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commit/galaxy-central: dannon: Datatypes controller should allow anonymous access.
by commits-noreply＠bitbucket.org 21 Oct '13

21 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6882fa888d10/ Changeset: 6882fa888d10 User: dannon Date: 2013-10-21 22:16:01 Summary: Datatypes controller should allow anonymous access. Affected #: 1 file diff -r d1fb4c641a79eb5451320397d4e22068d1c95bcf -r 6882fa888d10b469524669325a547a2c0f6c7e41 lib/galaxy/webapps/galaxy/api/datatypes.py --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/lib/galaxy/webapps/galaxy/api/datatypes.py @@ -4,13 +4,12 @@ from galaxy import web from galaxy.web.base.controller import BaseAPIController -from galaxy.datatypes.registry import Registry import logging log = logging.getLogger( __name__ ) class DatatypesController( BaseAPIController ): - @web.expose_api + @web.expose_api_anonymous def index( self, trans, **kwd ): """ GET /api/datatypes @@ -18,8 +17,7 @@ """ try: return trans.app.datatypes_registry.upload_file_formats - except Exception, exception: log.error( 'could not get datatypes: %s', str( exception ), exc_info=True ) trans.response.status = 500 - return { 'error': str( exception ) } \ No newline at end of file + return { 'error': str( exception ) } 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: Merge stable branch.
by commits-noreply＠bitbucket.org 21 Oct '13

21 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1fb4c641a79/ Changeset: d1fb4c641a79 User: natefoo Date: 2013-10-21 16:10:54 Summary: Merge stable branch. Affected #: 1 file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jgoecks: Trackster: add needed height config preference.
by commits-noreply＠bitbucket.org 19 Oct '13

19 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2778e2829d28/ Changeset: 2778e2829d28 User: jgoecks Date: 2013-10-19 21:59:43 Summary: Trackster: add needed height config preference. Affected #: 1 file diff -r 95815478f355009d925ea91e95e4db0a9d887ded -r 2778e2829d28bb053b12d47c6615c98052134a83 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -4220,7 +4220,8 @@ { key: 'show_sample_data', label: 'Show sample data', type: 'bool', default_value: true }, { key: 'show_labels', label: 'Show summary and sample labels', type: 'bool', default_value: true }, { key: 'summary_height', label: 'Locus summary height', type: 'float', default_value: 20 }, - { key: 'mode', type: 'string', default_value: this.mode, hidden: true } + { key: 'mode', type: 'string', default_value: this.mode, hidden: true }, + { key: 'height', type: 'int', default_value: 0, hidden: true } ] ), config_onchange: function() { 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: Enhance the Repair repository feature for tool shed repositories installed into Galaxy to handle repository and tool dependencies that are not only in an error status, but may also have one of the "installing" status values. This feature will now properly handle dependencies that are stuck in one of these installing states foe some reason. Existing system processes are not automatically killed (if they happen to exist), but warning messages are displayed.
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/95815478f355/ Changeset: 95815478f355 User: greg Date: 2013-10-18 22:43:29 Summary: Enhance the Repair repository feature for tool shed repositories installed into Galaxy to handle repository and tool dependencies that are not only in an error status, but may also have one of the "installing" status values. This feature will now properly handle dependencies that are stuck in one of these installing states foe some reason. Existing system processes are not automatically killed (if they happen to exist), but warning messages are displayed. Affected #: 7 files diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -3679,7 +3679,11 @@ """Return the repository's repository dependencies that are currently being installed.""" required_repositories_being_installed = [] for required_repository in self.repository_dependencies: - if required_repository.status == self.installation_status.INSTALLING: + if required_repository.status in [ self.installation_status.CLONING, + self.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, + self.installation_status.INSTALLING_TOOL_DEPENDENCIES, + self.installation_status.LOADING_PROPRIETARY_DATATYPES, + self.installation_status.SETTING_TOOL_VERSIONS ]: required_repositories_being_installed.append( required_repository ) return required_repositories_being_installed diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded 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 @@ -1185,6 +1185,21 @@ message=message, status=status ) + @web.expose + @web.require_admin + def repair_tool_shed_repositories( self, trans, tool_shed_repositories, repo_info_dicts, **kwd ): + """Repair specified tool shed repositories.""" + # The received lists of tool_shed_repositories and repo_info_dicts are ordered. + for index, tool_shed_repository in enumerate( tool_shed_repositories ): + repo_info_dict = repo_info_dicts[ index ] + repair_dict = repository_util.repair_tool_shed_repository( trans, + tool_shed_repository, + encoding_util.tool_shed_encode( repo_info_dict ) ) + tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] + return trans.response.send_redirect( web.url_for( controller='admin_toolshed', + action='monitor_repository_installation', + tool_shed_repository_ids=tsr_ids_for_monitoring ) ) + @web.json def repository_installation_status_updates( self, trans, ids=None, status_list=None ): # Avoid caching @@ -1208,21 +1223,6 @@ @web.expose @web.require_admin - def repair_tool_shed_repositories( self, trans, tool_shed_repositories, repo_info_dicts, **kwd ): - """Repair specified tool shed repositories.""" - # The received lists of tool_shed_repositories and repo_info_dicts are ordered. - for index, tool_shed_repository in enumerate( tool_shed_repositories ): - repo_info_dict = repo_info_dicts[ index ] - repair_dict = repository_util.repair_tool_shed_repository( trans, - tool_shed_repository, - encoding_util.tool_shed_encode( repo_info_dict ) ) - tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='monitor_repository_installation', - tool_shed_repository_ids=tsr_ids_for_monitoring ) ) - - @web.expose - @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): """ Select or change the tool panel section to contain the tools included in the tool shed repository being reinstalled. If there are updates diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -101,33 +101,7 @@ class StatusColumn( grids.TextColumn ): def get_value( self, trans, grid, tool_shed_repository ): - status_label = tool_shed_repository.status - if tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING, - trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS, - trans.model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, - trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, - trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]: - bgcolor = trans.model.ToolShedRepository.states.INSTALLING - elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, - trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: - bgcolor = trans.model.ToolShedRepository.states.UNINSTALLED - elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR ]: - bgcolor = trans.model.ToolShedRepository.states.ERROR - elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.DEACTIVATED ]: - bgcolor = trans.model.ToolShedRepository.states.WARNING - elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: - if tool_shed_repository.missing_repository_dependencies: - bgcolor = trans.model.ToolShedRepository.states.WARNING - status_label = '%s, missing repository dependencies' % status_label - elif tool_shed_repository.missing_tool_dependencies: - bgcolor = trans.model.ToolShedRepository.states.WARNING - status_label = '%s, missing tool dependencies' % status_label - else: - bgcolor = trans.model.ToolShedRepository.states.OK - else: - bgcolor = trans.model.ToolShedRepository.states.ERROR - rval = '<div class="count-box state-color-%s">%s</div>' % ( bgcolor, status_label ) - return rval + return suc.get_tool_shed_repository_status_label( trans, tool_shed_repository ) class ToolShedColumn( grids.TextColumn ): diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -758,7 +758,6 @@ log.debug( error_message ) repair_dict [ repository.name ] = error_message elif repository.status not in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: - # TODO: this may cause problems if the repository is currently being installed. shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) # Reset the repository attributes to the New state for installation. if metadata: @@ -793,7 +792,8 @@ work_dir = tempfile.mkdtemp( prefix="tmp-toolshed-itdep" ) # Reset missing tool dependencies. for tool_dependency in repository.missing_tool_dependencies: - if tool_dependency.status in [ trans.model.ToolDependency.installation_status.ERROR ]: + if tool_dependency.status in [ trans.model.ToolDependency.installation_status.ERROR, + trans.model.ToolDependency.installation_status.INSTALLING ]: tool_dependency_util.set_tool_dependency_attributes( trans, tool_dependency, trans.model.ToolDependency.installation_status.UNINSTALLED, diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1282,6 +1282,53 @@ log.exception( "Error attempting to get tool shed status for installed repository %s: %s" % ( str( repository.name ), str( e ) ) ) return {} +def get_tool_shed_repository_status_label( trans, tool_shed_repository=None, name=None, owner=None, changeset_revision=None, repository_clone_url=None ): + """Return a color-coded label for the status of the received tool-shed_repository installed into Galaxy.""" + if tool_shed_repository is None: + if name is not None and owner is not None and repository_clone_url is not None: + tool_shed = get_tool_shed_from_clone_url( repository_clone_url ) + tool_shed_repository = get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( trans.app, + tool_shed, + name, + owner, + changeset_revision ) + if tool_shed_repository: + status_label = tool_shed_repository.status + if tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING, + trans.model.ToolShedRepository.installation_status.SETTING_TOOL_VERSIONS, + trans.model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES, + trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES, + trans.model.ToolShedRepository.installation_status.LOADING_PROPRIETARY_DATATYPES ]: + bgcolor = trans.model.ToolShedRepository.states.INSTALLING + elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.NEW, + trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: + bgcolor = trans.model.ToolShedRepository.states.UNINSTALLED + elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR ]: + bgcolor = trans.model.ToolShedRepository.states.ERROR + elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.DEACTIVATED ]: + bgcolor = trans.model.ToolShedRepository.states.WARNING + elif tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.INSTALLED ]: + if tool_shed_repository.repository_dependencies_being_installed: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, %s' % ( status_label, trans.model.ToolShedRepository.installation_status.INSTALLING_REPOSITORY_DEPENDENCIES ) + elif tool_shed_repository.missing_repository_dependencies: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, missing repository dependencies' % status_label + elif tool_shed_repository.tool_dependencies_being_installed: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, %s' % (status_label, trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) + elif tool_shed_repository.missing_tool_dependencies: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, missing tool dependencies' % status_label + else: + bgcolor = trans.model.ToolShedRepository.states.OK + else: + bgcolor = trans.model.ToolShedRepository.states.ERROR + else: + bgcolor = trans.model.ToolShedRepository.states.WARNING + status_label = '%s, unknown status' % status_label + return '<div class="count-box state-color-%s">%s</div>' % ( bgcolor, status_label ) + def get_updated_changeset_revisions( trans, name, owner, changeset_revision ): """ Return a string of comma-separated changeset revision hashes for all available updates to the received changeset revision for the repository diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded templates/admin/tool_shed_repository/repair_repository.mako --- a/templates/admin/tool_shed_repository/repair_repository.mako +++ b/templates/admin/tool_shed_repository/repair_repository.mako @@ -18,27 +18,56 @@ %endif <div class="warningmessage"> - The following repositories will be inspected and repaired in the order listed to ensure each repository and all of it's tool dependencies are correctly - installed. Click <b>Repair</b> to inspect and repair these repositories. + <p> + The following repositories will be inspected and repaired in the order listed to ensure each repository and all of it's tool dependencies are + correctly installed. + </p> + <p> + Existing system processes associated with repositories or tool dependencies that are currently being installed will not be automatically + terminated. If possible, make sure no installation processes are still running for repositories whose status is or includes <b>cloning</b>, + <b>setting tool versions</b>, <b>installing repository dependencies</b>, or <b>installing tool dependencies</b> before clicking the <b>Repair</b> + button. + </p> + <p> + All repositories that do not display an <b>Installed</b> status will be removed from disk and reinstalled. + </p> + <p> + Click <b>Repair</b> to inspect and repair these repositories. + </p></div><div class="toolForm"> - <div class="toolFormTitle">Repair tool shed repository '${repository.name}'</div> - <br/><br/> - <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ), repair_dict=encoded_repair_dict )}" method="post" > - <% ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) %> + <div class="toolFormTitle">Repair tool shed repository <b>${repository.name}</b></div> + <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ) )}" method="post" > + <input type="hidden" name="repair_dict" value="${encoded_repair_dict}"/> + <% + from tool_shed.util.shed_util_common import get_tool_shed_repository_status_label + ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) + %><table class="grid"> - <tr><th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Owner</th><th bgcolor="#D8D8D8">Changeset revision</th></tr> + <tr> + <th bgcolor="#D8D8D8">Name</th> + <th bgcolor="#D8D8D8">Owner</th> + <th bgcolor="#D8D8D8">Changeset revision</th> + <th bgcolor="#D8D8D8">Status</th> + </tr> %for repo_info_dict in ordered_repo_info_dicts: <% for name, repo_info_tuple in repo_info_dict.items(): description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple break + status_label = get_tool_shed_repository_status_label( trans, + tool_shed_repository=None, + name=name, + owner=repository_owner, + changeset_revision=changeset_revision, + repository_clone_url=repository_clone_url ) %><tr><td>${name | h}</td><td>${repository_owner | h}</td><td>${changeset_revision | h}</td> + <td>${status_label}</td></tr> %endfor </table> diff -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 -r 95815478f355009d925ea91e95e4db0a9d887ded test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -969,7 +969,7 @@ self.check_for_strings( [ 'Metadata has been reset' ] ) def reset_metadata_on_selected_repositories( self, repository_ids ): - self.visit_url( '/admin/reset_metadata_on_selected_repositories' ) + self.visit_url( '/admin/reset_metadata_on_selected_repositories_in_tool_shed' ) kwd = dict( repository_ids=repository_ids ) self.submit_form( form_no=1, button="reset_metadata_on_selected_repositories_button", **kwd ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Tools API, show: remove unused flag, show io_details/link_details where possible; ToolParameters: improve polymorphism in to_dict
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/068afb09a7ba/ Changeset: 068afb09a7ba User: carlfeberhard Date: 2013-10-18 21:37:59 Summary: Tools API, show: remove unused flag, show io_details/link_details where possible; ToolParameters: improve polymorphism in to_dict Affected #: 2 files diff -r 799dca8ebe2375f962603382380dfc1da720764f -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -17,6 +17,7 @@ log = logging.getLogger(__name__) + class ToolParameter( object, Dictifiable ): """ Describes a parameter accepted by a tool. This is just a simple stub at the @@ -172,9 +173,10 @@ def to_dict( self, trans, view='collection', value_mapper=None ): """ to_dict tool parameter. This can be overridden by subclasses. """ - tool_dict = super( ToolParameter, self ).to_dict() - tool_dict[ 'html' ] = urllib.quote( self.get_html( trans ) ) + #TODO: removing html as it causes a lot of errors on subclasses - needs histories, etc. + #tool_dict[ 'html' ] = urllib.quote( self.get_html( trans ) ) + tool_dict[ 'model_class' ] = self.__class__.__name__ if hasattr( self, 'value' ): tool_dict[ 'value' ] = self.value return tool_dict @@ -193,6 +195,7 @@ else: return parameter_types[param_type]( tool, param ) + class TextToolParameter( ToolParameter ): """ Parameter that can take on any text value. @@ -210,12 +213,14 @@ self.size = elem.get( 'size' ) self.value = elem.get( 'value' ) self.area = string_as_bool( elem.get( 'area', False ) ) + def get_html_field( self, trans=None, value=None, other_values={} ): if value is None: value = self.value if self.area: return form_builder.TextArea( self.name, self.size, value ) else: return form_builder.TextField( self.name, self.size, value ) + def get_initial_value( self, trans, context, history=None ): return self.value @@ -266,6 +271,7 @@ if isinstance( value, int ): value = str( value ) return super( IntegerToolParameter, self ).get_html_field( trans=trans, value=value, other_values=other_values ) + def from_html( self, value, trans=None, other_values={} ): try: return int( value ) @@ -273,12 +279,14 @@ if not value and self.optional: return "" raise ValueError( "An integer is required" ) + def to_string( self, value, app ): """Convert a value to a string representation suitable for persisting""" if value is None: return "" else: return str( value ) + def to_python( self, value, app ): try: return int( value ) @@ -286,12 +294,14 @@ if not value and self.optional: return None raise err + def get_initial_value( self, trans, context, history=None ): if self.value: return int( self.value ) else: return None + class FloatToolParameter( TextToolParameter ): """ Parameter that takes a real number value. @@ -334,10 +344,12 @@ raise ValueError( "A real number is required" ) if self.min and self.max: self.validators.append( validation.InRangeValidator( None, self.min, self.max ) ) + def get_html_field( self, trans=None, value=None, other_values={} ): if isinstance( value, float ): value = str( value ) return super( FloatToolParameter, self ).get_html_field( trans=trans, value=value, other_values=other_values ) + def from_html( self, value, trans=None, other_values={} ): try: return float( value ) @@ -345,12 +357,14 @@ if not value and self.optional: return "" raise ValueError( "A real number is required" ) + def to_string( self, value, app ): """Convert a value to a string representation suitable for persisting""" if value is None: return "" else: return str( value ) + def to_python( self, value, app ): try: return float( value ) @@ -358,12 +372,14 @@ if not value and self.optional: return None raise err + def get_initial_value( self, trans, context, history=None ): try: return float( self.value ) except: return None + class BooleanToolParameter( ToolParameter ): """ Parameter that takes one of two values. @@ -387,31 +403,39 @@ self.truevalue = elem.get( 'truevalue', 'true' ) self.falsevalue = elem.get( 'falsevalue', 'false' ) self.checked = string_as_bool( elem.get( 'checked' ) ) + def get_html_field( self, trans=None, value=None, other_values={} ): checked = self.checked if value is not None: checked = form_builder.CheckboxField.is_checked( value ) return form_builder.CheckboxField( self.name, checked, refresh_on_change = self.refresh_on_change ) + def from_html( self, value, trans=None, other_values={} ): return form_builder.CheckboxField.is_checked( value ) + def to_html_value( self, value, app ): if value: return [ 'true', 'true' ] else: return [ 'true' ] + def to_python( self, value, app ): return ( value == 'True' ) + def get_initial_value( self, trans, context, history=None ): return self.checked + def to_param_dict_string( self, value, other_values={} ): if value: return self.truevalue else: return self.falsevalue + @property def legal_values( self ): return [ self.truevalue, self.falsevalue ] + class FileToolParameter( ToolParameter ): """ Parameter that takes an uploaded file as a value. @@ -431,8 +455,10 @@ """ ToolParameter.__init__( self, tool, elem ) self.ajax = string_as_bool( elem.get( 'ajax-upload' ) ) + def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.FileField( self.name, ajax = self.ajax, value = value ) + def from_html( self, value, trans=None, other_values={} ): # Middleware or proxies may encode files in special ways (TODO: this # should be pluggable) @@ -450,11 +476,13 @@ local_filename = local_filename ) return value + def get_required_enctype( self ): """ File upload elements require the multipart/form-data encoding """ return "multipart/form-data" + def to_string( self, value, app ): if value in [ None, '' ]: return None @@ -467,6 +495,7 @@ except: return None raise Exception( "FileToolParameter cannot be persisted" ) + def to_python( self, value, app ): if value is None: return None @@ -474,9 +503,11 @@ return value else: raise Exception( "FileToolParameter cannot be persisted" ) + def get_initial_value( self, trans, context, history=None ): return None + class FTPFileToolParameter( ToolParameter ): """ Parameter that takes a file uploaded via FTP as a value. @@ -486,36 +517,43 @@ Example: C{<param name="bins" type="file" />} """ ToolParameter.__init__( self, tool, elem ) + @property def visible( self ): if self.tool.app.config.ftp_upload_dir is None or self.tool.app.config.ftp_upload_site is None: return False return True + def get_html_field( self, trans=None, value=None, other_values={} ): if trans is None or trans.user is None: user_ftp_dir = None else: user_ftp_dir = trans.user_ftp_dir return form_builder.FTPFileField( self.name, user_ftp_dir, trans.app.config.ftp_upload_site, value = value ) + def from_html( self, value, trans=None, other_values={} ): try: assert type( value ) is list except: value = [ value ] return value + def to_string( self, value, app ): if value in [ None, '' ]: return None elif isinstance( value, unicode ) or isinstance( value, str ) or isinstance( value, list ): return value + def to_python( self, value, app ): if value is None: return None elif isinstance( value, unicode ) or isinstance( value, str ) or isinstance( value, list ): return value + def get_initial_value( self, trans, context, history=None ): return None + class HiddenToolParameter( ToolParameter ): """ Parameter that takes one of two values. @@ -532,10 +570,13 @@ def __init__( self, tool, elem ): ToolParameter.__init__( self, tool, elem ) self.value = elem.get( 'value' ) + def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.HiddenField( self.name, self.value ) + def get_initial_value( self, trans, context, history=None ): return self.value + def get_label( self ): return None @@ -543,26 +584,33 @@ ## can change, there needs to be a different way to specify this. I'm leaving ## it for now to avoid breaking any tools. + class BaseURLToolParameter( ToolParameter ): """ Returns a parameter the contains its value prepended by the current server base url. Used in all redirects. """ + def __init__( self, tool, elem ): ToolParameter.__init__( self, tool, elem ) self.value = elem.get( 'value', '' ) + def get_value( self, trans ): # url = trans.request.base + self.value url = url_for( self.value, qualified=True ) return url + def get_html_field( self, trans=None, value=None, other_values={} ): return form_builder.HiddenField( self.name, self.get_value( trans ) ) + def get_initial_value( self, trans, context, history=None ): return self.value + def get_label( self ): # BaseURLToolParameters are ultimately "hidden" parameters return None + class SelectToolParameter( ToolParameter ): """ Parameter that takes on one (or many) or a specific set of values. @@ -665,6 +713,7 @@ selected = string_as_bool( option.get( "selected", False ) ) self.static_options.append( ( option.text or value, value, selected ) ) self.is_dynamic = ( ( self.dynamic_options is not None ) or ( self.options is not None ) ) + def get_options( self, trans, other_values ): if self.options: return self.options.get_options( trans, other_values ) @@ -672,6 +721,7 @@ return eval( self.dynamic_options, self.tool.code_namespace, other_values ) else: return self.static_options + def get_legal_values( self, trans, other_values ): def _get_UnvalidatedValue_value( value ): if isinstance( value, UnvalidatedValue ): @@ -683,6 +733,7 @@ return set( v for _, v, _ in eval( self.dynamic_options, self.tool.code_namespace, other_values ) ) else: return self.legal_values + def get_html_field( self, trans=None, value=None, context={} ): # Dynamic options are not yet supported in workflow, allow # specifying the value as text for now. @@ -710,6 +761,7 @@ selected = ( optval in value ) field.add_option( text, optval, selected ) return field + def from_html( self, value, trans=None, context={} ): if self.need_late_validation( trans, context ): if self.multiple: @@ -747,11 +799,13 @@ if value not in legal_values: raise ValueError( "An invalid option was selected, please verify" ) return value + def to_html_value( self, value, app ): if isinstance( value, list ): return value else: return str( value ) + def to_param_dict_string( self, value, other_values={} ): if value is None: return "None" @@ -769,6 +823,7 @@ if isinstance( value, list ): value = self.separator.join( value ) return value + def value_to_basic( self, value, app ): if isinstance( value, UnvalidatedValue ): return { "__class__": "UnvalidatedValue", "value": value.value } @@ -778,10 +833,12 @@ # breaks multiple selection return { "__class__": "RuntimeValue" } return value + def value_from_basic( self, value, app, ignore_errors=False ): if isinstance( value, dict ) and value.get( "__class__", None ) == "UnvalidatedValue": return UnvalidatedValue( value["value"] ) return super( SelectToolParameter, self ).value_from_basic( value, app, ignore_errors=ignore_errors ) + def need_late_validation( self, trans, context ): """ Determine whether we need to wait to validate this parameters value @@ -826,6 +883,7 @@ return True # Dynamic, but all dependenceis are known and have values return False + def get_initial_value( self, trans, context, history=None ): # More working around dynamic options for workflow if self.need_late_validation( trans, context ): @@ -844,6 +902,7 @@ elif len( value ) == 1: value = value[0] return value + def value_to_display_text( self, value, app ): if isinstance( value, UnvalidatedValue ): suffix = "\n(value not yet validated)" @@ -863,6 +922,7 @@ if v in value: rval.append( t ) return "\n".join( rval ) + suffix + def get_dependencies( self ): """ Get the *names* of the other params this param depends on. @@ -876,17 +936,24 @@ d = super( SelectToolParameter, self ).to_dict( trans ) # Get options, value. - options = self.get_options( trans, [] ) - value = options[0][1] - for option in options: - if option[2]: - # Found selected option. - value = option[1] + options = [] + try: + options = self.get_options( trans, {} ) + except AssertionError, assertion: + # we dont/cant set other_values (the {} above), so params that require other params to be filled will error: + # required dependency in filter_options + # associated DataToolParam in get_column_list + pass - d.update( { - 'options': options, - 'value': value - } ) + d[ 'options' ] = options + if options: + value = options[0][1] + for option in options: + if option[2]: + # Found selected option. + value = option[1] + d[ 'value' ] = options + return d @@ -933,6 +1000,7 @@ def __init__( self, *args, **kwds ): super( GenomeBuildParameter, self ).__init__( *args, **kwds ) self.static_options = [ ( value, key, False ) for key, value in util.dbnames ] + def get_options( self, trans, other_values ): if not trans.history: yield 'unspecified', '?', False @@ -940,11 +1008,31 @@ last_used_build = trans.history.genome_build for dbkey, build_name in trans.db_builds: yield build_name, dbkey, ( dbkey == last_used_build ) + def get_legal_values( self, trans, other_values ): if not trans.history: return set( '?' ) return set( dbkey for dbkey, _ in trans.db_builds ) + def to_dict( self, trans, view='collection', value_mapper=None ): + # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here + d = ToolParameter.to_dict( self, trans ) + + # Get options, value - options is a generator here, so compile to list + options = list( self.get_options( trans, {} ) ) + value = options[0][1] + for option in options: + if option[2]: + # Found selected option. + value = option[1] + + d.update({ + 'options': options, + 'value': value + }) + return d + + class ColumnListParameter( SelectToolParameter ): """ Select list that consists of either the total number of columns or only @@ -1081,10 +1169,13 @@ return UnvalidatedValue( self.default_value ) return self.default_value return SelectToolParameter.get_initial_value( self, trans, context ) + def get_legal_values( self, trans, other_values ): return set( self.get_column_list( trans, other_values ) ) + def get_dependencies( self ): return [ self.data_ref ] + def need_late_validation( self, trans, context ): if super( ColumnListParameter, self ).need_late_validation( trans, context ): return True @@ -1245,7 +1336,6 @@ call_other_values.update( other_values.dict ) return eval( self.dynamic_options, self.tool.code_namespace, call_other_values ) - def get_options( self, trans=None, value=None, other_values={} ): if self.is_dynamic: if self.dynamic_options: @@ -1353,6 +1443,7 @@ else: rval = sanitize_param( rval ) return rval + def get_initial_value( self, trans, context, history=None ): def recurse_options( initial_values, options ): for option in options: @@ -1407,9 +1498,26 @@ """ return self.filtered.keys() + def to_dict( self, trans, view='collection', value_mapper=None ): + # skip SelectToolParameter (the immediate parent) bc we need to get options in a different way here + d = ToolParameter.to_dict( self, trans ) + + options = [] + try: + options = self.get_options( trans, {} ) + except KeyError, key_err: + # will sometimes error if self.is_dynamic and self.filtered + # bc we dont/cant fill out other_values above ({}) + pass + + d[ 'options' ] = options; + return d + + class DummyDataset( object ): pass + class DataToolParameter( ToolParameter ): # TODO, Nate: Make sure the following unit tests appropriately test the dataset security # components. Add as many additional tests as necessary. @@ -1720,6 +1828,7 @@ ref = ref() return ref + class HiddenDataToolParameter( HiddenToolParameter, DataToolParameter ): """ Hidden parameter that behaves as a DataToolParameter. As with all hidden @@ -1845,9 +1954,11 @@ """ def __init__( self, value ): self.value = value + def __str__( self ): return str( self.value ) + class RuntimeValue( object ): """ Wrapper to note a value that is not yet set, but will be required at diff -r 799dca8ebe2375f962603382380dfc1da720764f -r 068afb09a7ba896f1fdfee104d0b68c0a2e77de3 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,3 +1,5 @@ +import urllib + from galaxy import web, util from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin from galaxy.visualization.genomes import GenomeRegion @@ -44,8 +46,16 @@ GET /api/tools/{tool_id} Returns tool information, including parameters and inputs. """ + io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) + link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) try: - return self.app.toolbox.tools_by_id[ id ].to_dict( trans, for_display=True ) + id = urllib.unquote_plus( id ) + tool = self.app.toolbox.tools_by_id.get( id, None ) + if not tool: + trans.response.status = 404 + return { 'error': 'tool not found', 'id': id } + return tool.to_dict( trans, io_details=io_details, link_details=link_details ) + except Exception, exc: log.error( 'could not convert tool (%s) to dictionary: %s', id, str( exc ), exc_info=True ) trans.response.status = 500 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: HDA API, delete: fix namespacing on exceptions
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/799dca8ebe23/ Changeset: 799dca8ebe23 User: carlfeberhard Date: 2013-10-18 21:28:09 Summary: HDA API, delete: fix namespacing on exceptions Affected #: 1 file diff -r 99161bb83a3ec96fcc58ff14af9958fd8a19e0ce -r 799dca8ebe2375f962603382380dfc1da720764f lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -325,7 +325,8 @@ if purge: if not trans.app.config.allow_user_dataset_purge: - raise HTTPForbidden( detail='This instance does not allow user dataset purging' ) + raise exceptions.httpexceptions.HTTPForbidden( + detail='This instance does not allow user dataset purging' ) hda.purged = True trans.sa_session.add( hda ) @@ -345,11 +346,11 @@ trans.sa_session.flush() rval[ 'deleted' ] = True - except HTTPInternalServerError, http_server_err: + except exceptions.httpexceptions.HTTPInternalServerError, http_server_err: log.exception( 'HDA API, delete: uncaught HTTPInternalServerError: %s, %s\n%s', id, str( kwd ), str( http_server_err ) ) raise - except HTTPException, http_exc: + except exceptions.httpexceptions.HTTPException, http_exc: raise except Exception, exc: log.exception( 'HDA API, delete: uncaught exception: %s, %s\n%s', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: aswarren: API enable copying from one history to another
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0f8890ee9be5/ Changeset: 0f8890ee9be5 Branch: api_copy_history User: aswarren Date: 2013-08-02 00:02:54 Summary: API enable copying from one history to another Affected #: 1 file diff -r fe5867b89ec01bfde18591df8809526d85fb821e -r 0f8890ee9be56218a50dea5505a500e3fb9b3762 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -174,6 +174,7 @@ #TODO: copy existing, accessible hda - dataset controller, copy_datasets #TODO: convert existing, accessible hda - model.DatasetInstance(or hda.datatype).get_converter_types from_ld_id = payload.get( 'from_ld_id', None ) + from_hda_id= payload.get( 'from_hda_id', None ) try: history = self.get_history( trans, history_id, check_ownership=True, check_accessible=False ) except Exception, e: @@ -197,7 +198,19 @@ hda = ld.library_dataset_dataset_association.to_history_dataset_association( history, add_to_history=True ) trans.sa_session.flush() return hda.get_api_value() - + elif from_hda_id: + try: + hda = self.get_dataset(trans, from_hda_id) + assert trans.user.id == hda.history.user_id, "HistoryDatasetAssocation does not belong to current user" + except AssertionError, e: + trans.response.status=400 + return "HistoryDatasetAssocation does not belong to current user" + except Exception, e: + return str(e) + data_copy=hda.copy(copy_children = True) + result=history.add_dataset(data_copy) + trans.sa_session.flush() + return result.get_api_value() else: # TODO: implement other "upload" methods here. trans.response.status = 501 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: Restrict diff file size to something reasonable when browsing changesets in the Tool shed, and add some additional logging and error handling when setting metadata on repositories in the tool shed and Galaxy.
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/148a93733033/ Changeset: 148a93733033 User: greg Date: 2013-10-18 19:07:37 Summary: Restrict diff file size to something reasonable when browsing changesets in the Tool shed, and add some additional logging and error handling when setting metadata on repositories in the tool shed and Galaxy. Affected #: 7 files diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -517,10 +517,10 @@ message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) results[ 'unsuccessful_count' ] += 1 else: - message = "Successfully reset metadata on repository %s" % str( repository.name ) + message = "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), str( repository.owner ) ) results[ 'successful_count' ] += 1 except Exception, e: - message = "Error resetting metadata on repository %s: %s" % ( str( repository.name ), str( e ) ) + message = "Error resetting metadata on repository %s owned by %s: %s" % ( str( repository.name ), str( repository.owner ), str( e ) ) results[ 'unsuccessful_count' ] += 1 results[ 'repository_status' ].append( message ) stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -231,8 +231,11 @@ in addition to those repositories of type tool_dependency_definition. This param is ignored if the current user is not an admin user, in which case this same restriction is automatic. :param encoded_ids_to_skip (optional): a list of encoded repository ids for repositories that should not be processed. + :param skip_file (optional): A local file name that contains the encoded repository ids associated with repositories to skip. + This param can be used as an alternative to the above encoded_ids_to_skip. """ def handle_repository( trans, repository, results ): + log.debug( "Resetting metadata on repository %s" % str( repository.name ) ) repository_id = trans.security.encode_id( repository.id ) try: invalid_file_tups, metadata_dict = metadata_util.reset_all_metadata_on_repository_in_tool_shed( trans, repository_id ) @@ -240,12 +243,13 @@ message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) results[ 'unsuccessful_count' ] += 1 else: - message = "Successfully reset metadata on repository %s" % str( repository.name ) + message = "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), str( repository.user.username ) ) results[ 'successful_count' ] += 1 except Exception, e: - message = "Error resetting metadata on repository %s: %s" % ( str( repository.name ), str( e ) ) + message = "Error resetting metadata on repository %s owned by %s: %s" % ( str( repository.name ), str( repository.user.username ), str( e ) ) results[ 'unsuccessful_count' ] += 1 - results[ 'repository_status' ].append( message ) + status = '%s : %s' % ( str( repository.name ), message ) + results[ 'repository_status' ].append( status ) return results try: start_time = strftime( "%Y-%m-%d %H:%M:%S" ) @@ -255,6 +259,16 @@ unsuccessful_count=0 ) handled_repository_ids = [] encoded_ids_to_skip = payload.get( 'encoded_ids_to_skip', [] ) + skip_file = payload.get( 'skip_file', None ) + if skip_file and os.path.exists( skip_file ) and not encoded_ids_to_skip: + # Load the list of encoded_ids_to_skip from the skip_file. + # Contents of file must be 1 encoded repository id per line. + lines = open( skip_file, 'rb' ).readlines() + for line in lines: + if line.startswith( '#' ): + # Skip comments. + continue + encoded_ids_to_skip.append( line.rstrip( '\n' ) ) if trans.user_is_admin(): my_writable = util.asbool( payload.get( 'my_writable', False ) ) else: @@ -306,17 +320,18 @@ if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) else: - message = "Successfully reset metadata on repository %s" % str( repository.name ) + message = "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), str( repository.user.username ) ) except Exception, e: - message = "Error resetting metadata on repository %s: %s" % ( str( repository.name ), str( e ) ) - - results[ 'repository_status' ].append( message ) + message = "Error resetting metadata on repository %s owned by %s: %s" % ( str( repository.name ), str( repository.user.username ), str( e ) ) + status = '%s : %s' % ( str( repository.name ), message ) + results[ 'repository_status' ].append( status ) return results try: repository_id = payload.get( 'repository_id', None ) if repository_id is not None: repository = suc.get_repository_in_tool_shed( trans, repository_id ) start_time = strftime( "%Y-%m-%d %H:%M:%S" ) + log.debug( "%s...resetting metadata on repository %s" % ( start_time, str( repository.name ) ) ) results = handle_repository( trans, start_time, repository ) stop_time = strftime( "%Y-%m-%d %H:%M:%S" ) results[ 'stop_time' ] = stop_time diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/galaxy/webapps/tool_shed/controllers/hg.py --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -39,7 +39,9 @@ # Set metadata using the repository files on disk. error_message, status = set_repository_metadata( trans, repository ) if status == 'ok' and error_message: - log.debug( "Successfully reset metadata on repository %s, but encountered problem: %s" % ( repository.name, error_message ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s, but encountered problem: %s" % \ + ( str( repository.name ), str( repository.user.username ), error_message ) ) elif status != 'ok' and error_message: - log.debug( "Error resetting metadata on repository %s: %s" % ( repository.name, error_message ) ) + log.debug( "Error resetting metadata on repository %s owned by %s: %s" % \ + ( str( repository.name ), str( repository.user.username ), error_message ) ) return wsgi_app diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -42,6 +42,7 @@ from mercurial import commands from mercurial import hg +from mercurial import mdiff from mercurial import patch from mercurial import ui @@ -2856,11 +2857,19 @@ ctx_child = ctx.children()[ 0 ] else: ctx_child = None + diffs = [] + options_dict = suc.get_mercurial_default_options_dict( 'diff' ) + # Not quite sure if the following settings make any difference, but with a combination of them and the size check on each + # diff, we don't run out of memory when viewing the changelog of the cisortho2 repository on the test tool shed. + options_dict[ 'maxfile' ] = suc.MAXDIFFSIZE + options_dict[ 'maxtotal' ] = suc.MAXDIFFSIZE + diffopts = mdiff.diffopts( **options_dict ) + for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node(), opts=diffopts ): + if len( diff ) > suc.MAXDIFFSIZE: + diff = util.shrink_string_by_size( diff, suc.MAXDIFFSIZE ) + diffs.append( suc.to_html_string( diff ) ) modified, added, removed, deleted, unknown, ignored, clean = repo.status( node1=ctx_parent.node(), node2=ctx.node() ) anchors = modified + added + removed + deleted + unknown + ignored + clean - diffs = [] - for diff in patch.diff( repo, node1=ctx_parent.node(), node2=ctx.node() ): - diffs.append( suc.to_html_string( diff ) ) metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) # For rendering the prev button. if ctx_parent: diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/tool_shed/scripts/api/reset_metadata_on_repositories.py --- a/lib/tool_shed/scripts/api/reset_metadata_on_repositories.py +++ b/lib/tool_shed/scripts/api/reset_metadata_on_repositories.py @@ -25,33 +25,55 @@ else: return False +def read_skip_file( skip_file ): + encoded_ids_to_skip = [] + if os.path.exists( skip_file ): + # Contents of file must be 1 encoded repository id per line. + lines = open( skip_file, 'rb' ).readlines() + for line in lines: + if line.startswith( '#' ): + # Skip comments. + continue + encoded_ids_to_skip.append( line.rstrip( '\n' ) ) + return encoded_ids_to_skip + def main( options ): api_key = options.api base_tool_shed_url = options.tool_shed_url.rstrip( '/' ) my_writable = options.my_writable one_per_request = options.one_per_request skip_file = options.skip_file - encoded_ids_to_skip = [] - if skip_file and os.path.exists( skip_file ): - # Contents of file must be 1 encoded repository id per line. - contents = open( skip_file, 'rb' ).read() - if contents: - encoded_ids_to_skip = contents.split( '\n' ) + if skip_file: + encoded_ids_to_skip = read_skip_file( skip_file ) + else: + encoded_ids_to_skip = [] if string_as_bool( one_per_request ): url = '%s/api/repositories/repository_ids_for_setting_metadata?key=%s&my_writable=%s' % ( base_tool_shed_url, api_key, str( my_writable ) ) repository_ids = get( url, api_key ) for repository_id in repository_ids: if repository_id in encoded_ids_to_skip: + print "--------" print "Skipping repository with id %s because it is in skip file %s" % ( str( repository_id ), str( skip_file ) ) + print "--------" else: data = dict( repository_id=repository_id ) url = '%s/api/repositories/reset_metadata_on_repository' % base_tool_shed_url - submit( url, data, options.api ) + try: + submit( url, data, options.api ) + except Exception, e: + log.exception( ">>>>>>>>>>>>>>>Blew up on data: %s, exception: %s" % ( str( data ), str( e ) ) ) + # An nginx timeout undoubtedly occurred. + sys.exit( 1 ) else: data = dict( encoded_ids_to_skip=encoded_ids_to_skip, my_writable=my_writable ) url = '%s/api/repositories/reset_metadata_on_repositories' % base_tool_shed_url - submit( url, data, options.api ) + try: + submit( url, data, options.api ) + except Exception, e: + log.exception( str( e ) ) + # An nginx timeout undoubtedly occurred. + sys.exit( 1 ) if __name__ == '__main__': parser = argparse.ArgumentParser( description='Reset metadata on certain repositories in the Tool Shed via the Tool Shed API.' ) diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/tool_shed/util/metadata_util.py --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1772,17 +1772,19 @@ if trans.webapp.name == 'tool_shed': # We're in the tool shed. repository = suc.get_repository_in_tool_shed( trans, repository_id ) + owner = str( repository.user.username ) invalid_file_tups, metadata_dict = reset_all_metadata_on_repository_in_tool_shed( trans, repository_id ) else: # We're in Galaxy. repository = suc.get_installed_tool_shed_repository( trans, repository_id ) + owner = str( repository.owner ) invalid_file_tups, metadata_dict = reset_all_metadata_on_installed_repository( trans, repository_id ) if invalid_file_tups: message = tool_util.generate_message_for_invalid_tools( trans, invalid_file_tups, repository, None, as_html=False ) log.debug( message ) unsuccessful_count += 1 else: - log.debug( "Successfully reset metadata on repository %s" % str( repository.name ) ) + log.debug( "Successfully reset metadata on repository %s owned by %s" % ( str( repository.name ), owner ) ) successful_count += 1 except: log.exception( "Error attempting to reset metadata on repository %s", str( repository.name ) ) diff -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 -r 148a93733033814da72a7e7fc8139054626e9354 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -40,6 +40,7 @@ CHUNK_SIZE = 2**20 # 1Mb INITIAL_CHANGELOG_HASH = '000000000000' MAX_CONTENT_SIZE = 1048576 +MAXDIFFSIZE = 8000 MAX_DISPLAY_SIZE = 32768 DATATYPES_CONFIG_FILENAME = 'datatypes_conf.xml' REPOSITORY_DATA_MANAGER_CONFIG_FILENAME = 'data_manager_conf.xml' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History Panel: match arg order with Backbone when handling errors; pack scripts
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a5d98e64b173/ Changeset: a5d98e64b173 User: carlfeberhard Date: 2013-10-18 18:53:31 Summary: History Panel: match arg order with Backbone when handling errors; pack scripts Affected #: 8 files diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/mvc/dataset/hda-edit.js --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -50,15 +50,16 @@ purge_link.attr( 'href', [ "javascript", "void(0)" ].join( ':' ) ); purge_link.click( function( event ){ //TODO??: confirm? - var ajaxPromise = jQuery.ajax( purge_url ); - ajaxPromise.success( function( message, status, responseObj ){ + var xhr = jQuery.ajax( purge_url ); + xhr.success( function( message, status, responseObj ){ hdaView.model.set( 'purged', true ); hdaView.trigger( 'purged', hdaView ); }); - ajaxPromise.error( function( error, status, message ){ + xhr.error( function( error, status, message ){ //TODO: Exception messages are hidden within error page //!NOTE: that includes the 'Removal of datasets by users is not allowed in this Galaxy instance.' - hdaView.trigger( 'error', _l( "Unable to purge this dataset" ), error, status, message ); + view.trigger( 'error', + hdaView, xhr, { url: purge_url }, _l( "Unable to purge this dataset" ) ); }); }); } @@ -161,6 +162,7 @@ error: function() { // Something went wrong, so show HDA again. // TODO: an error notification would be good. + self.trigger( 'error', self, null, null, { url: delete_url }, _l( 'deletion failed' ) ); self.$el.show(); }, success: function() { @@ -521,7 +523,7 @@ url: this.urls.tags.get, error: function( xhr, status, error ){ view.log( "Tagging failed", xhr, status, error ); - view.trigger( 'error', _l( "Tagging failed" ), xhr, status, error ); + view.trigger( 'error', view, xhr, { url: view.urls.tags.get }, _l( "Tagging failed" ) ); }, success: function(tag_elt_html) { tagElt.html(tag_elt_html); @@ -546,7 +548,8 @@ loadAndDisplayAnnotation : function( event ){ //TODO: this is a drop in from history.mako - should use MV as well this.log( this + '.loadAndDisplayAnnotation', event ); - var annotationArea = this.$el.find( '.annotation-area' ), + var view = this, + annotationArea = this.$el.find( '.annotation-area' ), annotationElem = annotationArea.find( '.annotation-elt' ), setAnnotationUrl = this.urls.annotation.set; @@ -556,9 +559,10 @@ // Need to fill annotation element. $.ajax({ url: this.urls.annotation.get, - error: function(){ - view.log( "Annotation failed", xhr, status, error ); - view.trigger( 'error', _l( "Annotation failed" ), xhr, status, error ); + error: function( xhr, status, message ){ + view.log( "Annotation failed", xhr, status, message ); + view.trigger( 'error', + view, xhr, { url: view.urls.annotation.get }, _l( "Annotation failed" ) ); }, success: function( htmlFromAjax ){ if( htmlFromAjax === "" ){ diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/mvc/history/history-model.js --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -72,6 +72,10 @@ this.updateAfterDelay(); } }, this ); + + this.hdas.bind( 'error', function( model, xhr, options, msg ){ + this.trigger( 'error', model, xhr, options, msg ); + }, this ); }, setOwnEventHandlers : function(){ @@ -176,20 +180,26 @@ historyXhr.fail( function( xhr, status, error ){ //TODO: use ajax.status handlers here // keep rolling on a bad gateway - server restart - if( xhr.status === 502 ){ + + //if( xhr.status === 0 && xhr.readyState === 0 ){ + + if( ( xhr.status === 0 && xhr.readyState === 0 ) + || ( xhr.status === 502 ) ){ + + //if( xhr.status === 502 ){ + history.log( 'Bad Gateway error. Retrying...' ); setTimeout( function(){ - history.log( 'Bad Gateway error. Retrying...' ); //TODO: someway to throw error on X tries history.stateUpdater(); }, History.UPDATE_DELAY ); // if not interruption by iframe reload //TODO: remove when iframes are removed - } else if( !( ( xhr.readyState === 0 ) && ( xhr.status === 0 ) ) ){ + } else { history.log( 'stateUpdater error:', error, 'responseText:', xhr.responseText ); var msg = _l( 'An error occurred while getting updates from the server.' ) + ' ' + _l( 'Please contact a Galaxy administrator if the problem persists.' ); - history.trigger( 'error', msg, xhr, status, error ); + history.trigger( 'error', history, xhr, {}, msg ); } }); }, @@ -228,7 +238,7 @@ hdaIds, xhr, status, error, errorJson ); var msg = _l( 'An error occurred while getting dataset details from the server.' ) + ' ' + _l( 'Please contact a Galaxy administrator if the problem persists.' ); - history.trigger( 'error', msg, xhr, status, error ); + history.trigger( 'error', history, xhr, {}, msg ); } }, @@ -295,12 +305,13 @@ fetchDisplayApplications : function( ids ){ this.log( this + '.fetchDisplayApplications:', ids ); var history = this, + display_app_url = 'history/get_display_application_links', // if any ids passed place them in the query string data data = ( ids && _.isArray( ids ) )?({ hda_ids : ids.join( ',' ) }):({}); //TODO: hardcoded history.log( this + ': fetching display application data' ); - jQuery.ajax( 'history/get_display_application_links', { + jQuery.ajax( display_app_url, { data : data, success : function( displayAppList, status, xhr ){ //history.hdas.set( data, { merge: true } ); // doesn't work - clears all other attributes @@ -314,7 +325,7 @@ history.log( 'Error fetching display applications:', ids, xhr, status, error ); var msg = _l( 'An error occurred while getting display applications from the server.' ) + ' ' + _l( 'Please contact a Galaxy administrator if the problem persists.' ); - history.trigger( 'error', msg, xhr, status, error ); + history.trigger( 'error', history, xhr, { url: display_app_url }, msg ); } } }); @@ -322,7 +333,7 @@ toString : function(){ var nameString = ( this.get( 'name' ) )? - ( ',' + this.get( 'name' ) ) : ( '' ); + ( ', ' + this.get( 'name' ) ) : ( '' ); return 'History(' + this.get( 'id' ) + nameString + ')'; } }); diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -114,9 +114,21 @@ this.urls = {}; }, - // refresh function + errorHandler : function( model, xhr, options, msg ){ + // let 'lost contact' errors fail silently + if( xhr && ( ( xhr.status === 0 && xhr.readyState === 0 ) + || ( xhr.status === 502 ) ) ){ + this.log( 'lost contact with server', model, xhr, options, msg ); + return; + } + + // otherwise display a message + msg = msg || _l( 'An error occurred while getting updates from the server.' ) + ' ' + + _l( 'Please contact a Galaxy administrator if the problem persists.' ); + this.displayMessage( 'error', msg ); + }, + refresh : function() { - // refresh // TODO: refresh content without reloading frame window.location = window.location; }, @@ -128,8 +140,8 @@ this.model.bind( 'change:nice_size', this.updateHistoryDiskSize, this ); // don't need to re-render entire model on all changes, just render disk size when it changes - this.model.bind( 'error', function( msg, xhr, error, status ){ - this.displayMessage( 'error', msg ); + this.model.bind( 'error', function( model, xhr, options, msg ){ + this.errorHandler( model, xhr, options, msg ); this.model.attributes.error = undefined; }, this ); @@ -157,8 +169,8 @@ }, this ); // ---- self - this.bind( 'error', function( msg, xhr, error, status ){ - this.displayMessage( 'error', msg ); + this.bind( 'error', function( model, xhr, options, msg ){ + this.errorHandler( model, xhr, options, msg ); }); if( this.logger ){ @@ -380,8 +392,8 @@ hdaView.bind( 'body-collapsed', function( id ){ historyView.storage.get( 'expandedHdas' ).deleteKey( id ); }); - hdaView.bind( 'error', function( msg, xhr, status, error ){ - historyView.displayMessage( 'error', msg ); + hdaView.bind( 'error', function( model, xhr, options, msg ){ + historyView.errorHandler( model, xhr, options, msg ); }); }, @@ -488,7 +500,7 @@ url: view.urls.tag, error: function( xhr, error, status ) { panel.log( 'Error loading tag area html', xhr, error, status ); - panel.trigger( 'error', _l( "Tagging failed" ), xhr, error, status ); + panel.trigger( 'error', panel, {}, {}, _l( "Tagging failed" ) ); }, success: function(tag_elt_html) { //view.log( view + ' tag elt html (ajax)', tag_elt_html ); diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/mvc/dataset/hda-edit.js --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1,1 +1,1 @@ -var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){a.trigger("error",_l("Unable to purge this dataset"),h,g,i)})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:f+"/"+h+"?"+$.param(g)})}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",_l("Tagging failed"),g,e,f)},success:function(e){b.html(e);b.find("[title]").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(b){this.log(this+".loadAndDisplayAnnotation",b);var d=this.$el.find(".annotation-area"),c=d.find(".annotation-elt"),a=this.urls.annotation.set;if(d.is(":hidden")){if(!jQuery.trim(c.html())){$.ajax({url:this.urls.annotation.get,error:function(){view.log("Annotation failed",xhr,status,error);view.trigger("error",_l("Annotation failed"),xhr,status,error)},success:function(e){if(e===""){e="<em>"+_l("Describe or add notes to dataset")+"</em>"}c.html(e);d.find("[title]").tooltip();async_save_text(c.attr("id"),c.attr("id"),a,"new_annotation",18,true,4);d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:a+"/scatterplot?"+$.param(b),location:"center"});$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){f.Galaxy.modal.hide()},"View in saved visualization":function(){f.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e,buttons:{Cancel:function(){f.Galaxy.modal.hide()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){f.Galaxy.modal.hide();var g=$(this).val();c.id=g;f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})})}}})},"View in new visualization":function(){f.Galaxy.modal.hide();var g=a+"/trackster?"+$.param(c);f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:g})}}})}});return false}}; \ No newline at end of file +var HDAEditView=HDABaseView.extend(LoggableMixin).extend({initialize:function(a){HDABaseView.prototype.initialize.call(this,a);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_setUpBehaviors:function(c){HDABaseView.prototype._setUpBehaviors.call(this,c);var a=this,b=this.urls.purge,d=c.find("#historyItemPurger-"+this.model.get("id"));if(d){d.attr("href",["javascript","void(0)"].join(":"));d.click(function(e){var f=jQuery.ajax(b);f.success(function(i,g,h){a.model.set("purged",true);a.trigger("purged",a)});f.error(function(h,g,i){view.trigger("error",a,f,{url:b},_l("Unable to purge this dataset"))})})}},_render_warnings:function(){return $(jQuery.trim(HDABaseView.templates.messages(_.extend(this.model.toJSON(),{urls:this.urls}))))},_render_titleButtons:function(){var a=$('<div class="historyItemButtons"></div>');a.append(this._render_displayButton());a.append(this._render_editButton());a.append(this._render_deleteButton());return a},_render_editButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.UPLOAD)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.editButton=null;return null}var c=this.model.get("purged"),a=this.model.get("deleted"),b={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(a||c){b.enabled=false;if(c){b.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(a){b.title=_l("Undelete dataset to edit attributes")}}}this.editButton=new IconButtonView({model:new IconButton(b)});return this.editButton.render().$el},_render_deleteButton:function(){if((this.model.get("state")===HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){this.deleteButton=null;return null}var a=this,b=a.urls["delete"],c={title:_l("Delete"),href:b,id:"historyItemDeleter-"+this.model.get("id"),icon_class:"delete",on_click:function(){$.ajax({url:b,type:"POST",error:function(){a.trigger("error",a,null,null,{url:b},_l("deletion failed"));a.$el.show()},success:function(){a.model.set({deleted:true})}})}};if(this.model.get("deleted")||this.model.get("purged")){c={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}this.deleteButton=new IconButtonView({model:new IconButton(c)});return this.deleteButton.render().$el},_render_hdaSummary:function(){var a=_.extend(this.model.toJSON(),{urls:this.urls});if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){_.extend(a,{dbkey_unknown_and_editable:true})}return HDABaseView.templates.hdaSummary(a)},_render_errButton:function(){if(this.model.get("state")!==HistoryDatasetAssociation.STATES.ERROR){this.errButton=null;return null}this.errButton=new IconButtonView({model:new IconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",icon_class:"bug"})});return this.errButton.render().$el},_render_rerunButton:function(){this.rerunButton=new IconButtonView({model:new IconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",icon_class:"arrow-circle"})});return this.rerunButton.render().$el},_render_visualizationsButton:function(){var a=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(a))){this.visualizationsButton=null;return null}if(_.isObject(a[0])){return this._render_visualizationsFrameworkButton(a)}if(!this.urls.visualization){this.visualizationsButton=null;return null}var c=this.model.get("dbkey"),f=this.urls.visualization,d={},g={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(c){g.dbkey=c}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),href:this.urls.visualization,icon_class:"chart_curve"})});var b=this.visualizationsButton.render().$el;b.addClass("visualize-icon");function e(h){switch(h){case"trackster":return create_trackster_action_fn(f,g,c);case"scatterplot":return create_scatterplot_action_fn(f,g);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:f+"/"+h+"?"+$.param(g)})}}}if(a.length===1){b.attr("title",a[0]);b.click(e(a[0]))}else{_.each(a,function(i){var h=i.charAt(0).toUpperCase()+i.slice(1);d[_l(h)]=e(i)});make_popupmenu(b,d)}return b},_render_visualizationsFrameworkButton:function(a){if(!(this.model.hasData())||!(a&&!_.isEmpty(a))){this.visualizationsButton=null;return null}this.visualizationsButton=new IconButtonView({model:new IconButton({title:_l("Visualize"),icon_class:"chart_curve"})});var c=this.visualizationsButton.render().$el;c.addClass("visualize-icon");if(_.keys(a).length===1){c.attr("title",_.keys(a)[0]);c.attr("href",_.values(a)[0])}else{var d=[];_.each(a,function(e){d.push(e)});var b=new PopupMenu(c,d)}return c},_render_secondaryActionButtons:function(b){var c=$("<div/>"),a=this;c.attr("style","float: right;").attr("id","secondary-actions-"+this.model.get("id"));_.each(b,function(d){c.append(d.call(a))});return c},_render_tagButton:function(){if(!(this.model.hasData())||(!this.urls.tags.get)){this.tagButton=null;return null}this.tagButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset tags"),target:"galaxy_main",href:this.urls.tags.get,icon_class:"tags"})});return this.tagButton.render().$el},_render_annotateButton:function(){if(!(this.model.hasData())||(!this.urls.annotation.get)){this.annotateButton=null;return null}this.annotateButton=new IconButtonView({model:new IconButton({title:_l("Edit dataset annotation"),target:"galaxy_main",icon_class:"annotate"})});return this.annotateButton.render().$el},_render_tagArea:function(){if(!this.urls.tags.set){return null}return $(HDAEditView.templates.tagArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_annotationArea:function(){if(!this.urls.annotation.get){return null}return $(HDAEditView.templates.annotationArea(_.extend(this.model.toJSON(),{urls:this.urls})).trim())},_render_body_error:function(a){HDABaseView.prototype._render_body_error.call(this,a);var b=a.find("#primary-actions-"+this.model.get("id"));b.prepend(this._render_errButton())},_render_body_ok:function(a){a.append(this._render_hdaSummary());if(this.model.isDeletedOrPurged()){a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton]));return}a.append(this._render_primaryActionButtons([this._render_downloadButton,this._render_showParamsButton,this._render_rerunButton,this._render_visualizationsButton]));a.append(this._render_secondaryActionButtons([this._render_tagButton,this._render_annotateButton]));a.append('<div class="clear"/>');a.append(this._render_tagArea());a.append(this._render_annotationArea());a.append(this._render_displayAppArea());this._render_displayApps(a);a.append(this._render_peek())},events:{"click .historyItemTitle":"toggleBodyVisibility","click a.icon-button.tags":"loadAndDisplayTags","click a.icon-button.annotate":"loadAndDisplayAnnotation"},loadAndDisplayTags:function(c){this.log(this+".loadAndDisplayTags",c);var a=this,d=this.$el.find(".tag-area"),b=d.find(".tag-elt");if(d.is(":hidden")){if(!jQuery.trim(b.html())){$.ajax({url:this.urls.tags.get,error:function(g,e,f){a.log("Tagging failed",g,e,f);a.trigger("error",a,g,{url:a.urls.tags.get},_l("Tagging failed"))},success:function(e){b.html(e);b.find("[title]").tooltip();d.slideDown("fast")}})}else{d.slideDown("fast")}}else{d.slideUp("fast")}return false},loadAndDisplayAnnotation:function(c){this.log(this+".loadAndDisplayAnnotation",c);var a=this,e=this.$el.find(".annotation-area"),d=e.find(".annotation-elt"),b=this.urls.annotation.set;if(e.is(":hidden")){if(!jQuery.trim(d.html())){$.ajax({url:this.urls.annotation.get,error:function(h,f,g){a.log("Annotation failed",h,f,g);a.trigger("error",a,h,{url:a.urls.annotation.get},_l("Annotation failed"))},success:function(f){if(f===""){f="<em>"+_l("Describe or add notes to dataset")+"</em>"}d.html(f);e.find("[title]").tooltip();async_save_text(d.attr("id"),d.attr("id"),b,"new_annotation",18,true,4);e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},toString:function(){var a=(this.model)?(this.model+""):("(no model)");return"HDAView("+a+")"}});HDAEditView.templates={tagArea:Handlebars.templates["template-hda-tagArea"],annotationArea:Handlebars.templates["template-hda-annotationArea"]};function create_scatterplot_action_fn(a,b){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:a+"/scatterplot?"+$.param(b),location:"center"});$("div.popmenu-wrapper").remove();return false};return action}function create_trackster_action_fn(a,c,b){return function(){var d={};if(b){d["f-dbkey"]=b}$.ajax({url:a+"/list_tracks?"+$.param(d),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(e){var f=window.parent;f.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){f.Galaxy.modal.hide()},"View in saved visualization":function(){f.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:e,buttons:{Cancel:function(){f.Galaxy.modal.hide()},"Add to visualization":function(){$(f.document).find("input[name=id]:checked").each(function(){f.Galaxy.modal.hide();var g=$(this).val();c.id=g;f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:a+"/trackster?"+$.param(c)})})}}})},"View in new visualization":function(){f.Galaxy.modal.hide();var g=a+"/trackster?"+$.param(c);f.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:g})}}})}});return false}}; \ No newline at end of file diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/mvc/history/history-model.js --- a/static/scripts/packed/mvc/history/history-model.js +++ b/static/scripts/packed/mvc/history/history-model.js @@ -1,1 +1,1 @@ -var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.fetchDisplayApplications()}}this.setHdaEventHandlers();this.setOwnEventHandlers()},setHdaEventHandlers:function(){this.hdas.bind("state:ready",function(b,c,a){if(b.get("force_history_refresh")){this.updateAfterDelay()}},this)},setOwnEventHandlers:function(){if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.updateTimeoutId=null;a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},isRunning:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.RUNNING)||(a===HistoryDatasetAssociation.STATES.QUEUED))},isReady:function(){return !this.isRunning()},checkForUpdates:function(){if(this.isRunning()){this.updateAfterDelay()}else{this.trigger("ready")}return this},findHdasToUpdate:function(){var c=this,a=c.get("state_ids"),b=[];_.each(a,function(d,e){_.each(d,function(g){var f=c.hdas.get(g);if(!f||f.get("state")!==e){b.push(g)}})});return b},stateUpdater:function(){var c=this,a=this.get("state"),b=this.fetch();b.done(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=c.findHdasToUpdate();if(e.length){c.fetchHdaUpdates(e).done(function(f){c.checkForUpdates()})}else{c.checkForUpdates()}});b.fail(function(g,d,e){if(g.status===502){setTimeout(function(){c.log("Bad Gateway error. Retrying...");c.stateUpdater()},History.UPDATE_DELAY)}else{if(!((g.readyState===0)&&(g.status===0))){c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",h,i,d,e)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},fetchDisplayApplications:function(a){this.log(this+".fetchDisplayApplications:",a);var c=this,b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});c.log(this+": fetching display application data");jQuery.ajax("history/get_display_application_links",{data:b,success:function(f,d,e){_.each(f,function(h){var g=c.hdas.get(h.id);if(g){g.set(h)}})},error:function(g,d,e){if(!((g.readyState===0)&&(g.status===0))){c.log("Error fetching display applications:",a,g,d,e);var f=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",f,g,d,e)}}})},toString:function(){var a=(this.get("name"))?(","+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file +var History=Backbone.Model.extend(LoggableMixin).extend({defaults:{id:null,name:"Unnamed History",state:"new",diskSize:0,deleted:false},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("id")},initialize:function(b,c,a){a=a||null;this.log(this+".initialize:",b,c);this.hdas=new HDACollection();this.updateTimeoutId=null;if(c&&_.isArray(c)){this.hdas.add(c);this.checkForUpdates();if(this.hdas.length>0){this.fetchDisplayApplications()}}this.setHdaEventHandlers();this.setOwnEventHandlers()},setHdaEventHandlers:function(){this.hdas.bind("state:ready",function(b,c,a){if(b.get("force_history_refresh")){this.updateAfterDelay()}},this);this.hdas.bind("error",function(b,d,a,c){this.trigger("error",b,d,a,c)},this)},setOwnEventHandlers:function(){if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},hdaIdsFromStateIds:function(){return _.reduce(_.values(this.get("state_ids")),function(b,a){return b.concat(a)})},updateAfterDelay:function(){var a=this;this.updateTimeoutId=setTimeout(function(){a.updateTimeoutId=null;a.stateUpdater()},History.UPDATE_DELAY);return this.updateTimeoutId},isRunning:function(){var a=this.get("state");return((a===HistoryDatasetAssociation.STATES.RUNNING)||(a===HistoryDatasetAssociation.STATES.QUEUED))},isReady:function(){return !this.isRunning()},checkForUpdates:function(){if(this.isRunning()){this.updateAfterDelay()}else{this.trigger("ready")}return this},findHdasToUpdate:function(){var c=this,a=c.get("state_ids"),b=[];_.each(a,function(d,e){_.each(d,function(g){var f=c.hdas.get(g);if(!f||f.get("state")!==e){b.push(g)}})});return b},stateUpdater:function(){var c=this,a=this.get("state"),b=this.fetch();b.done(function(d){c.set(d);c.log("current history state:",c.get("state"),"(was)",a,"new size:",c.get("nice_size"));var e=c.findHdasToUpdate();if(e.length){c.fetchHdaUpdates(e).done(function(f){c.checkForUpdates()})}else{c.checkForUpdates()}});b.fail(function(g,d,e){if((g.status===0&&g.readyState===0)||(g.status===502)){c.log("Bad Gateway error. Retrying...");setTimeout(function(){c.stateUpdater()},History.UPDATE_DELAY)}else{c.log("stateUpdater error:",e,"responseText:",g.responseText);var f=_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");c.trigger("error",c,g,{},f)}})},fetchHdaUpdates:function(c){var a=this,b=jQuery.ajax({url:this.url()+"/contents?"+jQuery.param({ids:c.join(",")}),error:function(i,d,e){if((i.readyState===0)&&(i.status===0)){return}var g=JSON.parse(i.responseText);if(_.isArray(g)){var f=_.groupBy(g,function(j){if(_.has(j,"error")){return"errored"}return"ok"});a.log("fetched, errored datasets:",f.errored);a.updateHdas(g)}else{a.log("Error updating hdas from api history contents",c,i,d,e,g);var h=_l("An error occurred while getting dataset details from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");a.trigger("error",a,i,{},h)}},success:function(e,d,f){a.log(a+".fetchHdaUpdates, success:",d,f);a.updateHdas(e)}});return b},updateHdas:function(a){var c=this,b=[];c.log(c+".updateHdas:",a);_.each(a,function(e,f){var d=c.hdas.get(e.id);if(d){c.log("found existing model in list for id "+e.id+", updating...:");d.set(e)}else{c.log("NO existing model for id "+e.id+", creating...:");b.push(e)}});if(b.length){c.addHdas(b)}},addHdas:function(a){var b=this;_.each(a,function(c,d){var e=b.hdas.hidToCollectionIndex(c.hid);c.history_id=b.get("id");b.hdas.add(new HistoryDatasetAssociation(c),{at:e,silent:true})});b.hdas.trigger("add",a)},fetchDisplayApplications:function(a){this.log(this+".fetchDisplayApplications:",a);var d=this,c="history/get_display_application_links",b=(a&&_.isArray(a))?({hda_ids:a.join(",")}):({});d.log(this+": fetching display application data");jQuery.ajax(c,{data:b,success:function(g,e,f){_.each(g,function(i){var h=d.hdas.get(i.id);if(h){h.set(i)}})},error:function(h,e,f){if(!((h.readyState===0)&&(h.status===0))){d.log("Error fetching display applications:",a,h,e,f);var g=_l("An error occurred while getting display applications from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");d.trigger("error",d,h,{url:c},g)}}})},toString:function(){var a=(this.get("name"))?(", "+this.get("name")):("");return"History("+this.get("id")+a+")"}});History.UPDATE_DELAY=4000;var HistoryCollection=Backbone.Collection.extend(LoggableMixin).extend({model:History,urlRoot:"api/histories"}); \ No newline at end of file diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -var HistoryPanel=Backbone.View.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this._setUpEventHandlers();this.hdaViews={};this.urls={}},refresh:function(){window.location=window.location},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(d,c,b,a){this.displayMessage("error",d);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:purged",function(a){this.model.fetch()},this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(d,c,b,a){this.displayMessage("error",d)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_setUpWebStorage:function(b,a,c){this.storage=new PersistentStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var a in sessionStorage){if(a.indexOf("HistoryView.")===0){sessionStorage.removeItem(a)}}},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find("[title]").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)});b.bind("error",function(f,e,c,d){a.displayMessage("error",f)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",_l("Tagging failed"),h,g,f)},success:function(f){c.html(f);c.find("[title]").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("<div/>").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},scrollToTop:function(){$(document).scrollTop(0);return this},scrollIntoView:function(b,c){if(!c){$(document).scrollTop(b);return this}var a=window,d=this.$el.parent(),f=$(a).innerHeight(),e=(f/2)-(c/2);$(d).scrollTop(b-e);return this},scrollToId:function(b){if((!b)||(!this.hdaViews[b])){return this}var a=this.hdaViews[b].$el;this.scrollIntoView(a.offset().top,a.outerHeight());return this},scrollToHid:function(a){var b=this.model.hdas.getByHid(a);if(!b){return this}return this.scrollToId(b.id)},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file +var HistoryPanel=Backbone.View.extend(LoggableMixin).extend({el:"body.historyPage",HDAView:HDAEditView,events:{"click #history-tag":"loadAndDisplayTags","click #message-container":"removeMessage"},initialize:function(a){if(a.logger){this.logger=this.model.logger=a.logger}this.log(this+".initialize:",a);if(!a.urlTemplates){throw (this+" needs urlTemplates on initialize")}if(!a.urlTemplates.history){throw (this+" needs urlTemplates.history on initialize")}if(!a.urlTemplates.hda){throw (this+" needs urlTemplates.hda on initialize")}this.urlTemplates=a.urlTemplates.history;this.hdaUrlTemplates=a.urlTemplates.hda;this._setUpWebStorage(a.initiallyExpanded,a.show_deleted,a.show_hidden);this._setUpEventHandlers();this.hdaViews={};this.urls={}},errorHandler:function(b,d,a,c){if(d&&((d.status===0&&d.readyState===0)||(d.status===502))){this.log("lost contact with server",b,d,a,c);return}c=c||_l("An error occurred while getting updates from the server.")+" "+_l("Please contact a Galaxy administrator if the problem persists.");this.displayMessage("error",c)},refresh:function(){window.location=window.location},_setUpEventHandlers:function(){this.model.bind("change:nice_size",this.updateHistoryDiskSize,this);this.model.bind("error",function(b,d,a,c){this.errorHandler(b,d,a,c);this.model.attributes.error=undefined},this);this.model.hdas.bind("add",this.add,this);this.model.hdas.bind("reset",this.addAll,this);this.model.hdas.bind("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.bind("change:purged",function(a){this.model.fetch()},this);this.model.hdas.bind("state:ready",function(b,c,a){if((!b.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(b.get("id"))}},this);this.bind("error",function(b,d,a,c){this.errorHandler(b,d,a,c)});if(this.logger){this.bind("all",function(a){this.log(this+"",arguments)},this)}},_setUpWebStorage:function(b,a,c){this.storage=new PersistentStorage("HistoryView."+this.model.get("id"),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(b){this.storage.set("exandedHdas",b)}if((a===true)||(a===false)){this.storage.set("show_deleted",a)}if((c===true)||(c===false)){this.storage.set("show_hidden",c)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var a in sessionStorage){if(a.indexOf("HistoryView.")===0){sessionStorage.removeItem(a)}}},add:function(a){this.render()},addAll:function(){this.render()},handleHdaDeletionChange:function(a){if(a.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(a.get("id"))}},removeHdaView:function(c,b){var a=this.hdaViews[c];if(!a){return}a.remove(b);delete this.hdaViews[c];if(_.isEmpty(this.hdaViews)){this.render()}},render:function(){var b=this,d=b.toString()+".set-up",c=$("<div/>"),a=this.model.toJSON(),e=(this.$el.children().size()===0);a.urls=this._renderUrls(a);c.append(HistoryPanel.templates.historyPanel(a));c.find("[title]").tooltip({placement:"bottom"});if(!this.model.hdas.length||!this.renderItems(c.find("#"+this.model.get("id")+"-datasets"))){c.find("#emptyHistoryMessage").show()}$(b).queue(d,function(f){b.$el.fadeOut("fast",function(){f()})});$(b).queue(d,function(f){b.$el.html("");b.$el.append(c.children());b.$el.fadeIn("fast",function(){f()})});$(b).queue(d,function(f){this.log(b+" rendered:",b.$el);b._setUpBehaviours();if(e){b.trigger("rendered:initial")}else{b.trigger("rendered")}f()});$(b).dequeue(d);return this},_renderUrls:function(a){var b=this;b.urls={};_.each(this.urlTemplates,function(d,c){b.urls[c]=_.template(d,a)});return b.urls},renderItems:function(b){this.hdaViews={};var a=this,c=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(c,function(f){var e=f.get("id"),d=a.storage.get("expandedHdas").get(e);a.hdaViews[e]=new a.HDAView({model:f,expanded:d,urlTemplates:a.hdaUrlTemplates,logger:a.logger});a._setUpHdaListeners(a.hdaViews[e]);b.prepend(a.hdaViews[e].render().$el)});return c.length},_setUpHdaListeners:function(b){var a=this;b.bind("body-expanded",function(c){a.storage.get("expandedHdas").set(c,true)});b.bind("body-collapsed",function(c){a.storage.get("expandedHdas").deleteKey(c)});b.bind("error",function(d,f,c,e){a.errorHandler(d,f,c,e)})},_setUpBehaviours:function(){if(!(this.model.get("user")&&this.model.get("user").email)){return}var a=this.$("#history-annotation-area");this.$("#history-annotate").click(function(){if(a.is(":hidden")){a.slideDown("fast")}else{a.slideUp("fast")}return false});async_save_text("history-name-container","history-name",this.urls.rename,"new_name",18);async_save_text("history-annotation-container","history-annotation",this.urls.annotate,"new_annotation",18,true,4)},updateHistoryDiskSize:function(){this.$el.find("#history-size").text(this.model.get("nice_size"))},showQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(a.is(":hidden")){a.slideDown("fast")}},hideQuotaMessage:function(){var a=this.$el.find("#quota-message-container");if(!a.is(":hidden")){a.slideUp("fast")}},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(a){a.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},loadAndDisplayTags:function(d){this.log(this+".loadAndDisplayTags",d);var b=this,e=this.$el.find("#history-tag-area"),c=e.find(".tag-elt");this.log("\t tagArea",e," tagElt",c);if(e.is(":hidden")){if(!jQuery.trim(c.html())){var a=this;$.ajax({url:a.urls.tag,error:function(h,g,f){b.log("Error loading tag area html",h,g,f);b.trigger("error",b,{},{},_l("Tagging failed"))},success:function(f){c.html(f);c.find("[title]").tooltip();e.slideDown("fast")}})}else{e.slideDown("fast")}}else{e.slideUp("fast")}return false},displayMessage:function(c,d){var b=this.$el.find("#message-container"),a=$("<div/>").addClass(c+"message").text(d);b.html(a)},removeMessage:function(){var a=this.$el.find("#message-container");a.html(null)},scrollToTop:function(){$(document).scrollTop(0);return this},scrollIntoView:function(b,c){if(!c){$(document).scrollTop(b);return this}var a=window,d=this.$el.parent(),f=$(a).innerHeight(),e=(f/2)-(c/2);$(d).scrollTop(b-e);return this},scrollToId:function(b){if((!b)||(!this.hdaViews[b])){return this}var a=this.hdaViews[b].$el;this.scrollIntoView(a.offset().top,a.outerHeight());return this},scrollToHid:function(a){var b=this.model.hdas.getByHid(a);if(!b){return this}return this.scrollToId(b.id)},toString:function(){var a=this.model.get("name")||"";return"HistoryPanel("+a+")"}});HistoryPanel.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]}; \ No newline at end of file diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/viz/trackster.js --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1,1 +1,1 @@ -var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file +var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/backbone/backbone-relational","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("<a id='add-bookmark-button' class='icon-button menu-button plus-button' href='javascript:void(0);' title='Add bookmark'></a>");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey option[value='"+galaxy_config.app.default_dbkey+"']").attr("selected",true)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='<form id="new-browser-form" action="javascript:void(0);" method="post" onsubmit="return false;"><div class="form-row"><label for="new-title">Browser name:</label><div class="form-row-input"><input type="text" name="title" id="new-title" value="Unnamed"></input></div><div style="clear: both;"></div></div><div class="form-row"><label for="new-dbkey">Reference genome build (dbkey): </label><div class="form-row-input"><select name="dbkey" id="new-dbkey">';for(var f in e){g+='<option value="'+e[f][1]+'">'+e[f][0]+"</option>"}g+='</select></div><div style="clear: both;"></div></div><div class="form-row">Is the build not listed here? <a href="'+galaxy_config.root+'user/dbkeys?use_panels=True">Add a Custom Build</a></div></form>';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.prefs.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file diff -r febd7622924885dd0729ce00924289cc1f0eb741 -r a5d98e64b173e5fc11d0d7234a16fbc80c553317 static/scripts/packed/viz/trackster_ui.js --- a/static/scripts/packed/viz/trackster_ui.js +++ b/static/scripts/packed/viz/trackster_ui.js @@ -1,1 +1,1 @@ -define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file +define(["base","libs/underscore","viz/trackster/slotting","viz/trackster/painters","viz/trackster/tracks","viz/visualization"],function(a,f,e,c,d,h){var j=d.object_from_template;var b=function(l,k){if(!k){k={}}var m=new IconButtonCollection(f.map(l,function(n){return new IconButton(f.extend(n,k))}));return new IconButtonMenuView({collection:m})};var g=a.Base.extend({initialize:function(k){this.baseURL=k},createButtonMenu:function(){var k=this,l=b([{icon_class:"plus-button",title:"Add tracks",on_click:function(){h.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":view.dbkey},function(m){f.each(m,function(n){view.add_drawable(j(n,view,view))})})}},{icon_class:"block--plus",title:"Add group",on_click:function(){view.add_drawable(new d.DrawableGroup(view,view,{name:"New Group"}))}},{icon_class:"bookmarks",title:"Bookmarks",on_click:function(){force_right_panel(($("div#right").css("right")=="0px"?"hide":"show"))}},{icon_class:"globe",title:"Circster",on_click:function(){window.location=k.baseURL+"visualization/circster?id="+view.vis_id}},{icon_class:"disk--arrow",title:"Save",on_click:function(){Galaxy.modal.show({title:"Saving...",body:"progress"});var m=[];$(".bookmark").each(function(){m.push({position:$(this).children(".position").text(),annotation:$(this).children(".annotation").text()})});var n=(view.overview_drawable?view.overview_drawable.prefs.name:null),o={view:view.to_dict(),viewport:{chrom:view.chrom,start:view.low,end:view.high,overview:n},bookmarks:m};$.ajax({url:galaxy_config.root+"visualization/save",type:"POST",dataType:"json",data:{id:view.vis_id,title:view.prefs.name,dbkey:view.dbkey,type:"trackster",vis_json:JSON.stringify(o)}}).success(function(p){Galaxy.modal.hide();view.vis_id=p.vis_id;view.has_changes=false;window.history.pushState({},"",p.url+window.location.hash)}).error(function(){Galaxy.modal.show({title:"Could Not Save",body:"Could not save visualization. Please try again later.",buttons:{Cancel:function(){Galaxy.modal.hide()}}})})}},{icon_class:"cross-circle",title:"Close",on_click:function(){window.location=galaxy_config.root+"visualization"}}],{tooltip_config:{placement:"bottom"}});this.buttonMenu=l;return l},add_bookmarks:function(){var k=this,l=this.baseURL;Galaxy.modal.show({title:"Select dataset for new bookmarks",body:"progress"});$.ajax({url:this.baseURL+"/visualization/list_histories",data:{"f-dbkey":view.dbkey},error:function(){alert("Grid failed")},success:function(m){Galaxy.modal.show({title:"Select dataset for new bookmarks",body:m,buttons:{Cancel:function(){Galaxy.modal.hide()},Insert:function(){$("input[name=id]:checked,input[name=ldda_ids]:checked").first().each(function(){var n,o=$(this).val();if($(this).attr("name")==="id"){n={hda_id:o}}else{n={ldda_id:o}}$.ajax({url:this.baseURL+"/visualization/bookmarks_from_dataset",data:n,dataType:"json"}).then(function(p){for(i=0;i<p.data.length;i++){var q=p.data[i];k.add_bookmark(q[0],q[1])}})});Galaxy.modal.hide()}}})}})},add_bookmark:function(o,m,k){var q=$("#right .unified-panel-body"),s=$("<div/>").addClass("bookmark").appendTo(q);var t=$("<div/>").addClass("position").appendTo(s),p=$("<a href=''/>").text(o).appendTo(t).click(function(){view.go_to(o);return false}),n=$("<div/>").text(m).appendTo(s);if(k){var r=$("<div/>").addClass("delete-icon-container").prependTo(s).click(function(){s.slideUp("fast");s.remove();view.has_changes=true;return false}),l=$("<a href=''/>").addClass("icon-button delete").appendTo(r);n.make_text_editable({num_rows:3,use_textarea:true,help_text:"Edit bookmark note"}).addClass("annotation")}view.has_changes=true;return s},create_visualization:function(p,k,o,q,n){var m=this,l=new d.TracksterView(p);l.editor=true;$.when(l.load_chroms_deferred).then(function(B){if(k){var z=k.chrom,r=k.start,w=k.end,t=k.overview;if(z&&(r!==undefined)&&w){l.change_chrom(z,r,w)}else{l.change_chrom(B[0].chrom)}}else{l.change_chrom(B[0].chrom)}if(o){var u,s,v;for(var x=0;x<o.length;x++){l.add_drawable(j(o[x],l,l))}}l.update_intro_div();var A;for(var x=0;x<l.drawables.length;x++){if(l.drawables[x].prefs.name===t){l.set_overview(l.drawables[x]);break}}if(q){var y;for(var x=0;x<q.length;x++){y=q[x];m.add_bookmark(y.position,y.annotation,n)}}l.has_changes=false});return l},init_keyboard_nav:function(k){$(document).keydown(function(l){if($(l.srcElement).is(":input")){return}switch(l.which){case 37:k.move_fraction(0.25);break;case 38:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()-20);break;case 39:k.move_fraction(-0.25);break;case 40:var m=Math.round(k.viewport_container.height()/15);k.viewport_container.scrollTop(k.viewport_container.scrollTop()+20);break}})}});return{object_from_template:j,TracksterUI:g}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: natefoo: Log failures when setting peek.
by commits-noreply＠bitbucket.org 18 Oct '13

18 Oct '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/febd76229248/ Changeset: febd76229248 User: natefoo Date: 2013-10-18 17:43:01 Summary: Log failures when setting peek. Affected #: 1 file diff -r 503d939099fcd8913202300b83221a8d3269b9f9 -r febd7622924885dd0729ce00924289cc1f0eb741 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -227,6 +227,7 @@ out.append( '</th>' ) out.append( '</tr>' ) except Exception, exc: + log.exception( 'make_html_peek_header failed on HDA %s' % dataset.id ) raise Exception, "Can't create peek header %s" % str( exc ) return "".join( out ) @@ -254,6 +255,7 @@ out.append( '<td>%s</td>' % escape( elem ) ) out.append( '</tr>' ) except Exception, exc: + log.exception( 'make_html_peek_rows failed on HDA %s' % dataset.id ) raise Exception, "Can't create peek rows %s" % str( exc ) return "".join( out ) 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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