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

commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/315465b38434/ Changeset: 315465b38434 User: nsoranzo Date: 2014-01-15 17:51:36 Summary: PEP-8 and unused variables fixes. Affected #: 1 file diff -r 8deba81aad81fd565a7e33bad10bb8e741a6172b -r 315465b38434aff44e8863c6f2ea7e9ab549beb2 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -241,7 +241,7 @@ outputs = util.odict.odict() rval['history'] = trans.security.encode_id(history.id) rval['outputs'] = [] - for i, step in enumerate( workflow.steps ): + for step in workflow.steps: job = None if step.type == 'tool' or step.type is None: tool = self.app.toolbox.get_tool( step.tool_id ) @@ -285,7 +285,7 @@ """ try: stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) - except Exception,e: + except Exception, e: return ("Workflow with ID='%s' can not be found\n Exception: %s") % (workflow_id, str( e )) # check to see if user has permissions to selected workflow if stored_workflow.user != trans.user and not trans.user_is_admin(): @@ -293,7 +293,7 @@ trans.response.status = 400 return("Workflow is not owned by or shared with current user") - ret_dict = self._workflow_to_dict( trans, stored_workflow ); + ret_dict = self._workflow_to_dict( trans, stored_workflow ) if not ret_dict: #This workflow has a tool that's missing from the distribution trans.response.status = 400 @@ -309,7 +309,7 @@ copied from galaxy.web.controllers.workflows.py (delete) """ - workflow_id = id; + workflow_id = id try: stored_workflow = trans.sa_session.query(self.app.model.StoredWorkflow).get(trans.security.decode_id(workflow_id)) @@ -341,23 +341,23 @@ # currently assumes payload['workflow'] is a json representation of a workflow to be inserted into the database """ - data = payload['workflow']; + data = payload['workflow'] workflow, missing_tool_tups = self._workflow_from_dict( trans, data, source="API" ) # galaxy workflow newly created id - workflow_id = workflow.id; + workflow_id = workflow.id # api encoded, id - encoded_id = trans.security.encode_id(workflow_id); + encoded_id = trans.security.encode_id(workflow_id) # return list - rval= []; + rval = [] item = workflow.to_dict(value_mapper={'id':trans.security.encode_id}) item['url'] = url_for('workflow', id=encoded_id) - rval.append(item); + rval.append(item) - return item; + return item def _workflow_from_dict( self, trans, data, source=None ): """ @@ -386,7 +386,7 @@ # will be ( tool_id, tool_name, tool_version ). missing_tool_tups = [] # First pass to build step objects and populate basic values - for key, step_dict in data[ 'steps' ].iteritems(): + for step_dict in data[ 'steps' ].itervalues(): # Create the model class for the step step = model.WorkflowStep() steps.append( step ) @@ -530,7 +530,7 @@ step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) elif input_type == dict: # Input type is described by a dict, e.g. indexed parameters. - for partname, partval in val.items(): + for partval in val.values(): if type( partval ) == RuntimeValue: step_dict['inputs'].append( { "name" : name, "description" : "runtime parameter for tool %s" % module.get_name() } ) # User outputs https://bitbucket.org/galaxy/galaxy-central/commits/4fb2ce004601/ Changeset: 4fb2ce004601 User: nsoranzo Date: 2014-01-15 18:04:33 Summary: Let /api/workflows show() method display also importable workflows. Affected #: 1 file diff -r 315465b38434aff44e8863c6f2ea7e9ab549beb2 -r 4fb2ce004601f50d63c4884006d453eee580a85a lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -60,10 +60,10 @@ return "Malformed workflow id ( %s ) specified, unable to decode." % str(workflow_id) try: stored_workflow = trans.sa_session.query(trans.app.model.StoredWorkflow).get(decoded_workflow_id) - if stored_workflow.user != trans.user and not trans.user_is_admin(): + if stored_workflow.importable == False and stored_workflow.user != trans.user and not trans.user_is_admin(): if trans.sa_session.query(trans.app.model.StoredWorkflowUserShareAssociation).filter_by(user=trans.user, stored_workflow=stored_workflow).count() == 0: trans.response.status = 400 - return("Workflow is not owned by or shared with current user") + return("Workflow is neither importable, nor owned by or shared with current user") except: trans.response.status = 400 return "That workflow does not exist." https://bitbucket.org/galaxy/galaxy-central/commits/33af32773cba/ Changeset: 33af32773cba User: nsoranzo Date: 2014-01-15 18:22:51 Summary: Add show_published param to /api/workflows index() method to display also published workflows. Affected #: 1 file diff -r 4fb2ce004601f50d63c4884006d453eee580a85a -r 33af32773cba309fde44ced5fba78ce8fc64078b lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -5,7 +5,7 @@ """ import logging -from sqlalchemy import desc +from sqlalchemy import desc, or_ from galaxy import util from galaxy import web from galaxy import model @@ -26,10 +26,17 @@ GET /api/workflows Displays a collection of workflows. + + :param show_published: if True, show also published workflows + :type show_published: boolean """ + show_published = util.string_as_bool( kwd.get( 'show_published', 'False' ) ) rval = [] - for wf in trans.sa_session.query(trans.app.model.StoredWorkflow).filter_by( - user=trans.user, deleted=False).order_by( + filter1 = ( trans.app.model.StoredWorkflow.user == trans.user ) + if show_published: + filter1 = or_( filter1, ( trans.app.model.StoredWorkflow.published == True ) ) + for wf in trans.sa_session.query(trans.app.model.StoredWorkflow).filter( + filter1, trans.app.model.StoredWorkflow.table.c.deleted == False ).order_by( desc(trans.app.model.StoredWorkflow.table.c.update_time)).all(): item = wf.to_dict(value_mapper={'id':trans.security.encode_id}) encoded_id = trans.security.encode_id(wf.id) https://bitbucket.org/galaxy/galaxy-central/commits/f4be6a4360b6/ Changeset: f4be6a4360b6 User: nsoranzo Date: 2014-01-15 18:17:24 Summary: Move core code for importing a shared workflow to UsesStoredWorkflowMixin. Affected #: 4 files diff -r 33af32773cba309fde44ced5fba78ce8fc64078b -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -33,7 +33,7 @@ from galaxy.model.orm import eagerload, eagerload_all, desc from galaxy.security.validate_user_input import validate_publicname from galaxy.util.sanitize_html import sanitize_html -from galaxy.model.item_attrs import Dictifiable +from galaxy.model.item_attrs import Dictifiable, UsesAnnotations from galaxy.datatypes.interval import ChromatinInteractions from galaxy.datatypes.data import Text @@ -1497,7 +1497,7 @@ return return_message -class UsesStoredWorkflowMixin( SharableItemSecurityMixin ): +class UsesStoredWorkflowMixin( SharableItemSecurityMixin, UsesAnnotations ): """ Mixin for controllers that use StoredWorkflow objects. """ def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): @@ -1539,6 +1539,26 @@ # Connections by input name step.input_connections_by_name = dict( ( conn.input_name, conn ) for conn in step.input_connections ) + def _import_shared_workflow( self, trans, stored): + """ """ + # Copy workflow. + imported_stored = model.StoredWorkflow() + imported_stored.name = "imported: " + stored.name + imported_stored.latest_workflow = stored.latest_workflow + imported_stored.user = trans.user + # Save new workflow. + session = trans.sa_session + session.add( imported_stored ) + session.flush() + + # Copy annotations. + self.copy_item_annotation( session, stored.user, stored, imported_stored.user, imported_stored ) + for order_index, step in enumerate( stored.latest_workflow.steps ): + self.copy_item_annotation( session, stored.user, step, \ + imported_stored.user, imported_stored.latest_workflow.steps[order_index] ) + session.flush() + return imported_stored + class UsesFormDefinitionsMixin: """Mixin for controllers that use Galaxy form objects.""" diff -r 33af32773cba309fde44ced5fba78ce8fc64078b -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 lib/galaxy/webapps/galaxy/api/annotations.py --- a/lib/galaxy/webapps/galaxy/api/annotations.py +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -3,14 +3,13 @@ """ import logging from galaxy import web -from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.sanitize_html import sanitize_html from galaxy.web.base.controller import BaseAPIController, HTTPNotImplemented, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin, UsesStoredWorkflowMixin log = logging.getLogger( __name__ ) -class BaseAnnotationsController( BaseAPIController, UsesAnnotations, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin ): +class BaseAnnotationsController( BaseAPIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin ): @web.expose_api def index( self, trans, **kwd ): diff -r 33af32773cba309fde44ced5fba78ce8fc64078b -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 lib/galaxy/webapps/galaxy/controllers/page.py --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -1,7 +1,7 @@ from sqlalchemy import desc, and_ from galaxy import model, web from galaxy.web import error, url_for -from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings +from galaxy.model.item_attrs import UsesItemRatings from galaxy.web.base.controller import BaseUIController, SharableMixin, UsesHistoryMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin from galaxy.web.framework.helpers import time_ago, grids from galaxy import util @@ -274,7 +274,7 @@ # Default behavior: _BaseHTMLProcessor.unknown_endtag( self, tag ) -class PageController( BaseUIController, SharableMixin, UsesAnnotations, UsesHistoryMixin, +class PageController( BaseUIController, SharableMixin, UsesHistoryMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin, UsesItemRatings ): _page_list = PageListGrid() diff -r 33af32773cba309fde44ced5fba78ce8fc64078b -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 lib/galaxy/webapps/galaxy/controllers/workflow.py --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -19,7 +19,7 @@ from galaxy import web from galaxy.datatypes.data import Data from galaxy.jobs.actions.post import ActionBox -from galaxy.model.item_attrs import UsesAnnotations, UsesItemRatings +from galaxy.model.item_attrs import UsesItemRatings from galaxy.model.mapping import desc from galaxy.tools.parameters import RuntimeValue, visit_input_values from galaxy.tools.parameters.basic import DataToolParameter, DrillDownSelectToolParameter, SelectToolParameter, UnvalidatedValue @@ -132,7 +132,7 @@ self.tag_content += text -class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesAnnotations, UsesItemRatings ): +class WorkflowController( BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesItemRatings ): stored_list_grid = StoredWorkflowListGrid() published_list_grid = StoredWorkflowAllPublishedGrid() @@ -372,34 +372,17 @@ referer_message = "<a href='%s'>go to Galaxy's start page</a>" % url_for( '/' ) # Do import. - session = trans.sa_session stored = self.get_stored_workflow( trans, id, check_ownership=False ) if stored.importable == False: return trans.show_error_message( "The owner of this workflow has disabled imports via this link.<br>You can %s" % referer_message, use_panels=True ) elif stored.deleted: return trans.show_error_message( "You can't import this workflow because it has been deleted.<br>You can %s" % referer_message, use_panels=True ) - else: - # Copy workflow. - imported_stored = model.StoredWorkflow() - imported_stored.name = "imported: " + stored.name - imported_stored.latest_workflow = stored.latest_workflow - imported_stored.user = trans.user - # Save new workflow. - session = trans.sa_session - session.add( imported_stored ) - session.flush() + self._import_shared_workflow( trans, stored ) - # Copy annotations. - self.copy_item_annotation( session, stored.user, stored, imported_stored.user, imported_stored ) - for order_index, step in enumerate( stored.latest_workflow.steps ): - self.copy_item_annotation( session, stored.user, step, \ - imported_stored.user, imported_stored.latest_workflow.steps[order_index] ) - session.flush() - - # Redirect to load galaxy frames. - return trans.show_ok_message( - message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s.""" - % ( stored.name, web.url_for( controller='workflow' ), referer_message ), use_panels=True ) + # Redirect to load galaxy frames. + return trans.show_ok_message( + message="""Workflow "%s" has been imported. <br>You can <a href="%s">start using this workflow</a> or %s.""" + % ( stored.name, web.url_for( controller='workflow' ), referer_message ), use_panels=True ) @web.expose @web.require_login( "use Galaxy workflows" ) https://bitbucket.org/galaxy/galaxy-central/commits/2f7781fc4ce9/ Changeset: 2f7781fc4ce9 User: nsoranzo Date: 2014-01-15 18:28:21 Summary: Add /api/workflows/import method to import a workflow shared by other users. Affected #: 2 files diff -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 -r 2f7781fc4ce9dbb1768fd345621ec2a62000f2ae lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -6,20 +6,21 @@ import logging from sqlalchemy import desc, or_ +from galaxy import exceptions from galaxy import util from galaxy import web from galaxy import model from galaxy.tools.parameters import visit_input_values, DataToolParameter, RuntimeValue -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.web import _future_expose_api as expose_api +from galaxy.web.base.controller import BaseAPIController, url_for, UsesStoredWorkflowMixin from galaxy.workflow.modules import module_factory, ToolModule from galaxy.jobs.actions.post import ActionBox -from galaxy.model.item_attrs import UsesAnnotations from ..controllers.workflow import attach_ordered_steps log = logging.getLogger(__name__) -class WorkflowsAPIController(BaseAPIController, UsesAnnotations): +class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin): @web.expose_api def index(self, trans, **kwd): """ @@ -584,3 +585,31 @@ data['steps'][step.order_index] = step_dict return data + @expose_api + def import_shared_worflow(self, trans, payload, **kwd): + """ + POST /api/workflows/import + Import a workflow shared by other users. + + :param workflow_id: the workflow id (required) + :type workflow_id: str + + :raises: exceptions.MessageException, exceptions.ObjectNotFound + """ + # Pull parameters out of payload. + workflow_id = payload.get('workflow_id', None) + if workflow_id == None: + raise exceptions.ObjectAttributeMissingException( "Missing required parameter 'workflow_id'." ) + try: + stored_workflow = self.get_stored_workflow( trans, workflow_id, check_ownership=False ) + except: + raise exceptions.ObjectNotFound( "Malformed workflow id ( %s ) specified." % workflow_id ) + if stored_workflow.importable == False: + raise exceptions.MessageException( 'The owner of this workflow has disabled imports via this link.' ) + elif stored_workflow.deleted: + raise exceptions.MessageException( "You can't import this workflow because it has been deleted." ) + imported_workflow = self._import_shared_workflow( trans, stored_workflow ) + item = imported_workflow.to_dict(value_mapper={'id':trans.security.encode_id}) + encoded_id = trans.security.encode_id(imported_workflow.id) + item['url'] = url_for('workflow', id=encoded_id) + return item diff -r f4be6a4360b6c8c12f7eeed363c0dfe29dc8db41 -r 2f7781fc4ce9dbb1768fd345621ec2a62000f2ae lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -163,10 +163,11 @@ # "POST /api/workflows/import" => ``workflows.import_workflow()``. # Defines a named route "import_workflow". - webapp.mapper.connect("import_workflow", "/api/workflows/upload", controller="workflows", action="import_new_workflow", conditions=dict(method=["POST"])) - webapp.mapper.connect("workflow_dict", '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + webapp.mapper.connect( 'import_workflow', '/api/workflows/upload', controller='workflows', action='import_new_workflow', conditions=dict( method=['POST'] ) ) + webapp.mapper.connect( 'workflow_dict', '/api/workflows/{workflow_id}/download', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) # Preserve the following download route for now for dependent applications -- deprecate at some point - webapp.mapper.connect("workflow_dict", '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict(method=['GET'])) + webapp.mapper.connect( 'workflow_dict', '/api/workflows/download/{workflow_id}', controller='workflows', action='workflow_dict', conditions=dict( method=['GET'] ) ) + webapp.mapper.connect( 'import_shared_workflow', '/api/workflows/import', controller='workflows', action='import_shared_worflow', conditions=dict( method=['POST'] ) ) # ======================= # ===== LIBRARY API ===== Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: guerler: Charts: Improve button selection
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8deba81aad81/ Changeset: 8deba81aad81 User: guerler Date: 2014-01-16 07:38:06 Summary: Charts: Improve button selection Affected #: 4 files diff -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 -r 8deba81aad81fd565a7e33bad10bb8e741a6172b config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -48,9 +48,6 @@ // set elements this.setElement(this.portlet.$el); - - // reset create view - this.create.reset(); }, // execute command diff -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 -r 8deba81aad81fd565a7e33bad10bb8e741a6172b config/plugins/visualizations/charts/static/create.js --- a/config/plugins/visualizations/charts/static/create.js +++ b/config/plugins/visualizations/charts/static/create.js @@ -97,8 +97,8 @@ } }), 'back' : new Ui.ButtonIcon({ - icon : 'fa-list', - tooltip : 'Show Charts', + icon : 'fa-caret-left', + tooltip : 'Return', onclick : function() { self.$el.hide(); self.app.main.$el.show(); @@ -117,7 +117,10 @@ // elements this.setElement(this.portlet.$el); - // events + // hide back button on startup + this.portlet.hideOperation('back'); + + // model events var self = this; this.chart.on('change:title', function(chart) { self.title.value(chart.get('title')); @@ -125,6 +128,22 @@ this.chart.on('change:type', function(chart) { self.table.value(chart.get('type')); }); + + // collection events + this.app.charts.on('add', function(chart) { + self.portlet.showOperation('back'); + }); + this.app.charts.on('remove', function(chart) { + if (self.app.charts.length == 1) { + self.portlet.hideOperation('back'); + } + }); + this.app.charts.on('reset', function(chart) { + self.portlet.hideOperation('back'); + }); + + // reset + this.reset(); }, // reset diff -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 -r 8deba81aad81fd565a7e33bad10bb8e741a6172b config/plugins/visualizations/charts/static/library/portlet.js --- a/config/plugins/visualizations/charts/static/library/portlet.js +++ b/config/plugins/visualizations/charts/static/library/portlet.js @@ -45,6 +45,7 @@ // link functions var self = this; $.each(this.options.buttons, function(name, item) { + item.$el.prop('id', name); self.$buttons.append(item.$el); }); } else { @@ -57,6 +58,7 @@ // link functions var self = this; $.each(this.options.operations, function(name, item) { + item.$el.prop('id', name); self.$operations.append(item.$el); }); } @@ -96,13 +98,23 @@ }, // enable buttons - enableButton: function(name) { - this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', false); + enableButton: function(id) { + this.$buttons.find('#' + id).prop('disabled', false); }, // disable buttons - disableButton: function(name) { - this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); + disableButton: function(id) { + this.$buttons.find('#' + id).prop('disabled', true); + }, + + // enable operation + hideOperation: function(id) { + this.$operations.find('#' + id).hide(); + }, + + // disable operation + showOperation: function(id) { + this.$operations.find('#' + id).show(); }, // fill regular modal template diff -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 -r 8deba81aad81fd565a7e33bad10bb8e741a6172b config/plugins/visualizations/charts/static/library/ui.js --- a/config/plugins/visualizations/charts/static/library/ui.js +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -34,6 +34,7 @@ { // options optionsDefault: { + id : null, label : '', float : 'right', cls : 'btn-default', @@ -55,7 +56,7 @@ // element template: function(options) { - var str = '<button type="' + options.type + '" style="margin-right: 5px; float: ' + options.float + ';" type="button" class="btn ' + options.cls + '">'; + var str = '<button id="' + options.id + '" type="' + options.type + '" style="margin-right: 5px; float: ' + options.float + ';" type="button" class="btn ' + options.cls + '">'; if (options.icon) { str += '<i class="icon fa ' + options.icon + '"></i> ' ; } @@ -375,6 +376,7 @@ { // options optionsDefault: { + id : null, label : '', float : 'right', cls : 'icon-btn', @@ -403,7 +405,7 @@ // element template: function(options) { - var str = '<a style="margin-right: 5px; float: ' + options.float + ';" class="' + options.cls + '">'; + var str = '<a id="' + options.id + '" style="margin-right: 5px; float: ' + options.float + ';" class="' + options.cls + '">'; if (options.icon) { str += '<i class="icon fa ' + options.icon + '"></i>'; } Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Jan '14

15 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a4108edecdd5/ Changeset: a4108edecdd5 User: guerler Date: 2014-01-16 06:42:41 Summary: Charts: Show chart creation form on startup, add pie chart Affected #: 8 files diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r a4108edecdd5bfc9cc185866429bfa8297cab41e config/plugins/visualizations/charts/config/charts.xml --- a/config/plugins/visualizations/charts/config/charts.xml +++ b/config/plugins/visualizations/charts/config/charts.xml @@ -1,15 +1,21 @@ <?xml version="1.0" encoding="UTF-8"?><!DOCTYPE visualization SYSTEM "../../visualization.dtd"> -<visualization name="charts"> +<visualization name="Charts"><data_sources><data_source><model_class>HistoryDatasetAssociation</model_class><test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test><to_param param_attr="id">dataset_id</to_param></data_source> + <data_source> + <model_class>Visualization</model_class> + <test test_attr="type">charts</test> + <to_param param_attr="id">visualization_id</to_param> + </data_source></data_sources><params><param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + <param type="visualization" var_name_in_template="visualization">visualization_id</param></params><template>charts.mako</template></visualization> diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r a4108edecdd5bfc9cc185866429bfa8297cab41e config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -44,10 +44,13 @@ // create this.config.$el.hide(); - this.create.$el.hide(); + this.main.$el.hide(); // set elements this.setElement(this.portlet.$el); + + // reset create view + this.create.reset(); }, // execute command diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r a4108edecdd5bfc9cc185866429bfa8297cab41e config/plugins/visualizations/charts/static/charts/piechart.js --- a/config/plugins/visualizations/charts/static/charts/piechart.js +++ b/config/plugins/visualizations/charts/static/charts/piechart.js @@ -14,23 +14,37 @@ // render refresh : function(data) { - // add graph to screen - var self = this; - nv.addGraph(function() { - self.chart_3d = nv.models.pieChart() - .x(function(d) { return d.key }) - .y(function(d) { return d.y }) - .showLabels(true); + // loop through data groups + for (var key in data) { + // get group + var group = data[key]; + + // format chart data + var pie_data = []; + for (var key in group.values) { + var value = group.values[key]; + pie_data.push ({ + key : value.x, + y : value.y + }); + } + + // add graph to screen + var self = this; + nv.addGraph(function() { + self.chart_3d = nv.models.pieChart() + .donut(true) + .showLegend(false); - d3.select(self.options.svg_id) - .datum(data) - .transition().duration(1200) - .call(self.chart_3d); + d3.select(self.options.svg_id) + .datum(pie_data) + .call(self.chart_3d); - nv.utils.windowResize(self.chart_3d.update); - - return self.chart_3d; - }); + nv.utils.windowResize(self.chart_3d.update); + + return self.chart_3d; + }); + } } }); diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r a4108edecdd5bfc9cc185866429bfa8297cab41e config/plugins/visualizations/charts/static/create.js --- a/config/plugins/visualizations/charts/static/create.js +++ b/config/plugins/visualizations/charts/static/create.js @@ -29,7 +29,7 @@ // main elements this.message = new Ui.Message(); this.title = new Ui.Input({placeholder: 'Chart title'}); - this.dataset = new Ui.Input({value : app.options.dataset.id, disabled: true}); + this.dataset = new Ui.Input({value : app.options.dataset.id, disabled: true, visible: false}); // configure dataset this.groups = new Groups(this.app); @@ -91,14 +91,14 @@ operations : { 'save' : new Ui.ButtonIcon({ icon : 'fa-save', - tooltip : 'Save', + tooltip : 'Save Chart', onclick : function() { self._saveChart(); } }), 'back' : new Ui.ButtonIcon({ - icon : 'fa-caret-left', - tooltip : 'Return', + icon : 'fa-list', + tooltip : 'Show Charts', onclick : function() { self.$el.hide(); self.app.main.$el.show(); @@ -107,10 +107,9 @@ } }); this.portlet.append(this.message.$el); + this.portlet.append(this.dataset.$el); this.portlet.append((new Ui.Label({ label : 'Provide a chart title:'})).$el); this.portlet.append(this.title.$el); - this.portlet.append((new Ui.Label({ label : 'Select a dataset:'})).$el); - this.portlet.append(this.dataset.$el); this.portlet.append((new Ui.Label({ label : 'Select a chart type:'})).$el); this.portlet.append(this.table.$el); this.portlet.append(this.groups.$el); @@ -132,7 +131,7 @@ reset: function() { this.chart.reset(); this.chart.set('id', Utils.uuid()); - this.chart.set('dataset_id', app.options.dataset.id); + this.chart.set('dataset_id', this.app.options.dataset.id); this.chart.set('type', 'bardiagram'); this.chart.set('title', 'Chart title'); }, diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r a4108edecdd5bfc9cc185866429bfa8297cab41e config/plugins/visualizations/charts/static/groups.js --- a/config/plugins/visualizations/charts/static/groups.js +++ b/config/plugins/visualizations/charts/static/groups.js @@ -14,7 +14,7 @@ // table this.table = new Table({ - content : 'Add data sources to this table.', + content : 'Add data columns to this table.', ondblclick : function(group_id) { // get group var group = self.app.chart.groups.get(group_id); @@ -30,7 +30,7 @@ var self = this; this.portlet = new Portlet({ icon : '', - label : 'Configure data sources:', + label : 'Select data columns:', height : 100, operations : { 'new' : new Ui.ButtonIcon({ diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r a4108edecdd5bfc9cc185866429bfa8297cab41e config/plugins/visualizations/charts/static/library/ui.js --- a/config/plugins/visualizations/charts/static/library/ui.js +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -422,7 +422,8 @@ value : '', type : 'text', placeholder : '', - disabled : false + disabled : false, + visible : true }, // initialize @@ -440,6 +441,11 @@ if (this.options.disabled) { this.$el.prop('disabled', true); } + + // hide input field + if (!this.options.visible) { + this.$el.hide(); + } }, // value diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r a4108edecdd5bfc9cc185866429bfa8297cab41e config/plugins/visualizations/charts/static/models/types.js --- a/config/plugins/visualizations/charts/static/models/types.js +++ b/config/plugins/visualizations/charts/static/models/types.js @@ -39,7 +39,7 @@ } }, 'piechart' : { - title : 'Pie chart (under development)', + title : 'Pie chart', data : { y : { title : 'Values for y-axis' diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r a4108edecdd5bfc9cc185866429bfa8297cab41e config/plugins/visualizations/charts/static/plugins/nv.d3.js --- a/config/plugins/visualizations/charts/static/plugins/nv.d3.js +++ b/config/plugins/visualizations/charts/static/plugins/nv.d3.js @@ -2,5 +2,5 @@ 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t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return 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genome_build = ldda.dbkey, misc_info = ldda.info, diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -14,9 +14,9 @@ import urllib2 import zipfile from paste.httpexceptions import HTTPBadRequest +from galaxy import util, web from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound from galaxy.security import Action -from galaxy import util, web from galaxy.util.streamball import StreamBall from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin @@ -39,14 +39,12 @@ :returns: detailed dataset information from base controller .. seealso:: :attr:`galaxy.web.base.controller.UsesLibraryMixinItems.get_library_dataset` """ - # Get dataset. try: dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True ) except Exception, e: trans.response.status = 500 return str( e ) try: - # Default: return dataset as dict. rval = dataset.to_dict() except Exception, e: rval = "Error in dataset API at listing contents: " + str( e ) diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 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 @@ -971,8 +971,9 @@ @web.require_login( "deprecate repository" ) def deprecate( self, trans, **kwd ): """Mark a repository in the tool shed as deprecated or not deprecated.""" - # Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset revisions that may be associated with the - # repository. Revisions are not marked as not downlaodable because those that have installed the repository must be allowed to get updates. + # Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset + # revisions that may be associated with the repository. Revisions are not marked as not downlaodable + # because those that have installed the repository must be allowed to get updates. message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) @@ -2287,7 +2288,9 @@ status = 'warning' else: # Handle messaging for orphan tool dependency definitions. - orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata ) + orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, + repository, + metadata ) if orphan_message: message += orphan_message status = 'warning' @@ -2302,14 +2305,23 @@ skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) categories = suc.get_categories( trans ) selected_categories = [ rca.category_id for rca in repository.categories ] - containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) + containers_dict = container_util.build_repository_containers_for_tool_shed( trans, + repository, + changeset_revision, + repository_dependencies, + repository_metadata ) heads = suc.get_repository_heads( repo ) + deprecated_repository_dependency_tups = \ + repository_dependency_util.get_repository_dependency_tups_from_repository_metadata( trans.app, + repository_metadata, + deprecated_only=True ) return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, description=description, long_description=long_description, current_allow_push_list=current_allow_push_list, allow_push_select_field=allow_push_select_field, + deprecated_repository_dependency_tups=deprecated_repository_dependency_tups, repo=repo, heads=heads, repository=repository, diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -76,7 +76,7 @@ # Get the list of repository dependencies for this repository. status = self.install_model.ToolShedRepository.installation_status.INSTALLED repository_dependency_tups = \ - repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=status ) + repository_dependency_util.get_repository_dependency_tups_for_installed_repository( self.app, repository, status=status ) # Add an entry to self.installed_repository_dependencies_of_installed_repositories. if repository_tup not in self.installed_repository_dependencies_of_installed_repositories: debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) @@ -132,7 +132,7 @@ debug_msg += "to repository_dependencies_of_installed_repositories." log.debug( debug_msg ) repository_dependency_tups = \ - repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=None ) + repository_dependency_util.get_repository_dependency_tups_for_installed_repository( self.app, repository, status=None ) self.repository_dependencies_of_installed_repositories[ repository_tup ] = repository_dependency_tups def add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -303,10 +303,13 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ): """ - Return a dictionary of all repositories upon which the contents of the received repository_metadata record depend. The dictionary keys - are name-spaced values consisting of toolshed_base_url/repository_name/repository_owner/changeset_revision and the values are lists of - repository_dependency tuples consisting of ( toolshed_base_url, repository_name, repository_owner, changeset_revision ). This method - ensures that all required repositories to the nth degree are returned. + Return a dictionary of all repositories upon which the contents of the received + repository_metadata record depend. The dictionary keys are name-spaced values + consisting of: + toolshed_base_url/repository_name/repository_owner/changeset_revision + and the values are lists of repository_dependency tuples consisting of: + ( toolshed_base_url, repository_name, repository_owner, changeset_revision ). + This method ensures that all required repositories to the nth degree are returned. """ if handled_key_rd_dicts is None: handled_key_rd_dicts = [] @@ -331,8 +334,8 @@ all_repository_dependencies = initialize_all_repository_dependencies( current_repository_key, repository_dependencies_dict, all_repository_dependencies ) - # Handle the repository dependencies defined in the current repository, if any, and populate the various repository dependency objects for - # this round of processing. + # Handle the repository dependencies defined in the current repository, if any, and populate + # the various repository dependency objects for this round of processing. current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies = \ populate_repository_dependency_objects_for_processing( trans, current_repository_key, @@ -375,10 +378,41 @@ all_repository_dependencies = prune_invalid_repository_dependencies( all_repository_dependencies ) return all_repository_dependencies -def get_repository_dependency_tups_for_repository( app, repository, dependency_tups=None, status=None ): +def get_repository_dependency_tups_from_repository_metadata( app, repository_metadata, deprecated_only=False ): + """ + Return a list of of tuples defining repository objects required by the received repository. The returned + list defines the entire repository dependency tree. This method is called only from the Tool Shed. + """ + dependency_tups = [] + if repository_metadata is not None: + metadata = repository_metadata.metadata + if metadata: + repository_dependencies_dict = metadata.get( 'repository_dependencies', None ) + if repository_dependencies_dict is not None: + repository_dependency_tups = repository_dependencies_dict.get( 'repository_dependencies', None ) + if repository_dependency_tups is not None: + # The value of repository_dependency_tups is a list of repository dependency tuples like this: + # ['http://localhost:9009', 'package_samtools_0_1_18', 'devteam', 'ef37fc635cb9', 'False', 'False'] + for repository_dependency_tup in repository_dependency_tups: + toolshed, name, owner, changeset_revision, pir, oicct = \ + common_util.parse_repository_dependency_tuple( repository_dependency_tup ) + repository = suc.get_repository_by_name_and_owner( app, name, owner ) + if repository: + if deprecated_only: + if repository.deprecated: + dependency_tups.append( repository_dependency_tup ) + else: + dependency_tups.append( repository_dependency_tup ) + else: + log.debug( "Cannot locate repository %s owned by %s for inclusion in repository dependency tups." % \ + ( name, owner ) ) + return dependency_tups + +def get_repository_dependency_tups_for_installed_repository( app, repository, dependency_tups=None, status=None ): """ Return a list of of tuples defining tool_shed_repository objects (whose status can be anything) required by the - received repository. The returned list defines the entire repository dependency tree. + received repository. The returned list defines the entire repository dependency tree. This method is called + only from Galaxy. """ if dependency_tups is None: dependency_tups = [] @@ -393,7 +427,9 @@ continue if required_repository_tup not in dependency_tups: dependency_tups.append( required_repository_tup ) - return get_repository_dependency_tups_for_repository( app, required_repository, dependency_tups=dependency_tups ) + return get_repository_dependency_tups_for_installed_repository( app, + required_repository, + dependency_tups=dependency_tups ) return dependency_tups def get_repository_tuple_for_installed_repository_manager( repository ): @@ -657,12 +693,16 @@ containers_dict[ 'missing_repository_dependencies' ] = None return containers_dict -def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, key_rd_dicts_to_be_processed, - handled_key_rd_dicts, circular_repository_dependencies, all_repository_dependencies ): +def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, + key_rd_dicts_to_be_processed, handled_key_rd_dicts, + circular_repository_dependencies, all_repository_dependencies ): """ - The process that discovers all repository dependencies for a specified repository's changeset revision uses this method to populate the following items - for the current processing loop: filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies. - Each processing loop may discover more repository dependencies, so this method is repeatedly called until all repository dependencies have been discovered. + The process that discovers all repository dependencies for a specified repository's + changeset revision uses this method to populate the following items for the current + processing loop: filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, + handled_key_rd_dicts, all_repository_dependencies. Each processing loop may discover + more repository dependencies, so this method is repeatedly called until all repository + dependencies have been discovered. """ current_repository_key_rd_dicts = [] filtered_current_repository_key_rd_dicts = [] @@ -673,13 +713,15 @@ if current_repository_key_rd_dicts and current_repository_key: # Remove all repository dependencies that point to a revision within its own repository. current_repository_key_rd_dicts = remove_ropository_dependency_reference_to_self( current_repository_key_rd_dicts ) - current_repository_key_rd_dicts = get_updated_changeset_revisions_for_repository_dependencies( trans, current_repository_key_rd_dicts ) + current_repository_key_rd_dicts = get_updated_changeset_revisions_for_repository_dependencies( trans, + current_repository_key_rd_dicts ) for key_rd_dict in current_repository_key_rd_dicts: # Filter out repository dependencies that are required only if compiling the dependent repository's tool dependency. key_rd_dict = filter_only_if_compiling_contained_td( key_rd_dict ) if key_rd_dict: is_circular = False - if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ) and not in_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ) and not in_key_rd_dicts( key_rd_dict, + key_rd_dicts_to_be_processed ): filtered_current_repository_key_rd_dicts.append( key_rd_dict ) repository_dependency = key_rd_dict[ current_repository_key ] if current_repository_key in all_repository_dependencies: @@ -708,8 +750,10 @@ def prune_invalid_repository_dependencies( repository_dependencies ): """ - Eliminate all invalid entries in the received repository_dependencies dictionary. An entry is invalid if the value_list of the key/value pair is - empty. This occurs when an invalid combination of tool shed, name , owner, changeset_revision is used and a repository_metadata record is not found. + Eliminate all invalid entries in the received repository_dependencies dictionary. An entry + is invalid if the value_list of the key/value pair is empty. This occurs when an invalid + combination of tool shed, name , owner, changeset_revision is used and a repository_metadata + record is not found. """ valid_repository_dependencies = {} description = repository_dependencies.get( 'description', None ) @@ -752,7 +796,9 @@ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ common_util.parse_repository_dependency_tuple( repository_dependency ) if rd_toolshed == toolshed and rd_name == name and rd_owner == owner: - log.debug( "Removing repository dependency for repository %s owned by %s since it refers to a revision within itself." % ( name, owner ) ) + debug_msg = "Removing repository dependency for repository %s owned by %s " % ( name, owner ) + debug_msg += 'since it refers to a revision within itself.' + log.debug( debug_msg ) else: new_key_rd_dict = {} new_key_rd_dict[ key ] = repository_dependency diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -122,7 +122,7 @@ // CONTAINER tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); - tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar" >'); @@ -457,6 +457,7 @@ var self = this; this.modal = new mod_modal.GalaxyModal({ destructible : true, + bindClosingEvents: true, title : 'Dataset Details', body : template, buttons : { @@ -477,7 +478,6 @@ $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); } } - this.modal.bindEvents(); this.modal.show(); }, @@ -614,6 +614,7 @@ var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); self.modal = new mod_modal.GalaxyModal({ destructible : true, + bindClosingEvents: true, title : 'Import into History', body : history_modal_tmpl, buttons : { @@ -621,7 +622,6 @@ 'Close' : function() {self.modal.hideOrDestroy();} } }); - self.modal.bindEvents(); self.modal.show(); }, error: function(){ @@ -724,6 +724,7 @@ //send request $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') .appendTo('body').submit().remove(); + mod_toastr.info('Your download will begin soon'); }; }, @@ -737,6 +738,7 @@ var self = this; this.modal = new mod_modal.GalaxyModal({ destructible : true, + bindClosingEvents: true, title : 'Create New Folder', body : this.templateNewFolderInModal(), buttons : { @@ -744,7 +746,6 @@ 'Close' : function() {self.modal.hideOrDestroy(); self.modal = null;} } }); - this.modal.bindEvents(); this.modal.show(); }, @@ -810,7 +811,7 @@ tmpl_array = []; tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); tmpl_array.push(''); - tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); tmpl_array.push('<table class="table table-condensed">'); tmpl_array.push(' <thead>'); @@ -866,7 +867,7 @@ }, error: function(model, response){ if (response.statusCode().status === 403){ - mod_toastr.error('Please log in first. Redirecting to login page in 3s.'); + mod_toastr.info('Please log in first. Redirecting to login page in 3s.'); setTimeout(that.redirectToLogin, 3000); } else { mod_toastr.error('An error occured. Please try again.'); @@ -894,6 +895,7 @@ var self = this; this.modal = new mod_modal.GalaxyModal({ destructible : true, + bindClosingEvents: true, title : 'Create New Library', body : this.templateNewLibraryInModal(), buttons : { @@ -901,7 +903,6 @@ 'Close' : function() {self.modal.hideOrDestroy();} } }); - this.modal.bindEvents(); this.modal.show(); }, diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -16,50 +16,72 @@ height : null, width : null }, + + // flag whether the closing events are bound + eventsBound: false, // options options : { // by default the modal cannot be removed by the self.destroy() method // but only hidden through self.hide() - destructible: false + destructible: false, + // by default don't bind the events + bindClosingEvents: false }, // initialize initialize : function(options) { self = this; - if (options) + if (options){ this.create(options); + } }, hideOrDestroy: function(){ - if (this.options.destructible){ - self.destroy(); + self.visible = false; + + //unbinds event for ALL modals? + self.unbindEvents(); + + if (self.options.destructible){ + self.$el.remove(); // destroy } else { self.hide(); } }, + // hide modal, shouldn't be called directly but through hideOrDestroy() + // however hide() remains for backwards compatibility + hide: function(){ + this.visible = false; + this.$el.fadeOut('fast'); + }, + // bind the click-to-hide function bindEvents: function() { // bind the ESC key to hideOrDestroy() function $(document).on('keyup', function(event){ - if (event.keyCode == 27) { self.hideOrDestroy() } + if (event.keyCode == 27) { + self.hideOrDestroy() + } }) // bind the 'click anywhere' to hideOrDestroy() function... - $('html').on('click', function(event){ - self.hideOrDestroy() - }) + $('html').on('click', self.hideOrDestroy) // ...but don't hide if the click is on modal content $('.modal-content').on('click', function(event){ event.stopPropagation(); }) + + self.eventsBound = true; }, // unbind the click-to-hide function unbindEvents: function(){ // unbind the ESC key to hideOrDestroy() function $(document).off('keyup', function(event){ - if (event.keyCode == 27) { self.hideOrDestroy() } + if (event.keyCode == 27) { + self.hideOrDestroy() + } }) // unbind the 'click anywhere' to hideOrDestroy() function... $('html').off('click', function(event){ @@ -68,6 +90,8 @@ $('.modal-content').off('click', function(event){ event.stopPropagation(); }) + + self.eventsBound = false; }, // adds and displays a new frame/window @@ -76,59 +100,43 @@ this.initialize(options); // fix height - if (this.options.height) - { + if (this.options.height){ this.$body.css('height', this.options.height); this.$body.css('overflow', 'hidden'); - } else + } else{ this.$body.css('max-height', $(window).height() / 2); + } // fix width - if (this.options.width) + if (this.options.width){ this.$dialog.css('width', this.options.width); + } // show - if (this.visible) + if (this.visible){ this.$el.show(); - else + } else { this.$el.fadeIn('fast'); + } // set flag this.visible = true; }, - // hide modal, shouldn't be called directly but through hideOrDestroy() - hide: function(){ - // fade out - this.$el.fadeOut('fast'); - // set flag - this.visible = false; - // unbind events - this.unbindEvents(); - }, - - // destroy modal, shouldn't be called directly but through hideOrDestroy() - destroy: function(){ - // set flag - this.visible = false; - // unbind events - this.unbindEvents(); - // remove - this.$el.remove(); - }, - // create create: function(options) { // configure options this.options = _.defaults(options, this.optionsDefault); // check for progress bar request - if (this.options.body == 'progress') + if (this.options.body == 'progress'){ this.options.body = $('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'); + } // remove former element - if (this.$el) + if (this.$el){ this.$el.remove(); + } // create new element this.setElement(this.template(this.options.title)); @@ -144,8 +152,9 @@ this.$body.html(this.options.body); // configure background - if (!this.options.backdrop) + if (!this.options.backdrop){ this.$backdrop.removeClass('in'); + } // append buttons if (this.options.buttons) { @@ -160,6 +169,10 @@ // append to main element $(this.elMain).append($(this.el)); + + if (this.options.bindClosingEvents && !this.eventsBound){ + this.bindEvents(); + } }, // enable buttons diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(' <th class="button_heading">view</th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(" <td></td>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td></td>");r.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-folder-open"></span> browse</td>');r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(" <td>");r.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');r.push(' <span class="fa fa-eye"></span> details');r.push(" </button>");r.push(" </td>");r.push(' <td><%- content_item.get("name") %></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+r,{trigger:true,replace:true})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}this.modal.bindEvents();this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.bindEvents();s.modal.show()},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hideOrDestroy();r.modal=null}}});this.modal.bindEvents();this.modal.show()},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hideOrDestroy();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.error("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.bindEvents();this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(' <th class="button_heading">view</th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(" <td></td>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td></td>");r.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-folder-open"></span> browse</td>');r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(" <td>");r.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');r.push(' <span class="fa fa-eye"></span> details');r.push(" </button>");r.push(" </td>");r.push(' <td><%- content_item.get("name") %></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+r,{trigger:true,replace:true})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.show()},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hideOrDestroy();r.modal=null}}});this.modal.show()},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hideOrDestroy();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:g}}); \ No newline at end of file diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{destructible:false},initialize:function(b){self=this;if(b){this.create(b)}},hideOrDestroy:function(){if(this.options.destructible){self.destroy()}else{self.hide()}},bindEvents:function(){$(document).on("keyup",function(b){if(b.keyCode==27){self.hideOrDestroy()}});$("html").on("click",function(b){self.hideOrDestroy()});$(".modal-content").on("click",function(b){b.stopPropagation()})},unbindEvents:function(){$(document).off("keyup",function(b){if(b.keyCode==27){self.hideOrDestroy()}});$("html").off("click",function(b){self.hideOrDestroy()});$(".modal-content").off("click",function(b){b.stopPropagation()})},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false;this.unbindEvents()},destroy:function(){this.visible=false;this.unbindEvents();this.$el.remove()},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},eventsBound:false,options:{destructible:false,bindClosingEvents:false},initialize:function(b){self=this;if(b){this.create(b)}},hideOrDestroy:function(){self.visible=false;self.unbindEvents();if(self.options.destructible){self.$el.remove()}else{self.hide()}},hide:function(){this.visible=false;this.$el.fadeOut("fast")},bindEvents:function(){$(document).on("keyup",function(b){if(b.keyCode==27){self.hideOrDestroy()}});$("html").on("click",self.hideOrDestroy);$(".modal-content").on("click",function(b){b.stopPropagation()});self.eventsBound=true},unbindEvents:function(){$(document).off("keyup",function(b){if(b.keyCode==27){self.hideOrDestroy()}});$("html").off("click",function(b){self.hideOrDestroy()});$(".modal-content").off("click",function(b){b.stopPropagation()});self.eventsBound=false},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el));if(this.options.bindClosingEvents&&!this.eventsBound){this.bindEvents()}},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 templates/webapps/tool_shed/common/common.mako --- a/templates/webapps/tool_shed/common/common.mako +++ b/templates/webapps/tool_shed/common/common.mako @@ -51,6 +51,23 @@ </script></%def> +<%def name="render_deprecated_repository_dependencies_message( deprecated_repository_dependency_tups )"> + <div class="warningmessage"> + <% + from tool_shed.util.common_util import parse_repository_dependency_tuple + msg = '<ul>' + for deprecated_repository_dependency_tup in deprecated_repository_dependency_tups: + toolshed, name, owner, changeset_revision, pir, oicct = \ + parse_repository_dependency_tuple( deprecated_repository_dependency_tup ) + msg += '<li>Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b></li>' % \ + ( changeset_revision, name, owner ) + msg += '</ul>' + %> + This repository depends upon the following deprecated repositories<br/> + ${msg} + </div> +</%def> + <%def name="render_star_rating( name, rating, disabled=False )"><% if disabled: @@ -87,6 +104,20 @@ </div></%def> +<%def name="render_multiple_heads_message( heads )"> + <div class="warningmessage"> + <% + from tool_shed.util.shed_util_common import get_revision_label_from_ctx + heads_str = '' + for ctx in heads: + heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx, include_date=True ) + %> + Contact the administrator of this Tool Shed as soon as possible and let them know that + this repository has the following multiple heads which must be merged.<br/> + ${heads_str} + </div> +</%def> + <%def name="render_review_comment( comment_text )"><style type="text/css"> #reviews_table{ table-layout:fixed; diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -87,6 +87,14 @@ multiple_heads = len( heads ) > 1 else: multiple_heads = False + + if repository_metadata is None: + revision_installable = False + else: + if repository_metadata.downloadable is None: + revision_installable = 'unknown' + else: + revision_installable = repository_metadata.downloadable %><%! @@ -119,18 +127,12 @@ <div class="warningmessage"> This repository has been marked as deprecated, so some tool shed features may be restricted. </div> -%elif multiple_heads: - <div class="warningmessage"> - <% - from tool_shed.util.shed_util_common import get_revision_label_from_ctx - heads_str = '' - for ctx in heads: - heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx, include_date=True ) - %> - Contact the administrator of this Tool Shed as soon as possible and let them know that - this repository has the following multiple heads which must be merged.<br/> - ${heads_str} - </div> +%endif: +%if multiple_heads: + ${render_multiple_heads_message( heads )} +%endif +%if deprecated_repository_dependency_tups: + ${render_deprecated_repository_dependencies_message( deprecated_repository_dependency_tups )} %endif %if len( changeset_revision_select_field.options ) > 1: @@ -207,7 +209,11 @@ ${repository.user.username | h} </div><div class="form-row"> - <label>Times downloaded:</label> + <label>This revision can be installed:</label> + ${revision_installable} + </div> + <div class="form-row"> + <label>Times cloned / installed:</label> ${repository.times_downloaded | h} </div> %if is_admin: diff -r a4108edecdd5bfc9cc185866429bfa8297cab41e -r ed3e84645aa2488b5fc046ed50e3fdfd9fd52588 templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -30,6 +30,14 @@ multiple_heads = len( heads ) > 1 else: multiple_heads = False + + if repository_metadata is None: + revision_installable = False + else: + if repository_metadata.downloadable is None: + revision_installable = 'unknown' + else: + revision_installable = repository_metadata.downloadable %><%! @@ -66,18 +74,12 @@ <div class="warningmessage"> This repository has been marked as deprecated, so some tool shed features may be restricted. </div> -%elif multiple_heads: - <div class="warningmessage"> - <% - from tool_shed.util.shed_util_common import get_revision_label_from_ctx - heads_str = '' - for ctx in heads: - heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx, include_date=True ) - %> - Contact the administrator of this Tool Shed as soon as possible and let them know that - this repository has the following multiple heads which must be merged.<br/> - ${heads_str} - </div> +%endif: +%if multiple_heads: + ${render_multiple_heads_message( heads )} +%endif +%if deprecated_repository_dependency_tups: + ${render_deprecated_repository_dependencies_message( deprecated_repository_dependency_tups )} %endif %if len( changeset_revision_select_field.options ) > 1: @@ -142,7 +144,11 @@ ${repository.user.username | h} </div><div class="form-row"> - <label>Times downloaded:</label> + <label>This revision can be installed:</label> + ${revision_installable} + </div> + <div class="form-row"> + <label>Times cloned / installed:</label> ${repository.times_downloaded} </div> %if trans.user_is_admin(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 15 Jan '14

15 Jan '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4e2f60de42fa/ Changeset: 4e2f60de42fa Branch: search User: kellrott Date: 2014-01-14 17:14:42 Summary: Default merge Affected #: 376 files diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/config/charts.xml --- /dev/null +++ b/config/plugins/visualizations/charts/config/charts.xml @@ -0,0 +1,15 @@ +<?xml version="1.0" encoding="UTF-8"?> +<!DOCTYPE visualization SYSTEM "../../visualization.dtd"> +<visualization name="charts"> + <data_sources> + <data_source> + <model_class>HistoryDatasetAssociation</model_class> + <test type="isinstance" test_attr="datatype" result_type="datatype">tabular.Tabular</test> + <to_param param_attr="id">dataset_id</to_param> + </data_source> + </data_sources> + <params> + <param type="dataset" var_name_in_template="hda" required="true">dataset_id</param> + </params> + <template>charts.mako</template> +</visualization> diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/sample.txt --- /dev/null +++ b/config/plugins/visualizations/charts/sample.txt @@ -0,0 +1,9 @@ +43 55 63 99 28 85 20 31 47 14 +1 63 94 83 94 74 7 73 51 7 +8 34 2 94 87 21 72 51 3 84 +5 50 40 30 59 43 19 77 30 80 +22 55 69 43 77 72 12 54 53 56 +36 34 81 28 59 64 54 29 57 69 +57 90 93 32 45 98 40 16 52 83 +6 17 39 86 10 11 38 69 19 50 +67 51 47 22 58 27 65 49 92 96 \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/app.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/app.js @@ -0,0 +1,67 @@ +// dependencies +define(['library/portlet', 'library/ui', 'library/utils', + 'main', 'viewport', 'create', 'config', + 'models/datasets', 'models/chart', 'models/charts', 'models/types'], + function( Portlet, Ui, Utils, + Main, Viewport, Create, Config, + Datasets, Chart, Charts, Types + ) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(options) + { + // link options + this.options = options; + + // link galaxy + this.modal = parent.Galaxy.modal; + + // create chart objects + this.types = new Types(); + this.chart = new Chart(); + this.charts = new Charts(this); + + // create dataset handler + this.datasets = new Datasets(this); + + // create views + this.main = new Main(this); + this.viewport = new Viewport(this); + this.config = new Config(this); + this.create = new Create(this); + + // portlet + this.portlet = new Portlet({icon : 'fa-bar-chart-o', label : 'Charts'}); + this.portlet.append(this.main.$el); + this.portlet.append(this.config.$el); + this.portlet.append(this.create.$el); + + // append main + this.main.append(this.viewport.$el); + + // create + this.config.$el.hide(); + this.create.$el.hide(); + + // set elements + this.setElement(this.portlet.$el); + }, + + // execute command + execute: function(options) { + }, + + // unload + onunload: function() { + }, + + // log + log: function(location, message) { + console.log(location + ' ' + message); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/charts/bardiagram.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/bardiagram.js @@ -0,0 +1,34 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.d3_chart = nv.models.multiBarChart(); + + self.d3_chart.xAxis.tickFormat(d3.format('.2f')) + self.d3_chart.yAxis.tickFormat(d3.format('.1f')) + + d3.select(self.options.svg_id) + .datum(data) + .call(self.d3_chart); + + nv.utils.windowResize(self.d3_chart.update); + }); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/charts/horizontal.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/horizontal.js @@ -0,0 +1,33 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.d3_chart = nv.models.multiBarHorizontalChart(); + + self.d3_chart.xAxis.tickFormat(function() { return ''; }); + + d3.select(self.options.svg_id) + .datum(data) + .call(self.d3_chart); + + nv.utils.windowResize(self.d3_chart.update); + }); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/charts/line.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/line.js @@ -0,0 +1,39 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.chart_3d = nv.models.lineChart(); + + self.chart_3d.xAxis + .tickFormat(d3.format(',f')); + + self.chart_3d.yAxis + .tickFormat(d3.format(',.2f')); + + d3.select(self.options.svg_id) + .datum(data) + .call(self.chart_3d); + + nv.utils.windowResize(self.chart_3d.update); + + return self.chart_3d; + }); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/charts/linewithfocus.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/linewithfocus.js @@ -0,0 +1,37 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.chart_3d = nv.models.lineWithFocusChart(); + + self.chart_3d.xAxis + .tickFormat(d3.format(',f')); + + self.chart_3d.yAxis + .tickFormat(d3.format(',.2f')); + + d3.select(self.options.svg_id) + .datum(data) + .call(self.chart_3d); + + nv.utils.windowResize(self.chart_3d.update); + }); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/charts/piechart.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/piechart.js @@ -0,0 +1,37 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.chart_3d = nv.models.pieChart() + .x(function(d) { return d.key }) + .y(function(d) { return d.y }) + .showLabels(true); + + d3.select(self.options.svg_id) + .datum(data) + .transition().duration(1200) + .call(self.chart_3d); + + nv.utils.windowResize(self.chart_3d.update); + + return self.chart_3d; + }); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/charts/scatterplot.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/scatterplot.js @@ -0,0 +1,37 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + self.d3_chart = nv.models.scatterChart() + .showDistX(true) + .showDistY(true) + .color(d3.scale.category10().range()); + + self.d3_chart.xAxis.tickFormat(d3.format('.02f')) + self.d3_chart.yAxis.tickFormat(d3.format('.02f')) + + d3.select(self.options.svg_id) + .datum(data) + .call(self.d3_chart); + + nv.utils.windowResize(self.d3_chart.update); + }); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/charts/stackedarea.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/charts/stackedarea.js @@ -0,0 +1,59 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + this.app = app; + this.options = options; + this.chart = options.chart; + }, + + // render + refresh : function(data) + { + // add graph to screen + var self = this; + nv.addGraph(function() { + // check data + var valid = true; + var length = 0; + for (var key in data) { + // evalute length + if (length == 0) { + length = data[key].values.length; + } else { + if (length != data[key].values.length) { + valid = false; + break; + } + } + } + if (!valid) { + return; + } + + // make plot + self.d3_chart = nv.models.stackedAreaChart() + .x(function(d) { + return d.x + }) + .y(function(d) { + return d.y + }) + .clipEdge(true); + + self.d3_chart.xAxis.tickFormat(function() { return ''; }); + + d3.select(self.options.svg_id) + .datum(data) + .call(self.d3_chart); + + nv.utils.windowResize(self.d3_chart.update); + }); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/config.js @@ -0,0 +1,219 @@ +// dependencies +define(['library/portlet', 'library/table', 'library/ui', 'library/utils', 'models/group'], + function(Portlet, Table, Ui, Utils, Group) { + +// chart config +return Backbone.View.extend( +{ + // model + group: new Group(), + + // columns + columns: [], + + // initialize + initialize: function(app, options) { + // link app + this.app = app; + + // get current chart object + this.chart = this.app.chart; + + // ui elements + this.message = new Ui.Message(); + this.label = new Ui.Input({placeholder: 'Group label'}); + this.table = new Table({content: 'No data column.'}); + + // add table to portlet + var self = this; + this.portlet = new Portlet({ + icon : 'fa-edit', + label : 'Define group properties:', + operations : { + 'save' : new Ui.ButtonIcon({ + icon : 'fa-save', + tooltip : 'Save', + onclick : function() { + // save/add group + self._saveGroup(); + } + }), + 'back' : new Ui.ButtonIcon({ + icon : 'fa-caret-left', + tooltip : 'Return', + onclick : function() { + self.$el.hide(); + self.app.create.$el.show(); + } + }) + } + }); + this.portlet.append(this.message.$el); + this.portlet.append(this.label.$el); + this.portlet.append(this.table.$el); + + // add element + this.setElement(this.portlet.$el); + + // change + var self = this; + this.chart.on('change:dataset_id', function() { + self._refreshDataset(); + }); + this.chart.on('change:type', function() { + self._refreshType(); + }); + this.group.on('change:label', function() { + self._refreshLabel(); + }); + this.group.on('change', function() { + self._refreshGroup(); + }); + }, + + // show + show: function() { + this.$el.show(); + }, + + // reset + reset: function() { + this.group.reset(); + this.group.set('id', Utils.uuid()); + this.group.set('label', 'Group label'); + }, + + // update dataset + _refreshDataset: function() { + // identify datasets + var dataset_id = this.chart.get('dataset_id'); + + // check if dataset is available + if (!dataset_id) { + return; + } + + // get dataset + var dataset = this.app.datasets.get({id : dataset_id}); + + // check + if (!dataset) { + this.app.log('Config::render()', 'Failed to retrieve dataset.'); + return; + } + + // configure columns + this.columns = []; + var meta = dataset.metadata_column_types; + for (var key in meta){ + this.columns.push({ + 'label' : key + ' [' + meta[key] + ']', + 'value' : key + }); + } + + // update select fields + for (var key in this.list) { + this.list[key].update(this.columns); + } + }, + + // update + _refreshType: function() { + // configure chart type + var self = this; + var chart_type = this.chart.get('type'); + if (chart_type) { + var chart_settings = this.app.types.get(chart_type); + + // table + this.table.removeAll(); + this.list = {}; + for (var id in chart_settings.data) { + // create select field + var data_def = chart_settings.data[id]; + var select = new Ui.Select({ + id : 'select_' + id, + gid : id, + data : this.columns, + onchange : function(value) { + self.group.set(this.gid, value); + } + }); + + // add row to table + this.table.add(data_def.title); + this.table.add(select.$el); + this.table.append(id); + + // add select field to list + this.list[id] = select; + } + } + }, + + // update + _refreshGroup: function() { + // update select fields + for (var id in this.list) { + var col = this.group.get(id); + if (col === undefined) { + col = 0; + } + this.list[id].value(col); + } + }, + + // update label + _refreshLabel: function() { + var label_text = this.group.get('label'); + if (label_text === undefined) { + label_text = ''; + } + this.label.value(label_text); + }, + + // create group + _saveGroup: function() { + // get current chart + var chart = this.chart; + + // update group object + var group = this.group; + for (var key in this.list) { + group.set(key, this.list[key].value()); + } + + // add label + group.set({ + dataset_id : this.chart.get('dataset_id'), + label : this.label.value(), + date : Utils.time() + }); + + // validate + if (!group.get('label')) { + this.message.update({message : 'Please enter a label for your group.'}); + return; + } + + // get groups of current chart + var groups = this.chart.groups; + + // create/update group + var group_update = groups.get(group.id); + if (group_update) { + group_update.set(group.attributes); + } else { + groups.add(group.clone()); + } + + // hide + this.$el.hide(); + + // update main + this.app.create.$el.show(); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/create.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/create.js @@ -0,0 +1,189 @@ +// dependencies +define(['library/portlet', 'library/table', 'library/ui', 'library/utils', 'models/chart', 'groups'], + function(Portlet, Table, Ui, Utils, Chart, Groups) { + +// widget +return Backbone.View.extend( +{ + // defaults options + optionsDefault: { + header : true, + content : 'No content available.' + }, + + // current chart + chart : null, + + // initialize + initialize: function(app, options) + { + // link application + this.app = app; + + // get current chart object + this.chart = this.app.chart; + + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // main elements + this.message = new Ui.Message(); + this.title = new Ui.Input({placeholder: 'Chart title'}); + this.dataset = new Ui.Input({value : app.options.dataset.id, disabled: true}); + + // configure dataset + this.groups = new Groups(this.app); + + // table + var self = this; + this.table = new Table({ + header : false, + onconfirm : function(type) { + if (self.chart.groups.length > 0) { + // show modal + self.app.modal.show({ + title : 'Switching the chart type?', + body : 'You configured data sources. If you switch chart types your configurations will be removed.', + buttons : { + 'Cancel' : function() { + // hide modal + self.app.modal.hide(); + }, + 'Continue' : function() { + // hide modal + self.app.modal.hide(); + + // confirm + self.table.confirm(type); + } + } + }); + } else { + // confirm + self.table.confirm(type); + } + }, + onchange : function(type) { + // update chart type + self.chart.set({type: type}); + + // reset groups + self.chart.groups.reset(); + }, + content: 'No chart types available' + }); + + // add types + var types_n = 0; + var types = app.types.attributes; + for (var id in types){ + var chart_type = types[id]; + this.table.add (++types_n + '.'); + this.table.add (chart_type.title); + this.table.append(id); + } + + // add table to portlet + var self = this; + this.portlet = new Portlet({ + icon : 'fa-edit', + label : 'Create a new chart:', + operations : { + 'save' : new Ui.ButtonIcon({ + icon : 'fa-save', + tooltip : 'Save', + onclick : function() { + self._saveChart(); + } + }), + 'back' : new Ui.ButtonIcon({ + icon : 'fa-caret-left', + tooltip : 'Return', + onclick : function() { + self.$el.hide(); + self.app.main.$el.show(); + } + }) + } + }); + this.portlet.append(this.message.$el); + this.portlet.append((new Ui.Label({ label : 'Provide a chart title:'})).$el); + this.portlet.append(this.title.$el); + this.portlet.append((new Ui.Label({ label : 'Select a dataset:'})).$el); + this.portlet.append(this.dataset.$el); + this.portlet.append((new Ui.Label({ label : 'Select a chart type:'})).$el); + this.portlet.append(this.table.$el); + this.portlet.append(this.groups.$el); + + // elements + this.setElement(this.portlet.$el); + + // events + var self = this; + this.chart.on('change:title', function(chart) { + self.title.value(chart.get('title')); + }); + this.chart.on('change:type', function(chart) { + self.table.value(chart.get('type')); + }); + }, + + // reset + reset: function() { + this.chart.reset(); + this.chart.set('id', Utils.uuid()); + this.chart.set('dataset_id', app.options.dataset.id); + this.chart.set('type', 'bardiagram'); + this.chart.set('title', 'Chart title'); + }, + + // set chart + setChart: function(new_chart) { + this.chart.copy(new_chart); + }, + + // create chart + _saveChart: function() { + // update chart data + this.chart.set({ + type : this.table.value(), + title : this.title.value(), + dataset_id : this.dataset.value(), + date : Utils.time() + }); + + // validate + if (!this.chart.get('title')) { + this.message.update({message : 'Please enter a title for your chart.'}); + return; + } + + if (!this.chart.get('type')) { + this.message.update({message : 'Please select a chart type.'}); + return; + } + + if (this.chart.groups.length == 0) { + this.message.update({message : 'Please configure at least one data source.'}); + return; + } + + // create/get chart + var current = this.app.charts.get(this.chart.id); + if (!current) { + current = this.chart.clone(); + this.app.charts.add(current); + } + + // update chart model + current.copy(this.chart); + + // hide + this.$el.hide(); + + // update main + this.app.main.$el.show(); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/groups.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/groups.js @@ -0,0 +1,154 @@ +// dependencies +define(['library/portlet', 'library/table', 'library/ui', 'library/utils'], function(Portlet, Table, Ui, Utils) { + +// chart config +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) { + // link app + this.app = app; + + // get current chart object + this.chart = this.app.chart; + + // table + this.table = new Table({ + content : 'Add data sources to this table.', + ondblclick : function(group_id) { + // get group + var group = self.app.chart.groups.get(group_id); + + // show edit + self.app.create.$el.hide(); + self.app.config.show(); + self.app.config.group.set(group.attributes); + } + }); + + // add table to portlet + var self = this; + this.portlet = new Portlet({ + icon : '', + label : 'Configure data sources:', + height : 100, + operations : { + 'new' : new Ui.ButtonIcon({ + icon : 'fa-plus', + tooltip: 'Create', + onclick: function() { + self.app.create.$el.hide(); + self.app.config.show(); + self.app.config.reset(); + } + }), + 'edit' : new Ui.ButtonIcon({ + icon : 'fa-pencil', + tooltip: 'Edit', + onclick: function() { + // check if element has been selected + var group_id = self.table.value(); + if (!group_id) { + return; + } + + // get group + var group = self.app.chart.groups.get(group_id); + + // show edit + self.app.create.$el.hide(); + self.app.config.show(); + self.app.config.group.set(group.attributes); + } + }), + 'delete' : new Ui.ButtonIcon({ + icon : 'fa-minus', + tooltip: 'Delete', + onclick: function() { + // check if element has been selected + var id = self.table.value(); + if (!id) { + return; + } + // remove group from chart + self.chart.groups.remove(id); + } + }) + } + }); + this.portlet.append(this.table.$el); + + // add element + this.setElement(this.portlet.$el); + + // change + var self = this; + this.chart.on('change', function() { + self._refresh(); + }); + this.chart.on('reset', function() { + self._removeGroupAll(); + }); + this.chart.on('change:type', function() { + self.app.config.trigger('change'); + }); + this.chart.groups.on('add', function(group) { + self._addGroup(group); + }); + this.chart.groups.on('remove', function(group) { + self._removeGroup(group); + }); + this.chart.groups.on('reset', function(group) { + self._removeGroupAll(); + }); + this.chart.groups.on('change', function(group) { + self._removeGroup(group); + self._addGroup(group); + }); + }, + + // refresh + _refresh: function() { + this._removeGroupAll(); + var self = this; + var groups = this.chart.groups; + if (groups) { + groups.each(function(group) { self._addGroup(group); }); + } + }, + + // add + _addGroup: function(group) { + // make custom info string + var info = '['; + var chart_type = this.chart.get('type'); + if (chart_type) { + var chart_settings = this.app.types.get(chart_type); + for (var key in chart_settings.data) { + info += key + '=' + group.get(key) + ', ' + } + } + info = info.substring(0, info.length - 2) + ']'; + + // add to table + this.table.add(group.get('label')); + this.table.add(info); + this.table.add('Last changed: ' + group.get('date')); + this.table.prepend(group.id); + this.table.value(group.id); + }, + + // remove + _removeGroup: function(group) { + // remove from to table + this.table.remove(group.id); + }, + + // data config reset + _removeGroupAll: function() { + // reset options table + this.table.removeAll(); + } +}); + +}); \ No newline at end of file diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/library/portlet.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/portlet.js @@ -0,0 +1,142 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// return +return Backbone.View.extend( +{ + // visibility + visible: false, + + // defaults options + optionsDefault: { + label : '', + icon : 'fa-tasks', + buttons : null, + body : null, + height : null, + operations : null, + placement : 'bottom', + overflow : 'auto' + }, + + // content + $content : null, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // link content + this.$content = this.$el.find('#content'); + + // set content height + if (this.options.height) { + this.$el.find('#body').css('height', this.options.height); + this.$el.find('#content').css('overflow', this.options.overflow); + } + + // append buttons + this.$buttons = $(this.el).find('#buttons'); + if (this.options.buttons) { + // link functions + var self = this; + $.each(this.options.buttons, function(name, item) { + self.$buttons.append(item.$el); + }); + } else { + this.$buttons.remove(); + } + + // append operations + this.$operations = $(this.el).find('#operations'); + if (this.options.operations) { + // link functions + var self = this; + $.each(this.options.operations, function(name, item) { + self.$operations.append(item.$el); + }); + } + + // add body + if(this.options.body) { + this.append(this.options.body); + } + }, + + // append + append: function($el) { + this.$content.append(Utils.wrap($el)); + }, + + // content + content: function() { + return this.$content; + }, + + // hide modal + show: function(){ + // fade in + this.$el.fadeIn('fast'); + + // set flag + this.visible = true; + }, + + // hide modal + hide: function(){ + // fade out + this.$el.fadeOut('fast'); + + // set flag + this.visible = false; + }, + + // enable buttons + enableButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', false); + }, + + // disable buttons + disableButton: function(name) { + this.$buttons.find('#' + String(name).toLowerCase()).prop('disabled', true); + }, + + // fill regular modal template + template: function(options) { + var tmpl = '<div class="toolForm">'; + + if (options.label) { + tmpl += '<div id="title" class="toolFormTitle" style="padding-bottom: 7px;">' + + '<div id="operations" style="float: right;"></div>' + + '<div>'; + + if (options.icon) + tmpl += '<i style="font-size: 1.2em" class="icon fa ' + options.icon + '"> </i>'; + + tmpl += options.label + + '</div>' + + '</div>'; + } + tmpl += '<div id="body" class="toolFormBody">'; + + if (options.placement == 'top') { + tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'; + } + + tmpl += '<div id="content" class="content" style="height: inherit; padding: 10px;"></div>'; + + if (options.placement == 'bottom') { + tmpl += '<div id="buttons" class="buttons" style="height: 50px; padding: 10px;"></div>'; + } + + tmpl += '</div>' + + '</div>'; + return tmpl; + } +}); + +}); diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/library/table.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/table.js @@ -0,0 +1,188 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// return +return Backbone.View.extend( +{ + // current row + row: null, + + // count rows + row_count: 0, + + // defaults options + optionsDefault: { + content : 'No content available.', + onchange : null, + ondblclick : null, + onconfirm : null + }, + + // events + events : { + 'click' : 'onclick', + 'dblclick' : 'ondblclick' + }, + + // first + first: true, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(options)); + + // initialize row + this.row = $('<tr></tr>'); + }, + + // add header cell + addHeader: function($el) { + var wrapper = $('<th></th>'); + wrapper.append($el); + this.row.append(wrapper); + }, + + // header + appendHeader: function() { + // append header row + $(this.el).find('thead').append(this.row); + + // row + this.row = $('<tr></tr>'); + }, + + // add row cell + add: function($el) { + var wrapper = $('<td></td>'); + wrapper.append($el); + this.row.append(wrapper); + }, + + // append + append: function(id) { + this.commit(id); + }, + + // prepend + prepend: function(id) { + this.commit(id, true); + }, + + // commit + commit: function(id, prepend) { + // add + this.row.attr('id', id); + + // add row + if (prepend) { + $(this.el).find('tbody').prepend(this.row); + } else { + $(this.el).find('tbody').append(this.row); + } + + // row + this.row = $('<tr></tr>'); + + // row count + this.row_count++; + this.refresh(); + }, + + // remove + remove: function(id) { + $(this.el).find('#' + id).remove(); + this.row_count--; + this.refresh(); + }, + + // remove + removeAll: function() { + $(this.el).find('tbody').html(''); + this.row_count = 0; + this.refresh(); + }, + + // value + value: function(new_value) { + // get current id/value + this.before = this.$el.find('.current').attr('id'); + + // check if new_value is defined + if (new_value !== undefined) { + this.$el.find('tr').removeClass('current'); + if (new_value) { + this.$el.find('#' + new_value).addClass('current'); + } + } + + // get current id/value + var after = this.$el.find('.current').attr('id'); + if(after === undefined) { + return null; + } else { + // fire onchange + if (after != this.before && this.options.onchange) { + this.options.onchange(new_value); + } + + // return current value + return after; + } + }, + + // confirm new value + confirm: function(new_value) { + this.value(new_value); + }, + + // onclick + onclick: function(e) { + // get values + var old_value = this.value(); + var new_value = $(e.target).closest('tr').attr('id'); + + // check equality + if (new_value && old_value != new_value) { + if (this.options.onconfirm) { + this.options.onconfirm(new_value); + } else { + this.confirm(new_value); + } + } + }, + + // onclick + ondblclick: function(e) { + var value = this.value(); + if (value && this.options.ondblclick) { + this.options.ondblclick(value); + } + }, + + // refresh + refresh: function() { + if (this.row_count == 0) { + this.$el.find('tmessage').show(); + } else { + this.$el.find('tmessage').hide(); + } + }, + + // load html template + template: function(options) + { + return '<div>' + + '<table class="grid">' + + '<thead></thead>' + + '<tbody style="cursor: pointer;"></tbody>' + + '</table>' + + '<tmessage>' + options.content + '</tmessage>' + + '<div>'; + } +}); + +}); diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/library/ui.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -0,0 +1,472 @@ +// dependencies +define(['library/utils', 'library/ui.select'], function(Utils, Select) { + +// plugin +var Label = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + }, + + // template + template: function(options) { + return '<label><b>' + options.label + '</b></label>'; + }, + + // value + value: function() { + return options.label; + } +}); + +// plugin +var Button = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '', + float : 'right', + cls : 'btn-default', + type : 'submit', + icon : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + }, + + // element + template: function(options) { + var str = '<button type="' + options.type + '" style="margin-right: 5px; float: ' + options.float + ';" type="button" class="btn ' + options.cls + '">'; + if (options.icon) { + str += '<i class="icon fa ' + options.icon + '"></i> ' ; + } + str += options.label + + '</button>'; + return str; + } +}); + +// plugin +var Anchor = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + }, + + // element + template: function(options) { + return '<div><a href="javascript:void(0)">' + options.label + '</a></div>'; + } +}); + +// plugin +var Message = Backbone.View.extend( +{ + // options + optionsDefault: { + message : '', + status : 'info', + persistent : false + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement('<div></div>'); + }, + + // update + update : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // show message + if (options.message != '') { + this.$el.html(this.template(this.options)); + this.$el.fadeIn(); + + // check if message is persistent + if (!options.persistent) { + // set timer + var self = this; + window.setTimeout(function() { + if (self.$el.is(':visible')) { + self.$el.fadeOut(); + } else { + self.$el.hide(); + } + }, 3000); + } + } else { + this.$el.fadeOut(); + } + }, + + // element + template: function(options) { + return '<div class="alert alert-' + options.status + '" style="padding: 2px 2px 2px 10px;">' + options.message + '</div>'; + } +}); + +// plugin +var Searchbox = Backbone.View.extend( +{ + // options + optionsDefault: { + onclick : null, + searchword : '' + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add click event + var self = this; + if (this.options.onclick) { + this.$el.on('submit', function(e) { + var search_field = self.$el.find('#search'); + self.options.onclick(search_field.val()); + }); + } + }, + + // element + template: function(options) { + return '<div class="search">' + + '<form onsubmit="return false;">' + + '<input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="' + options.searchword + '">' + + '<button type="submit" class="btn search-btn">' + + '<i class="fa fa-search"></i>' + + '</button>' + + '</form>' + + '</div>'; + } +}); + +// plugin +var Title = Backbone.View.extend( +{ + // options + optionsDefault: { + label : 'Unlabeled', + body : null + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + if (this.options.body) { + this.$el.find('.body').append(this.options.body); + } + }, + + // element + template: function(options) { + return '<div id="title" class="title">' + + options.label + ':' + + '</div>'; + } +}); + +// tab +var ButtonMenu = Backbone.View.extend( +{ + // main options + options: + { + id : '', + title : '', + target : '', + href : '', + onunload : null, + onclick : null, + visible : true, + icon : null, + tag : '' + }, + + // optional sub menu + $menu: null, + + // initialize + initialize: function (options) + { + // read in defaults + if (options) + this.options = _.defaults(options, this.options); + + // add template for tab + this.setElement($(this._template(this.options))); + + // find root + var $root = $(this.el).find('.root'); + + // link head + var self = this; + $root.on('click', function(e) + { + // prevent default + e.preventDefault(); + + // add click event + if(self.options.onclick) { + self.options.onclick(); + } + }); + + // visiblity + if (!this.options.visible) + this.hide(); + }, + + // show + show: function() + { + $(this.el).show(); + }, + + // hide + hide: function() + { + $(this.el).hide(); + }, + + // add menu item + addMenu: function (options) + { + // menu option defaults + var menuOptions = { + title : '', + target : '', + href : '', + onclick : null, + divider : false, + icon : null + } + + // read in defaults + if (options) + menuOptions = _.defaults(options, menuOptions); + + // check if submenu element is available + if (!this.$menu) + { + // insert submenu element into root + $(this.el).append(this._templateMenu()); + + // update element link + this.$menu = $(this.el).find('.menu'); + } + + // create + var $item = $(this._templateMenuItem(menuOptions)); + + // add events + $item.on('click', function(e) + { + // prevent default + e.preventDefault(); + + // add click event + if(menuOptions.onclick) { + menuOptions.onclick(); + } + }); + + // append menu + this.$menu.append($item); + + // append divider + if (menuOptions.divider) + this.$menu.append($(this._templateDivider())); + }, + + // fill template header + _templateMenuItem: function (options) + { + var tmpl = '<li>' + + '<a href="' + options.href + '" target="' + options.target + '">'; + + if (options.icon) + tmpl += '<i class="fa ' + options.icon + '"></i>'; + + tmpl += ' ' + options.title + + '</a>' + + '</li>'; + return tmpl; + }, + + // fill template header + _templateMenu: function () + { + return '<ul class="menu dropdown-menu pull-right" role="menu"></ul>'; + }, + + _templateDivider: function() + { + return '<li class="divider"></li>'; + }, + + // fill template + _template: function (options) + { + // start template + var tmpl = '<div id="' + options.id + '" class="button-menu btn-group">' + + '<button type="button" class="root btn btn-default dropdown-toggle" data-toggle="dropdown">'; + + if (options.icon) + tmpl += '<i class="fa ' + options.icon + '"></i>'; + + '</button>' + + '</div>'; + + // return template + return tmpl; + } +}); + +// plugin +var ButtonIcon = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '', + float : 'right', + cls : 'icon-btn', + type : 'submit', + icon : '', + tooltip : '' + }, + + // initialize + initialize : function(options) { + // get options + if (options) + this.options = _.defaults(options, this.optionsDefault); + else + this.options = this.optionsDefault; + + // create new element + this.setElement(this.template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + + // add tooltip + $(this.el).tooltip({title: options.tooltip, placement: 'bottom'}); + }, + + // element + template: function(options) { + var str = '<a style="margin-right: 5px; float: ' + options.float + ';" class="' + options.cls + '">'; + if (options.icon) { + str += '<i class="icon fa ' + options.icon + '"></i>'; + } + str += options.label + + '</a>'; + return str; + } +}); + + +// plugin +var Input = Backbone.View.extend( +{ + // options + optionsDefault: { + value : '', + type : 'text', + placeholder : '', + disabled : false + }, + + // initialize + initialize : function(options) { + // get options + if (options) + this.options = _.defaults(options, this.optionsDefault); + else + this.options = this.optionsDefault; + + // create new element + this.setElement(this.template(this.options)); + + // disable input field + if (this.options.disabled) { + this.$el.prop('disabled', true); + } + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.$el.val(new_val); + } + return this.$el.val(); + }, + + // element + template: function(options) { + return '<input id="' + options.id + '" type="' + options.type + '" value="' + options.value + '" placeholder="' + options.placeholder + '" class="form-control">'; + } +}); + +// return +return { + Label : Label, + Button : Button, + ButtonIcon : ButtonIcon, + Input : Input, + Anchor : Anchor, + Message : Message, + Searchbox : Searchbox, + Title : Title, + Select : Select, + ButtonMenu : ButtonMenu +} +}); diff -r e30627f8eac5e1db3d58b654aa59f14834c399e8 -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d config/plugins/visualizations/charts/static/library/ui.select.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/ui.select.js @@ -0,0 +1,117 @@ +// dependencies +define(['library/utils'], function(Utils) { + + +// plugin +return Backbone.View.extend( +{ + // options + optionsDefault: { + id : '', + cls : '' + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add change event + var self = this; + if (this.options.onchange) { + this.$el.on('change', function() { self.options.onchange(self.value()) }); + } + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.$el.val(new_val); + } + return this.$el.val(); + }, + + // label + label : function () { + return this.$el.find('option:selected').text(); + }, + + // disabled + disabled: function() { + return this.$el.is(':disabled'); + }, + + // render + update: function(options) { + // selected + var selected = this.$el.val(); + + // remove all options + $(this.el).find('option').remove(); + + // add new options + for (var key in options.data) { + $(this.el).append(this.templateOption(options.data[key])); + } + + // check if selected value exists + var exists = 0 != $(this.el).find('option[value=' + selected + ']').length; + + // add selected value + if (exists) + $(this.el).val(selected); + }, + + // update from url + updateUrl : function(options, callback) { + // get json + var self = this; + Utils.get(options.url, function(json) { + // write data into array + var data = []; + for (key in json) { + data.push({label: json[key].name, value: json[key].id}); + } + + // check if disabled. do not update disabled select elements. + if (!self.disabled()) { + self.update({data: data}); + } + + // callback + if (callback) { + callback(); + } + }); + }, + + // option + templateOption: function(options) { + return '<option value="' + options.value + '">' + options.label + '</option>'; + }, + + // element + template: function(options) { + var tmpl = '<select id="' + options.id + '" class="select ' + options.cls + ' ' + options.id + '">'; + for (key in options.data) { + // options + var item = options.data[key]; + + // identify selected value + var tag = ''; + if (item.value == options.selected || item.value == '') { + tag = 'selected'; + } + + // add template string + tmpl += '<option value="' + item.value + '" ' + tag + '>' + item.label + '</option>'; + } + tmpl += '</select>'; + return tmpl; + } +}); + +}); This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/2113355e2eb0/ Changeset: 2113355e2eb0 Branch: search User: kellrott Date: 2014-01-14 17:27:10 Summary: Adding update_time to ldda to_dict Affected #: 1 file diff -r 4e2f60de42fa5a00251bdf0d4e17edb2c9a9710d -r 2113355e2eb0fc2b2c34300bf9b117b6105780d2 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2217,6 +2217,7 @@ library_dataset_id = ldda.library_dataset_id, file_size = file_size, file_name = ldda.file_name, + update_time = ldda.update_time.isoformat(), data_type = ldda.ext, genome_build = ldda.dbkey, misc_info = ldda.info, https://bitbucket.org/galaxy/galaxy-central/commits/985e3d88f9ac/ Changeset: 985e3d88f9ac Branch: search User: kellrott Date: 2014-01-14 19:35:43 Summary: Adding update_time to hda to_dict Affected #: 1 file diff -r 2113355e2eb0fc2b2c34300bf9b117b6105780d2 -r 985e3d88f9ac85a90de7aa541b5844037cccd120 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1779,6 +1779,7 @@ visible = hda.visible, state = hda.state, file_size = int( hda.get_size() ), + update_time = hda.update_time.isoformat(), data_type = hda.ext, genome_build = hda.dbkey, misc_info = hda.info, https://bitbucket.org/galaxy/galaxy-central/commits/29bb29e0b3f9/ Changeset: 29bb29e0b3f9 User: jmchilton Date: 2014-01-16 04:59:36 Summary: Merged in kellrott/galaxy-central/search (pull request #296) Adding update_time to dataset to_dict methods Affected #: 1 file diff -r c28f10187bb86e0f18d36c1a7086af8615c87c97 -r 29bb29e0b3f9004304896403d15a09482d8e3c03 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1779,6 +1779,7 @@ visible = hda.visible, state = hda.state, file_size = int( hda.get_size() ), + update_time = hda.update_time.isoformat(), data_type = hda.ext, genome_build = hda.dbkey, misc_info = hda.info, @@ -2217,6 +2218,7 @@ library_dataset_id = ldda.library_dataset_id, file_size = file_size, file_name = ldda.file_name, + update_time = ldda.update_time.isoformat(), data_type = ldda.ext, genome_build = ldda.dbkey, misc_info = ldda.info, 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: martenson: javascript library and modal refactoring, automatic even binding if flag provided
by commits-noreply＠bitbucket.org 15 Jan '14

15 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c28f10187bb8/ Changeset: c28f10187bb8 User: martenson Date: 2014-01-16 00:11:09 Summary: javascript library and modal refactoring, automatic even binding if flag provided Affected #: 5 files diff -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d -r c28f10187bb86e0f18d36c1a7086af8615c87c97 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -14,9 +14,9 @@ import urllib2 import zipfile from paste.httpexceptions import HTTPBadRequest +from galaxy import util, web from galaxy.exceptions import ItemAccessibilityException, MessageException, ItemDeletionException, ObjectNotFound from galaxy.security import Action -from galaxy import util, web from galaxy.util.streamball import StreamBall from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin @@ -39,14 +39,12 @@ :returns: detailed dataset information from base controller .. seealso:: :attr:`galaxy.web.base.controller.UsesLibraryMixinItems.get_library_dataset` """ - # Get dataset. try: dataset = self.get_library_dataset( trans, id = id, check_ownership=False, check_accessible=True ) except Exception, e: trans.response.status = 500 return str( e ) try: - # Default: return dataset as dict. rval = dataset.to_dict() except Exception, e: rval = "Error in dataset API at listing contents: " + str( e ) diff -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d -r c28f10187bb86e0f18d36c1a7086af8615c87c97 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -122,7 +122,7 @@ // CONTAINER tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">'); - tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar" >'); @@ -457,6 +457,7 @@ var self = this; this.modal = new mod_modal.GalaxyModal({ destructible : true, + bindClosingEvents: true, title : 'Dataset Details', body : template, buttons : { @@ -477,7 +478,6 @@ $(this.modal.elMain).find('#dataset_import_single').val(self.lastSelectedHistory); } } - this.modal.bindEvents(); this.modal.show(); }, @@ -614,6 +614,7 @@ var history_modal_tmpl = _.template(self.templateBulkImportInModal(), {histories : histories.models}); self.modal = new mod_modal.GalaxyModal({ destructible : true, + bindClosingEvents: true, title : 'Import into History', body : history_modal_tmpl, buttons : { @@ -621,7 +622,6 @@ 'Close' : function() {self.modal.hideOrDestroy();} } }); - self.modal.bindEvents(); self.modal.show(); }, error: function(){ @@ -724,6 +724,7 @@ //send request $('<form action="'+ url +'" method="'+ (method||'post') +'">'+inputs+'</form>') .appendTo('body').submit().remove(); + mod_toastr.info('Your download will begin soon'); }; }, @@ -737,6 +738,7 @@ var self = this; this.modal = new mod_modal.GalaxyModal({ destructible : true, + bindClosingEvents: true, title : 'Create New Folder', body : this.templateNewFolderInModal(), buttons : { @@ -744,7 +746,6 @@ 'Close' : function() {self.modal.hideOrDestroy(); self.modal = null;} } }); - this.modal.bindEvents(); this.modal.show(); }, @@ -810,7 +811,7 @@ tmpl_array = []; tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">'); tmpl_array.push(''); - tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>'); + tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>'); tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>'); tmpl_array.push('<table class="table table-condensed">'); tmpl_array.push(' <thead>'); @@ -866,7 +867,7 @@ }, error: function(model, response){ if (response.statusCode().status === 403){ - mod_toastr.error('Please log in first. Redirecting to login page in 3s.'); + mod_toastr.info('Please log in first. Redirecting to login page in 3s.'); setTimeout(that.redirectToLogin, 3000); } else { mod_toastr.error('An error occured. Please try again.'); @@ -894,6 +895,7 @@ var self = this; this.modal = new mod_modal.GalaxyModal({ destructible : true, + bindClosingEvents: true, title : 'Create New Library', body : this.templateNewLibraryInModal(), buttons : { @@ -901,7 +903,6 @@ 'Close' : function() {self.modal.hideOrDestroy();} } }); - this.modal.bindEvents(); this.modal.show(); }, diff -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d -r c28f10187bb86e0f18d36c1a7086af8615c87c97 static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -16,50 +16,72 @@ height : null, width : null }, + + // flag whether the closing events are bound + eventsBound: false, // options options : { // by default the modal cannot be removed by the self.destroy() method // but only hidden through self.hide() - destructible: false + destructible: false, + // by default don't bind the events + bindClosingEvents: false }, // initialize initialize : function(options) { self = this; - if (options) + if (options){ this.create(options); + } }, hideOrDestroy: function(){ - if (this.options.destructible){ - self.destroy(); + self.visible = false; + + //unbinds event for ALL modals? + self.unbindEvents(); + + if (self.options.destructible){ + self.$el.remove(); // destroy } else { self.hide(); } }, + // hide modal, shouldn't be called directly but through hideOrDestroy() + // however hide() remains for backwards compatibility + hide: function(){ + this.visible = false; + this.$el.fadeOut('fast'); + }, + // bind the click-to-hide function bindEvents: function() { // bind the ESC key to hideOrDestroy() function $(document).on('keyup', function(event){ - if (event.keyCode == 27) { self.hideOrDestroy() } + if (event.keyCode == 27) { + self.hideOrDestroy() + } }) // bind the 'click anywhere' to hideOrDestroy() function... - $('html').on('click', function(event){ - self.hideOrDestroy() - }) + $('html').on('click', self.hideOrDestroy) // ...but don't hide if the click is on modal content $('.modal-content').on('click', function(event){ event.stopPropagation(); }) + + self.eventsBound = true; }, // unbind the click-to-hide function unbindEvents: function(){ // unbind the ESC key to hideOrDestroy() function $(document).off('keyup', function(event){ - if (event.keyCode == 27) { self.hideOrDestroy() } + if (event.keyCode == 27) { + self.hideOrDestroy() + } }) // unbind the 'click anywhere' to hideOrDestroy() function... $('html').off('click', function(event){ @@ -68,6 +90,8 @@ $('.modal-content').off('click', function(event){ event.stopPropagation(); }) + + self.eventsBound = false; }, // adds and displays a new frame/window @@ -76,59 +100,43 @@ this.initialize(options); // fix height - if (this.options.height) - { + if (this.options.height){ this.$body.css('height', this.options.height); this.$body.css('overflow', 'hidden'); - } else + } else{ this.$body.css('max-height', $(window).height() / 2); + } // fix width - if (this.options.width) + if (this.options.width){ this.$dialog.css('width', this.options.width); + } // show - if (this.visible) + if (this.visible){ this.$el.show(); - else + } else { this.$el.fadeIn('fast'); + } // set flag this.visible = true; }, - // hide modal, shouldn't be called directly but through hideOrDestroy() - hide: function(){ - // fade out - this.$el.fadeOut('fast'); - // set flag - this.visible = false; - // unbind events - this.unbindEvents(); - }, - - // destroy modal, shouldn't be called directly but through hideOrDestroy() - destroy: function(){ - // set flag - this.visible = false; - // unbind events - this.unbindEvents(); - // remove - this.$el.remove(); - }, - // create create: function(options) { // configure options this.options = _.defaults(options, this.optionsDefault); // check for progress bar request - if (this.options.body == 'progress') + if (this.options.body == 'progress'){ this.options.body = $('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>'); + } // remove former element - if (this.$el) + if (this.$el){ this.$el.remove(); + } // create new element this.setElement(this.template(this.options.title)); @@ -144,8 +152,9 @@ this.$body.html(this.options.body); // configure background - if (!this.options.backdrop) + if (!this.options.backdrop){ this.$backdrop.removeClass('in'); + } // append buttons if (this.options.buttons) { @@ -160,6 +169,10 @@ // append to main element $(this.elMain).append($(this.el)); + + if (this.options.bindClosingEvents && !this.eventsBound){ + this.bindEvents(); + } }, // enable buttons diff -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d -r c28f10187bb86e0f18d36c1a7086af8615c87c97 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(' <th class="button_heading">view</th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(" <td></td>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td></td>");r.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-folder-open"></span> browse</td>');r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(" <td>");r.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');r.push(' <span class="fa fa-eye"></span> details');r.push(" </button>");r.push(" </td>");r.push(' <td><%- content_item.get("name") %></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+r,{trigger:true,replace:true})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}this.modal.bindEvents();this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.bindEvents();s.modal.show()},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+='<input type="hidden" name="'+v[0]+'" value="'+v[1]+'" />'});$('<form action="'+s+'" method="'+(u||"post")+'">'+r+"</form>").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hideOrDestroy();r.modal=null}}});this.modal.bindEvents();this.modal.show()},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hideOrDestroy();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push(" <form>");tmpl_array.push(' <input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push(' <input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push(' <input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push(" </form>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.error("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.bindEvents();this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');r.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');r.push('<div id="library_folder_toolbar" >');r.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');r.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');r.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');r.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');r.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');r.push(" </button>");r.push(' <ul class="dropdown-menu" role="menu">');r.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');r.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');r.push(" </ul>");r.push(" </div>");r.push("</div>");r.push('<div class="library_breadcrumb">');r.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');r.push("<% } else { %>");r.push('<span title="You are in this folder"><%- path_item[1] %></span>');r.push("<% } %>");r.push("<% }); %>");r.push("</div>");r.push('<table id="folder_table" class="table table-condensed">');r.push(" <thead>");r.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');r.push(' <th class="button_heading">view</th>');r.push(" <th>name</th>");r.push(" <th>data type</th>");r.push(" <th>size</th>");r.push(" <th>date (UTC)</th>");r.push(" </thead>");r.push(" <tbody>");r.push(" <td></td>");r.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" <td></td>");r.push(" </tr>");r.push(" <% _.each(items, function(content_item) { %>");r.push(' <tr class="folder_row light" id="<%- content_item.id %>">');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" <td></td>");r.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');r.push(' <span class="fa fa-folder-open"></span> browse</td>');r.push(' <td><%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' <span class="muted">(empty folder)</span>');r.push(" <% } %>");r.push(" </td>");r.push(" <td>folder</td>");r.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');r.push(" <% } else { %>");r.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');r.push(" <td>");r.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');r.push(' <span class="fa fa-eye"></span> details');r.push(" </button>");r.push(" </td>");r.push(' <td><%- content_item.get("name") %></td>');r.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');r.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');r.push(" <% } %> ");r.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');r.push(" </tr>");r.push(" <% }); %>");r.push(" ");r.push(" </tbody>");r.push("</table>");r.push("</div>");return r.join("")},templateDatasetModal:function(){var r=[];r.push('<div id="dataset_info_modal">');r.push(' <table class="table table-striped table-condensed">');r.push(" <tr>");r.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');r.push(' <td><%= _.escape(item.get("name")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Data type</th>');r.push(' <td><%= _.escape(item.get("data_type")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Genome build</th>');r.push(' <td><%= _.escape(item.get("genome_build")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Size</th>');r.push(" <td><%= _.escape(size) %></td>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Date uploaded (UTC)</th>');r.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Uploaded by</th>');r.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');r.push(" </tr>");r.push(' <tr scope="row">');r.push(' <th scope="row">Data Lines</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');r.push(" </tr>");r.push(' <th scope="row">Comment Lines</th>');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');r.push(" <% } else { %>");r.push(' <td scope="row">unknown</td>');r.push(" <% } %>");r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Number of Columns</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Column Types</th>');r.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');r.push(" </tr>");r.push(" <tr>");r.push(' <th scope="row">Miscellaneous information</th>');r.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');r.push(" </tr>");r.push(" </table>");r.push(' <pre class="peek">');r.push(" </pre>");r.push("</div>");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');r.push("Select history: ");r.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');r.push(" <% _.each(histories, function(history) { %>");r.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');r.push(" <% }); %>");r.push("</select>");r.push("</span>");return r.join("")},templateProgressBar:function(){var r=[];r.push('<div class="import_text">');r.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");r.push("</div>");r.push('<div class="progress">');r.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');r.push(' <span class="completion_span">0% Complete</span>');r.push(" </div>");r.push("</div>");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w<s.attributes.folder.models.length;w++){var v=s.attributes.folder.models[w];if(v.get("type")==="file"){v.set("readable_size",t.size_to_string(v.get("file_size")))}}var y=s.full_path;var z;if(y.length===1){z=0}else{z=y[y.length-2][0]}var x=_.template(t.templateFolder(),{path:s.full_path,items:s.attributes.folder.models,id:r.id,upper_folder_id:z});t.$el.html(x)},error:function(){n.error("An error occured :(")}})},size_to_string:function(r){var s="";if(r>=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+r,{trigger:true,replace:true})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. 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Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:g}}); \ No newline at end of file diff -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d -r c28f10187bb86e0f18d36c1a7086af8615c87c97 static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{destructible:false},initialize:function(b){self=this;if(b){this.create(b)}},hideOrDestroy:function(){if(this.options.destructible){self.destroy()}else{self.hide()}},bindEvents:function(){$(document).on("keyup",function(b){if(b.keyCode==27){self.hideOrDestroy()}});$("html").on("click",function(b){self.hideOrDestroy()});$(".modal-content").on("click",function(b){b.stopPropagation()})},unbindEvents:function(){$(document).off("keyup",function(b){if(b.keyCode==27){self.hideOrDestroy()}});$("html").off("click",function(b){self.hideOrDestroy()});$(".modal-content").off("click",function(b){b.stopPropagation()})},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false;this.unbindEvents()},destroy:function(){this.visible=false;this.unbindEvents();this.$el.remove()},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},eventsBound:false,options:{destructible:false,bindClosingEvents:false},initialize:function(b){self=this;if(b){this.create(b)}},hideOrDestroy:function(){self.visible=false;self.unbindEvents();if(self.options.destructible){self.$el.remove()}else{self.hide()}},hide:function(){this.visible=false;this.$el.fadeOut("fast")},bindEvents:function(){$(document).on("keyup",function(b){if(b.keyCode==27){self.hideOrDestroy()}});$("html").on("click",self.hideOrDestroy);$(".modal-content").on("click",function(b){b.stopPropagation()});self.eventsBound=true},unbindEvents:function(){$(document).off("keyup",function(b){if(b.keyCode==27){self.hideOrDestroy()}});$("html").off("click",function(b){self.hideOrDestroy()});$(".modal-content").off("click",function(b){b.stopPropagation()});self.eventsBound=false},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el));if(this.options.bindClosingEvents&&!this.eventsBound){this.bindEvents()}},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ 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.

1 0

commit/galaxy-central: greg: Display messages for repositories in the tool shed that have dependencies on deprecated repositories.
by commits-noreply＠bitbucket.org 15 Jan '14

15 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9fe1a6fc375b/ Changeset: 9fe1a6fc375b User: greg Date: 2014-01-15 21:35:41 Summary: Display messages for repositories in the tool shed that have dependencies on deprecated repositories. Affected #: 6 files diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d 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 @@ -971,8 +971,9 @@ @web.require_login( "deprecate repository" ) def deprecate( self, trans, **kwd ): """Mark a repository in the tool shed as deprecated or not deprecated.""" - # Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset revisions that may be associated with the - # repository. Revisions are not marked as not downlaodable because those that have installed the repository must be allowed to get updates. + # Marking a repository in the tool shed as deprecated has no effect on any downloadable changeset + # revisions that may be associated with the repository. Revisions are not marked as not downlaodable + # because those that have installed the repository must be allowed to get updates. message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) @@ -2287,7 +2288,9 @@ status = 'warning' else: # Handle messaging for orphan tool dependency definitions. - orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, repository, metadata ) + orphan_message = tool_dependency_util.generate_message_for_orphan_tool_dependencies( trans, + repository, + metadata ) if orphan_message: message += orphan_message status = 'warning' @@ -2302,14 +2305,23 @@ skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) categories = suc.get_categories( trans ) selected_categories = [ rca.category_id for rca in repository.categories ] - containers_dict = container_util.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) + containers_dict = container_util.build_repository_containers_for_tool_shed( trans, + repository, + changeset_revision, + repository_dependencies, + repository_metadata ) heads = suc.get_repository_heads( repo ) + deprecated_repository_dependency_tups = \ + repository_dependency_util.get_repository_dependency_tups_from_repository_metadata( trans.app, + repository_metadata, + deprecated_only=True ) return trans.fill_template( '/webapps/tool_shed/repository/manage_repository.mako', repo_name=repo_name, description=description, long_description=long_description, current_allow_push_list=current_allow_push_list, allow_push_select_field=allow_push_select_field, + deprecated_repository_dependency_tups=deprecated_repository_dependency_tups, repo=repo, heads=heads, repository=repository, diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -76,7 +76,7 @@ # Get the list of repository dependencies for this repository. status = self.install_model.ToolShedRepository.installation_status.INSTALLED repository_dependency_tups = \ - repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=status ) + repository_dependency_util.get_repository_dependency_tups_for_installed_repository( self.app, repository, status=status ) # Add an entry to self.installed_repository_dependencies_of_installed_repositories. if repository_tup not in self.installed_repository_dependencies_of_installed_repositories: debug_msg = "Adding an entry for revision %s of repository %s owned by %s " % ( installed_changeset_revision, name, owner ) @@ -132,7 +132,7 @@ debug_msg += "to repository_dependencies_of_installed_repositories." log.debug( debug_msg ) repository_dependency_tups = \ - repository_dependency_util.get_repository_dependency_tups_for_repository( self.app, repository, status=None ) + repository_dependency_util.get_repository_dependency_tups_for_installed_repository( self.app, repository, status=None ) self.repository_dependencies_of_installed_repositories[ repository_tup ] = repository_dependency_tups def add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( self, tool_dependency ): diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -303,10 +303,13 @@ key_rd_dicts_to_be_processed=None, all_repository_dependencies=None, handled_key_rd_dicts=None, circular_repository_dependencies=None ): """ - Return a dictionary of all repositories upon which the contents of the received repository_metadata record depend. The dictionary keys - are name-spaced values consisting of toolshed_base_url/repository_name/repository_owner/changeset_revision and the values are lists of - repository_dependency tuples consisting of ( toolshed_base_url, repository_name, repository_owner, changeset_revision ). This method - ensures that all required repositories to the nth degree are returned. + Return a dictionary of all repositories upon which the contents of the received + repository_metadata record depend. The dictionary keys are name-spaced values + consisting of: + toolshed_base_url/repository_name/repository_owner/changeset_revision + and the values are lists of repository_dependency tuples consisting of: + ( toolshed_base_url, repository_name, repository_owner, changeset_revision ). + This method ensures that all required repositories to the nth degree are returned. """ if handled_key_rd_dicts is None: handled_key_rd_dicts = [] @@ -331,8 +334,8 @@ all_repository_dependencies = initialize_all_repository_dependencies( current_repository_key, repository_dependencies_dict, all_repository_dependencies ) - # Handle the repository dependencies defined in the current repository, if any, and populate the various repository dependency objects for - # this round of processing. + # Handle the repository dependencies defined in the current repository, if any, and populate + # the various repository dependency objects for this round of processing. current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies = \ populate_repository_dependency_objects_for_processing( trans, current_repository_key, @@ -375,10 +378,41 @@ all_repository_dependencies = prune_invalid_repository_dependencies( all_repository_dependencies ) return all_repository_dependencies -def get_repository_dependency_tups_for_repository( app, repository, dependency_tups=None, status=None ): +def get_repository_dependency_tups_from_repository_metadata( app, repository_metadata, deprecated_only=False ): + """ + Return a list of of tuples defining repository objects required by the received repository. The returned + list defines the entire repository dependency tree. This method is called only from the Tool Shed. + """ + dependency_tups = [] + if repository_metadata is not None: + metadata = repository_metadata.metadata + if metadata: + repository_dependencies_dict = metadata.get( 'repository_dependencies', None ) + if repository_dependencies_dict is not None: + repository_dependency_tups = repository_dependencies_dict.get( 'repository_dependencies', None ) + if repository_dependency_tups is not None: + # The value of repository_dependency_tups is a list of repository dependency tuples like this: + # ['http://localhost:9009', 'package_samtools_0_1_18', 'devteam', 'ef37fc635cb9', 'False', 'False'] + for repository_dependency_tup in repository_dependency_tups: + toolshed, name, owner, changeset_revision, pir, oicct = \ + common_util.parse_repository_dependency_tuple( repository_dependency_tup ) + repository = suc.get_repository_by_name_and_owner( app, name, owner ) + if repository: + if deprecated_only: + if repository.deprecated: + dependency_tups.append( repository_dependency_tup ) + else: + dependency_tups.append( repository_dependency_tup ) + else: + log.debug( "Cannot locate repository %s owned by %s for inclusion in repository dependency tups." % \ + ( name, owner ) ) + return dependency_tups + +def get_repository_dependency_tups_for_installed_repository( app, repository, dependency_tups=None, status=None ): """ Return a list of of tuples defining tool_shed_repository objects (whose status can be anything) required by the - received repository. The returned list defines the entire repository dependency tree. + received repository. The returned list defines the entire repository dependency tree. This method is called + only from Galaxy. """ if dependency_tups is None: dependency_tups = [] @@ -393,7 +427,9 @@ continue if required_repository_tup not in dependency_tups: dependency_tups.append( required_repository_tup ) - return get_repository_dependency_tups_for_repository( app, required_repository, dependency_tups=dependency_tups ) + return get_repository_dependency_tups_for_installed_repository( app, + required_repository, + dependency_tups=dependency_tups ) return dependency_tups def get_repository_tuple_for_installed_repository_manager( repository ): @@ -657,12 +693,16 @@ containers_dict[ 'missing_repository_dependencies' ] = None return containers_dict -def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, key_rd_dicts_to_be_processed, - handled_key_rd_dicts, circular_repository_dependencies, all_repository_dependencies ): +def populate_repository_dependency_objects_for_processing( trans, current_repository_key, repository_dependencies_dict, + key_rd_dicts_to_be_processed, handled_key_rd_dicts, + circular_repository_dependencies, all_repository_dependencies ): """ - The process that discovers all repository dependencies for a specified repository's changeset revision uses this method to populate the following items - for the current processing loop: filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, handled_key_rd_dicts, all_repository_dependencies. - Each processing loop may discover more repository dependencies, so this method is repeatedly called until all repository dependencies have been discovered. + The process that discovers all repository dependencies for a specified repository's + changeset revision uses this method to populate the following items for the current + processing loop: filtered_current_repository_key_rd_dicts, key_rd_dicts_to_be_processed, + handled_key_rd_dicts, all_repository_dependencies. Each processing loop may discover + more repository dependencies, so this method is repeatedly called until all repository + dependencies have been discovered. """ current_repository_key_rd_dicts = [] filtered_current_repository_key_rd_dicts = [] @@ -673,13 +713,15 @@ if current_repository_key_rd_dicts and current_repository_key: # Remove all repository dependencies that point to a revision within its own repository. current_repository_key_rd_dicts = remove_ropository_dependency_reference_to_self( current_repository_key_rd_dicts ) - current_repository_key_rd_dicts = get_updated_changeset_revisions_for_repository_dependencies( trans, current_repository_key_rd_dicts ) + current_repository_key_rd_dicts = get_updated_changeset_revisions_for_repository_dependencies( trans, + current_repository_key_rd_dicts ) for key_rd_dict in current_repository_key_rd_dicts: # Filter out repository dependencies that are required only if compiling the dependent repository's tool dependency. key_rd_dict = filter_only_if_compiling_contained_td( key_rd_dict ) if key_rd_dict: is_circular = False - if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ) and not in_key_rd_dicts( key_rd_dict, key_rd_dicts_to_be_processed ): + if not in_key_rd_dicts( key_rd_dict, handled_key_rd_dicts ) and not in_key_rd_dicts( key_rd_dict, + key_rd_dicts_to_be_processed ): filtered_current_repository_key_rd_dicts.append( key_rd_dict ) repository_dependency = key_rd_dict[ current_repository_key ] if current_repository_key in all_repository_dependencies: @@ -708,8 +750,10 @@ def prune_invalid_repository_dependencies( repository_dependencies ): """ - Eliminate all invalid entries in the received repository_dependencies dictionary. An entry is invalid if the value_list of the key/value pair is - empty. This occurs when an invalid combination of tool shed, name , owner, changeset_revision is used and a repository_metadata record is not found. + Eliminate all invalid entries in the received repository_dependencies dictionary. An entry + is invalid if the value_list of the key/value pair is empty. This occurs when an invalid + combination of tool shed, name , owner, changeset_revision is used and a repository_metadata + record is not found. """ valid_repository_dependencies = {} description = repository_dependencies.get( 'description', None ) @@ -752,7 +796,9 @@ toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ common_util.parse_repository_dependency_tuple( repository_dependency ) if rd_toolshed == toolshed and rd_name == name and rd_owner == owner: - log.debug( "Removing repository dependency for repository %s owned by %s since it refers to a revision within itself." % ( name, owner ) ) + debug_msg = "Removing repository dependency for repository %s owned by %s " % ( name, owner ) + debug_msg += 'since it refers to a revision within itself.' + log.debug( debug_msg ) else: new_key_rd_dict = {} new_key_rd_dict[ key ] = repository_dependency diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d templates/webapps/tool_shed/common/common.mako --- a/templates/webapps/tool_shed/common/common.mako +++ b/templates/webapps/tool_shed/common/common.mako @@ -51,6 +51,23 @@ </script></%def> +<%def name="render_deprecated_repository_dependencies_message( deprecated_repository_dependency_tups )"> + <div class="warningmessage"> + <% + from tool_shed.util.common_util import parse_repository_dependency_tuple + msg = '<ul>' + for deprecated_repository_dependency_tup in deprecated_repository_dependency_tups: + toolshed, name, owner, changeset_revision, pir, oicct = \ + parse_repository_dependency_tuple( deprecated_repository_dependency_tup ) + msg += '<li>Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b></li>' % \ + ( changeset_revision, name, owner ) + msg += '</ul>' + %> + This repository depends upon the following deprecated repositories<br/> + ${msg} + </div> +</%def> + <%def name="render_star_rating( name, rating, disabled=False )"><% if disabled: @@ -87,6 +104,20 @@ </div></%def> +<%def name="render_multiple_heads_message( heads )"> + <div class="warningmessage"> + <% + from tool_shed.util.shed_util_common import get_revision_label_from_ctx + heads_str = '' + for ctx in heads: + heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx, include_date=True ) + %> + Contact the administrator of this Tool Shed as soon as possible and let them know that + this repository has the following multiple heads which must be merged.<br/> + ${heads_str} + </div> +</%def> + <%def name="render_review_comment( comment_text )"><style type="text/css"> #reviews_table{ table-layout:fixed; diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -87,6 +87,14 @@ multiple_heads = len( heads ) > 1 else: multiple_heads = False + + if repository_metadata is None: + revision_installable = False + else: + if repository_metadata.downloadable is None: + revision_installable = 'unknown' + else: + revision_installable = repository_metadata.downloadable %><%! @@ -119,18 +127,12 @@ <div class="warningmessage"> This repository has been marked as deprecated, so some tool shed features may be restricted. </div> -%elif multiple_heads: - <div class="warningmessage"> - <% - from tool_shed.util.shed_util_common import get_revision_label_from_ctx - heads_str = '' - for ctx in heads: - heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx, include_date=True ) - %> - Contact the administrator of this Tool Shed as soon as possible and let them know that - this repository has the following multiple heads which must be merged.<br/> - ${heads_str} - </div> +%endif: +%if multiple_heads: + ${render_multiple_heads_message( heads )} +%endif +%if deprecated_repository_dependency_tups: + ${render_deprecated_repository_dependencies_message( deprecated_repository_dependency_tups )} %endif %if len( changeset_revision_select_field.options ) > 1: @@ -207,7 +209,11 @@ ${repository.user.username | h} </div><div class="form-row"> - <label>Times downloaded:</label> + <label>This revision can be installed:</label> + ${revision_installable} + </div> + <div class="form-row"> + <label>Times cloned / installed:</label> ${repository.times_downloaded | h} </div> %if is_admin: diff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f -r 9fe1a6fc375b3fad14dac271ed8f85e02fc6ef6d templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -30,6 +30,14 @@ multiple_heads = len( heads ) > 1 else: multiple_heads = False + + if repository_metadata is None: + revision_installable = False + else: + if repository_metadata.downloadable is None: + revision_installable = 'unknown' + else: + revision_installable = repository_metadata.downloadable %><%! @@ -66,18 +74,12 @@ <div class="warningmessage"> This repository has been marked as deprecated, so some tool shed features may be restricted. </div> -%elif multiple_heads: - <div class="warningmessage"> - <% - from tool_shed.util.shed_util_common import get_revision_label_from_ctx - heads_str = '' - for ctx in heads: - heads_str += '%s<br/>' % get_revision_label_from_ctx( ctx, include_date=True ) - %> - Contact the administrator of this Tool Shed as soon as possible and let them know that - this repository has the following multiple heads which must be merged.<br/> - ${heads_str} - </div> +%endif: +%if multiple_heads: + ${render_multiple_heads_message( heads )} +%endif +%if deprecated_repository_dependency_tups: + ${render_deprecated_repository_dependencies_message( deprecated_repository_dependency_tups )} %endif %if len( changeset_revision_select_field.options ) > 1: @@ -142,7 +144,11 @@ ${repository.user.username | h} </div><div class="form-row"> - <label>Times downloaded:</label> + <label>This revision can be installed:</label> + ${revision_installable} + </div> + <div class="form-row"> + <label>Times cloned / installed:</label> ${repository.times_downloaded} </div> %if trans.user_is_admin(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 15 Jan '14

15 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/73dcfbfc744c/ Changeset: 73dcfbfc744c Branch: stable User: dan Date: 2013-12-12 23:09:29 Summary: When setting external metadata using _handle_metadata_externally (e.g. local and lwr runners) use the requirments of the set metadata tool to determine dependencies. Resolves issue seen with missing samtools command when samtools is not in the path, but has been installed with the dependency system. Affected #: 4 files diff -r a96ca602209ca2d4d732cced9530a62b3e4134a8 -r 73dcfbfc744c2336749df0276a5a727d672c6add lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -585,6 +585,9 @@ tool_xml_text = """ <tool id="__SET_METADATA__" name="Set External Metadata" version="1.0.1" tool_type="set_metadata"><type class="SetMetadataTool" module="galaxy.tools"/> + <requirements> + <requirement type="package">samtools</requirement> + </requirements><action module="galaxy.tools.actions.metadata" class="SetMetadataToolAction"/><command>$__SET_EXTERNAL_METADATA_COMMAND_LINE__</command><inputs> diff -r a96ca602209ca2d4d732cced9530a62b3e4134a8 -r 73dcfbfc744c2336749df0276a5a727d672c6add lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -196,7 +196,7 @@ log.exception( "from_work_dir specified a location not in the working directory: %s, %s" % ( source_file, job_wrapper.working_directory ) ) return output_pairs - def _handle_metadata_externally(self, job_wrapper): + def _handle_metadata_externally( self, job_wrapper, resolve_requirements=False ): """ Set metadata externally. Used by the local and lwr job runners where this shouldn't be attached to command-line to execute. @@ -211,6 +211,12 @@ #we don't want to overwrite metadata that was copied over in init_meta(), as per established behavior kwds={ 'overwrite' : False } ) log.debug( 'executing external set_meta script for job %d: %s' % ( job_wrapper.job_id, external_metadata_script ) ) + if resolve_requirements: + dependency_shell_commands = self.app.datatypes_registry.set_external_metadata_tool.build_dependency_shell_commands() + if dependency_shell_commands: + if isinstance( dependency_shell_commands, list ): + dependency_shell_commands = "&&".join( dependency_shell_commands ) + external_metadata_script = "%s&&%s" % ( dependency_shell_commands, external_metadata_script ) external_metadata_proc = subprocess.Popen( args=external_metadata_script, shell=True, env=os.environ, diff -r a96ca602209ca2d4d732cced9530a62b3e4134a8 -r 73dcfbfc744c2336749df0276a5a727d672c6add lib/galaxy/jobs/runners/local.py --- a/lib/galaxy/jobs/runners/local.py +++ b/lib/galaxy/jobs/runners/local.py @@ -110,7 +110,7 @@ job_wrapper.fail( "failure running job", exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - self._handle_metadata_externally( job_wrapper ) + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job! try: job_wrapper.finish( stdout, stderr, exit_code ) diff -r a96ca602209ca2d4d732cced9530a62b3e4134a8 -r 73dcfbfc744c2336749df0276a5a727d672c6add lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -154,7 +154,7 @@ job_wrapper.fail( message, exception=True ) log.exception("failure running job %d" % job_wrapper.job_id) return - self._handle_metadata_externally( job_wrapper ) + self._handle_metadata_externally( job_wrapper, resolve_requirements=True ) # Finish the job try: job_wrapper.finish( stdout, stderr ) https://bitbucket.org/galaxy/galaxy-central/commits/4e280310697b/ Changeset: 4e280310697b Branch: stable User: jmchilton Date: 2013-12-13 22:43:26 Summary: Use null object pattern to simplify logic related to no dependency manager being set. Fixes bug introduced in 4241eff related to dependency_manager being None if tool_dependency_dir is not set. Affected #: 4 files diff -r 73dcfbfc744c2336749df0276a5a727d672c6add -r 4e280310697b806aa0e08c80f342e2c93f1558f0 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -704,10 +704,7 @@ if self.command_line and self.command_line.startswith( 'python' ): self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root # Shell fragment to inject dependencies - if self.app.config.use_tool_dependencies: - self.dependency_shell_commands = self.tool.build_dependency_shell_commands() - else: - self.dependency_shell_commands = None + self.dependency_shell_commands = self.tool.build_dependency_shell_commands() # We need command_line persisted to the db in order for Galaxy to re-queue the job # if the server was stopped and restarted before the job finished job.command_line = self.command_line @@ -1451,10 +1448,7 @@ if self.command_line and self.command_line.startswith( 'python' ): self.galaxy_lib_dir = os.path.abspath( "lib" ) # cwd = galaxy root # Shell fragment to inject dependencies - if self.app.config.use_tool_dependencies: - self.dependency_shell_commands = self.tool.build_dependency_shell_commands() - else: - self.dependency_shell_commands = None + self.dependency_shell_commands = self.tool.build_dependency_shell_commands() # We need command_line persisted to the db in order for Galaxy to re-queue the job # if the server was stopped and restarted before the job finished task.command_line = self.command_line diff -r 73dcfbfc744c2336749df0276a5a727d672c6add -r 4e280310697b806aa0e08c80f342e2c93f1558f0 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -40,7 +40,7 @@ from galaxy.tools.actions import DefaultToolAction from galaxy.tools.actions.data_source import DataSourceToolAction from galaxy.tools.actions.data_manager import DataManagerToolAction -from galaxy.tools.deps import DependencyManager, INDETERMINATE_DEPENDENCY +from galaxy.tools.deps import build_dependency_manager from galaxy.tools.deps.requirements import parse_requirements_from_xml from galaxy.tools.parameters import check_param, params_from_strings, params_to_strings from galaxy.tools.parameters.basic import (BaseURLToolParameter, @@ -696,14 +696,7 @@ return stored.latest_workflow def init_dependency_manager( self ): - if self.app.config.use_tool_dependencies: - dependency_manager_kwds = { - 'default_base_path': self.app.config.tool_dependency_dir, - 'conf_file': self.app.config.dependency_resolvers_config_file, - } - self.dependency_manager = DependencyManager( **dependency_manager_kwds ) - else: - self.dependency_manager = None + self.dependency_manager = build_dependency_manager( self.app.config ) @property def sa_session( self ): diff -r 73dcfbfc744c2336749df0276a5a727d672c6add -r 4e280310697b806aa0e08c80f342e2c93f1558f0 lib/galaxy/tools/deps/__init__.py --- a/lib/galaxy/tools/deps/__init__.py +++ b/lib/galaxy/tools/deps/__init__.py @@ -15,6 +15,31 @@ from galaxy.util.submodules import submodules +def build_dependency_manager( config ): + if config.use_tool_dependencies: + dependency_manager_kwds = { + 'default_base_path': config.tool_dependency_dir, + 'conf_file': config.dependency_resolvers_config_file, + } + dependency_manager = DependencyManager( **dependency_manager_kwds ) + else: + dependency_manager = NullDependencyManager() + + return dependency_manager + + +class NullDependencyManager( object ): + + def uses_tool_shed_dependencies(self): + return False + + def dependency_shell_commands( self, requirements, **kwds ): + return [] + + def find_dep( self, name, version=None, type='package', **kwds ): + return INDETERMINATE_DEPENDENCY + + class DependencyManager( object ): """ A DependencyManager attempts to resolve named and versioned dependencies by diff -r 73dcfbfc744c2336749df0276a5a727d672c6add -r 4e280310697b806aa0e08c80f342e2c93f1558f0 lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -458,7 +458,7 @@ tool_dependency = tool_dependencies[ index ] if tool_dependency.can_install: try: - dependencies_ignored = app.toolbox.dependency_manager and not app.toolbox.dependency_manager.uses_tool_shed_dependencies() + dependencies_ignored = not app.toolbox.dependency_manager.uses_tool_shed_dependencies() if dependencies_ignored: log.info("Skipping package %s, tool shed dependency resolver not enabled." % package_name) # Tool dependency resolves have been configured and they do not Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Tweaks to scripts/api/common.py to fix JSONDecodeError removal and clean up code.
by commits-noreply＠bitbucket.org 15 Jan '14

15 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d2f73445ce7a/ Changeset: d2f73445ce7a User: dannon Date: 2014-01-15 15:05:38 Summary: Tweaks to scripts/api/common.py to fix JSONDecodeError removal and clean up code. Affected #: 1 file diff -r d0302907cbbfbfbc8561bd3b2fe4a667161e67ff -r d2f73445ce7ada2f13947aa7c7c8506743d40d3f scripts/api/common.py --- a/scripts/api/common.py +++ b/scripts/api/common.py @@ -1,3 +1,6 @@ +""" +Common methods used by the API sample scripts. +""" import json import logging import os @@ -9,17 +12,16 @@ sys.path = new_path from galaxy import eggs -import pkg_resources +eggs.require( "pycrypto" ) -pkg_resources.require( "pycrypto" ) from Crypto.Cipher import Blowfish -from Crypto.Util.randpool import RandomPool -from Crypto.Util import number log = logging.getLogger( __name__ ) def make_url( api_key, url, args=None ): - # Adds the API Key to the URL if it's not already there. + """ + Adds the API Key to the URL if it's not already there. + """ if args is None: args = [] argsep = '&' @@ -30,29 +32,37 @@ return url + argsep + '&'.join( [ '='.join( t ) for t in args ] ) def get( api_key, url ): - # Do the actual GET. + """ + Do the actual GET. + """ url = make_url( api_key, url ) try: return json.loads( urllib2.urlopen( url ).read() ) - except json.decoder.JSONDecodeError, e: - print "URL did not return JSON data" + except ValueError, e: + print "URL did not return JSON data: %s" % e sys.exit(1) def post( api_key, url, data ): - # Do the actual POST. + """ + Do the actual POST. + """ url = make_url( api_key, url ) req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data ) ) return json.loads( urllib2.urlopen( req ).read() ) def put( api_key, url, data ): - # Do the actual PUT + """ + Do the actual PUT + """ url = make_url( api_key, url ) req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data )) req.get_method = lambda: 'PUT' return json.loads( urllib2.urlopen( req ).read() ) def __del( api_key, url, data ): - # Do the actual DELETE + """ + Do the actual DELETE + """ url = make_url( api_key, url ) req = urllib2.Request( url, headers = { 'Content-Type': 'application/json' }, data = json.dumps( data )) req.get_method = lambda: 'DELETE' @@ -60,7 +70,9 @@ def display( api_key, url, return_formatted=True ): - # Sends an API GET request and acts as a generic formatter for the JSON response. + """ + Sends an API GET request and acts as a generic formatter for the JSON response. + """ try: r = get( api_key, url ) except urllib2.HTTPError, e: @@ -97,8 +109,10 @@ print 'response is unknown type: %s' % type( r ) def submit( api_key, url, data, return_formatted=True ): - # Sends an API POST request and acts as a generic formatter for the JSON response. - # 'data' will become the JSON payload read by Galaxy. + """ + Sends an API POST request and acts as a generic formatter for the JSON response. + 'data' will become the JSON payload read by Galaxy. + """ try: r = post( api_key, url, data ) except urllib2.HTTPError, e: @@ -131,8 +145,10 @@ print r def update( api_key, url, data, return_formatted=True ): - # Sends an API PUT request and acts as a generic formatter for the JSON response. - # 'data' will become the JSON payload read by Galaxy. + """ + Sends an API PUT request and acts as a generic formatter for the JSON response. + 'data' will become the JSON payload read by Galaxy. + """ try: r = put( api_key, url, data ) except urllib2.HTTPError, e: @@ -147,10 +163,12 @@ print 'Response' print '--------' print r - + def delete( api_key, url, data, return_formatted=True ): - # Sends an API DELETE request and acts as a generic formatter for the JSON response. - # 'data' will become the JSON payload read by Galaxy. + """ + Sends an API DELETE request and acts as a generic formatter for the JSON response. + 'data' will become the JSON payload read by Galaxy. + """ try: r = __del( api_key, url, data ) except urllib2.HTTPError, e: @@ -166,12 +184,14 @@ print '--------' print r -# utility method to encode ID's def encode_id( config_id_secret, obj_id ): + """ + utility method to encode ID's + """ id_cipher = Blowfish.new( config_id_secret ) # Convert to string s = str( obj_id ) - # Pad to a multiple of 8 with leading "!" + # Pad to a multiple of 8 with leading "!" s = ( "!" * ( 8 - len(s) % 8 ) ) + s # Encrypt return id_cipher.encrypt( s ).encode( 'hex' ) 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: inithello: Fix tool configuration reload for changes in 5f6c670.
by commits-noreply＠bitbucket.org 15 Jan '14

15 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d0302907cbbf/ Changeset: d0302907cbbf User: inithello Date: 2014-01-15 14:54:33 Summary: Fix tool configuration reload for changes in 5f6c670. Affected #: 1 file diff -r 833d5e848479b04c0e90923b9dc4c168d78b4d7e -r d0302907cbbfbfbc8561bd3b2fe4a667161e67ff templates/admin/reload_tool.mako --- a/templates/admin/reload_tool.mako +++ b/templates/admin/reload_tool.mako @@ -1,5 +1,6 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> +<% from galaxy.tools import Tool, ToolSection %><script type="text/javascript"> $().ready(function() { @@ -26,13 +27,13 @@ </label><select name="tool_id"> %for key, val in toolbox.tool_panel.items(): - %if key.startswith( 'tool' ): + %if isinstance( val, Tool ): <option value="${val.id}">${val.name}</option> - %elif key.startswith( 'section' ): + %elif isinstance( val, ToolSection ): <optgroup label="${val.name}"><% section = val %> %for section_key, section_val in section.elems.items(): - %if section_key.startswith( 'tool' ): + %if isinstance( section_val, Tool ): <% selected_str = "" %> %if section_val.id == tool_id: <% selected_str = " selected=\"selected\"" %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix object not found wording.
by commits-noreply＠bitbucket.org 15 Jan '14

15 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/833d5e848479/ Changeset: 833d5e848479 User: dannon Date: 2014-01-15 14:46:53 Summary: Fix object not found wording. Affected #: 1 file diff -r fa698b544051c61a6b895f04840309a7807ce5a7 -r 833d5e848479b04c0e90923b9dc4c168d78b4d7e lib/galaxy/exceptions/error_codes.json --- a/lib/galaxy/exceptions/error_codes.json +++ b/lib/galaxy/exceptions/error_codes.json @@ -52,6 +52,6 @@ { "name": "USER_OBJECT_NOT_FOUND", "code": 404001, - "message": "No such object not found." + "message": "No such object found." } ] 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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