_runner_external_id}</td> @@ -125,32 +133,3 @@ </div></div></form> -<form name="jobs" action="${h.url_for(controller='admin', action='jobs')}" method="POST"> - <p/> - <div class="toolForm"> - <div class="toolFormTitle"> - Administrative Job Lock - </div> - <div class="toolFormBody"> - <div class="form-row"> - <input type="hidden" name="ajl_submit" value="True"/> - %if job_lock==True: - <p>Job dispatching is currently <strong>locked</strong>.</p> - <label> - <input type='checkbox' name='job_lock' checked='checked' /> - Prevent jobs from dispatching. - </label> - %else: - <p>Job dispatching is currently <strong>unlocked</strong>.</p> - <label> - <input type='checkbox' name='job_lock' /> - Prevent jobs from dispatching. - </label> - %endif - </div> - <div class="form-row"> - <input type="submit" class="primary-button" name="submit" value="Update"> - </div> - </div> - </div> -</form> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Trackster: prevent data requests for very small regions by using a (configurable) minimum region size. This improves performance when zoomed in on small regions. Pack scripts.
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9852dd712f5c/ changeset: 9852dd712f5c user: jgoecks date: 2013-02-19 16:16:21 summary: Trackster: prevent data requests for very small regions by using a (configurable) minimum region size. This improves performance when zoomed in on small regions. Pack scripts. affected #: 4 files diff -r ddb55ff5fd1cdb5c2510eef55ab8d427c9e54003 -r 9852dd712f5c628d1f635fe643f036eb2b930863 static/scripts/packed/viz/trackster/tracks.js --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1,1 +1,1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var 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P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite 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ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new f(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset()},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close 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focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=this.viewport_container.width()/(this.high-this.low);var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new Y.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,ao){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;aq=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ap=[],ai=function(ar){return(ar&&"track" in ar)};while((ac*S*ag)<ah){var am=this._get_tile_bounds(ac,ag),an=this.draw_helper(ad,am,ag,this.tiles_div,aq);if(ai(an)){ap.push(an)}else{ak=false}ac+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ap,ae,aq,ao)}},postdraw_actions:function(ad,ae,ag,ac){var af=ab.find(ad,function(ah){return ah.has_icons});if(af){ab.each(ad,function(ah){if(!ah.has_icons){ah.html_elt.css("padding-top",D)}})}},draw_helper:function(ac,af,ar,ah,ai,ao){var an=this,aw=this._gen_tile_cache_key(ai,af);if(!ao){ao={}}var av=(ac?undefined:an.tile_cache.get_elt(aw));if(av){an.show_tile(av,ah,ai);return av}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}}if(al){q(at,ao.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),au=af.get("start"),ad=af.get("end"),ap=Math.ceil((ad-au)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ap);ae.width=ap;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var av=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(av!==undefined){an.tile_cache.set_elt(aw,av);an.show_tile(av,ah,ai)}return av}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,ah,av,aj,al,at){var aq=this,aB=this._gen_tile_cache_key(al,ah);if(!at){at={}}var aA=(ad?undefined:aq.tile_cache.get_elt(aB));if(aA){aq.show_tile(aA,aj,al);return aA}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(ah,aq.mode,av,aq.data_url_extra_params);if(V(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ah,aq.mode,av,view.reference_track.data_url_extra_params);if(V(am)){ao=false}}ak.push(am)}if(ao){q(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ay=ah.get("start"),ae=ah.get("end"),az=0,ar=Math.ceil((ae-ay)*al)+this.left_offset,ap=0,af=[],ax;var ac=0;for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);az=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];am=ak[az+1];aA=aq.draw_tile(aw,au,af[ax],av,ah,al,am)}this.tile_cache.set_elt(aB,aA);this.show_tile(aA,aj,al);return aA}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.hide_contents();return null}},draw_tile:function(ak,al,ag,af,ai,am){var ae=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){this.hide_contents();return}var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ah=0,aj=ak.length;ah<aj;ah++){var ac=Math.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();return new b(ae,ai,af,ad,ak)}this.hide_contents()}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return false}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","mvc/data","viz/trackster/filters"],function(ab,x,l,u,L,Y,i){var q=ab.extend;var V=function(ac){return("isResolved" in ac)};var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();if(ap.offsetY<aq){$(this).insertBefore(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable_before(am,ar);return}else{if(ap.offsetY>ah){$(this).insertAfter(ai);var ar=n[ai.attr("id")];ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al<ak.length;al++){aj=$(ak.get(al));aq=aj.position().top;ah=aq+aj.outerHeight();if(aj.is(ag)&&this!==aj.get(0)&&ap.offsetY>=aq&&ap.offsetY<=ah){if(ap.offsetY-aq<ah-ap.offsetY){aj.find(".content-div").prepend(this)}else{aj.find(".content-div").append(this)}if(am.container){am.container.remove_drawable(am)}n[aj.attr("id")].add_drawable(am);return}}for(al=0;al<ak.length;al++){aj=$(ak.get(al));if(ap.offsetY<aj.position().top&&!(aj.hasClass("reference-track")||aj.hasClass("intro"))){break}}if(al===ak.length){if(this!==ak.get(al-1)){at.append(this);n[at.attr("id")].move_drawable(am,al)}}else{if(this!==ak.get(al)){$(this).insertBefore(ak.get(al));n[at.attr("id")].move_drawable(am,(ap.deltaY>0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var aa=16,G=9,D=20,A=100,I=12000,S=400,K=5000,w=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",E="No data for this chrom/contig.",v="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",y="Tool cannot be rerun: ",a="Loading data...",U="Ready for display",Q=10,H=20;function W(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.name=af.name;this.view=ad;this.container=ac;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name}],saved_values:af.prefs,onchange:function(){this.track.set_name(this.track.config.values.name)}});this.prefs=this.config.values;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.content_visible=true;this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("<div/>").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("<div style='clear: both'/>"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("<div style='clear: both'/>").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var af=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ac=function(){ad.config.update_from_form($(".dialog-box"));hide_modal();$(window).unbind("keypress.check_enter_esc")},ae=function(ag){if((ag.keyCode||ag.which)===27){af()}else{if((ag.keyCode||ag.which)===13){ac()}}};$(window).bind("keypress.check_enter_esc",ae);show_modal("Configure",ad.config.build_form(),{Cancel:af,OK:ac})}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.remove()}}];q(r.prototype,{init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.content_visible){return true}return false},request_draw:function(){},_draw:function(){},to_dict:function(){},set_name:function(ac){this.old_name=this.name;this.name=ac;this.name_div.text(this.name)},revert_name:function(){if(this.old_name){this.name=this.old_name;this.name_div.text(this.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("<a/>").attr("href","javascript:void(0);").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad<ac.length;ad++){ae=ac[ad];this.add_action_icon(ae.name,ae.title,ae.css_class,ae.on_click_fn,ae.prepend,ae.hide)}},update_icons:function(){},hide_contents:function(){},show_contents:function(){},get_drawables:function(){}});var z=function(ad,ac,ae){r.call(this,ad,ac,ae);this.obj_type=ae.obj_type;this.drawables=[]};q(z.prototype,r.prototype,{unpack_drawables:function(ae){this.drawables=[];var ad;for(var ac=0;ac<ae.length;ac++){ad=p(ae[ac],this.view,this);this.add_drawable(ad)}},init:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].init()}},_draw:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac]._draw()}},to_dict:function(){var ad=[];for(var ac=0;ac<this.drawables.length;ac++){ad.push(this.drawables[ac].to_dict())}return{name:this.name,prefs:this.prefs,obj_type:this.obj_type,drawables:ad}},add_drawable:function(ac){this.drawables.push(ac);ac.container=this;this.changed()},add_drawable_before:function(ae,ac){this.changed();var ad=this.drawables.indexOf(ac);if(ad!==-1){this.drawables.splice(ad,0,ae);return true}return false},replace_drawable:function(ae,ac,ad){var af=this.drawables.indexOf(ae);if(af!==-1){this.drawables[af]=ac;if(ad){ae.container_div.replaceWith(ac.container_div)}this.changed()}return af},remove_drawable:function(ad){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);ad.container=null;this.changed();return true}return false},move_drawable:function(ad,ae){var ac=this.drawables.indexOf(ad);if(ac!==-1){this.drawables.splice(ac,1);this.drawables.splice(ae,0,ad);this.changed();return true}return false},get_drawables:function(){return this.drawables}});var P=function(ad,ac,af){q(af,{obj_type:"DrawableGroup",drag_handle_class:"group-handle"});z.call(this,ad,ac,af);this.content_div=$("<div/>").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,z.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw(true)}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("<div/>").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("<div/>").addClass("track-header");ac.append($("<div/>").addClass(this.drag_handle_class));this.name_div=$("<div/>").addClass("track-name").text(this.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al<ae;al++){ai=this.drawables[al];if(ai.get_type()!==ag){can_composite=false;break}if(ai instanceof c){ac++}}if(ao||ac===1){this.action_icons.composite_icon.show()}else{this.action_icons.composite_icon.hide();$(".bs-tooltip").remove()}if(ac>1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];ap[ad.name]=[ad]}for(al=1;al<this.drawables.length;al++){ai=this.drawables[al];for(ak=0;ak<ai.filters_manager.filters.length;ak++){ad=ai.filters_manager.filters[ak];if(ad.name in ap){ap[ad.name].push(ad)}}}this.filters_manager.remove_all();var af,ah,aj,am;for(var an in ap){af=ap[an];if(af.length===ac){ah=new i.NumberFilter({name:af[0].name,index:af[0].index});this.filters_manager.add_filter(ah)}}if(this.filters_manager.filters.length>0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac<this.drawables.length;ac++){this.drawables[ac].filters_manager=this.saved_filters_managers[ac]}this.saved_filters_managers=[]},setup_multitrack_filtering:function(){if(this.filters_manager.filters.length>0){this.saved_filters_managers=[];for(var ac=0;ac<this.drawables.length;ac++){drawable=this.drawables[ac];this.saved_filters_managers.push(drawable.filters_manager);drawable.filters_manager=this.filters_manager}}this.filters_manager.init_filters()},show_composite_track:function(){var ag=[];for(var ad=0;ad<this.drawables.length;ad++){ag.push(this.drawables[ad].name)}var ae="Composite Track of "+this.drawables.length+" tracks ("+ag.join(", ")+")";var af=new f(this.view,this.view,{name:ae,drawables:this.drawables});var ac=this.container.replace_drawable(this,af,true);af.request_draw()},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);this.update_icons()},remove_drawable:function(ac){z.prototype.remove_drawable.call(this,ac);this.update_icons()},to_dict:function(){if(this.filters_manager.visible()){this._restore_filter_managers()}var ac=q(z.prototype.to_dict.call(this),{filters:this.filters_manager.to_dict()});if(this.filters_manager.visible()){this.setup_multitrack_filtering()}return ac},request_draw:function(ac,ae){for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].request_draw(ac,ae)}}});var Z=Backbone.View.extend({initialize:function(ac){q(ac,{obj_type:"View"});z.call(this,"View",ac.container,ac);this.chrom=null;this.vis_id=ac.vis_id;this.dbkey=ac.dbkey;this.label_tracks=[];this.tracks_to_be_redrawn=[];this.max_low=0;this.max_high=0;this.zoom_factor=3;this.min_separation=30;this.has_changes=false;this.load_chroms_deferred=null;this.render();this.canvas_manager=new x.CanvasManager(this.container.get(0).ownerDocument);this.reset()},render:function(){this.requested_redraw=false;var ae=this.container,ac=this;this.top_container=$("<div/>").addClass("top-container").appendTo(ae);this.browser_content_div=$("<div/>").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("<div/>").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("<div/>").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("<div/>").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("<div/>").addClass("intro").appendTo(this.viewport_container).hide();var af=$("<div/>").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){x.select_datasets(select_datasets_url,add_track_async_url,{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("<div/>").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("<div/>").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("<div/>").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("<div/>").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("<div/>").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("<a/>").attr("href","javascript:void(0);").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("<div/>").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("<div/>").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("<div/>").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("<div/>").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("<select/>").attr({name:"chrom"}).css("width","15em").append("<option value=''>Loading</option>").appendTo(this.nav_controls);var ad=function(ag){if(ag.type==="focusout"||(ag.keyCode||ag.which)===13||(ag.keyCode||ag.which)===27){if((ag.keyCode||ag.which)!==27){ac.go_to($(this).val())}$(this).hide();$(this).val("");ac.location_span.show();ac.chrom_select.show()}};this.nav_input=$("<input/>").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("<span/>").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_drawables(),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("<input/>").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("<a/>").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("<a/>").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("<div />").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new X(this,{content_div:this.top_labeltrack}));this.add_label_track(new X(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")}});q(Z.prototype,z.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=w;var ac=this,ad=$.Deferred();$.ajax({url:chrom_url+"/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){ac.add_label_track(new B(ac))}ac.chrom_data=ag.chrom_info;var aj='<option value="">Select Chrom/Contig</option>';for(var ai=0,af=ac.chrom_data.length;ai<af;ai++){var ah=ac.chrom_data[ai].chrom;aj+='<option value="'+ah+'">'+ah+"</option>"}if(ag.prev_chroms){aj+='<option value="previous">Previous '+w+"</option>"}if(ag.next_chroms){aj+='<option value="next">Next '+w+"</option>"}ac.chrom_select.html(aj);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-w});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+w});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();ae.request_redraw(true);for(var ag=0,ac=ae.drawables.length;ag<ac;ag++){var af=ae.drawables[ag];if(af.init){af.init()}}if(ae.reference_track){ae.reference_track.init()}}if(ad!==undefined&&aj!==undefined){ae.low=Math.max(ad,0);ae.high=Math.min(aj,ae.max_high)}else{ae.low=0;ae.high=ae.max_high}ae.reset_overview();ae.request_redraw()}},go_to:function(ag){ag=ag.replace(/ |,/g,"");var ak=this,ac,af,ad=ag.split(":"),ai=ad[0],aj=ad[1];if(aj!==undefined){try{var ah=aj.split("-");ac=parseInt(ah[0],10);af=parseInt(ah[1],10)}catch(ae){return false}}ak.change_chrom(ai,ac,af)},move_fraction:function(ae){var ac=this;var ad=ac.high-ac.low;this.move_delta(ae*ad)},move_delta:function(af){var ac=this;var ae=ac.high-ac.low;if(ac.low-af<ac.max_low){ac.low=ac.max_low;ac.high=ac.max_low+ae}else{if(ac.high-af>ac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw();var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){z.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){z.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ak,ac,aj,al){var ai=this,ah=(al?[al]:ai.drawables),ae;var ad;for(var ag=0;ag<ah.length;ag++){ad=ah[ag];ae=-1;for(var af=0;af<ai.tracks_to_be_redrawn.length;af++){if(ai.tracks_to_be_redrawn[af][0]===ad){ae=af;break}}if(ae<0){ai.tracks_to_be_redrawn.push([ad,ac,aj])}else{ai.tracks_to_be_redrawn[ag][1]=ac;ai.tracks_to_be_redrawn[ag][2]=aj}}if(!this.requested_redraw){requestAnimationFrame(function(){ai._redraw(ak)});this.requested_redraw=true}},_redraw:function(am){this.requested_redraw=false;var aj=this.low,af=this.high;if(aj<this.max_low){aj=this.max_low}if(af>this.max_high){af=this.max_high}var al=this.high-this.low;if(this.high!==0&&al<this.min_separation){af=aj+this.min_separation}this.low=Math.floor(aj);this.high=Math.ceil(af);this.update_location(this.low,this.high);this.resolution_b_px=(this.high-this.low)/this.viewport_container.width();this.resolution_px_b=1/this.resolution_b_px;var ac=(this.low/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var ai=((this.high-this.low)/(this.max_high-this.max_low)*this.overview_viewport.width())||0;var an=13;this.overview_box.css({left:ac,width:Math.max(an,ai)}).show();if(ai<an){this.overview_box.css("left",ac-(an-ai)/2)}if(this.overview_highlight){this.overview_highlight.css({left:ac,width:ai})}if(!am){var ae,ad,ak;for(var ag=0,ah=this.tracks_to_be_redrawn.length;ag<ah;ag++){ae=this.tracks_to_be_redrawn[ag][0];ad=this.tracks_to_be_redrawn[ag][1];ak=this.tracks_to_be_redrawn[ag][2];if(ae){ae._draw(ad,ak)}}this.tracks_to_be_redrawn=[];for(ag=0,ah=this.label_tracks.length;ag<ah;ag++){this.label_tracks[ag]._draw()}}},zoom_in:function(ad,ae){if(this.max_high===0||this.high-this.low<=this.min_separation){return}var af=this.high-this.low,ag=af/2+this.low,ac=(af/this.zoom_factor)/2;if(ad){ag=ad/this.viewport_container.width()*(this.high-this.low)+this.low}this.low=Math.round(ag-ac);this.high=Math.round(ag+ac);this.changed();this.request_redraw()},zoom_out:function(){if(this.max_high===0){return}var ad=this.high-this.low,ae=ad/2+this.low,ac=(ad*this.zoom_factor)/2;this.low=Math.round(ae-ac);this.high=Math.round(ae+ac);this.changed();this.request_redraw()},resize_window:function(){this.viewport_container.height(this.container.height()-this.top_container.height()-this.bottom_container.height());this.request_redraw()},set_overview:function(ae){if(this.overview_drawable){if(this.overview_drawable.dataset_id===ae.dataset_id){return}this.overview_viewport.find(".track").remove()}var ad=ae.copy({content_div:this.overview_viewport}),ac=this;ad.header_div.hide();ad.is_overview=true;ac.overview_drawable=ad;this.overview_drawable.postdraw_actions=function(){ac.overview_highlight.show().height(ac.overview_drawable.content_div.height());ac.overview_viewport.height(ac.overview_drawable.content_div.height()+ac.overview_box.outerHeight());ac.overview_close.show();ac.resize_window()};ac.overview_drawable.request_draw();this.changed()},reset_overview:function(){$(".bs-tooltip").remove();this.overview_viewport.find(".track-tile").remove();this.overview_viewport.height(this.default_overview_height);this.overview_box.height(this.default_overview_height);this.overview_close.hide();this.overview_highlight.hide();view.resize_window();view.overview_drawable=null}});var s=function(ae,aj,af){this.track=ae;this.name=aj.name;this.params=[];var aq=aj.params;for(var ag=0;ag<aq.length;ag++){var al=aq[ag],ad=al.name,ap=al.label,ah=unescape(al.html),ar=al.value,an=al.type;if(an==="number"){this.params.push(new e(ad,ap,ah,(ad in af?af[ad]:ar),al.min,al.max))}else{if(an==="select"){this.params.push(new N(ad,ap,ah,(ad in af?af[ad]:ar)))}else{console.log("WARNING: unrecognized tool parameter type:",ad,an)}}}this.parent_div=$("<div/>").addClass("dynamic-tool").hide();this.parent_div.bind("drag",function(au){au.stopPropagation()}).click(function(au){au.stopPropagation()}).bind("dblclick",function(au){au.stopPropagation()});var ao=$("<div class='tool-name'>").appendTo(this.parent_div).text(this.name);var am=this.params;var ak=this;$.each(this.params,function(av,ay){var ax=$("<div>").addClass("param-row").appendTo(ak.parent_div);var au=$("<div>").addClass("param-label").text(ay.label).appendTo(ax);var aw=$("<div/>").addClass("param-input").html(ay.html).appendTo(ax);aw.find(":input").val(ay.value);$("<div style='clear: both;'/>").appendTo(ax)});this.parent_div.find("input").click(function(){$(this).select()});var at=$("<div>").addClass("param-row").appendTo(this.parent_div);var ai=$("<input type='submit'>").attr("value","Run on complete dataset").appendTo(at);var ac=$("<input type='submit'>").attr("value","Run on visible region").css("margin-left","3em").appendTo(at);ac.click(function(){ak.run_on_region()});ai.click(function(){ak.run_on_dataset()});if("visible" in af&&af.visible){this.parent_div.show()}};q(s.prototype,{update_params:function(){for(var ac=0;ac<this.params.length;ac++){this.params[ac].update_value()}},state_dict:function(){var ad={};for(var ac=0;ac<this.params.length;ac++){ad[this.params[ac].name]=this.params[ac].value}ad.visible=this.parent_div.is(":visible");return ad},get_param_values_dict:function(){var ac={};this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();ac[ad]=ae});return ac},get_param_values:function(){var ac=[];this.parent_div.find(":input").each(function(){var ad=$(this).attr("name"),ae=$(this).val();if(ad){ac[ac.length]=ae}});return ac},run_on_dataset:function(){var ac=this;ac.run({target_dataset_id:this.track.original_dataset_id,tool_id:ac.name},null,function(ad){show_modal(ac.name+" is Running",ac.name+" is running on the complete dataset. Tool outputs are in dataset's history.",{Close:hide_modal})})},run_on_region:function(){var ai=new x.GenomeRegion({chrom:this.track.view.chrom,start:this.track.view.low,end:this.track.view.high}),ad={target_dataset_id:this.track.original_dataset_id,action:"rerun",tool_id:this.name,regions:[ai.toJSON()]},ah=this.track,ae=ad.tool_id+ah.tool_region_and_parameters_str(ai),ac;if(ah.container===view){var ag=new P(view,view,{name:this.name});var af=ah.container.replace_drawable(ah,ag,false);ag.container_div.insertBefore(ah.view.content_div.children()[af]);ag.add_drawable(ah);ah.container_div.appendTo(ag.content_div);ac=ag}else{ac=ah.container}var aj=new ah.constructor(view,ac,{name:ae,hda_ldda:"hda"});aj.init_for_tool_data();aj.change_mode(ah.mode);aj.set_filters_manager(ah.filters_manager.copy(aj));aj.update_icons();ac.add_drawable(aj);aj.tiles_div.text("Starting job.");this.update_params();this.run(ad,aj,function(ak){aj.set_dataset(new Y.Dataset(ak));aj.tiles_div.text("Running job.");aj.init()})},run:function(ac,ae,af){ac.inputs=this.get_param_values_dict();var ad=new l.ServerStateDeferred({ajax_settings:{url:galaxy_paths.get("tool_url"),data:JSON.stringify(ac),dataType:"json",contentType:"application/json",type:"POST"},interval:2000,success_fn:function(ag){return ag!=="pending"}});$.when(ad.go()).then(function(ag){if(ag==="no converter"){ae.container_div.addClass("error");ae.content_div.text(J)}else{if(ag.error){ae.container_div.addClass("error");ae.content_div.text(y+ag.message)}else{af(ag)}}})}});var N=function(ad,ac,ae,af){this.name=ad;this.label=ac;this.html=$(ae);this.value=af};q(N.prototype,{update_value:function(){this.value=$(this.html).val()}});var e=function(ae,ad,ag,ah,af,ac){N.call(this,ae,ad,ag,ah);this.min=af;this.max=ac};q(e.prototype,N.prototype,{update_value:function(){N.prototype.update_value.call(this);this.value=parseFloat(this.value)}});var C=function(ac,ad){L.Scaler.call(this,ad);this.filter=ac};C.prototype.gen_val=function(ac){if(this.filter.high===Number.MAX_VALUE||this.filter.low===-Number.MAX_VALUE||this.filter.low===this.filter.high){return this.default_val}return((parseFloat(ac[this.filter.index])-this.filter.low)/(this.filter.high-this.filter.low))};var F=function(ac){this.track=ac.track;this.params=ac.params;this.values={};this.restore_values((ac.saved_values?ac.saved_values:{}));this.onchange=ac.onchange};q(F.prototype,{restore_values:function(ac){var ad=this;$.each(this.params,function(ae,af){if(ac[af.key]!==undefined){ad.values[af.key]=ac[af.key]}else{ad.values[af.key]=af.default_value}})},build_form:function(){var af=this;var ac=$("<div />");var ae;function ad(ak,ag){for(var ao=0;ao<ak.length;ao++){ae=ak[ao];if(ae.hidden){continue}var ai="param_"+ao;var at=af.values[ae.key];var av=$("<div class='form-row' />").appendTo(ag);av.append($("<label />").attr("for",ai).text(ae.label+":"));if(ae.type==="bool"){av.append($('<input type="checkbox" />').attr("id",ai).attr("name",ai).attr("checked",at))}else{if(ae.type==="text"){av.append($('<input type="text"/>').attr("id",ai).val(at).click(function(){$(this).select()}))}else{if(ae.type==="select"){var aq=$("<select />").attr("id",ai);for(var am=0;am<ae.options.length;am++){$("<option/>").text(ae.options[am].label).attr("value",ae.options[am].value).appendTo(aq)}aq.val(at);av.append(aq)}else{if(ae.type==="color"){var au=$("<div/>").appendTo(av),ap=$("<input />").attr("id",ai).attr("name",ai).val(at).css("float","left").appendTo(au).click(function(ax){$(".bs-tooltip").removeClass("in");var aw=$(this).siblings(".bs-tooltip").addClass("in");aw.css({left:$(this).position().left+$(this).width()+5,top:$(this).position().top-($(aw).height()/2)+($(this).height()/2)}).show();aw.click(function(ay){ay.stopPropagation()});$(document).bind("click.color-picker",function(){aw.hide();$(document).unbind("click.color-picker")});ax.stopPropagation()}),an=$("<a href='javascript:void(0)'/>").addClass("icon-button arrow-circle").appendTo(au).attr("title","Set new random color").tooltip(),ar=$("<div class='bs-tooltip right' style='position: absolute;' />").appendTo(au).hide(),aj=$("<div class='tooltip-inner' style='text-align: inherit'></div>").appendTo(ar),ah=$("<div class='tooltip-arrow'></div>").appendTo(ar),al=$.farbtastic(aj,{width:100,height:100,callback:ap,color:at});au.append($("<div/>").css("clear","both"));(function(aw){an.click(function(){aw.setColor(l.get_random_color())})})(al)}else{av.append($("<input />").attr("id",ai).attr("name",ai).val(at))}}}}if(ae.help){av.append($("<div class='help'/>").text(ae.help))}}}ad(this.params,ac);return ac},update_from_form:function(ac){var ae=this;var ad=false;$.each(this.params,function(af,ah){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="float"){ag=parseFloat(ag)}else{if(ah.type==="int"){ag=parseInt(ag)}else{if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}}}if(ag!==ae.values[ah.key]){ae.values[ah.key]=ag;ad=true}}});if(ad){this.onchange();this.track.changed()}}});var b=function(ac,ag,ae,ad,af){this.track=ac;this.region=ag;this.low=ag.get("start");this.high=ag.get("end");this.resolution=ae;this.html_elt=$("<div class='track-tile'/>").append(ad).height($(ad).attr("height"));this.data=af;this.stale=false};b.prototype.predisplay_actions=function(){};var j=function(ac,ah,ae,ad,af,ag){b.call(this,ac,ah,ae,ad,af);this.max_val=ag};q(j.prototype,b.prototype);var O=function(af,an,ag,ae,ai,ap,aj,aq,ad,am){b.call(this,af,an,ag,ae,ai);this.mode=aj;this.all_slotted=ad;this.feature_mapper=am;this.has_icons=false;if(aq){this.has_icons=true;var ak=this;ae=this.html_elt.children()[0],message_div=$("<div/>").addClass("tile-message").css({height:D-1,width:ae.width}).prependTo(this.html_elt);var al=new x.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),ao=ai.length,ah=$("<a href='javascript:void(0);'/>").addClass("icon more-down").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("<a href='javascript:void(0);'/>").addClass("icon more-across").attr("title","For speed, only the first "+ao+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ah.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.DEEP_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()});ac.click(function(){ak.stale=true;af.data_manager.get_more_data(al,af.mode,ak.resolution,{},af.data_manager.BROAD_DATA_REQ);$(".bs-tooltip").hide();af.request_draw(true)}).dblclick(function(ar){ar.stopPropagation()})}};q(O.prototype,b.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ak=at[0],ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al<ai.length;al++){ah=ai[al];ap[ah.name]=at[ah.index]}var af=$("<div/>").attr("id",ak).addClass("feature-popup"),au=$("<table/>"),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("<tr/>").appendTo(au);$("<th/>").appendTo(av).text(ar);$("<td/>").attr("align","left").appendTo(av).text(typeof(aq)==="number"?W(aq,2):aq)}af.append($("<div class='feature-popup-inner'>").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"))-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"))+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=new Y.Dataset({id:ae.dataset_id,hda_ldda:ae.hda_ldda});this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new x.GenomeDataManager({dataset:this.dataset,genome:new x.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=0;this.content_div=$("<div class='track-content'>").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.dynamic_tool_div.toggle();if(ac.dynamic_tool_div.is(":visible")){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".bs-tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='<strong>Tool</strong>: <%= track.tool.name %><br/><strong>Dataset</strong>: <%= track.name %><br/><strong>Region(s)</strong>: <select name="regions"><option value="cur">current viewing area</option><option value="bookmarks">bookmarks</option><option value="both">current viewing area and bookmarks</option></select>',ae=ab.template(af,{track:ac});var ah=function(){hide_modal();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new x.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new x.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}hide_modal();window.location.href=galaxy_paths.get("sweepster_url")+"?"+$.param({dataset_id:ac.dataset_id,hda_ldda:ac.hda_ldda,regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};show_modal("Visualize tool parameter space and output from different parameter settings?",ae,{No:ah,Yes:ad})}},r.prototype.action_icons_def[2]],can_draw:function(){if(this.dataset_id&&r.prototype.can_draw.call(this)){return true}return false},build_container_div:function(){return $("<div/>").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("<div class='track-header'/>");if(this.view.editor){this.drag_div=$("<div/>").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("<div/>").addClass("track-name").appendTo(ac).text(this.name).attr("id",this.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},on_resize:function(){},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("<div class='track-resize'>");$(ac.container_div).hover(function(){if(ac.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.values.height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.values.mode?this.config.values.mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae<ac;ae++){var ah=ad.display_modes[ae];ag[ah]=function(aj){return function(){ad.change_mode(aj);ad.icons_div.show();ad.container_div.mouseleave(function(){ad.icons_div.hide()})}}(ah)}make_popupmenu(this.action_icons.mode_icon,ag)},build_action_icons:function(){r.prototype.build_action_icons.call(this,this.action_icons_def);if(this.display_modes!==undefined){this.set_display_modes(this.display_modes)}},hide_contents:function(){this.tiles_div.hide();this.container_div.find(".yaxislabel, .track-resize").hide()},show_contents:function(){this.tiles_div.show();this.container_div.find(".yaxislabel, .track-resize").show();this.request_draw()},get_type:function(){if(this instanceof X){return"LabelTrack"}else{if(this instanceof B){return"ReferenceTrack"}else{if(this instanceof h){return"LineTrack"}else{if(this instanceof T){return"ReadTrack"}else{if(this instanceof R){return"VcfTrack"}else{if(this instanceof f){return"CompositeTrack"}else{if(this instanceof c){return"FeatureTrack"}}}}}}}return""},init:function(ae){var ad=this;ad.enabled=false;ad.tile_cache.clear();ad.data_manager.clear();ad.content_div.css("height","auto");ad.tiles_div.text("").children().remove();ad.container_div.removeClass("nodata error pending");if(!ad.dataset_id){return}var ac=$.Deferred(),af={hda_ldda:ad.hda_ldda,data_type:this.dataset_check_type,chrom:ad.view.chrom,retry:ae};$.getJSON(this.dataset.url(),af,function(ag){if(!ag||ag==="error"||ag.kind==="error"){ad.container_div.addClass("error");ad.tiles_div.text(o);if(ag.message){ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("View error").click(function(){show_modal("Trackster Error","<pre>"+ag.message+"</pre>",{Close:hide_modal})}));ad.tiles_div.append($("<span/>").text(" "));ad.tiles_div.append($("<a href='javascript:void(0);'></a>").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(E)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(v);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when(ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){},get_drawables:function(){return this}});var M=function(ae,ad,af){g.call(this,ae,ad,af);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in af?af.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=("tool" in af&&af.tool?new s(this,af.tool,af.tool_state):null);this.tile_cache=new x.Cache(Q);if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){this.dynamic_tool_div=this.tool.parent_div;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("<div/>").addClass("tiles").appendTo(this.content_div);this.overlay_div=$("<div/>").addClass("overlay").appendTo(this.content_div);if(af.mode){this.change_mode(af.mode)}};q(M.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw(true)},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),name:this.name,hda_ldda:this.hda_ldda,dataset_id:this.dataset_id,prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.values.mode=ad;ac.tile_cache.clear();ac.request_draw();this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ad,ac){this.view.request_redraw(false,ad,ac,this)},before_draw:function(){},_draw:function(ad,ao){if(!this.can_draw()){return}var al=this.view.low,ah=this.view.high,aj=ah-al,ae=this.view.container.width(),aq=this.view.resolution_px_b,ag=this.view.resolution_b_px;if(this.is_overview){al=this.view.max_low;ah=this.view.max_high;ag=(view.max_high-view.max_low)/ae;aq=1/ag}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(ag*S)),ak=true,ap=[],ai=function(ar){return(ar&&"track" in ar)};while((ac*S*ag)<ah){var am=this._get_tile_bounds(ac,ag),an=this.draw_helper(ad,am,ag,this.tiles_div,aq);if(ai(an)){ap.push(an)}else{ak=false}ac+=1}if(!ao){this.tiles_div.children(".remove").removeClass("remove").remove()}var af=this;if(ak){this.tiles_div.children(".remove").remove();af.postdraw_actions(ap,ae,aq,ao)}},postdraw_actions:function(ad,ae,ag,ac){var af=ab.find(ad,function(ah){return ah.has_icons});if(af){ab.each(ad,function(ah){if(!ah.has_icons){ah.html_elt.css("padding-top",D)}})}},draw_helper:function(ac,af,ar,ah,ai,ao){var an=this,aw=this._gen_tile_cache_key(ai,af);if(!ao){ao={}}var av=(ac?undefined:an.tile_cache.get_elt(aw));if(av){an.show_tile(av,ah,ai);return av}var al=true;var at=an.data_manager.get_data(af,an.mode,ar,an.data_url_extra_params);if(V(at)){al=false}var aj;if(view.reference_track&&ai>view.canvas_manager.char_width_px){aj=view.reference_track.data_manager.get_data(af,an.mode,ar,view.reference_track.data_url_extra_params);if(V(aj)){al=false}}if(al){q(at,ao.more_tile_data);var ak=an.mode;if(ak==="Auto"){ak=an.get_mode(at);an.update_auto_mode(ak)}var ae=an.view.canvas_manager.new_canvas(),au=af.get("start"),ad=af.get("end"),ap=Math.ceil((ad-au)*ai)+an.left_offset,am=an.get_canvas_height(at,ak,ai,ap);ae.width=ap;ae.height=am;var aq=ae.getContext("2d");aq.translate(this.left_offset,0);var av=an.draw_tile(at,aq,ak,ar,af,ai,aj);if(av!==undefined){an.tile_cache.set_elt(aw,av);an.show_tile(av,ah,ai)}return av}var ag=$.Deferred();$.when(at,aj).then(function(){view.request_redraw(false,false,false,an);ag.resolve()});return ag},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},draw_tile:function(ac,ad,ah,af,ag,ai,ae){console.log("Warning: TiledTrack.draw_tile() not implemented.")},show_tile:function(ae,ah,ai){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ai;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{ah.append(ac)}ae.html_elt.height("auto");this.max_height_px=Math.max(this.max_height_px,ae.html_elt.height());ae.html_elt.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},_get_tile_bounds:function(ac,ad){var af=Math.floor(ac*S*ad),ag=Math.ceil(S*ad),ae=(af+ag<=this.view.max_high?af+ag:this.view.max_high);return new x.GenomeRegion({chrom:this.view.chrom,start:af,end:ae})},tool_region_and_parameters_str:function(ae){var ac=this,ad=(ae!==undefined?ae.toString():"all");return" - region=["+ad+"], parameters=["+ac.tool.get_param_values().join(", ")+"]"},data_and_mode_compatible:function(ac,ad){return true},can_subset:function(ac){return false},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state";this.normal_postdraw_actions=this.postdraw_actions;this.postdraw_actions=function(ae,af,ah,ac){var ad=this;ad.normal_postdraw_actions(ae,af,ah,ac);ad.dataset_check_type="converted_datasets_state";ad.data_query_wait=K;var ag=new l.ServerStateDeferred({url:ad.dataset_state_url,url_params:{dataset_id:ad.dataset_id,hda_ldda:ad.hda_ldda},interval:ad.data_query_wait,success_fn:function(ai){return ai!=="pending"}});$.when(ag.go()).then(function(){ad.data_manager.set("data_type","data")});ad.postdraw_actions=ad.normal_postdraw_actions}}});var X=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(X.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},_draw:function(){var ae=this.view,af=ae.high-ae.low,ai=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/ai)*ai,ag=this.view.container.width(),ad=$("<div style='position: relative; height: 1.3em;'></div>");while(ac<ae.high){var ah=(ac-ae.low)/af*ag;ad.append($("<div class='label'>"+commatize(ac)+"</div>").css({position:"absolute",left:ah-1}));ac+=ai}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){M.call(this,ad,ac,ag);this.drawables=[];this.left_offset=0;if("drawables" in ag){var af;for(var ae=0;ae<ag.drawables.length;ae++){af=ag.drawables[ae];this.drawables[ae]=p(af,ad,null);if(af.left_offset>this.left_offset){this.left_offset=af.left_offset}}this.enabled=true}if(this.drawables.length!==0){this.set_display_modes(this.drawables[0].display_modes,this.drawables[0].mode)}this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,M.prototype,{action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".bs-tooltip").remove();ac.show_group()}}].concat(M.prototype.action_icons_def),to_dict:z.prototype.to_dict,add_drawable:z.prototype.add_drawable,unpack_drawables:z.prototype.unpack_drawables,change_mode:function(ac){M.prototype.change_mode.call(this,ac);for(var ad=0;ad<this.drawables.length;ad++){this.drawables[ad].change_mode(ac)}},init:function(){var ae=[];for(var ad=0;ad<this.drawables.length;ad++){ae.push(this.drawables[ad].init())}var ac=this;$.when.apply($,ae).then(function(){ac.enabled=true;ac.request_draw()})},update_icons:function(){this.action_icons.filters_icon.hide();this.action_icons.tools_icon.hide();this.action_icons.param_space_viz_icon.hide()},can_draw:r.prototype.can_draw,draw_helper:function(ad,ah,av,aj,al,at){var aq=this,aB=this._gen_tile_cache_key(al,ah);if(!at){at={}}var aA=(ad?undefined:aq.tile_cache.get_elt(aB));if(aA){aq.show_tile(aA,aj,al);return aA}var ak=[],aq,ao=true,aw,am;for(var ax=0;ax<this.drawables.length;ax++){aq=this.drawables[ax];aw=aq.data_manager.get_data(ah,aq.mode,av,aq.data_url_extra_params);if(V(aw)){ao=false}ak.push(aw);am=null;if(view.reference_track&&al>view.canvas_manager.char_width_px){am=view.reference_track.data_manager.get_data(ah,aq.mode,av,view.reference_track.data_url_extra_params);if(V(am)){ao=false}}ak.push(am)}if(ao){q(aw,at.more_tile_data);this.tile_predraw_init();var ag=aq.view.canvas_manager.new_canvas(),ay=ah.get("start"),ae=ah.get("end"),az=0,ar=Math.ceil((ae-ay)*al)+this.left_offset,ap=0,af=[],ax;var ac=0;for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];var an=aq.mode;if(an==="Auto"){an=aq.get_mode(aw);aq.update_auto_mode(an)}af.push(an);ac=aq.get_canvas_height(aw,an,al,ar);if(ac>ap){ap=ac}}ag.width=ar;ag.height=(at.height?at.height:ap);az=0;var au=ag.getContext("2d");au.translate(this.left_offset,0);au.globalAlpha=0.5;au.globalCompositeOperation="source-over";for(ax=0;ax<this.drawables.length;ax++,az+=2){aq=this.drawables[ax];aw=ak[az];am=ak[az+1];aA=aq.draw_tile(aw,au,af[ax],av,ah,al,am)}this.tile_cache.set_elt(aB,aA);this.show_tile(aA,aj,al);return aA}var ai=$.Deferred(),aq=this;$.when.apply($,ak).then(function(){view.request_redraw(false,false,false,aq);ai.resolve()});return ai},show_group:function(){var af=new P(this.view,this.container,{name:this.name}),ac;for(var ae=0;ae<this.drawables.length;ae++){ac=this.drawables[ae];ac.update_icons();af.add_drawable(ac);ac.container=af;af.content_div.append(ac.container_div)}var ad=this.container.replace_drawable(this,af,true);af.request_draw()},tile_predraw_init:function(){var af=Number.MAX_VALUE,ac=-af,ad;for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];if(ad instanceof h){if(ad.prefs.min_value<af){af=ad.prefs.min_value}if(ad.prefs.max_value>ac){ac=ad.prefs.max_value}}}for(var ae=0;ae<this.drawables.length;ae++){ad=this.drawables[ae];ad.prefs.min_value=af;ad.prefs.max_value=ac}},postdraw_actions:function(ae,ah,aj,ad){M.prototype.postdraw_actions.call(this,ae,ah,aj,ad);var ag=-1;for(var af=0;af<ae.length;af++){var ac=ae[af].html_elt.find("canvas").height();if(ac>ag){ag=ac}}for(var af=0;af<ae.length;af++){var ai=ae[af];if(ai.html_elt.find("canvas").height()!==ag){this.draw_helper(true,ai.index,ai.resolution,ai.html_elt.parent(),aj,{height:ag});ai.html_elt.remove()}}}});var B=function(ac){M.call(this,ac,{content_div:ac.top_labeltrack},{resize:false});ac.reference_track=this;this.left_offset=200;this.visible_height_px=12;this.container_div.addClass("reference-track");this.content_div.css("background","none");this.content_div.css("min-height","0px");this.content_div.css("border","none");this.data_url=reference_url+"/"+this.view.dbkey;this.data_url_extra_params={reference:true};this.data_manager=new x.ReferenceTrackDataManager({data_url:this.data_url});this.hide_contents()};q(B.prototype,r.prototype,M.prototype,{build_header_div:function(){},init:function(){this.data_manager.clear();this.enabled=true},can_draw:r.prototype.can_draw,draw_helper:function(ae,af,ac,ag,ah,ad){if(ah>this.view.canvas_manager.char_width_px){return M.prototype.draw_helper.call(this,ae,af,ac,ag,ah,ad)}else{this.hide_contents();return null}},draw_tile:function(ak,al,ag,af,ai,am){var ae=this;if(am>this.view.canvas_manager.char_width_px){if(ak.data===null){this.hide_contents();return}var ad=al.canvas;al.font=al.canvas.manager.default_font;al.textAlign="center";ak=ak.data;for(var ah=0,aj=ak.length;ah<aj;ah++){var ac=Math.floor(ah*am);al.fillText(ak[ah],ac,10)}this.show_contents();return new b(ae,ai,af,ad,ak)}this.hide_contents()}});var h=function(ae,ad,af){var ac=this;this.display_modes=["Histogram","Line","Filled","Intensity"];this.mode="Histogram";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"color",label:"Color",type:"color",default_value:l.get_random_color()},{key:"min_value",label:"Min Value",type:"float",default_value:undefined},{key:"max_value",label:"Max Value",type:"float",default_value:undefined},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:32,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(h.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;$("#linetrack_"+this.dataset_id+"_minval").text(this.prefs.min_value);this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;$("#linetrack_"+this.dataset_id+"_maxval").text(this.prefs.max_value);this.tile_cache.clear();this.request_draw()},predraw_init:function(){var ac=this;ac.vertical_range=undefined;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.hda_ldda},function(ad){ac.container_div.addClass("line-track");var ag=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=ag.min,ai=ag.max;ae=Math.floor(Math.min(0,Math.max(ae,ag.mean-2*ag.sd)));ai=Math.ceil(Math.max(0,Math.min(ai,ag.mean+2*ag.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ai;$("#track_"+ac.dataset_id+"_minval").val(ac.prefs.min_value);$("#track_"+ac.dataset_id+"_maxval").val(ac.prefs.max_value)}ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.total_frequency=ag.total_frequency;ac.container_div.find(".yaxislabel").remove();var ah=$("<div/>").text(W(ac.prefs.min_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_min_value(aj)}},help_text:"Set min value"}).addClass("yaxislabel bottom").attr("id","linetrack_"+ac.dataset_id+"_minval").prependTo(ac.container_div),af=$("<div/>").text(W(ac.prefs.max_value,3)).make_text_editable({num_cols:6,on_finish:function(aj){$(".bs-tooltip").remove();var aj=parseFloat(aj);if(!isNaN(aj)){ac.set_max_value(aj)}},help_text:"Set max value"}).addClass("yaxislabel top").attr("id","linetrack_"+ac.dataset_id+"_maxval").prependTo(ac.container_div)})},draw_tile:function(al,aj,ae,ad,ag,ak){var ac=aj.canvas,af=ag.get("start"),ai=ag.get("end"),ah=new L.LinePainter(al.data,af,ai,this.prefs,ae);ah.draw(aj,ac.width,ac.height,ak);return new b(this,ag,ad,ac,al.data)},can_subset:function(ac){return false}});var t=function(ae,ad,af){var ac=this;this.display_modes=["Heatmap"];this.mode="Heatmap";M.call(this,ae,ad,af);this.hda_ldda=af.hda_ldda;this.dataset_id=af.dataset_id;this.original_dataset_id=this.dataset_id;this.left_offset=0;this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"pos_color",label:"Positive Color",type:"color",default_value:"#FF8C00"},{key:"neg_color",label:"Negative Color",type:"color",default_value:"#4169E1"},{key:"min_value",label:"Min Value",type:"float",default_value:-1},{key:"max_value",label:"Max Value",type:"float",default_value:1},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:500,hidden:true}],saved_values:af.prefs,onchange:function(){ac.set_name(ac.prefs.name);ac.vertical_range=ac.prefs.max_value-ac.prefs.min_value;ac.set_min_value(ac.prefs.min_value);ac.set_max_value(ac.prefs.max_value)}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.vertical_range=this.config.values.max_value-this.config.values.min_value};q(t.prototype,r.prototype,M.prototype,{on_resize:function(){this.request_draw(true)},set_min_value:function(ac){this.prefs.min_value=ac;this.tile_cache.clear();this.request_draw()},set_max_value:function(ac){this.prefs.max_value=ac;this.tile_cache.clear();this.request_draw()},draw_tile:function(ac,ae,ai,ag,ah,aj){var af=ae.canvas,ad=new L.DiagonalHeatmapPainter(ac.data,ah.get("start"),ah.get("end"),this.prefs,ai);ad.draw(ae,af.width,af.height,aj);return new b(this,ah,ag,af,ac.data)}});var c=function(af,ae,ah){var ad=this;this.display_modes=["Auto","Coverage","Dense","Squish","Pack"];M.call(this,af,ae,ah);var ag=l.get_random_color(),ac=l.get_random_color([ag,"#FFFFFF"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:ag},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true,help:"Show the number of items in each bin when drawing summary histogram"},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"connector_style",label:"Connector style",type:"select",default_value:"fishbones",options:[{label:"Line with arrows",value:"fishbone"},{label:"Arcs",value:"arcs"}]},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"height",type:"int",default_value:this.visible_height_px,hidden:true}],saved_values:ah.prefs,onchange:function(){ad.set_name(ad.prefs.name);ad.tile_cache.clear();ad.set_painter_from_config();ad.request_draw()}});this.prefs=this.config.values;this.visible_height_px=this.config.values.height;this.container_div.addClass("feature-track");this.hda_ldda=ah.hda_ldda;this.dataset_id=ah.dataset_id;this.original_dataset_id=ah.dataset_id;this.show_labels_scale=0.001;this.showing_details=false;this.summary_draw_height=30;this.slotters={};this.start_end_dct={};this.left_offset=200;this.set_painter_from_config()};q(c.prototype,r.prototype,M.prototype,{set_dataset:function(ac){this.dataset_id=ac.get("id");this.hda_ldda=ac.get("hda_ldda");this.dataset=ac;this.data_manager.set("dataset",ac)},set_painter_from_config:function(){if(this.config.values.connector_style==="arcs"){this.painter=L.ArcLinkedFeaturePainter}else{this.painter=L.LinkedFeaturePainter}},before_draw:function(){this.max_height_px=0},postdraw_actions:function(ar,am,ah,ag){M.prototype.postdraw_actions.call(this,ar,ag);var al=this,ao;if(al.mode==="Coverage"){var ad=-1;for(ao=0;ao<ar.length;ao++){var an=ar[ao].max_val;if(an>ad){ad=an}}for(ao=0;ao<ar.length;ao++){var au=ar[ao];if(au.max_val!==ad){au.html_elt.remove();al.draw_helper(true,au.index,au.resolution,au.html_elt.parent(),ah,{more_tile_data:{max:ad}})}}}if(al.filters_manager){var ai=al.filters_manager.filters;for(var aq=0;aq<ai.length;aq++){ai[aq].update_ui_elt()}var at=false,ac,aj;for(ao=0;ao<ar.length;ao++){if(ar[ao].data.length){ac=ar[ao].data[0];for(var aq=0;aq<ai.length;aq++){aj=ai[aq];if(aj.applies_to(ac)&&aj.min!==aj.max){at=true;break}}}}if(al.filters_available!==at){al.filters_available=at;if(!al.filters_available){al.filters_manager.hide()}al.update_icons()}}this.container_div.find(".yaxislabel").remove();var af=ar[0];if(af instanceof j){var ak=(this.prefs.histogram_max?this.prefs.histogram_max:af.max_val),ae=$("<div/>").text(ak).make_text_editable({num_cols:12,on_finish:function(av){$(".bs-tooltip").remove();var av=parseFloat(av);al.prefs.histogram_max=(!isNaN(av)?av:null);al.tile_cache.clear();al.request_draw()},help_text:"Set max value; leave blank to use default"}).addClass("yaxislabel top").css("color",this.prefs.label_color);this.container_div.prepend(ae)}if(af instanceof O){var ap=true;for(ao=0;ao<ar.length;ao++){if(!ar[ao].all_slotted){ap=false;break}}if(!ap){this.action_icons.show_more_rows_icon.show()}else{this.action_icons.show_more_rows_icon.hide()}}else{this.action_icons.show_more_rows_icon.hide()}},update_auto_mode:function(ac){var ac;if(this.mode==="Auto"){if(ac==="no_detail"){ac="feature spans"}else{if(ac==="summary_tree"){ac="coverage histogram"}}this.action_icons.mode_icon.attr("title","Set display mode (now: Auto/"+ac+")")}},incremental_slots:function(ag,ac,af){var ad=this.view.canvas_manager.dummy_context,ae=this.slotters[ag];if(!ae||(ae.mode!==af)){ae=new (u.FeatureSlotter)(ag,af,A,function(ah){return ad.measureText(ah)});this.slotters[ag]=ae}return ae.slot_features(ac)},get_mode:function(ac){if(ac.dataset_type==="summary_tree"){mode="summary_tree"}else{if(ac.extra_info==="no_detail"||this.is_overview){mode="no_detail"}else{if(this.view.high-this.view.low>I){mode="Squish"}else{mode="Pack"}}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="summary_tree"||ag==="Coverage"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(aa,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,ar,af,aj,ae){var ap=this,ad=aq.canvas,ay=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(ao==="summary_tree"||ao==="Coverage"){var aA=new L.SummaryTreePainter(am,ay,ac,this.prefs);aA.draw(aq,ad.width,ad.height,aj);return new j(ap,af,ar,ad,am.data,am.max)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var at=0,av=am.data.length;at<av;at++){var ah=am.data[at];var au=false;var al;for(var ax=0,aC=ak.length;ax<aC;ax++){al=ak[ax];al.update_attrs(ah);if(!al.keep(ah)){au=true;break}}if(!au){ai.push(ah);if(!(ah[0] in an)){all_slotted=false}}}}var aB=(this.filters_manager.alpha_filter?new C(this.filters_manager.alpha_filter):null);var az=(this.filters_manager.height_filter?new C(this.filters_manager.height_filter):null);var aA=new (this.painter)(ai,ay,ac,this.prefs,ao,aB,az,ae);var aw=null;aq.fillStyle=this.prefs.block_color;aq.font=aq.canvas.manager.default_font;aq.textAlign="right";if(am.data){aw=aA.draw(aq,ad.width,ad.height,aj,an);aw.translation=-ag}return new O(ap,af,ar,ad,am.data,aj,ao,am.message,all_slotted,aw)},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="summary_tree"}else{if(ac.extra_info==="no_detail"||ac.dataset_type==="summary_tree"){return false}else{return true}}}},can_subset:function(ac){if(ac.dataset_type==="summary_tree"||ac.message||ac.extra_info==="no_detail"){return false}return true}});var R=function(ad,ac,ae){c.call(this,ad,ac,ae);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ae.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter};q(R.prototype,r.prototype,M.prototype,c.prototype);var T=function(ae,ad,ag){c.call(this,ae,ad,ag);var af=l.get_random_color(),ac=l.get_random_color([af,"#ffffff"]);this.config=new F({track:this,params:[{key:"name",label:"Name",type:"text",default_value:this.name},{key:"block_color",label:"Block and sense strand color",type:"color",default_value:af},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:ac},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"histogram_max",label:"Histogram maximum",type:"float",default_value:null,help:"Clear value to set automatically"},{key:"mode",type:"string",default_value:this.mode,hidden:true}],saved_values:ag.prefs,onchange:function(){this.track.set_name(this.track.prefs.name);this.track.tile_cache.clear();this.track.request_draw()}});this.prefs=this.config.values;this.painter=L.ReadPainter;this.update_icons()};q(T.prototype,r.prototype,M.prototype,c.prototype);var d={LineTrack:h,FeatureTrack:c,VcfTrack:R,ReadTrack:T,DiagonalHeatmapTrack:t,CompositeTrack:f,DrawableGroup:P};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new d[af](ad,ac,ae)}};return{TracksterView:Z,DrawableGroup:P,LineTrack:h,FeatureTrack:c,DiagonalHeatmapTrack:t,ReadTrack:T,VcfTrack:R,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff -r ddb55ff5fd1cdb5c2510eef55ab8d427c9e54003 -r 9852dd712f5c628d1f635fe643f036eb2b930863 static/scripts/packed/viz/visualization.js --- a/static/scripts/packed/viz/visualization.js +++ b/static/scripts/packed/viz/visualization.js @@ -1,1 +1,1 @@ -define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,p){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){show_modal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=function(u){return("isResolved" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_paths.attributes.image_path+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=x.indexOf(v);if(u!==-1){if(w[v].stale){x.splice(u,1);delete w[v]}else{this.move_key_to_end(v,u)}}return w[v]},set_elt:function(v,x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=this.attributes.num_elements;if(!y[v]){if(z.length>=w){var u=z.shift();delete y[u]}z.push(v)}y[v]=x;return x},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,init_data:null,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(A,z,w,y){var B=this.get_elt(A);if(B&&(j(B)||this.get("data_mode_compatible")(B,z))){return B}var C=this.get("key_ary"),v=this.get("obj_cache"),D,u;for(var x=0;x<C.length;x++){D=C[x];u=new g({from_str:D});if(u.contains(A)){B=v[D];if(j(B)||(this.get("data_mode_compatible")(B,z)&&this.get("can_subset")(B))){this.move_key_to_end(D,x);return B}}}return this.load_data(A,z,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}else{if(u.dataset_type==="summary_tree"){w.level=Math.min(u.level-1,2)}}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},get_elt:function(u){return q.prototype.get_elt.call(this,u.toString())},set_elt:function(v,u){return q.prototype.set_elt.call(this,v.toString(),u)}});var n=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,w,x,u,v)}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){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_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<=w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}return u},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=i.Dataset.extend({initialize:function(u){this.set("id",u.dataset_id);this.set("config",p.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this,init_data:v}))}});var o=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=o.extend({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,ReferenceTrackDataManager:n,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file +define(["libs/underscore","mvc/data","viz/trackster/util","utils/config"],function(s,i,l,p){var a=function(u,x,w,v){$.ajax({url:u,data:w,error:function(){alert("Grid failed")},success:function(y){show_modal("Select datasets for new tracks",y,{Cancel:function(){hide_modal()},Add:function(){var z=[];$("input[name=id]:checked,input[name=ldda_ids]:checked").each(function(){var A={data_type:"track_config",hda_ldda:"hda"},B=$(this).val();if($(this).attr("name")!=="id"){A.hda_ldda="ldda"}z[z.length]=$.ajax({url:x+"/"+B,data:A,dataType:"json"})});$.when.apply($,z).then(function(){var A=(arguments[0] instanceof Array?$.map(arguments,function(B){return B[0]}):[arguments[0]]);v(A)});hide_modal()}})}})};var j=function(u){return("isResolved" in u)};var f=function(u){this.default_font=u!==undefined?u:"9px Monaco, Lucida Console, monospace";this.dummy_canvas=this.new_canvas();this.dummy_context=this.dummy_canvas.getContext("2d");this.dummy_context.font=this.default_font;this.char_width_px=this.dummy_context.measureText("A").width;this.patterns={};this.load_pattern("right_strand","/visualization/strand_right.png");this.load_pattern("left_strand","/visualization/strand_left.png");this.load_pattern("right_strand_inv","/visualization/strand_right_inv.png");this.load_pattern("left_strand_inv","/visualization/strand_left_inv.png")};s.extend(f.prototype,{load_pattern:function(u,y){var v=this.patterns,w=this.dummy_context,x=new Image();x.src=galaxy_paths.attributes.image_path+y;x.onload=function(){v[u]=w.createPattern(x,"repeat")}},get_pattern:function(u){return this.patterns[u]},new_canvas:function(){var u=$("<canvas/>")[0];if(window.G_vmlCanvasManager){G_vmlCanvasManager.initElement(u)}u.manager=this;return u}});var q=Backbone.Model.extend({defaults:{num_elements:20,obj_cache:null,key_ary:null},initialize:function(u){this.clear()},get_elt:function(v){var w=this.attributes.obj_cache,x=this.attributes.key_ary,u=x.indexOf(v);if(u!==-1){if(w[v].stale){x.splice(u,1);delete w[v]}else{this.move_key_to_end(v,u)}}return w[v]},set_elt:function(v,x){var y=this.attributes.obj_cache,z=this.attributes.key_ary,w=this.attributes.num_elements;if(!y[v]){if(z.length>=w){var u=z.shift();delete y[u]}z.push(v)}y[v]=x;return x},move_key_to_end:function(v,u){this.attributes.key_ary.splice(u,1);this.attributes.key_ary.push(v)},clear:function(){this.attributes.obj_cache={};this.attributes.key_ary=[]},size:function(){return this.attributes.key_ary.length},most_recently_added:function(){return this.size()===0?null:this.attributes.key_ary[this.attributes.key_ary.length-1]}});var d=q.extend({defaults:s.extend({},q.prototype.defaults,{dataset:null,genome:null,init_data:null,min_region_size:500,filters_manager:null,data_type:"data",data_mode_compatible:function(u,v){return true},can_subset:function(u){return false}}),initialize:function(u){q.prototype.initialize.call(this);var v=this.get("init_data");if(v){this.add_data(v)}},add_data:function(u){if(this.get("num_elements")<u.length){this.set("num_elements",u.length)}var v=this;s.each(u,function(w){v.set_data(w.region,w)})},data_is_ready:function(){var x=this.get("dataset"),w=$.Deferred(),u=(this.get("data_type")==="raw_data"?"state":this.get("data_type")==="data"?"converted_datasets_state":"error"),v=new l.ServerStateDeferred({ajax_settings:{url:this.get("dataset").url(),data:{hda_ldda:x.get("hda_ldda"),data_type:u},dataType:"json"},interval:5000,success_fn:function(y){return y!=="pending"}});$.when(v.go()).then(function(y){w.resolve(y==="ok"||y==="data")});return w},search_features:function(u){var v=this.get("dataset"),w={query:u,hda_ldda:v.get("hda_ldda"),data_type:"features"};return $.getJSON(v.url(),w)},load_data:function(C,B,v,A){var y=this.get("dataset"),x={data_type:this.get("data_type"),chrom:C.get("chrom"),low:C.get("start"),high:C.get("end"),mode:B,resolution:v,hda_ldda:y.get("hda_ldda")};$.extend(x,A);var E=this.get("filters_manager");if(E){var F=[];var u=E.filters;for(var z=0;z<u.length;z++){F.push(u[z].name)}x.filter_cols=JSON.stringify(F)}var w=this,D=$.getJSON(y.url(),x,function(G){w.set_data(C,G)});this.set_data(C,D);return D},get_data:function(A,z,w,y){var B=this.get_elt(A);if(B&&(j(B)||this.get("data_mode_compatible")(B,z))){return B}var C=this.get("key_ary"),v=this.get("obj_cache"),D,u;for(var x=0;x<C.length;x++){D=C[x];u=new g({from_str:D});if(u.contains(A)){B=v[D];if(j(B)||(this.get("data_mode_compatible")(B,z)&&this.get("can_subset")(B))){this.move_key_to_end(D,x);return B}}}if(A.length()<this.attributes.min_region_size){var E=new g({from_str:this.most_recently_added()});if(!E||(A.get("start")>E.get("start"))){A.set("end",A.get("start")+this.attributes.min_region_size)}else{A.set("start",A.get("end")-this.attributes.min_region_size)}A.set("genome",this.attributes.genome);A.trim()}return this.load_data(A,z,w,y)},set_data:function(v,u){this.set_elt(v,u)},DEEP_DATA_REQ:"deep",BROAD_DATA_REQ:"breadth",get_more_data:function(C,B,x,A,y){var E=this._mark_stale(C);if(!(E&&this.get("data_mode_compatible")(E,B))){console.log("ERROR: problem with getting more data: current data is not compatible");return}var w=C.get("start");if(y===this.DEEP_DATA_REQ){$.extend(A,{start_val:E.data.length+1})}else{if(y===this.BROAD_DATA_REQ){w=(E.max_high?E.max_high:E.data[E.data.length-1][2])+1}}var D=C.copy().set("start",w);var v=this,z=this.load_data(D,B,x,A),u=$.Deferred();this.set_data(C,u);$.when(z).then(function(F){if(F.data){F.data=E.data.concat(F.data);if(F.max_low){F.max_low=E.max_low}if(F.message){F.message=F.message.replace(/[0-9]+/,F.data.length)}}v.set_data(C,F);u.resolve(F)});return u},can_get_more_detailed_data:function(v){var u=this.get_elt(v);return(u.dataset_type==="bigwig"&&u.data.length<8000)},get_more_detailed_data:function(x,z,v,y,w){var u=this._mark_stale(x);if(!u){console.log("ERROR getting more detailed data: no current data");return}if(!w){w={}}if(u.dataset_type==="bigwig"){w.num_samples=1000*y}else{if(u.dataset_type==="summary_tree"){w.level=Math.min(u.level-1,2)}}return this.load_data(x,z,v,w)},_mark_stale:function(v){var u=this.get_elt(v);if(!u){console.log("ERROR: no data to mark as stale: ",this.get("dataset"),v.toString())}u.stale=true;return u},get_genome_wide_data:function(u){var w=this,y=true,x=s.map(u.get("chroms_info").chrom_info,function(A){var z=w.get_elt(new g({chrom:A.chrom,start:0,end:A.len}));if(!z){y=false}return z});if(y){return x}var v=$.Deferred();$.getJSON(this.get("dataset").url(),{data_type:"genome_data"},function(z){w.add_data(z.data);v.resolve(z.data)});return v},get_elt:function(u){return q.prototype.get_elt.call(this,u.toString())},set_elt:function(v,u){return q.prototype.set_elt.call(this,v.toString(),u)}});var n=d.extend({initialize:function(u){var v=new Backbone.Model();v.urlRoot=u.data_url;this.set("dataset",v)},load_data:function(w,x,u,v){if(u>1){return{data:null}}return d.prototype.load_data.call(this,w,x,u,v)}});var c=Backbone.Model.extend({defaults:{name:null,key:null,chroms_info:null},initialize:function(u){this.id=u.dbkey},get_chroms_info:function(){return this.attributes.chroms_info.chrom_info},get_chrom_region:function(u){var v=s.find(this.get_chroms_info(),function(w){return w.chrom===u});return new g({chrom:v.chrom,end:v.len})},get_chrom_len:function(u){return s.find(this.get_chroms_info(),function(v){return v.chrom===u}).len}});var g=Backbone.RelationalModel.extend({defaults:{chrom:null,start:0,end:0,genome:null},initialize:function(v){if(v.from_str){var x=v.from_str.split(":"),w=x[0],u=x[1].split("-");this.set({chrom:w,start:parseInt(u[0],10),end:parseInt(u[1],10)})}},copy:function(){return new g({chrom:this.get("chrom"),start:this.get("start"),end:this.get("end")})},length:function(){return this.get("end")-this.get("start")},toString:function(){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_overlap:function(B){var v=this.get("chrom"),A=B.get("chrom"),z=this.get("start"),x=B.get("start"),y=this.get("end"),w=B.get("end"),u;if(v&&A&&v!==A){return g.overlap_results.DIF_CHROMS}if(z<x){if(y<x){u=g.overlap_results.BEFORE}else{if(y<w){u=g.overlap_results.OVERLAP_START}else{u=g.overlap_results.CONTAINS}}}else{if(z>x){if(z>w){u=g.overlap_results.AFTER}else{if(y<=w){u=g.overlap_results.CONTAINED_BY}else{u=g.overlap_results.OVERLAP_END}}}else{u=(y>=w?g.overlap_results.CONTAINS:g.overlap_results.CONTAINED_BY)}}return u},trim:function(u){if(this.attributes.start<0){this.attributes.start=0}if(this.attributes.genome){var v=this.attributes.genome.get_chrom_len(this.attributes.chrom);if(this.attributes.end>v){this.attributes.end=v-1}}return this},contains:function(u){return this.compute_overlap(u)===g.overlap_results.CONTAINS},overlaps:function(u){return s.intersection([this.compute_overlap(u)],[g.overlap_results.DIF_CHROMS,g.overlap_results.BEFORE,g.overlap_results.AFTER]).length===0}},{overlap_results:{DIF_CHROMS:1000,BEFORE:1001,CONTAINS:1002,OVERLAP_START:1003,OVERLAP_END:1004,CONTAINED_BY:1005,AFTER:1006}});var m=Backbone.Collection.extend({model:g});var e=Backbone.RelationalModel.extend({defaults:{region:null,note:""},relations:[{type:Backbone.HasOne,key:"region",relatedModel:g}]});var r=Backbone.Collection.extend({model:e});var t=i.Dataset.extend({initialize:function(u){this.set("id",u.dataset_id);this.set("config",p.ConfigSettingCollection.from_config_dict(u.prefs));this.get("config").add([{key:"name",value:this.get("name")},{key:"color"}]);var v=this.get("preloaded_data");if(v){v=v.data}else{v=[]}this.set("data_manager",new d({dataset:this,init_data:v}))}});var o=Backbone.RelationalModel.extend({defaults:{title:"",type:""},url:galaxy_paths.get("visualization_url"),save:function(){return $.ajax({url:this.url(),type:"POST",dataType:"json",data:{vis_json:JSON.stringify(this)}})}});var k=o.extend({defaults:s.extend({},o.prototype.defaults,{dbkey:"",tracks:null,bookmarks:null,viewport:null}),relations:[{type:Backbone.HasMany,key:"tracks",relatedModel:t}],add_tracks:function(u){this.get("tracks").add(u)}});var b=Backbone.Model.extend({});var h=Backbone.Router.extend({initialize:function(v){this.view=v.view;this.route(/([\w]+)$/,"change_location");this.route(/([\w]+\:[\d,]+-[\d,]+)$/,"change_location");var u=this;u.view.on("navigate",function(w){u.navigate(w)})},change_location:function(u){this.view.go_to(u)}});return{BackboneTrack:t,BrowserBookmark:e,BrowserBookmarkCollection:r,Cache:q,CanvasManager:f,Genome:c,GenomeDataManager:d,GenomeRegion:g,GenomeRegionCollection:m,GenomeVisualization:k,ReferenceTrackDataManager:n,TrackBrowserRouter:h,TrackConfig:b,Visualization:o,select_datasets:a}}); \ No newline at end of file diff -r ddb55ff5fd1cdb5c2510eef55ab8d427c9e54003 -r 9852dd712f5c628d1f635fe643f036eb2b930863 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -2222,6 +2222,14 @@ obj_dict.data_manager : new visualization.GenomeDataManager({ dataset: this.dataset, + // HACK: simulate 'genome' attributes from view for now. + // View should eventually use Genome object. + genome: new visualization.Genome({ + key: view.dbkey, + chroms_info: { + chrom_info: view.chrom_data + } + }), data_mode_compatible: this.data_and_mode_compatible, can_subset: this.can_subset })); diff -r ddb55ff5fd1cdb5c2510eef55ab8d427c9e54003 -r 9852dd712f5c628d1f635fe643f036eb2b930863 static/scripts/viz/visualization.js --- a/static/scripts/viz/visualization.js +++ b/static/scripts/viz/visualization.js @@ -166,21 +166,33 @@ return value; }, - // Move key to end of cache. Keys are removed from the front, so moving a key to the end - // delays the key's removal. + /** + * Move key to end of cache. Keys are removed from the front, so moving a key to the end + * delays the key's removal. + */ move_key_to_end: function(key, index) { this.attributes.key_ary.splice(index, 1); this.attributes.key_ary.push(key); }, + /** + * Clear all elements from the cache. + */ clear: function() { this.attributes.obj_cache = {}; this.attributes.key_ary = []; }, - // Returns the number of elements in the cache. + /** Returns the number of elements in the cache. */ size: function() { return this.attributes.key_ary.length; + }, + + /** Returns key most recently added to cache. */ + most_recently_added: function() { + return this.size() === 0 ? null : + // Most recent key is at the end of key array. + this.attributes.key_ary[this.attributes.key_ary.length - 1]; } }); @@ -190,7 +202,9 @@ var GenomeDataManager = Cache.extend({ defaults: _.extend({}, Cache.prototype.defaults, { dataset: null, + genome: null, init_data: null, + min_region_size: 200, filters_manager: null, data_type: "data", data_mode_compatible: function(entry, mode) { return true; }, @@ -356,6 +370,28 @@ } } + // If needed, extend region to make it minimum size. + if (region.length() < this.attributes.min_region_size) { + // IDEA: alternative heuristic is to find adjacent cache entry to region and use that to extend. + // This would prevent bad extensions when zooming in/out while still preserving the behavior + // below. + + // Use heuristic to extend region: extend relative to last data request. + var last_request = new GenomeRegion({from_str: this.most_recently_added()}); + if (!last_request || (region.get('start') > last_request.get('start'))) { + // This request is after the last request, so extend right. + region.set('end', region.get('start') + this.attributes.min_region_size); + } + else { + // This request is after the last request, so extend left. + region.set('start', region.get('end') - this.attributes.min_region_size); + } + + // Trim region to avoid invalid coordinates. + region.set('genome', this.attributes.genome); + region.trim(); + } + return this.load_data(region, mode, resolution, extra_params); }, @@ -574,6 +610,7 @@ * Returns a GenomeRegion object denoting a complete chromosome. */ get_chrom_region: function(chr_name) { + // FIXME: use findWhere in underscore 1.4 var chrom_info = _.find(this.get_chroms_info(), function(chrom_info) { return chrom_info.chrom === chr_name; }); @@ -581,6 +618,14 @@ chrom: chrom_info.chrom, end: chrom_info.len }); + }, + + /** Returns the length of a chromosome. */ + get_chrom_len: function(chr_name) { + // FIXME: use findWhere in underscore 1.4 + return _.find(this.get_chroms_info(), function(chrom_info) { + return chrom_info.chrom === chr_name; + }).len; } }); @@ -591,7 +636,8 @@ defaults: { chrom: null, start: 0, - end: 0 + end: 0, + genome: null }, /** @@ -645,24 +691,24 @@ first_end = this.get('end'), second_end = a_region.get('end'), overlap; - // Look at chroms. + // Compare chroms. if (first_chrom && second_chrom && first_chrom !== second_chrom) { return GenomeRegion.overlap_results.DIF_CHROMS; } - // Look at regions. + // Compare regions. if (first_start < second_start) { if (first_end < second_start) { overlap = GenomeRegion.overlap_results.BEFORE; } - else if (first_end <= second_end) { + else if (first_end < second_end) { overlap = GenomeRegion.overlap_results.OVERLAP_START; } - else { // first_end > second_end + else { // first_end >= second_end overlap = GenomeRegion.overlap_results.CONTAINS; } } - else { // first_start >= second_start + else if (first_start > second_start) { if (first_start > second_end) { overlap = GenomeRegion.overlap_results.AFTER; } @@ -673,9 +719,34 @@ overlap = GenomeRegion.overlap_results.OVERLAP_END; } } + else { // first_start === second_start + overlap = (first_end >= second_end ? + GenomeRegion.overlap_results.CONTAINS : + GenomeRegion.overlap_results.CONTAINED_BY); + } return overlap; }, + + /** + * Trim a region to match genome's constraints. + */ + trim: function(genome) { + // Assume that all chromosome/contigs start at 0. + if (this.attributes.start < 0) { + this.attributes.start = 0; + } + + // Only try to trim the end if genome is set. + if (this.attributes.genome) { + var chrom_len = this.attributes.genome.get_chrom_len(this.attributes.chrom); + if (this.attributes.end > chrom_len) { + this.attributes.end = chrom_len - 1; + } + } + + return this; + }, /** * Returns true if this region contains a given 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: natefoo: Properly handle subdirectory collection in a job output's extra_files_path.
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ddb55ff5fd1c/ changeset: ddb55ff5fd1c user: natefoo date: 2013-02-19 16:07:14 summary: Properly handle subdirectory collection in a job output's extra_files_path. affected #: 1 file diff -r 90f3b97fba53d68f955ddce9de97d12e10763b45 -r ddb55ff5fd1cdb5c2510eef55ab8d427c9e54003 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2635,19 +2635,26 @@ """ for name, hda in output.items(): temp_file_path = os.path.join( job_working_directory, "dataset_%s_files" % ( hda.dataset.id ) ) + extra_dir = None try: - a_files = os.listdir( temp_file_path ) - if len( a_files ) > 0: - for f in a_files: + # This skips creation of directories - object store + # automatically creates them. However, empty directories will + # not be created in the object store at all, which might be a + # problem. + for root, dirs, files in os.walk( temp_file_path ): + extra_dir = root.replace(job_working_directory, '', 1).lstrip(os.path.sep) + for f in files: self.app.object_store.update_from_file(hda.dataset, - extra_dir="dataset_%d_files" % hda.dataset.id, + extra_dir=extra_dir, alt_name = f, - file_name = os.path.join(temp_file_path, f), + file_name = os.path.join(root, f), create = True, preserve_symlinks = True ) - # Clean up after being handled by object store. - # FIXME: If the object (e.g., S3) becomes async, this will - # cause issues so add it to the object store functionality? + # Clean up after being handled by object store. + # FIXME: If the object (e.g., S3) becomes async, this will + # cause issues so add it to the object store functionality? + if extra_dir is not None: + # there was an extra_files_path dir, attempt to remove it shutil.rmtree(temp_file_path) except Exception, e: log.debug( "Error in collect_associated_files: %s" % ( e ) ) 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: Small fixes for trackster resolution calculation.
by Bitbucket 19 Feb '13

19 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/90f3b97fba53/ changeset: 90f3b97fba53 user: jgoecks date: 2013-02-19 14:56:32 summary: Small fixes for trackster resolution calculation. affected #: 1 file diff -r 1f073bb32539ea9d978c04a892a36d995561cb30 -r 90f3b97fba53d68f955ddce9de97d12e10763b45 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1427,11 +1427,12 @@ // -- Drawing code -- - // Calculate resolution in both pixels/base and bases/pixel; round bases/pixels for tile calculations. - // TODO: require minimum difference in new resolution to update? + // Calculate resolution in both pixels/base and bases/pixel. + // TODO: require minimum difference in new resolution to update? This + // would help alleviate issues when window is being resized. this.resolution_b_px = (this.high - this.low) / this.viewport_container.width(); - this.resolution_px_b = this.viewport_container.width() / (this.high - this.low); - + this.resolution_px_b = 1 / this.resolution_b_px; + // Overview var left_px = ( this.low / (this.max_high - this.max_low) * this.overview_viewport.width() ) || 0; var width_px = ( (this.high - this.low)/(this.max_high - this.max_low) * this.overview_viewport.width() ) || 0; Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by Bitbucket 19 Feb '13

19 Feb '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0f1ae0dc3ff/ changeset: a0f1ae0dc3ff user: sfk date: 2013-02-18 00:46:39 summary: Fixed a small bug when jobwrapper was referenced but it didnt exist affected #: 1 file diff -r 09c81e81952d4768d63fde4840f31958d8e23041 -r a0f1ae0dc3ff4474e46b8e54aea4b999d8e0d0e0 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -607,7 +607,7 @@ try: self.job_runners[runner_name].stop_job( job ) except KeyError: - log.error( 'stop(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) + log.error( 'stop(): (%s) Invalid job runner: %s' % ( job.get_id(), runner_name ) ) # Job and output dataset states have already been updated, so nothing is done here. def recover( self, job, job_wrapper ): https://bitbucket.org/galaxy/galaxy-central/commits/1f073bb32539/ changeset: 1f073bb32539 user: natefoo date: 2013-02-19 14:53:25 summary: Merged in sfk/galaxy-central-random-bug-fix (pull request #126) Fixed a small bug when jobwrapper was referenced but it didnt exist affected #: 1 file diff -r 31aca8c9901ecf4ad852f7114d6550d997374888 -r 1f073bb32539ea9d978c04a892a36d995561cb30 lib/galaxy/jobs/handler.py --- a/lib/galaxy/jobs/handler.py +++ b/lib/galaxy/jobs/handler.py @@ -607,7 +607,7 @@ try: self.job_runners[runner_name].stop_job( job ) except KeyError: - log.error( 'stop(): (%s) Invalid job runner: %s' % ( job_wrapper.job_id, runner_name ) ) + log.error( 'stop(): (%s) Invalid job runner: %s' % ( job.get_id(), runner_name ) ) # Job and output dataset states have already been updated, so nothing is done here. def recover( self, job, job_wrapper ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fix for installing a repository from the tool shed that includes a repository dependency defintion where the required repository is owned by a user other than the dependent repository.
by Bitbucket 18 Feb '13

18 Feb '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8da37d3985ab/ changeset: 8da37d3985ab branch: stable user: greg date: 2013-02-18 21:28:06 summary: Fix for installing a repository from the tool shed that includes a repository dependency defintion where the required repository is owned by a user other than the dependent repository. affected #: 3 files diff -r 337e5b6bd7dc5696087c436e54192149c1bc8bc3 -r 8da37d3985ab9c489760e64d4e3eb707dfbeb4b8 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -714,7 +714,11 @@ for rd_tup in rd_tups: tool_shed, name, owner, changeset_revision = rd_tup # Updates to installed repository revisions may have occurred, so make sure to locate the appropriate repository revision if one exists. - repository, current_changeset_revision = repository_was_previously_installed( trans, tool_shed, name, repo_info_tuple ) + # We need to create a temporary repo_info_tuple that includes the correct repository owner which we get from the current rd_tup. The current + # tuple looks like: ( description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, installed_td ) + tmp_clone_url = suc.generate_clone_url_from_repo_info_tup( rd_tup ) + tmp_repo_info_tuple = ( None, tmp_clone_url, changeset_revision, None, owner, None, None ) + repository, current_changeset_revision = repository_was_previously_installed( trans, tool_shed, name, tmp_repo_info_tuple ) if repository: new_rd_tup = [ tool_shed, name, owner, changeset_revision, repository.id, repository.status ] if repository.status == trans.model.ToolShedRepository.installation_status.INSTALLED: diff -r 337e5b6bd7dc5696087c436e54192149c1bc8bc3 -r 8da37d3985ab9c489760e64d4e3eb707dfbeb4b8 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -953,6 +953,12 @@ return '%s://%s%s/repos/%s/%s' % ( protocol, username, base, repository.user.username, repository.name ) else: return '%s/repos/%s/%s' % ( base_url, repository.user.username, repository.name ) +def generate_clone_url_from_repo_info_tup( repo_info_tup ): + """Generate teh URL for cloning a repositoyr given a tuple of toolshed, name, owner, changeset_revision.""" + # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab'] + toolshed, name, owner, changeset_revision = repo_info_tup + # Don't include the changeset_revision in clone urls. + return url_join( toolshed, 'repos', owner, name ) def generate_datatypes_metadata( datatypes_config, metadata_dict ): """Update the received metadata_dict with information from the parsed datatypes_config.""" tree = ElementTree.parse( datatypes_config ) diff -r 337e5b6bd7dc5696087c436e54192149c1bc8bc3 -r 8da37d3985ab9c489760e64d4e3eb707dfbeb4b8 lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1461,12 +1461,15 @@ repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, repository_id, changeset_revision ) metadata = repository_metadata.metadata - if not includes_tools and 'tools' in metadata: - includes_tools = True - if not has_repository_dependencies and 'repository_dependencies' in metadata: - has_repository_dependencies = True - if not includes_tool_dependencies and 'tool_dependencies' in metadata: - includes_tool_dependencies = True + if not includes_tools: + if 'tools' in metadata: + includes_tools = True + if not has_repository_dependencies: + if 'repository_dependencies' in metadata: + has_repository_dependencies = True + if not includes_tool_dependencies: + if 'tool_dependencies' in metadata: + includes_tool_dependencies = True repo_dir = repository.repo_path( trans.app ) repo = hg.repository( suc.get_configured_ui(), repo_dir ) ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0