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

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b76dd608c500/ Changeset: b76dd608c500 User: guerler Date: 2014-01-16 20:10:32 Summary: Charts: Add configuration model, link all view functions to model events Affected #: 8 files diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r b76dd608c500d8421d0ec51f6b638b7324ecead6 config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -1,10 +1,10 @@ // dependencies define(['library/portlet', 'library/ui', 'library/utils', 'views/charts', 'views/viewport', 'views/chart', 'views/group', - 'models/datasets', 'models/chart', 'models/charts', 'models/types'], + 'models/config', 'models/datasets', 'models/chart', 'models/charts', 'models/group', 'models/types'], function( Portlet, Ui, Utils, ChartsView, ViewportView, ChartView, GroupView, - Datasets, Chart, Charts, Types + Config, Datasets, Chart, Charts, Group, Types ) { // widget @@ -19,10 +19,14 @@ // link galaxy this.modal = parent.Galaxy.modal; + // create configuration model + this.config = new Config(); + // create chart models this.types = new Types(); this.chart = new Chart(); this.charts = new Charts(); + this.group = new Group(); // create dataset handler this.datasets = new Datasets(this); diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r b76dd608c500d8421d0ec51f6b638b7324ecead6 config/plugins/visualizations/charts/static/models/chart.js --- a/config/plugins/visualizations/charts/static/models/chart.js +++ b/config/plugins/visualizations/charts/static/models/chart.js @@ -22,8 +22,9 @@ // reset reset: function() { - this.clear().set(this.defaults); + this.clear({silent: true}).set(this.defaults); this.groups.reset(); + this.trigger('reset', this); }, // copy diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r b76dd608c500d8421d0ec51f6b638b7324ecead6 config/plugins/visualizations/charts/static/models/config.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/models/config.js @@ -0,0 +1,16 @@ +// dependencies +define([], function() { + + +// model +return Backbone.Model.extend( +{ + // options + defaults : { + query_limit : 20, + query_pace : 1000, + query_max : 5 + } +}); + +}); \ No newline at end of file diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r b76dd608c500d8421d0ec51f6b638b7324ecead6 config/plugins/visualizations/charts/static/models/group.js --- a/config/plugins/visualizations/charts/static/models/group.js +++ b/config/plugins/visualizations/charts/static/models/group.js @@ -1,23 +1,14 @@ // dependencies -define(['library/utils'], function(Utils) { - +define([], function() { // model return Backbone.Model.extend( { - // defaults - defaults : { - }, - - // initialize - initialize: function(options) - { - }, - // reset reset: function() { - this.clear().set(this.defaults); + this.clear({silent: true}).set(this.defaults); + this.trigger('reset', this); } }); diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r b76dd608c500d8421d0ec51f6b638b7324ecead6 config/plugins/visualizations/charts/static/views/chart.js --- a/config/plugins/visualizations/charts/static/views/chart.js +++ b/config/plugins/visualizations/charts/static/views/chart.js @@ -125,6 +125,9 @@ this.chart.on('change:type', function(chart) { self.table.value(chart.get('type')); }); + this.chart.on('reset', function(chart) { + self._resetChart(); + }); // collection events this.app.charts.on('add', function(chart) { @@ -140,23 +143,17 @@ }); // reset - this.reset(); + this._resetChart(); }, // reset - reset: function() { - this.chart.reset(); + _resetChart: function() { this.chart.set('id', Utils.uuid()); this.chart.set('dataset_id', this.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 diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r b76dd608c500d8421d0ec51f6b638b7324ecead6 config/plugins/visualizations/charts/static/views/charts.js --- a/config/plugins/visualizations/charts/static/views/charts.js +++ b/config/plugins/visualizations/charts/static/views/charts.js @@ -16,12 +16,12 @@ ondblclick : function(chart_id) { // get chart var chart = self.app.charts.get(chart_id); - + self.app.chart.copy(chart); + // show edit self.$el.hide(); // update model and show create - self.app.chart_view.setChart(chart); self.app.chart_view.$el.show(); }, onchange : function(chart_id) { @@ -41,7 +41,7 @@ tooltip: 'Create', onclick: function() { self.$el.hide(); - self.app.chart_view.reset(); + self.app.chart.reset(); self.app.chart_view.$el.show(); } }), @@ -57,11 +57,11 @@ // get chart var chart = self.app.charts.get(chart_id); + self.app.chart.copy(chart); // show edit self.$el.hide(); self.app.chart_view.$el.show(); - self.app.chart_view.setChart(chart); } }), 'delete' : new Ui.ButtonIcon({ diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r b76dd608c500d8421d0ec51f6b638b7324ecead6 config/plugins/visualizations/charts/static/views/group.js --- a/config/plugins/visualizations/charts/static/views/group.js +++ b/config/plugins/visualizations/charts/static/views/group.js @@ -1,13 +1,10 @@ // dependencies -define(['library/portlet', 'library/table', 'library/ui', 'library/utils', 'models/group'], - function(Portlet, Table, Ui, Utils, Group) { +define(['library/portlet', 'library/table', 'library/ui', 'library/utils'], + function(Portlet, Table, Ui, Utils) { // chart config return Backbone.View.extend( { - // model - group: new Group(), - // columns columns: [], @@ -18,6 +15,7 @@ // get current chart object this.chart = this.app.chart; + this.group = this.app.group; // ui elements this.message = new Ui.Message(); @@ -69,6 +67,9 @@ this.group.on('change', function() { self._refreshGroup(); }); + this.group.on('reset', function() { + self._resetGroup(); + }); }, // show @@ -77,8 +78,7 @@ }, // reset - reset: function() { - this.group.reset(); + _resetGroup: function() { this.group.set('id', Utils.uuid()); this.group.set('label', 'Group label'); }, diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r b76dd608c500d8421d0ec51f6b638b7324ecead6 config/plugins/visualizations/charts/static/views/groups.js --- a/config/plugins/visualizations/charts/static/views/groups.js +++ b/config/plugins/visualizations/charts/static/views/groups.js @@ -37,9 +37,9 @@ icon : 'fa-plus', tooltip: 'Create', onclick: function() { + self.app.group.reset(); self.app.chart_view.$el.hide(); self.app.group_view.show(); - self.app.group_view.reset(); } }), 'edit' : new Ui.ButtonIcon({ https://bitbucket.org/galaxy/galaxy-central/commits/dec86d2bd3b1/ Changeset: dec86d2bd3b1 User: guerler Date: 2014-01-16 20:10:56 Summary: Merge Affected #: 8 files diff -r b76dd608c500d8421d0ec51f6b638b7324ecead6 -r dec86d2bd3b10c16c91ec2847840c62b5e2bfe59 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -602,7 +602,11 @@ if check_migrate_tools: # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. from tool_shed.galaxy_install.migrate.check import verify_tools - verify_tools( self, install_db_url, config_file, self.config.database_engine_options ) + if combined_install_database: + install_database_options = self.config.database_engine_options + else: + install_database_options = self.config.install_database_engine_options + verify_tools( self, install_db_url, config_file, install_database_options ) from galaxy.model import mapping self.model = mapping.init( self.config.file_path, diff -r b76dd608c500d8421d0ec51f6b638b7324ecead6 -r dec86d2bd3b10c16c91ec2847840c62b5e2bfe59 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -734,8 +734,7 @@ self.tags = [] def _next_hid( self ): - # TODO: override this with something in the database that ensures - # better integrity + # this is overriden in mapping.py db_next_hid() method if len( self.datasets ) == 0: return 1 else: @@ -3446,4 +3445,7 @@ self.context = context class APIKeys( object ): - pass + def __init__( self, id=None, user_id=None, key=None): + self.id = id + self.user_id = user_id + self.key = key diff -r b76dd608c500d8421d0ec51f6b638b7324ecead6 -r dec86d2bd3b10c16c91ec2847840c62b5e2bfe59 lib/galaxy/webapps/galaxy/api/authenticate.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -0,0 +1,77 @@ +""" +API key retrieval through BaseAuth +""" + +from galaxy import util, web +from pprint import pprint +from galaxy.web.base.controller import BaseAPIController +from base64 import b64decode, b64encode +from urllib import quote, unquote +from galaxy.exceptions import ObjectNotFound +from paste.httpexceptions import HTTPBadRequest + +import logging +log = logging.getLogger( __name__ ) + +class AuthenticationController( BaseAPIController ): + + @web.expose_api_anonymous + def get_api_key( self, trans, **kwd ): + """ + def get_api_key( self, trans, **kwd ) + * GET /api/authenticate/baseauth + returns an API key for authenticated user based on BaseAuth headers + """ + email, password = self._decode_baseauth( trans.environ.get( 'HTTP_AUTHORIZATION' ) ) + + user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).all() + + if (len(user) is not 1): + # DB is inconsistent and we have more users with same email + raise ObjectNotFound + else: + user = user[0] + is_valid_user = user.check_password( password ) + + if (is_valid_user): + user_id = user.id + api_key_row = trans.sa_session.query( trans.app.model.APIKeys ).filter( trans.app.model.APIKeys.table.c.user_id == user_id ).first() + else: + trans.response.status = 500 + return "invalid password" + + return dict( api_key= api_key_row.key ) + + def _decode_baseauth( self, encoded_str ): + """Decode an encrypted HTTP basic authentication string. Returns a tuple of + the form (email, password), and raises a HTTPBadRequest exception if + nothing could be decoded. + """ + split = encoded_str.strip().split(' ') + + # If split is only one element, try to decode the email and password + # directly. + if len(split) == 1: + try: + email, password = b64decode(split[0]).split(':') + except: + raise HTTPBadRequest + + # If there are only two elements, check the first and ensure it says + # 'basic' so that we know we're about to decode the right thing. If not, + # bail out. + elif len(split) == 2: + if split[0].strip().lower() == 'basic': + try: + email, password = b64decode(split[1]).split(':') + except: + raise HTTPBadRequest + else: + raise HTTPBadRequest + + # If there are more than 2 elements, something crazy must be happening. + # Bail. + else: + raise HTTPBadRequest + + return unquote(email), unquote(password) diff -r b76dd608c500d8421d0ec51f6b638b7324ecead6 -r dec86d2bd3b10c16c91ec2847840c62b5e2bfe59 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 @@ -2,7 +2,6 @@ API operations on the datasets from library. """ import glob -import logging import operator import os import os.path diff -r b76dd608c500d8421d0ec51f6b638b7324ecead6 -r dec86d2bd3b10c16c91ec2847840c62b5e2bfe59 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -169,6 +169,16 @@ 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'] ) ) + # ============================ + # ===== AUTHENTICATE API ===== + # ============================ + + webapp.mapper.connect( 'api_key_retrieval', + '/api/authenticate/baseauth/', + controller='authenticate', + action='get_api_key', + conditions=dict( method=[ "GET" ] ) ) + # ======================= # ===== LIBRARY API ===== # ======================= diff -r b76dd608c500d8421d0ec51f6b638b7324ecead6 -r dec86d2bd3b10c16c91ec2847840c62b5e2bfe59 lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -129,7 +129,7 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, changeset_revision ) - if not repository_metadata: + if repository_metadata is None: # The changeset_revision column in the repository_metadata table has been updated with a new # value value, so find the changeset_revision to which we need to update. repo_dir = repository.repo_path( trans.app ) @@ -139,7 +139,7 @@ encoded_repository_id, new_changeset_revision ) changeset_revision = new_changeset_revision - if repository_metadata: + if repository_metadata is not None: encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id ) repository_metadata_dict = repository_metadata.to_dict( view='collection', value_mapper=self.__get_value_mapper( trans ) ) @@ -168,7 +168,8 @@ def __get_value_mapper( self, trans ): value_mapper = { 'id' : trans.security.encode_id, - 'repository_id' : trans.security.encode_id } + 'repository_id' : trans.security.encode_id, + 'user_id' : trans.security.encode_id } return value_mapper @web.expose_api diff -r b76dd608c500d8421d0ec51f6b638b7324ecead6 -r dec86d2bd3b10c16c91ec2847840c62b5e2bfe59 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -68,7 +68,8 @@ def __get_value_mapper( self, trans ): value_mapper = { 'id' : trans.security.encode_id, - 'repository_id' : trans.security.encode_id } + 'repository_id' : trans.security.encode_id, + 'user_id' : trans.security.encode_id } return value_mapper @web.expose_api_anonymous @@ -159,15 +160,33 @@ repository_dependency_repository_metadata = \ suc.get_repository_metadata_by_changeset_revision( trans, repository_dependency_id, changeset_revision ) if repository_dependency_repository_metadata is None: - log.debug( 'Cannot locate repository_metadata with id %s for repository dependency %s owned by %s.' % \ - ( str( repository_dependency_id ), str( name ), str( owner ) ) ) - continue + # The changeset_revision column in the repository_metadata table has been updated with a new + # value value, so find the changeset_revision to which we need to update. + repo_dir = repository_dependency.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository_dependency, + repo, + changeset_revision ) + repository_dependency_repository_metadata = \ + suc.get_repository_metadata_by_changeset_revision( trans, + repository_dependency_id, + new_changeset_revision ) + if repository_dependency_repository_metadata is None: + decoded_repository_dependency_id = trans.security.decode_id( repository_dependency_id ) + debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \ + ( decoded_repository_dependency_id, str( name ), str( owner ) ) + debug_msg += 'using either of these changeset_revisions: %s, %s.' % \ + ( str( changeset_revision ), str( new_changeset_revision ) ) + log.debug( debug_msg ) + continue + else: + changeset_revision = new_changeset_revision repository_dependency_repository_metadata_id = trans.security.encode_id( repository_dependency_repository_metadata.id ) repository_dependency_dict = repository_dependency.to_dict( view='element', value_mapper=self.__get_value_mapper( trans ) ) # We have to add the changeset_revision of of the repository dependency. repository_dependency_dict[ 'changeset_revision' ] = changeset_revision - repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', + repository_dependency_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=repository_dependency_repository_metadata_id ) repository_dependencies_dicts.append( repository_dependency_dict ) diff -r b76dd608c500d8421d0ec51f6b638b7324ecead6 -r dec86d2bd3b10c16c91ec2847840c62b5e2bfe59 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -724,8 +724,8 @@ def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ): """ - Return the installable changeset_revision in the repository changelog after the changeset to which after_changeset_revision refers. If there - isn't one, return None. + Return the installable changeset_revision in the repository changelog after the changeset to which + after_changeset_revision refers. If there isn't one, return None. """ changeset_revisions = get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) if len( changeset_revisions ) == 1: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Fixes in the tool shed api for mapping the repository user_id and for handling repository_dependency changeset_revision values that have been updated.
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11bdc0f5c964/ Changeset: 11bdc0f5c964 User: greg Date: 2014-01-16 20:07:28 Summary: Fixes in the tool shed api for mapping the repository user_id and for handling repository_dependency changeset_revision values that have been updated. Affected #: 3 files diff -r 1ffcb550e2f9464bf71a5f5154dff71ba0dd6379 -r 11bdc0f5c964a18e5a810abc283f7f1ec5e9f5ff lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -129,7 +129,7 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, encoded_repository_id, changeset_revision ) - if not repository_metadata: + if repository_metadata is None: # The changeset_revision column in the repository_metadata table has been updated with a new # value value, so find the changeset_revision to which we need to update. repo_dir = repository.repo_path( trans.app ) @@ -139,7 +139,7 @@ encoded_repository_id, new_changeset_revision ) changeset_revision = new_changeset_revision - if repository_metadata: + if repository_metadata is not None: encoded_repository_metadata_id = trans.security.encode_id( repository_metadata.id ) repository_metadata_dict = repository_metadata.to_dict( view='collection', value_mapper=self.__get_value_mapper( trans ) ) @@ -168,7 +168,8 @@ def __get_value_mapper( self, trans ): value_mapper = { 'id' : trans.security.encode_id, - 'repository_id' : trans.security.encode_id } + 'repository_id' : trans.security.encode_id, + 'user_id' : trans.security.encode_id } return value_mapper @web.expose_api diff -r 1ffcb550e2f9464bf71a5f5154dff71ba0dd6379 -r 11bdc0f5c964a18e5a810abc283f7f1ec5e9f5ff lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -68,7 +68,8 @@ def __get_value_mapper( self, trans ): value_mapper = { 'id' : trans.security.encode_id, - 'repository_id' : trans.security.encode_id } + 'repository_id' : trans.security.encode_id, + 'user_id' : trans.security.encode_id } return value_mapper @web.expose_api_anonymous @@ -159,15 +160,33 @@ repository_dependency_repository_metadata = \ suc.get_repository_metadata_by_changeset_revision( trans, repository_dependency_id, changeset_revision ) if repository_dependency_repository_metadata is None: - log.debug( 'Cannot locate repository_metadata with id %s for repository dependency %s owned by %s.' % \ - ( str( repository_dependency_id ), str( name ), str( owner ) ) ) - continue + # The changeset_revision column in the repository_metadata table has been updated with a new + # value value, so find the changeset_revision to which we need to update. + repo_dir = repository_dependency.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + new_changeset_revision = suc.get_next_downloadable_changeset_revision( repository_dependency, + repo, + changeset_revision ) + repository_dependency_repository_metadata = \ + suc.get_repository_metadata_by_changeset_revision( trans, + repository_dependency_id, + new_changeset_revision ) + if repository_dependency_repository_metadata is None: + decoded_repository_dependency_id = trans.security.decode_id( repository_dependency_id ) + debug_msg = 'Cannot locate repository_metadata with id %d for repository dependency %s owned by %s ' % \ + ( decoded_repository_dependency_id, str( name ), str( owner ) ) + debug_msg += 'using either of these changeset_revisions: %s, %s.' % \ + ( str( changeset_revision ), str( new_changeset_revision ) ) + log.debug( debug_msg ) + continue + else: + changeset_revision = new_changeset_revision repository_dependency_repository_metadata_id = trans.security.encode_id( repository_dependency_repository_metadata.id ) repository_dependency_dict = repository_dependency.to_dict( view='element', value_mapper=self.__get_value_mapper( trans ) ) # We have to add the changeset_revision of of the repository dependency. repository_dependency_dict[ 'changeset_revision' ] = changeset_revision - repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', + repository_dependency_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', id=repository_dependency_repository_metadata_id ) repository_dependencies_dicts.append( repository_dependency_dict ) diff -r 1ffcb550e2f9464bf71a5f5154dff71ba0dd6379 -r 11bdc0f5c964a18e5a810abc283f7f1ec5e9f5ff lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -724,8 +724,8 @@ def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ): """ - Return the installable changeset_revision in the repository changelog after the changeset to which after_changeset_revision refers. If there - isn't one, return None. + Return the installable changeset_revision in the repository changelog after the changeset to which + after_changeset_revision refers. If there isn't one, return None. """ changeset_revisions = get_ordered_metadata_changeset_revisions( repository, repo, downloadable=True ) if len( changeset_revisions ) == 1: 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: jmchilton: Fix database engine options when verifying tools using separate install database.
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1ffcb550e2f9/ Changeset: 1ffcb550e2f9 User: jmchilton Date: 2014-01-16 20:00:30 Summary: Fix database engine options when verifying tools using separate install database. Bug report and fix thanks to Jim Johnson. Affected #: 1 file diff -r dd0bf9c3d0e42246964c8d65785ece1feec6b98e -r 1ffcb550e2f9464bf71a5f5154dff71ba0dd6379 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -602,7 +602,11 @@ if check_migrate_tools: # Alert the Galaxy admin to tools that have been moved from the distribution to the tool shed. from tool_shed.galaxy_install.migrate.check import verify_tools - verify_tools( self, install_db_url, config_file, self.config.database_engine_options ) + if combined_install_database: + install_database_options = self.config.database_engine_options + else: + install_database_options = self.config.install_database_engine_options + verify_tools( self, install_db_url, config_file, install_database_options ) from galaxy.model import mapping self.model = mapping.init( self.config.file_path, 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: martenson: remove doubled import
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dd0bf9c3d0e4/ Changeset: dd0bf9c3d0e4 User: martenson Date: 2014-01-16 19:35:51 Summary: remove doubled import Affected #: 1 file diff -r 3149e4f0836584708c417c42e36250709026d18c -r dd0bf9c3d0e42246964c8d65785ece1feec6b98e 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 @@ -2,7 +2,6 @@ API operations on the datasets from library. """ import glob -import logging import operator import os import os.path 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: removed obvious bugs in api_key retrieval through API using basic authentication
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3149e4f08365/ Changeset: 3149e4f08365 User: martenson Date: 2014-01-16 19:30:53 Summary: removed obvious bugs in api_key retrieval through API using basic authentication Affected #: 1 file diff -r a24014287a29cddcd4ef392a4bde59a833c3ecab -r 3149e4f0836584708c417c42e36250709026d18c lib/galaxy/webapps/galaxy/api/authenticate.py --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -10,7 +10,6 @@ from galaxy.exceptions import ObjectNotFound from paste.httpexceptions import HTTPBadRequest - import logging log = logging.getLogger( __name__ ) @@ -23,7 +22,7 @@ * GET /api/authenticate/baseauth returns an API key for authenticated user based on BaseAuth headers """ - email, password = _decode_baseauth( trans.environ.get( 'HTTP_AUTHORIZATION' ) ) + email, password = self._decode_baseauth( trans.environ.get( 'HTTP_AUTHORIZATION' ) ) user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).all() @@ -41,38 +40,38 @@ trans.response.status = 500 return "invalid password" - return dict('api_key', api_key_row.key) + return dict( api_key= api_key_row.key ) -def _decode_baseauth( encoded_str ): - """Decode an encrypted HTTP basic authentication string. Returns a tuple of - the form (email, password), and raises a DecodeError exception if - nothing could be decoded. - """ - split = encoded_str.strip().split(' ') + def _decode_baseauth( self, encoded_str ): + """Decode an encrypted HTTP basic authentication string. Returns a tuple of + the form (email, password), and raises a HTTPBadRequest exception if + nothing could be decoded. + """ + split = encoded_str.strip().split(' ') - # If split is only one element, try to decode the email and password - # directly. - if len(split) == 1: - try: - email, password = b64decode(split[0]).split(':') - except: - raise HTTPBadRequest + # If split is only one element, try to decode the email and password + # directly. + if len(split) == 1: + try: + email, password = b64decode(split[0]).split(':') + except: + raise HTTPBadRequest - # If there are only two elements, check the first and ensure it says - # 'basic' so that we know we're about to decode the right thing. If not, - # bail out. - elif len(split) == 2: - if split[0].strip().lower() == 'basic': - try: - email, password = b64decode(split[1]).split(':') - except: - raise DecodeError + # If there are only two elements, check the first and ensure it says + # 'basic' so that we know we're about to decode the right thing. If not, + # bail out. + elif len(split) == 2: + if split[0].strip().lower() == 'basic': + try: + email, password = b64decode(split[1]).split(':') + except: + raise HTTPBadRequest + else: + raise HTTPBadRequest + + # If there are more than 2 elements, something crazy must be happening. + # Bail. else: raise HTTPBadRequest - # If there are more than 2 elements, something crazy must be happening. - # Bail. - else: - raise HTTPBadRequest - - return unquote(email), unquote(password) + return unquote(email), unquote(password) 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: api_key retrieval through API using basic authentication
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a24014287a29/ Changeset: a24014287a29 User: martenson Date: 2014-01-16 19:20:10 Summary: api_key retrieval through API using basic authentication Affected #: 3 files diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r a24014287a29cddcd4ef392a4bde59a833c3ecab lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -734,8 +734,7 @@ self.tags = [] def _next_hid( self ): - # TODO: override this with something in the database that ensures - # better integrity + # this is overriden in mapping.py db_next_hid() method if len( self.datasets ) == 0: return 1 else: @@ -3446,4 +3445,7 @@ self.context = context class APIKeys( object ): - pass + def __init__( self, id=None, user_id=None, key=None): + self.id = id + self.user_id = user_id + self.key = key diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r a24014287a29cddcd4ef392a4bde59a833c3ecab lib/galaxy/webapps/galaxy/api/authenticate.py --- /dev/null +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -0,0 +1,78 @@ +""" +API key retrieval through BaseAuth +""" + +from galaxy import util, web +from pprint import pprint +from galaxy.web.base.controller import BaseAPIController +from base64 import b64decode, b64encode +from urllib import quote, unquote +from galaxy.exceptions import ObjectNotFound +from paste.httpexceptions import HTTPBadRequest + + +import logging +log = logging.getLogger( __name__ ) + +class AuthenticationController( BaseAPIController ): + + @web.expose_api_anonymous + def get_api_key( self, trans, **kwd ): + """ + def get_api_key( self, trans, **kwd ) + * GET /api/authenticate/baseauth + returns an API key for authenticated user based on BaseAuth headers + """ + email, password = _decode_baseauth( trans.environ.get( 'HTTP_AUTHORIZATION' ) ) + + user = trans.sa_session.query( trans.app.model.User ).filter( trans.app.model.User.table.c.email == email ).all() + + if (len(user) is not 1): + # DB is inconsistent and we have more users with same email + raise ObjectNotFound + else: + user = user[0] + is_valid_user = user.check_password( password ) + + if (is_valid_user): + user_id = user.id + api_key_row = trans.sa_session.query( trans.app.model.APIKeys ).filter( trans.app.model.APIKeys.table.c.user_id == user_id ).first() + else: + trans.response.status = 500 + return "invalid password" + + return dict('api_key', api_key_row.key) + +def _decode_baseauth( encoded_str ): + """Decode an encrypted HTTP basic authentication string. Returns a tuple of + the form (email, password), and raises a DecodeError exception if + nothing could be decoded. + """ + split = encoded_str.strip().split(' ') + + # If split is only one element, try to decode the email and password + # directly. + if len(split) == 1: + try: + email, password = b64decode(split[0]).split(':') + except: + raise HTTPBadRequest + + # If there are only two elements, check the first and ensure it says + # 'basic' so that we know we're about to decode the right thing. If not, + # bail out. + elif len(split) == 2: + if split[0].strip().lower() == 'basic': + try: + email, password = b64decode(split[1]).split(':') + except: + raise DecodeError + else: + raise HTTPBadRequest + + # If there are more than 2 elements, something crazy must be happening. + # Bail. + else: + raise HTTPBadRequest + + return unquote(email), unquote(password) diff -r ee176b881f3784ab658254ff4d471bcd113f05ce -r a24014287a29cddcd4ef392a4bde59a833c3ecab lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -169,6 +169,16 @@ 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'] ) ) + # ============================ + # ===== AUTHENTICATE API ===== + # ============================ + + webapp.mapper.connect( 'api_key_retrieval', + '/api/authenticate/baseauth/', + controller='authenticate', + action='get_api_key', + conditions=dict( method=[ "GET" ] ) ) + # ======================= # ===== LIBRARY API ===== # ======================= 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: guerler: Charts: Update view organization
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ee176b881f37/ Changeset: ee176b881f37 User: guerler Date: 2014-01-16 18:24:47 Summary: Charts: Update view organization Affected #: 14 files diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/app.js --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -1,9 +1,9 @@ // dependencies define(['library/portlet', 'library/ui', 'library/utils', - 'main', 'viewport', 'create', 'config', + 'views/charts', 'views/viewport', 'views/chart', 'views/group', 'models/datasets', 'models/chart', 'models/charts', 'models/types'], function( Portlet, Ui, Utils, - Main, Viewport, Create, Config, + ChartsView, ViewportView, ChartView, GroupView, Datasets, Chart, Charts, Types ) { @@ -19,32 +19,32 @@ // link galaxy this.modal = parent.Galaxy.modal; - // create chart objects + // create chart models this.types = new Types(); this.chart = new Chart(); - this.charts = new Charts(this); + this.charts = new Charts(); // 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); + this.charts_view = new ChartsView(this); + this.group_view = new GroupView(this); + this.chart_view = new ChartView(this); + this.viewport_view = new ViewportView(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.$el); + this.portlet.append(this.charts_view.$el); + this.portlet.append(this.group_view.$el); + this.portlet.append(this.chart_view.$el); // append main - this.main.append(this.viewport.$el); + this.charts_view.append(this.viewport_view.$el); // create - this.config.$el.hide(); - this.main.$el.hide(); + this.group_view.$el.hide(); + this.charts_view.$el.hide(); // set elements this.setElement(this.portlet.$el); diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/config.js --- a/config/plugins/visualizations/charts/static/config.js +++ /dev/null @@ -1,219 +0,0 @@ -// dependencies -define(['library/portlet', 'library/table', 'library/ui', 'library/utils', 'models/group'], - function(Portlet, Table, Ui, Utils, Group) { - -// chart config -return Backbone.View.extend( -{ - // model - group: new Group(), - - // columns - columns: [], - - // initialize - initialize: function(app, options) { - // link app - this.app = app; - - // get current chart object - this.chart = this.app.chart; - - // ui elements - this.message = new Ui.Message(); - this.label = new Ui.Input({placeholder: 'Group label'}); - this.table = new Table({content: 'No data column.'}); - - // add table to portlet - var self = this; - this.portlet = new Portlet({ - icon : 'fa-edit', - label : 'Define group properties:', - operations : { - 'save' : new Ui.ButtonIcon({ - icon : 'fa-save', - tooltip : 'Save', - onclick : function() { - // save/add group - self._saveGroup(); - } - }), - 'back' : new Ui.ButtonIcon({ - icon : 'fa-caret-left', - tooltip : 'Return', - onclick : function() { - self.$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 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/create.js --- a/config/plugins/visualizations/charts/static/create.js +++ /dev/null @@ -1,207 +0,0 @@ -// 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, visible: false}); - - // 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 Chart', - 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(this.dataset.$el); - this.portlet.append((new Ui.Label({ label : 'Provide a chart title:'})).$el); - this.portlet.append(this.title.$el); - this.portlet.append((new Ui.Label({ label : 'Select a chart type:'})).$el); - this.portlet.append(this.table.$el); - this.portlet.append(this.groups.$el); - - // elements - this.setElement(this.portlet.$el); - - // hide back button on startup - this.portlet.hideOperation('back'); - - // model events - var self = this; - this.chart.on('change:title', function(chart) { - self.title.value(chart.get('title')); - }); - this.chart.on('change:type', function(chart) { - self.table.value(chart.get('type')); - }); - - // collection events - this.app.charts.on('add', function(chart) { - self.portlet.showOperation('back'); - }); - this.app.charts.on('remove', function(chart) { - if (self.app.charts.length == 1) { - self.portlet.hideOperation('back'); - } - }); - this.app.charts.on('reset', function(chart) { - self.portlet.hideOperation('back'); - }); - - // reset - this.reset(); - }, - - // reset - reset: function() { - this.chart.reset(); - this.chart.set('id', Utils.uuid()); - this.chart.set('dataset_id', this.app.options.dataset.id); - this.chart.set('type', 'bardiagram'); - this.chart.set('title', 'Chart title'); - }, - - // set chart - setChart: function(new_chart) { - this.chart.copy(new_chart); - }, - - // create chart - _saveChart: function() { - // update chart data - this.chart.set({ - type : this.table.value(), - title : this.title.value(), - dataset_id : this.dataset.value(), - date : Utils.time() - }); - - // validate - if (!this.chart.get('title')) { - this.message.update({message : 'Please enter a title for your chart.'}); - return; - } - - if (!this.chart.get('type')) { - this.message.update({message : 'Please select a chart type.'}); - return; - } - - if (this.chart.groups.length == 0) { - this.message.update({message : 'Please configure at least one data source.'}); - return; - } - - // create/get chart - var current = this.app.charts.get(this.chart.id); - if (!current) { - current = this.chart.clone(); - this.app.charts.add(current); - } - - // update chart model - current.copy(this.chart); - - // hide - this.$el.hide(); - - // update main - this.app.main.$el.show(); - } -}); - -}); \ No newline at end of file diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/groups.js --- a/config/plugins/visualizations/charts/static/groups.js +++ /dev/null @@ -1,154 +0,0 @@ -// dependencies -define(['library/portlet', 'library/table', 'library/ui', 'library/utils'], function(Portlet, Table, Ui, Utils) { - -// chart config -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) { - // link app - this.app = app; - - // get current chart object - this.chart = this.app.chart; - - // table - this.table = new Table({ - content : 'Add data columns to this table.', - ondblclick : function(group_id) { - // get group - var group = self.app.chart.groups.get(group_id); - - // show edit - self.app.create.$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 : 'Select data columns:', - 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 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce 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 @@ -48,14 +48,14 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement(this.template(this.options)); + this.setElement(this._template(this.options)); // add event $(this.el).on('click', options.onclick); }, // element - template: function(options) { + _template: function(options) { 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> ' ; @@ -80,14 +80,14 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement(this.template(this.options)); + this.setElement(this._template(this.options)); // add event $(this.el).on('click', options.onclick); }, // element - template: function(options) { + _template: function(options) { return '<div><a href="javascript:void(0)">' + options.label + '</a></div>'; } }); @@ -218,7 +218,7 @@ var ButtonMenu = Backbone.View.extend( { // main options - options: + optionsDefault: { id : '', title : '', @@ -237,9 +237,8 @@ // initialize initialize: function (options) { - // read in defaults - if (options) - this.options = _.defaults(options, this.options); + // get options + this.options = Utils.merge(options, this.optionsDefault); // add template for tab this.setElement($(this._template(this.options))); @@ -290,9 +289,8 @@ icon : null } - // read in defaults - if (options) - menuOptions = _.defaults(options, menuOptions); + // get options + menuOptions = Utils.merge(options, menuOptions); // check if submenu element is available if (!this.$menu) @@ -388,10 +386,7 @@ // initialize initialize : function(options) { // get options - if (options) - this.options = _.defaults(options, this.optionsDefault); - else - this.options = this.optionsDefault; + this.options = Utils.merge(options, this.optionsDefault); // create new element this.setElement(this.template(this.options)); @@ -430,11 +425,8 @@ // initialize initialize : function(options) { - // get options - if (options) - this.options = _.defaults(options, this.optionsDefault); - else - this.options = this.optionsDefault; + // configure options + this.options = Utils.merge(options, this.optionsDefault); // create new element this.setElement(this.template(this.options)); diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/library/ui.select.js --- a/config/plugins/visualizations/charts/static/library/ui.select.js +++ b/config/plugins/visualizations/charts/static/library/ui.select.js @@ -1,14 +1,14 @@ // dependencies define(['library/utils'], function(Utils) { - // plugin return Backbone.View.extend( { // options optionsDefault: { - id : '', - cls : '' + id : '', + cls : '', + empty : 'No data available' }, // initialize @@ -17,21 +17,41 @@ this.options = Utils.merge(options, this.optionsDefault); // create new element - this.setElement(this.template(this.options)); + this.setElement(this._template(this.options)); // add change event var self = this; if (this.options.onchange) { - this.$el.on('change', function() { self.options.onchange(self.value()) }); + this.$el.on('change', function() { self.options.onchange(self.value()); }); } + + // refresh + this._refresh(); }, // value - value : function (new_val) { - if (new_val !== undefined) { - this.$el.val(new_val); + value : function (new_value) { + // get current id/value + var before = this.$el.val(); + + // check if new_value is defined + if (new_value !== undefined) { + this.$el.val(new_value); } - return this.$el.val(); + + // get current id/value + var after = this.$el.val(); + if(after === undefined) { + return null; + } else { + // fire onchange + if ((after != before && this.options.onchange) || this.$el.find('option').length == 1) { + this.options.onchange(after); + } + + // return current value + return after; + } }, // label @@ -43,6 +63,35 @@ disabled: function() { return this.$el.is(':disabled'); }, + + // enable + enable: function() { + this.$el.prop('disabled', false); + }, + + // disable + disable: function() { + this.$el.prop('disabled', true); + }, + + // add + add: function(options) { + // add options + $(this.el).append(this._templateOption(options)); + + // refresh + this._refresh(); + }, + + // remove + remove: function(value) { + // remove option + $(this.el).find('option[value=' + value + ']').remove(); + $(this.el).trigger('change'); + + // refresh + this._refresh(); + }, // render update: function(options) { @@ -54,47 +103,46 @@ // add new options for (var key in options.data) { - $(this.el).append(this.templateOption(options.data[key])); + $(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 (this._exists(selected)) + $(this.el).val(selected); - // add selected value - if (exists) - $(this.el).val(selected); + // refresh + this._refresh(); }, - // 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(); - } - }); + // refresh + _refresh: function() { + // remove placeholder + $(this.el).find('option[value=null]').remove(); + + // count remaining entries + var remaining = $(this.el).find('option').length; + if (remaining == 0) { + // append placeholder + $(this.el).append(this._templateOption({value : 'null', label : this.options.empty})); + this.disable(); + } else { + this.enable(); + } + }, + + // exists + _exists: function(value) { + // check if selected value exists + return 0 != $(this.el).find('option[value=' + value + ']').length; }, // option - templateOption: function(options) { + _templateOption: function(options) { return '<option value="' + options.value + '">' + options.label + '</option>'; }, // element - template: function(options) { + _template: function(options) { var tmpl = '<select id="' + options.id + '" class="select ' + options.cls + ' ' + options.id + '">'; for (key in options.data) { // options diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/library/utils.js --- a/config/plugins/visualizations/charts/static/library/utils.js +++ b/config/plugins/visualizations/charts/static/library/utils.js @@ -6,21 +6,6 @@ request('GET', url, {}, success, error); }; -// delete -function del (url, success, error) { - request('DELETE', url, {}, success, error); -}; - -// post -function post (url, data, success, error) { - request('POST', url, data, success, error); -}; - -// put -function put (url, data, success, error) { - request('PUT', url, data, success, error); -}; - // generic function to send json to url function request (method, url, data, success, error) { @@ -134,11 +119,8 @@ return { cssLoadFile : cssLoadFile, cssGetAttribute : cssGetAttribute, + get : get, merge : merge, - get : get, - post : post, - del : del, - put : put, request: request, uuid: uuid, wrap : wrap, diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/main.js --- a/config/plugins/visualizations/charts/static/main.js +++ /dev/null @@ -1,150 +0,0 @@ -// dependencies -define(['library/portlet', 'library/table', 'library/ui', 'library/utils'], function(Portlet, Table, Ui, Utils) { - -// widget -return Backbone.View.extend( -{ - // initialize - initialize: function(app, options) - { - // link app - this.app = app; - - // table - this.table = new Table({ - content : 'Add charts to this table.', - ondblclick : function(chart_id) { - // get chart - var chart = self.app.charts.get(chart_id); - - // show edit - self.$el.hide(); - - // update model and show create - self.app.create.setChart(chart); - self.app.create.$el.show(); - }, - onchange : function(chart_id) { - self.app.viewport.show(chart_id); - } - }); - - // add table to portlet - var self = this; - this.portlet = new Portlet({ - icon : 'fa-list', - label : 'List of created charts:', - height : 100, - operations : { - 'new' : new Ui.ButtonIcon({ - icon : 'fa-plus', - tooltip: 'Create', - onclick: function() { - self.$el.hide(); - self.app.create.reset(); - self.app.create.$el.show(); - } - }), - 'edit' : new Ui.ButtonIcon({ - icon : 'fa-pencil', - tooltip: 'Edit', - onclick: function() { - // check if element has been selected - var chart_id = self.table.value(); - if (!chart_id) { - return; - } - - // get chart - var chart = self.app.charts.get(chart_id); - - // show edit - self.$el.hide(); - self.app.create.$el.show(); - self.app.create.setChart(chart); - } - }), - 'delete' : new Ui.ButtonIcon({ - icon : 'fa-minus', - tooltip: 'Delete', - onclick: function() { - - // check if element has been selected - var chart_id = self.table.value(); - if (!chart_id) { - return; - } - - // title - var chart = self.app.charts.get(chart_id); - - // show modal - self.app.modal.show({ - title : 'Are you sure?', - body : 'The selected chart "' + chart.get('title') + '" will be irreversibly deleted.', - buttons : { - 'Cancel' : function() {self.app.modal.hide();}, - 'Delete' : function() { - // hide modal - self.app.modal.hide(); - - // remove chart - self.app.charts.remove(chart_id); - } - } - }); - } - }), - } - }); - this.portlet.append(this.table.$el); - - // append to main - this.$el.append(this.portlet.$el); - - // events - var self = this; - this.app.charts.on('add', function(chart) { - // add - self._addChart(chart); - }); - this.app.charts.on('remove', function(chart) { - // remove - self._removeChart(chart); - }); - this.app.charts.on('change', function(chart) { - // replace - self._removeChart(chart); - self._addChart(chart); - }); - }, - - // append - append : function($el) { - this.$el.append(Utils.wrap('')); - this.$el.append($el); - }, - - // add - _addChart: function(chart) { - // add title to table - this.table.add(chart.get('title')); - - // get chart type - var type = this.app.types.get(chart.get('type')); - this.table.add(type.title); - - // add additional columns - this.table.add('Last change: ' + chart.get('date')); - this.table.prepend(chart.get('id')); - this.table.value(chart.get('id')); - }, - - // remove - _removeChart: function(chart) { - // remove from to table - this.table.remove(chart.id); - } -}); - -}); \ No newline at end of file diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/viewport.js --- a/config/plugins/visualizations/charts/static/viewport.js +++ /dev/null @@ -1,202 +0,0 @@ -// dependencies -define(['library/portlet', 'library/ui', 'library/utils'], - function(Portlet, Ui, Utils) { - -// widget -return Backbone.View.extend( -{ - // list - list: {}, - - // options - optionsDefault : - { - height : 300 - }, - - // initialize - initialize: function(app, options) - { - // link app - this.app = app; - - // link options - this.options = Utils.merge(options, this.optionsDefault); - - // add table to portlet - this.portlet = new Portlet({ - height : this.options.height, - overflow : 'hidden' - }); - - // set this element - this.setElement(this.portlet.$el); - - // events - var self = this; - - // add - this.app.charts.on('add', function(chart) { - self._addChart(chart); - }); - - // remove - this.app.charts.on('remove', function(chart) { - self._removeChart(chart.id); - }); - - // replace - this.app.charts.on('change', function(chart) { - self._removeChart(chart.id); - self._addChart(chart); - }); - }, - - // show - show: function(id) { - // hide all - this.$el.find('svg').hide(); - - var item = this.list[id]; - if (item) { - // show selected chart - this.$el.find(item.svg_id).show(); - - // this trigger d3 update events - $(window).trigger('resize'); - } - }, - - // add - _addChart: function(chart) { - // make sure that svg does not exist already - this._removeChart(chart.id); - - // create id - var svg_id = '#svg_' + chart.id; - - // create element - var chart_el = $(this._template({id: svg_id, height : this.options.height})); - - // add to portlet - this.portlet.append(chart_el); - - // backup id - this.list[chart.id] = { - svg_id : svg_id - } - - // identify chart type - var chart_type = chart.get('type'); - var chart_settings = this.app.types.get(chart_type); - - // create chart view - var self = this; - require(['charts/' + chart_type], function(ChartView) { - // create chart - var view = new ChartView(self.app, {svg_id : svg_id, chart : chart}); - - // reset chart data - var chart_data = []; - - // request data - var chart_index = 0; - chart.groups.each(function(group) { - - // add group data - chart_data.push({ - key : (chart_index + 1) + ':' + group.get('label'), - values : [] - }); - - // get data - for (var key in chart_settings.data) { - // configure request - var data_options = { - view : view, - data : chart_data, - index : chart_index, - dataset_id : group.get('dataset_id'), - column : group.get(key), - column_key : key - } - - // make request - self._data(data_options); - } - - // count - chart_index++; - }); - - // add view - self.list[chart.id].view = view; - }); - }, - - // data - _data: function(options) { - // gather objects - var view = options.view; - var data = options.data; - - // gather parameters - var index = options.index; - var column = options.column; - var dataset_id = options.dataset_id; - var column_key = options.column_key; - var group_data = data[options.index]; - - // send request - self.app.datasets.get({id : dataset_id, column: column}, function(dataset) { - // select column - var values = dataset.values[column]; - var n_values = values.length; - - // read column values - var column_values = []; - for (var i = 0; i < n_values; i++) { - var value = values[i]; - if(!isNaN(value)) { - column_values.push(value); - } else { - column_values.push(0) - } - } - - // write column values - for (var i = 0; i < n_values; i++) { - // make sure dictionary exists - if (group_data.values[i] === undefined) { - group_data.values[i] = { - x : i, - y : 0 - } - } - - // write data - group_data.values[i][column_key] = column_values[i]; - } - - // refresh view - view.refresh(data); - }); - - }, - - // remove - _removeChart: function(id) { - var item = this.list[id]; - if (item) { - d3.select(item.svg_id).remove(); - $(item.svg_id).remove(); - } - }, - - // template - _template: function(options) { - return '<svg id="' + options.id.substr(1) + '"style="height: ' + options.height + 'px;"></svg>'; - } -}); - -}); \ No newline at end of file diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/views/chart.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/views/chart.js @@ -0,0 +1,204 @@ +// dependencies +define(['library/portlet', 'library/table', 'library/ui', 'library/utils', 'models/chart', 'views/groups'], + function(Portlet, Table, Ui, Utils, Chart, GroupsView) { + +// widget +return Backbone.View.extend( +{ + // defaults options + optionsDefault: { + header : true, + content : 'No content available.' + }, + + // 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, visible: false}); + + // configure dataset + this.groups_view = new GroupsView(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 Chart', + onclick : function() { + self._saveChart(); + } + }), + 'back' : new Ui.ButtonIcon({ + icon : 'fa-caret-left', + tooltip : 'Return', + onclick : function() { + self.$el.hide(); + self.app.charts_view.$el.show(); + } + }) + } + }); + this.portlet.append(this.message.$el); + this.portlet.append(this.dataset.$el); + this.portlet.append((new Ui.Label({ label : 'Provide a chart title:'})).$el); + this.portlet.append(this.title.$el); + this.portlet.append((new Ui.Label({ label : 'Select a chart type:'})).$el); + this.portlet.append(this.table.$el); + this.portlet.append(this.groups_view.$el); + + // elements + this.setElement(this.portlet.$el); + + // hide back button on startup + this.portlet.hideOperation('back'); + + // model events + var self = this; + this.chart.on('change:title', function(chart) { + self.title.value(chart.get('title')); + }); + this.chart.on('change:type', function(chart) { + self.table.value(chart.get('type')); + }); + + // collection events + this.app.charts.on('add', function(chart) { + self.portlet.showOperation('back'); + }); + this.app.charts.on('remove', function(chart) { + if (self.app.charts.length == 1) { + self.portlet.hideOperation('back'); + } + }); + this.app.charts.on('reset', function(chart) { + self.portlet.hideOperation('back'); + }); + + // reset + this.reset(); + }, + + // reset + reset: function() { + this.chart.reset(); + this.chart.set('id', Utils.uuid()); + this.chart.set('dataset_id', this.app.options.dataset.id); + this.chart.set('type', 'bardiagram'); + this.chart.set('title', 'Chart title'); + }, + + // set chart + setChart: function(new_chart) { + this.chart.copy(new_chart); + }, + + // create chart + _saveChart: function() { + // update chart data + this.chart.set({ + type : this.table.value(), + title : this.title.value(), + dataset_id : this.dataset.value(), + date : Utils.time() + }); + + // validate + if (!this.chart.get('title')) { + this.message.update({message : 'Please enter a title for your chart.'}); + return; + } + + if (!this.chart.get('type')) { + this.message.update({message : 'Please select a chart type.'}); + return; + } + + if (this.chart.groups.length == 0) { + this.message.update({message : 'Please configure at least one data source.'}); + return; + } + + // create/get chart + var current = this.app.charts.get(this.chart.id); + if (!current) { + current = this.chart.clone(); + this.app.charts.add(current); + } + + // update chart model + current.copy(this.chart); + + // hide + this.$el.hide(); + + // update main + this.app.charts_view.$el.show(); + } +}); + +}); \ No newline at end of file diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/views/charts.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/views/charts.js @@ -0,0 +1,150 @@ +// dependencies +define(['library/portlet', 'library/table', 'library/ui', 'library/utils'], function(Portlet, Table, Ui, Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) + { + // link app + this.app = app; + + // table + this.table = new Table({ + content : 'Add charts to this table.', + ondblclick : function(chart_id) { + // get chart + var chart = self.app.charts.get(chart_id); + + // show edit + self.$el.hide(); + + // update model and show create + self.app.chart_view.setChart(chart); + self.app.chart_view.$el.show(); + }, + onchange : function(chart_id) { + self.app.viewport_view.show(chart_id); + } + }); + + // add table to portlet + var self = this; + this.portlet = new Portlet({ + icon : 'fa-list', + label : 'List of created charts:', + height : 100, + operations : { + 'new' : new Ui.ButtonIcon({ + icon : 'fa-plus', + tooltip: 'Create', + onclick: function() { + self.$el.hide(); + self.app.chart_view.reset(); + self.app.chart_view.$el.show(); + } + }), + 'edit' : new Ui.ButtonIcon({ + icon : 'fa-pencil', + tooltip: 'Edit', + onclick: function() { + // check if element has been selected + var chart_id = self.table.value(); + if (!chart_id) { + return; + } + + // get chart + var chart = self.app.charts.get(chart_id); + + // show edit + self.$el.hide(); + self.app.chart_view.$el.show(); + self.app.chart_view.setChart(chart); + } + }), + 'delete' : new Ui.ButtonIcon({ + icon : 'fa-minus', + tooltip: 'Delete', + onclick: function() { + + // check if element has been selected + var chart_id = self.table.value(); + if (!chart_id) { + return; + } + + // title + var chart = self.app.charts.get(chart_id); + + // show modal + self.app.modal.show({ + title : 'Are you sure?', + body : 'The selected chart "' + chart.get('title') + '" will be irreversibly deleted.', + buttons : { + 'Cancel' : function() {self.app.modal.hide();}, + 'Delete' : function() { + // hide modal + self.app.modal.hide(); + + // remove chart + self.app.charts.remove(chart_id); + } + } + }); + } + }), + } + }); + this.portlet.append(this.table.$el); + + // append to main + this.$el.append(this.portlet.$el); + + // events + var self = this; + this.app.charts.on('add', function(chart) { + // add + self._addChart(chart); + }); + this.app.charts.on('remove', function(chart) { + // remove + self._removeChart(chart); + }); + this.app.charts.on('change', function(chart) { + // replace + self._removeChart(chart); + self._addChart(chart); + }); + }, + + // append + append : function($el) { + this.$el.append(Utils.wrap('')); + this.$el.append($el); + }, + + // add + _addChart: function(chart) { + // add title to table + this.table.add(chart.get('title')); + + // get chart type + var type = this.app.types.get(chart.get('type')); + this.table.add(type.title); + + // add additional columns + this.table.add('Last change: ' + chart.get('date')); + this.table.prepend(chart.get('id')); + this.table.value(chart.get('id')); + }, + + // remove + _removeChart: function(chart) { + // remove from to table + this.table.remove(chart.id); + } +}); + +}); \ No newline at end of file diff -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 -r ee176b881f3784ab658254ff4d471bcd113f05ce config/plugins/visualizations/charts/static/views/group.js --- /dev/null +++ b/config/plugins/visualizations/charts/static/views/group.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.$el.hide(); + self.app.chart_view.$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.$el.hide(); + + // update main + this.app.chart_view.$el.show(); + } +}); + +}); \ No newline at end of file This diff is so big that we needed to truncate the remainder. 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 deletion of test methods after tests have been run.
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7b889da9b563/ Changeset: 7b889da9b563 User: inithello Date: 2014-01-16 17:30:25 Summary: Fix deletion of test methods after tests have been run. Affected #: 3 files diff -r 659a29d112f622db5dabb65e4105535b5aee3b30 -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -498,6 +498,7 @@ functional.test_toolbox.toolbox = app.toolbox # When testing data managers, do not test toolbox. functional.test_toolbox.build_tests( + app=app, testing_shed_tools=testing_shed_tools, master_api_key=master_api_key, user_api_key=get_user_api_key(), diff -r 659a29d112f622db5dabb65e4105535b5aee3b30 -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py +++ b/test/functional/test_toolbox.py @@ -72,13 +72,13 @@ raise -def build_tests( testing_shed_tools=False, master_api_key=None, user_api_key=None ): +def build_tests( app=None, testing_shed_tools=False, master_api_key=None, user_api_key=None ): """ If the module level variable `toolbox` is set, generate `ToolTestCase` classes for all of its tests and put them into this modules globals() so they can be discovered by nose. """ - if toolbox is None: + if app is None: return # Push all the toolbox tests to module level @@ -88,9 +88,8 @@ for key, val in G.items(): if key.startswith( 'TestForTool_' ): del G[ key ] - - for i, tool_id in enumerate( toolbox.tools_by_id ): - tool = toolbox.get_tool( tool_id ) + for i, tool_id in enumerate( app.toolbox.tools_by_id ): + tool = app.toolbox.get_tool( tool_id ) if isinstance( tool, TOOL_TYPES_NO_TEST ): #We do not test certain types of tools (e.g. Data Manager tools) as part of ToolTestCase continue diff -r 659a29d112f622db5dabb65e4105535b5aee3b30 -r 7b889da9b563bc8245977dceb5aa4b8965857aa2 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -595,21 +595,16 @@ """ tests_to_delete = [] tools_to_delete_by_id = [] - # Push all the toolbox tests to module level - G = globals() - # Eliminate all previous tests from G. - for key, val in G.items(): - if key.startswith( 'TestForTool_' ): - del G[ key ] - # Find all tests previously generated by twill. for key in test_toolbox.__dict__: if key.startswith( 'TestForTool_' ): - log.debug( 'Tool test %s discovered in test_toolbox.' % str( key ) ) # We can't delete this test just yet, we're still iterating over __dict__. tests_to_delete.append( key ) tool_id = key.replace( 'TestForTool_', '' ) for app_tool_id in app.toolbox.tools_by_id: - if app_tool_id.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ): + # Revisit this code if at some point we notice that Twill re-runs tests that should have been deleted. + # Undoubtedly the following if statement will need to be enhanced to find the tool id in question. For + # example, the following or is required because Twill replaces some spaces with underscores in test names. + if app_tool_id == tool_id or app_tool_id.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ): tools_to_delete_by_id.append( tool_id ) # Delete the discovered twill-generated tests. for key in tests_to_delete: @@ -617,16 +612,12 @@ log.debug( 'Deleting test %s from test_toolbox.' % str( key ) ) del test_toolbox.__dict__[ key ] for tool_id in tools_to_delete_by_id: - if tool_id in app.toolbox.tools_by_id: - log.debug( 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) ) - del app.toolbox.tools_by_id[ tool_id ] + log.debug( 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) ) + del app.toolbox.tools_by_id[ tool_id ] def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, install_and_test_statistics_dict ): """Test tools contained in the received repository.""" - # Set the global variable 'test_toolbox', so that test.functional.test_toolbox will generate the - # appropriate test methods. - test_toolbox.toolbox = app.toolbox # Get the attributes that identify the repository whose contained tools are being tested. name = str( repository.name ) owner = str( repository.owner ) @@ -635,7 +626,8 @@ # Generate the test methods for this installed repository. We need to pass testing_shed_tools=True here # or twill will look in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test # files. - test_toolbox.build_tests( testing_shed_tools=True, + test_toolbox.build_tests( app=app, + testing_shed_tools=True, master_api_key=install_and_test_base_util.default_galaxy_master_api_key ) # Set up nose to run the generated functional tests. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) 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 16 Jan '14

16 Jan '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4f1f6bb5bf5e/ Changeset: 4f1f6bb5bf5e User: jmchilton Date: 2014-01-16 16:30:01 Summary: Add tool execution tests for various exceptional conditions. Tool action raising exception, redirecting, and returning an error message. Affected #: 1 file diff -r ff018b067bb21760335de776f7e97a987d86c7e6 -r 4f1f6bb5bf5e975f4d40a8feeeed77795a6d69aa test/unit/tools/test_execution.py --- a/test/unit/tools/test_execution.py +++ b/test/unit/tools/test_execution.py @@ -15,6 +15,10 @@ from galaxy.util.odict import odict from tools_support import UsesApp +from galaxy import eggs +eggs.require( "Paste" ) +from paste import httpexceptions + # Simple tool with just one text parameter and output. SIMPLE_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"><command>echo "$param1" < $out1</command> @@ -92,6 +96,41 @@ # Didn't specify a rerun_remap_id so this should be None assert self.tool_action.execution_call_args[ 0 ][ "rerun_remap_job_id" ] is None + def test_execute_exception( self ): + self.__init_tool( SIMPLE_TOOL_CONTENTS ) + self.tool_action.raise_exception( ) + template, template_vars = self.__handle_with_incoming( + param1="moo", + runtool_btn="dummy", + ) + assert template == "message.mako" + assert template_vars[ "status" ] == "error" + assert "Error executing tool" in template_vars[ "message" ] + + def test_execute_errors( self ): + self.__init_tool( SIMPLE_TOOL_CONTENTS ) + self.tool_action.return_error( ) + template, template_vars = self.__handle_with_incoming( + param1="moo", + runtool_btn="dummy", + ) + assert template == "message.mako" + assert template_vars[ "status" ] == "error" + assert "Test Error Message" in template_vars[ "message" ], template_vars + + def test_redirect( self ): + self.__init_tool( SIMPLE_TOOL_CONTENTS ) + self.tool_action.expect_redirect = True + redirect_raised = False + try: + template, template_vars = self.__handle_with_incoming( + param1="moo", + runtool_btn="dummy", + ) + except httpexceptions.HTTPFound: + redirect_raised = True + assert redirect_raised + def test_remap_job( self ): self.__init_tool( SIMPLE_TOOL_CONTENTS ) template, template_vars = self.__handle_with_incoming( @@ -237,12 +276,31 @@ def __init__( self, expected_trans ): self.expected_trans = expected_trans self.execution_call_args = [] + self.expect_redirect = False + self.exception_after_exection = None + self.error_message_after_excution = None def execute( self, tool, trans, **kwds ): assert self.expected_trans == trans self.execution_call_args.append( kwds ) + num_calls = len( self.execution_call_args ) + if self.expect_redirect: + raise httpexceptions.HTTPFound( "http://google.com" ) + if self.exception_after_exection is not None: + if num_calls > self.exception_after_exection: + raise Exception( "Test Exception" ) + if self.error_message_after_excution is not None: + if num_calls > self.error_message_after_excution: + return None, "Test Error Message" + return None, odict(dict(out1="1")) + def raise_exception( self, after_execution=0 ): + self.exception_after_exection = after_execution + + def return_error( self, after_execution=0 ): + self.error_message_after_excution = after_execution + class MockTrans( object ): https://bitbucket.org/galaxy/galaxy-central/commits/659a29d112f6/ Changeset: 659a29d112f6 User: jmchilton Date: 2014-01-16 16:30:01 Summary: Rearrange __handle_execute and handle_input in Tool... Slightly cleaner this way (fewer exit points) and will enable extensions I am making downstream. Affected #: 1 file diff -r 4f1f6bb5bf5e975f4d40a8feeeed77795a6d69aa -r 659a29d112f622db5dabb65e4105535b5aee3b30 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1871,7 +1871,7 @@ errors, params = self.__check_param_values( trans, incoming, state, old_errors, process_state, history=history, source=source ) if self.__should_refresh_state( incoming ): - return self.__handle_state_refresh( trans, state, errors ) + template, template_vars = self.__handle_state_refresh( trans, state, errors ) else: # User actually clicked next or execute. @@ -1879,18 +1879,30 @@ # error messages if errors: error_message = "One or more errors were found in the input you provided. The specific errors are marked below." - return "tool_form.mako", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message ) + template = "tool_form.mako" + template_vars = dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message ) # If we've completed the last page we can execute the tool elif all_pages or state.page == self.last_page: - return self.__handle_tool_execute( trans, rerun_remap_job_id, params, history ) + tool_executed, result = self.__handle_tool_execute( trans, rerun_remap_job_id, params, history ) + if tool_executed: + template = 'tool_executed.mako' + template_vars = dict( out_data=result ) + else: + template = 'message.mako' + template_vars = dict( status='error', message=result, refresh_frames=[] ) # Otherwise move on to the next page else: - return self.__handle_page_advance( trans, state, errors ) + template, template_vars = self.__handle_page_advance( trans, state, errors ) + return template, template_vars def __should_refresh_state( self, incoming ): return not( 'runtool_btn' in incoming or 'URL' in incoming or 'ajax_upload' in incoming ) def __handle_tool_execute( self, trans, rerun_remap_job_id, params, history ): + """ + Return a pair with whether execution is successful as well as either + resulting output data or an error message indicating the problem. + """ try: _, out_data = self.execute( trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id ) except httpexceptions.HTTPFound, e: @@ -1898,16 +1910,16 @@ raise e except Exception, e: log.exception('Exception caught while attempting tool execution:') - return 'message.mako', dict( status='error', message='Error executing tool: %s' % str(e), refresh_frames=[] ) - try: - assert isinstance( out_data, odict ) - return 'tool_executed.mako', dict( out_data=out_data ) - except: + message = 'Error executing tool: %s' % str(e) + return False, message + if isinstance( out_data, odict ): + return True, out_data + else: if isinstance( out_data, str ): message = out_data else: - message = 'Failure executing tool (odict not returned from tool execution)' - return 'message.mako', dict( status='error', message=message, refresh_frames=[] ) + message = 'Failure executing tool (invalid data returned from tool execution)' + return False, message def __handle_state_refresh( self, trans, state, errors ): try: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Explicitly require UsesAnnotations mixin for the annotations api controller *after* UsesStoredWorkflowMixin.
by commits-noreply＠bitbucket.org 16 Jan '14

16 Jan '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff018b067bb2/ Changeset: ff018b067bb2 User: dannon Date: 2014-01-16 15:56:31 Summary: Explicitly require UsesAnnotations mixin for the annotations api controller *after* UsesStoredWorkflowMixin. Affected #: 1 file diff -r 2f7781fc4ce9dbb1768fd345621ec2a62000f2ae -r ff018b067bb21760335de776f7e97a987d86c7e6 lib/galaxy/webapps/galaxy/api/annotations.py --- a/lib/galaxy/webapps/galaxy/api/annotations.py +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -3,13 +3,14 @@ """ 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, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin ): +class BaseAnnotationsController( BaseAPIController, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin, UsesStoredWorkflowMixin, UsesAnnotations ): @web.expose_api def index( self, trans, **kwd ): 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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