- galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2729: Bug fixes, enhancements, code refactoring and ...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8cbdd73ab68c changeset: 2729:8cbdd73ab68c user: Greg Von Kuster <greg(a)bx.psu.edu> date: Sat Sep 19 00:25:14 2009 -0400 description: Bug fixes, enhancements, code refactoring and re-introduction of functional tests for library templates. - Fixed bug where exception was thrown when chosing a role in the admin view - The contents of inherited templates will no longer be displayed in the inherited container - Old versions of library datasets will not be displayed in the lbrary browser - Added the job.traceback information to the dataset error report - Moved the get_form_wigets method the forms.py to the FormDefinition class, renaming it to get_wigets 15 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/web/controllers/admin.py lib/galaxy/web/controllers/dataset.py lib/galaxy/web/controllers/forms.py lib/galaxy/web/controllers/library.py lib/galaxy/web/controllers/library_admin.py lib/galaxy/web/controllers/library_dataset.py lib/galaxy/web/controllers/requests.py lib/galaxy/web/controllers/requests_admin.py templates/admin/library/browse_library.mako templates/library/browse_library.mako templates/library/new_dataset.mako test/base/twilltestcase.py test/functional/test_forms_and_requests.py test/functional/test_security_and_libraries.py diffs (1993 lines): diff -r 9d615c906e6c -r 8cbdd73ab68c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Fri Sep 18 22:41:11 2009 -0400 +++ b/lib/galaxy/model/__init__.py Sat Sep 19 00:25:14 2009 -0400 @@ -14,6 +14,7 @@ from galaxy.datatypes.metadata import MetadataCollection from galaxy.security import RBACAgent, get_permitted_actions from galaxy.util.hash_util import * +from galaxy.web.form_builder import * import logging log = logging.getLogger( __name__ ) @@ -686,10 +687,23 @@ self.name = name or "Unnamed library" self.description = description self.root_folder = root_folder - def get_info_association( self, restrict=False ): + def get_info_association( self, restrict=False, inherited=False ): if self.info_association: - return self.info_association[0] - return None + return self.info_association[0], inherited + return None, inherited + def get_template_widgets( self, trans, get_contents=True ): + # See if we have any associated templates - the returned value for + # inherited is not applicable at the library level + info_association, inherited = self.get_info_association() + if info_association: + template = info_association.template + if get_contents: + # See if we have any field contents + info = info_association.info + if info: + return template.get_widgets( trans.user, contents=info.content ) + return template.get_widgets( trans.user ) + return [] class LibraryFolder( object ): def __init__( self, name=None, description=None, item_count=0, order_id=None ): @@ -708,19 +722,35 @@ folder.parent_id = self.id folder.order_id = self.item_count self.item_count += 1 - def get_info_association( self, restrict=False ): + def get_info_association( self, restrict=False, inherited=False ): # If restrict is True, we will return this folder's info_association, not inheriting. # If restrict is False, we'll return the next available info_association in the - # inheritable hierarchy + # inheritable hierarchy. True is also returned if the info_association was inherited, + # and False if not. This enables us to eliminate displaying the any contents of the inherited + # template. if self.info_association: - return self.info_association[0] + return self.info_association[0], inherited if restrict: - return None + return None, inherited if self.parent: - return self.parent.get_info_association() + return self.parent.get_info_association( inherited=True ) if self.library_root: - return self.library_root[0].get_info_association() - return None + return self.library_root[0].get_info_association( inherited=True ) + return None, inherited + def get_template_widgets( self, trans, get_contents=True ): + # See if we have any associated templates + info_association, inherited = self.get_info_association() + if info_association: + template = info_association.template + # See if we have any field contents, but only if the info_association was + # not inherited ( we do not want to display the inherited contents ). + if not inherited and get_contents: + info = info_association.info + if info: + return template.get_widgets( trans.user, info.content ) + else: + return template.get_widgets( trans.user ) + return [] @property def active_library_datasets( self ): # This needs to be a list @@ -839,15 +869,31 @@ return ldda def clear_associated_files( self, metadata_safe = False, purge = False ): return - def get_info_association( self, restrict=False ): + def get_info_association( self, restrict=False, inherited=False ): # If restrict is True, we will return this ldda's info_association whether it # exists or not. If restrict is False, we'll return the next available info_association - # in the inheritable hierarchy + # in the inheritable hierarchy. True is also returned if the info_association was inherited, + # and False if not. This enables us to eliminate displaying the any contents of the inherited + # template. if self.info_association: - return self.info_association[0] + return self.info_association[0], inherited if restrict: - return None - return self.library_dataset.folder.get_info_association() + return None, inherited + return self.library_dataset.folder.get_info_association( inherited=True ) + def get_template_widgets( self, trans, get_contents=True ): + # See if we have any associated templates + info_association, inherited = self.get_info_association() + if info_association: + template = info_association.template + # See if we have any field contents, but only if the info_association was + # not inherited ( we do not want to display the inherited contents ). + if not inherited and get_contents: + info = info_association.info + if info: + return template.get_widgets( trans.user, info.content ) + else: + return template.get_widgets( trans.user ) + return [] class LibraryInfoAssociation( object ): def __init__( self, library, form_definition, info ): @@ -1030,6 +1076,62 @@ if f['layout'] == str(layout_index): fields_dict[i] = f return fields_dict + def get_widgets( self, user, contents=[], **kwd ): + ''' + Return the list of widgets that comprise a form definition, + including field contents if any. + ''' + params = util.Params( kwd ) + widgets = [] + for index, field in enumerate( self.fields ): + field_name = 'field_%i' % index + # determine the value of the field + if field_name in kwd: + # the user had already filled out this field and the same form is re-rendered + # due to some reason like required fields have been left out. + if field[ 'type' ] == 'CheckboxField': + value = CheckboxField.is_checked( util.restore_text( params.get( field_name, False ) ) ) + else: + value = util.restore_text( params.get( field_name, '' ) ) + elif contents: + # this field has a saved value + value = str( contents[ index ] ) + else: + # if none of the above, then leave the field empty + if field[ 'type' ] == 'CheckboxField': + # Since we do not have contents, set checkbox value to False + value = False + else: + # Set other field types to empty string + value = '' + # create the field widget + field_widget = eval( field[ 'type' ] )( field_name ) + if field[ 'type' ] == 'TextField': + field_widget.set_size( 40 ) + field_widget.value = value + elif field[ 'type' ] == 'TextArea': + field_widget.set_size( 3, 40 ) + field_widget.value = value + elif field['type'] == 'AddressField': + field_widget.user = user + field_widget.value = value + field_widget.params = params + elif field[ 'type' ] == 'SelectField': + for option in field[ 'selectlist' ]: + if option == value: + field_widget.add_option( option, option, selected=True ) + else: + field_widget.add_option( option, option ) + elif field[ 'type' ] == 'CheckboxField': + field_widget.checked = value + if field[ 'required' ] == 'required': + req = 'Required' + else: + req = 'Optional' + widgets.append( dict( label=field[ 'label' ], + widget=field_widget, + helptext='%s (%s)' % ( field[ 'helptext' ], req ) ) ) + return widgets class FormDefinitionCurrent( object ): def __init__(self, form_definition=None): diff -r 9d615c906e6c -r 8cbdd73ab68c lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri Sep 18 22:41:11 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Sat Sep 19 00:25:14 2009 -0400 @@ -3,7 +3,6 @@ from galaxy import util, datatypes from galaxy.web.base.controller import * from galaxy.model.orm import * -from galaxy.web.controllers.forms import get_all_forms, get_form_widgets from galaxy.web.framework.helpers import time_ago, iff, grids import logging log = logging.getLogger( __name__ ) @@ -242,7 +241,7 @@ # whose DatasetPermissions is associated with the Role # [ ( LibraryDatasetDatasetAssociation [ action, action ] ) ] library_dataset_actions = {} - for dp in role.actions: + for dp in role.dataset_actions: for ldda in trans.app.model.LibraryDatasetDatasetAssociation \ .filter( trans.app.model.LibraryDatasetDatasetAssociation.dataset_id==dp.dataset_id ) \ .all(): diff -r 9d615c906e6c -r 8cbdd73ab68c lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri Sep 18 22:41:11 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Sat Sep 19 00:25:14 2009 -0400 @@ -35,6 +35,9 @@ ----------------------------------------------------------------------------- job info: ${info} +----------------------------------------------------------------------------- +job traceback: +${traceback} ----------------------------------------------------------------------------- (This is an automated message). """ @@ -76,6 +79,7 @@ tool_id=job.tool_id, stderr=job.stderr, stdout=job.stdout, + traceback=job.traceback, info=job.info ) ) frm = to_address # Check email a bit diff -r 9d615c906e6c -r 8cbdd73ab68c lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Fri Sep 18 22:41:11 2009 -0400 +++ b/lib/galaxy/web/controllers/forms.py Sat Sep 19 00:25:14 2009 -0400 @@ -500,10 +500,6 @@ Return all the latest forms from the form_definition_current table if all_versions is set to True. Otherwise return all the versions of all the forms from the form_definition table. - - TODO: when we add the concept of a form_definition_type ( e.g., - 'request_header', 'request_sample', 'library_template' ), filter - the query if received filter is not None. ''' if all_versions: return trans.app.model.FormDefinition.query().all() @@ -515,64 +511,3 @@ return [ fdc.latest_form for fdc in fdc_list ] else: return [ fdc.latest_form for fdc in fdc_list if fdc.latest_form.type == form_type ] - - - -def get_form_widgets( trans, form, contents=[], user=None, **kwd ): - ''' - Return the list of widgets that comprise a form definition, - including field contents if any. - ''' - params = util.Params( kwd ) - if not user: - user = trans.user - widgets = [] - for index, field in enumerate( form.fields ): - field_name = 'field_%i' % index - # determine the value of the field - if field_name in kwd: - # the user had already filled out this field and the same form is re-rendered - # due to some reason like required fields have been left out. - if field[ 'type' ] == 'CheckboxField': - value = CheckboxField.is_checked( util.restore_text( params.get( field_name, False ) ) ) - else: - value = util.restore_text( params.get( field_name, '' ) ) - elif contents: - # this field has a saved value - value = str(contents[ index ]) - else: - # if none of the above, then leave the field empty - if field[ 'type' ] == 'CheckboxField': - # Since we do not have contents, set checkbox value to False - value = False - else: - # Set other field types to empty string - value = '' - # create the field widget - field_widget = eval( field[ 'type' ] )( field_name ) - if field[ 'type' ] == 'TextField': - field_widget.set_size( 40 ) - field_widget.value = value - elif field[ 'type' ] == 'TextArea': - field_widget.set_size( 3, 40 ) - field_widget.value = value - elif field['type'] == 'AddressField': - field_widget.user = user - field_widget.value = value - field_widget.params = params - elif field[ 'type' ] == 'SelectField': - for option in field[ 'selectlist' ]: - if option == value: - field_widget.add_option( option, option, selected=True ) - else: - field_widget.add_option( option, option ) - elif field[ 'type' ] == 'CheckboxField': - field_widget.checked = value - if field[ 'required' ] == 'required': - req = 'Required' - else: - req = 'Optional' - widgets.append( dict( label=field[ 'label' ], - widget=field_widget, - helptext='%s (%s)' % ( field[ 'helptext' ], req ) ) ) - return widgets diff -r 9d615c906e6c -r 8cbdd73ab68c lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Fri Sep 18 22:41:11 2009 -0400 +++ b/lib/galaxy/web/controllers/library.py Sat Sep 19 00:25:14 2009 -0400 @@ -3,7 +3,7 @@ from galaxy.datatypes import sniff from galaxy import util from galaxy.util.odict import odict -from galaxy.web.controllers.forms import get_all_forms, get_form_widgets +from galaxy.web.controllers.forms import get_all_forms from galaxy.util.streamball import StreamBall import logging, tempfile, zipfile, tarfile, os, sys @@ -149,16 +149,7 @@ messagetype='error' ) ) if action == 'information': # See if we have any associated templates - if library.info_association: - template = library.info_association[0].template - # See if we have any field contents - info = library.info_association[0].info - if info: - widgets = get_form_widgets( trans, template, info.content ) - else: - widgets = get_form_widgets( trans, template ) - else: - widgets = [] + widgets = library.get_template_widgets( trans ) if params.get( 'rename_library_button', False ): old_name = library.name new_name = util.restore_text( params.name ) @@ -479,17 +470,7 @@ msg=util.sanitize_text( msg ), messagetype='error' ) ) # See if we have any associated templates - info_association = ldda.get_info_association() - if info_association: - template = info_association.template - # See if we have any field contents - info = info_association.info - if info: - widgets = get_form_widgets( trans, template, info.content ) - else: - widgets = get_form_widgets( trans, template ) - else: - widgets = [] + widgets = ldda.get_template_widgets( trans ) if action == 'permissions': if params.get( 'update_roles_button', False ): # The user clicked the Save button on the 'Associate With Roles' form @@ -782,6 +763,8 @@ msg=util.sanitize_text( msg ), messagetype='error' ) ) if not id or replace_dataset: + # See if we have any inherited templates, but do not inherit contents. + widgets = folder.get_template_widgets( trans, get_contents=False ) upload_option = params.get( 'upload_option', 'upload_file' ) # No dataset(s) specified, so display the upload form. Send list of data formats to the form # so the "extension" select list can be populated dynamically @@ -806,6 +789,7 @@ last_used_build=last_used_build, roles=roles, history=history, + widgets=widgets, msg=msg, messagetype=messagetype, replace_dataset=replace_dataset ) @@ -968,17 +952,7 @@ messagetype=messagetype ) elif action == 'information': # See if we have any associated templates - info_association = folder.get_info_association() - if info_association: - template = info_association.template - # See if we have any field contents - info = info_association.info - if info: - widgets = get_form_widgets( trans, template, info.content ) - else: - widgets = get_form_widgets( trans, template ) - else: - widgets = [] + widgets = folder.get_template_widgets( trans ) if params.get( 'rename_folder_button', False ): if trans.app.security_agent.can_modify_library_item( user, roles, folder ): old_name = folder.name diff -r 9d615c906e6c -r 8cbdd73ab68c lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Fri Sep 18 22:41:11 2009 -0400 +++ b/lib/galaxy/web/controllers/library_admin.py Sat Sep 19 00:25:14 2009 -0400 @@ -2,7 +2,7 @@ from galaxy import util from galaxy.web.base.controller import * from galaxy.model.orm import * -from galaxy.web.controllers.forms import get_all_forms, get_form_widgets +from galaxy.web.controllers.forms import get_all_forms # Older py compatibility try: set() @@ -96,17 +96,7 @@ return trans.fill_template( '/admin/library/new_library.mako', msg=msg, messagetype=messagetype ) elif action == 'information': # See if we have any associated templates - info_association = library.get_info_association() - if info_association: - template = info_association.template - # See if we have any field contents - info = info_association.info - if info: - widgets = get_form_widgets( trans, template, info.content ) - else: - widgets = get_form_widgets( trans, template ) - else: - widgets = [] + widgets = library.get_template_widgets( trans ) if params.get( 'rename_library_button', False ): old_name = library.name new_name = util.restore_text( params.name ) @@ -293,17 +283,7 @@ messagetype=messagetype ) elif action == 'information': # See if we have any associated templates - info_association = folder.get_info_association() - if info_association: - template = info_association.template - # See if we have any field contents - info = info_association.info - if info: - widgets = get_form_widgets( trans, template, info.content ) - else: - widgets = get_form_widgets( trans, template ) - else: - widgets = [] + widgets = folder.get_template_widgets( trans ) if params.get( 'rename_folder_button', False ): old_name = folder.name new_name = util.restore_text( params.name ) @@ -478,13 +458,8 @@ msg=util.sanitize_text( msg ), messagetype=messagetype ) ) elif not id or replace_dataset: - # See if we have any associated templates - info_association = folder.get_info_association() - if info_association: - template = info_association.template - widgets = get_form_widgets( trans, template ) - else: - widgets = [] + # See if we have any inherited templates, but do not inherit contents. + widgets = folder.get_template_widgets( trans, get_contents=False ) upload_option = params.get( 'upload_option', 'upload_file' ) # No dataset(s) specified, so display the upload form. Send list of data formats to the form # so the "extension" select list can be populated dynamically @@ -536,17 +511,7 @@ msg=util.sanitize_text( msg ), messagetype='error' ) ) # See if we have any associated templates - info_association = ldda.get_info_association() - if info_association: - template = info_association.template - # See if we have any field contents - info = info_association.info - if info: - widgets = get_form_widgets( trans, template, info.content ) - else: - widgets = get_form_widgets( trans, template ) - else: - widgets = [] + widgets = ldda.get_template_widgets( trans ) if action == 'permissions': if params.get( 'update_roles_button', False ): permissions = {} @@ -1019,8 +984,9 @@ # Since information templates are inherited, the template fields can be displayed on the information # page for a folder or library dataset when it has no info_association object. If the user has added # field contents on an inherited template via a parent's info_association, we'll need to create a new - # form_values and info_association for the current object. - info_association = library_item.get_info_association( restrict=True ) + # form_values and info_association for the current object. The value for the returned inherited variable + # is not applicable at this level. + info_association, inherited = library_item.get_info_association( restrict=True ) if info_association: template = info_association.template info = info_association.info @@ -1031,7 +997,7 @@ form_values.flush() else: # Inherit the next available info_association so we can get the template - info_association = library_item.get_info_association() + info_association, inherited = library_item.get_info_association() template = info_association.template # Create a new FormValues object form_values = trans.app.model.FormValues( template, field_contents ) diff -r 9d615c906e6c -r 8cbdd73ab68c lib/galaxy/web/controllers/library_dataset.py --- a/lib/galaxy/web/controllers/library_dataset.py Fri Sep 18 22:41:11 2009 -0400 +++ b/lib/galaxy/web/controllers/library_dataset.py Sat Sep 19 00:25:14 2009 -0400 @@ -205,7 +205,7 @@ template_field_contents = [] template = None folder = trans.app.model.LibraryFolder.get( folder_id ) - info_association = folder.get_info_association() + info_association, inherited = folder.get_info_association() if info_association: template = info_association.template for field_index in range( len( template.fields ) ): diff -r 9d615c906e6c -r 8cbdd73ab68c lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Fri Sep 18 22:41:11 2009 -0400 +++ b/lib/galaxy/web/controllers/requests.py Sat Sep 19 00:25:14 2009 -0400 @@ -9,7 +9,6 @@ from galaxy.web.form_builder import * from datetime import datetime, timedelta from cgi import escape, FieldStorage -from galaxy.web.controllers.forms import get_form_widgets log = logging.getLogger( __name__ ) @@ -480,7 +479,7 @@ libraries[ library ] = hidden_folder_ids libui = self.__library_ui(libraries, **kwd) widgets = widgets + libui - widgets = widgets + get_form_widgets(trans, request_type.request_form, contents=[], **kwd) + widgets = widgets + request_type.request_form.get_widgets( user, **kwd ) return trans.fill_template( '/requests/new_request.mako', select_request_type=select_request_type, request_type=request_type, @@ -722,7 +721,7 @@ libraries[ library ] = hidden_folder_ids libui = self.__library_ui(libraries, request, **kwd) widgets = widgets + libui - widgets = widgets + get_form_widgets(trans, request.type.request_form, request.values.content, **kwd) + widgets = widgets + request.type.request_form.get_widgets( user, request.values.content, **kwd ) return trans.fill_template( '/requests/edit_request.mako', select_request_type=select_request_type, request_type=request.type, diff -r 9d615c906e6c -r 8cbdd73ab68c lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Fri Sep 18 22:41:11 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Sat Sep 19 00:25:14 2009 -0400 @@ -7,7 +7,6 @@ import logging, tempfile, zipfile, tarfile, os, sys from galaxy.web.form_builder import * from datetime import datetime, timedelta -from galaxy.web.controllers.forms import get_form_widgets from galaxy.web.controllers.forms import get_all_forms log = logging.getLogger( __name__ ) @@ -178,7 +177,7 @@ # libraries selectbox libui = self.__library_ui(trans, request.user, request, **kwd) widgets = widgets + libui - widgets = widgets + get_form_widgets(trans, request.type.request_form, request.values.content, request.user, **kwd) + widgets = widgets + request.type.request_form.get_widgets( request.user, request.values.content, **kwd ) return trans.fill_template( '/admin/requests/edit_request.mako', select_request_type=select_request_type, request_type=request.type, @@ -687,7 +686,7 @@ # libraries selectbox libui = self.__library_ui(trans, user, **kwd) widgets = widgets + libui - widgets = widgets + get_form_widgets(trans, request_type.request_form, contents=[], user=user, **kwd) + widgets = widgets + request_type.request_form.get_widgets( user, **kwd ) return trans.fill_template( '/admin/requests/new_request.mako', select_request_type=select_request_type, request_type=request_type, diff -r 9d615c906e6c -r 8cbdd73ab68c templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Fri Sep 18 22:41:11 2009 -0400 +++ b/templates/admin/library/browse_library.mako Sat Sep 19 00:25:14 2009 -0400 @@ -85,48 +85,48 @@ else: current_version = False %> - <div class="historyItemWrapper historyItem historyItem-${ldda.state}" id="libraryItem-${ldda.id}"> - ## Header row for library items (name, state, action buttons) - <div class="historyItemTitleBar"> - <table cellspacing="0" cellpadding="0" border="0" width="100%"> - <tr> - <td width="*"> - %if selected: - <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/> - %else: - <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> - %endif - <span class="libraryItemDeleted-${ldda.deleted}"> - <a href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a> - </span> - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> - %if not library.deleted and not folder.deleted and not library_dataset.deleted: - <div popupmenu="dataset-${ldda.id}-popup"> - <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> - ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use - ##<a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a> - <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> - %if current_version: + %if current_version: + <div class="historyItemWrapper historyItem historyItem-${ldda.state}" id="libraryItem-${ldda.id}"> + ## Header row for library items (name, state, action buttons) + <div class="historyItemTitleBar"> + <table cellspacing="0" cellpadding="0" border="0" width="100%"> + <tr> + <td width="*"> + %if selected: + <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/> + %else: + <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> + %endif + <span class="libraryItemDeleted-${ldda.deleted}"> + <a href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True, deleted=deleted, show_deleted=show_deleted )}"><b>${ldda.name[:50]}</b></a> + </span> + <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> + %if not library.deleted and not folder.deleted and not library_dataset.deleted: + <div popupmenu="dataset-${ldda.id}-popup"> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> + ## We're disabling the ability to add templates at the LDDA and LibraryDataset level, but will leave this here for possible future use + ##<a class="action-button" href="${h.url_for( controller='library_admin', action='info_template', library_id=library.id, library_dataset_id=library_dataset.id, new_template=True )}">Add an information template to this dataset</a> + <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> <a class="action-button" href="${h.url_for( controller='library_admin', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> - %endif - %if ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> - %endif - <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a> - </div> - %elif not library.deleted and not folder.deleted and library_dataset.deleted: - <div popupmenu="dataset-${ldda.id}-popup"> - <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Undelete this dataset</a> - </div> - %endif - </td> - <td width="300">${ldda.message}</td> - <td width="150">${uploaded_by}</td> - <td width="60">${ldda.create_time.strftime( "%Y-%m-%d" )}</td> - </tr> - </table> + %if ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library_admin', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> + %endif + <a class="action-button" confirm="Click OK to delete dataset '${ldda.name}'." href="${h.url_for( controller='library_admin', action='delete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Delete this dataset</a> + </div> + %elif not library.deleted and not folder.deleted and library_dataset.deleted: + <div popupmenu="dataset-${ldda.id}-popup"> + <a class="action-button" href="${h.url_for( controller='library_admin', action='undelete_library_item', library_id=library.id, library_item_id=library_dataset.id, library_item_type='library_dataset' )}">Undelete this dataset</a> + </div> + %endif + </td> + <td width="300">${ldda.message}</td> + <td width="150">${uploaded_by}</td> + <td width="60">${ldda.create_time.strftime( "%Y-%m-%d" )}</td> + </tr> + </table> + </div> </div> - </div> + %endif </%def> <%def name="render_folder( folder, folder_pad, deleted, show_deleted, created_ldda_ids, library_id, root_folder=False )"> diff -r 9d615c906e6c -r 8cbdd73ab68c templates/library/browse_library.mako --- a/templates/library/browse_library.mako Fri Sep 18 22:41:11 2009 -0400 +++ b/templates/library/browse_library.mako Sat Sep 19 00:25:14 2009 -0400 @@ -91,52 +91,53 @@ uploaded_by = 'anonymous' if ldda == library_dataset.library_dataset_dataset_association: current_version = True + can_modify_library_dataset = trans.app.security_agent.can_modify_library_item( user, roles, library_dataset ) + can_manage_library_dataset = trans.app.security_agent.can_manage_library_item( user, roles, library_dataset ) else: current_version = False - can_modify_library_dataset = trans.app.security_agent.can_modify_library_item( user, roles, library_dataset ) - can_manage_library_dataset = trans.app.security_agent.can_manage_library_item( user, roles, library_dataset ) %> - - <tr class="datasetRow" - %if parent is not None: - parent="${parent}" - style="display: none;" + %if current_version: + <tr class="datasetRow" + %if parent is not None: + parent="${parent}" + style="display: none;" + %endif + > + <td style="padding-left: ${pad+20}px;"> + %if selected: + <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/> + %else: + <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> + %endif + <a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a> + <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> + <div popupmenu="dataset-${ldda.id}-popup"> + %if can_modify_library_dataset: + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> + %else: + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, information=True )}">View this dataset's information</a> + %endif + %if can_manage_library_dataset: + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> + %endif + %if can_modify_library_dataset: + <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> + %endif + %if ldda.has_data: + <a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library.id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a> + <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> + %endif + </div> + </td> + <td>${ldda.message}</td> + <td>${uploaded_by}</td> + <td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td> + </tr> + <% + my_row = row_counter.count + row_counter.increment() + %> %endif - > - <td style="padding-left: ${pad+20}px;"> - %if selected: - <input type="checkbox" name="ldda_ids" value="${ldda.id}" checked/> - %else: - <input type="checkbox" name="ldda_ids" value="${ldda.id}"/> - %endif - <a href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, info=True )}"><b>${ldda.name[:60]}</b></a> - <a id="dataset-${ldda.id}-popup" class="popup-arrow" style="display: none;">▼</a> - <div popupmenu="dataset-${ldda.id}-popup"> - %if can_modify_library_dataset: - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, edit_info=True )}">Edit this dataset's information</a> - %else: - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, information=True )}">View this dataset's information</a> - %endif - %if can_manage_library_dataset: - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, id=ldda.id, permissions=True )}">Edit this dataset's permissions</a> - %endif - %if current_version and can_modify_library_dataset: - <a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=folder.id, replace_id=library_dataset.id )}">Upload a new version of this dataset</a> - %endif - %if ldda.has_data: - <a class="action-button" href="${h.url_for( controller='library', action='datasets', library_id=library.id, ldda_ids=str( ldda.id ), do_action='add' )}">Import this dataset into your current history</a> - <a class="action-button" href="${h.url_for( controller='library', action='download_dataset_from_folder', id=ldda.id, library_id=library.id )}">Download this dataset</a> - %endif - </div> - </td> - <td>${ldda.message}</td> - <td>${uploaded_by}</td> - <td>${ldda.create_time.strftime( "%Y-%m-%d" )}</td> - </tr> - <% - my_row = row_counter.count - row_counter.increment() - %> </%def> <%def name="render_folder( folder, folder_pad, created_ldda_ids, library_id, hidden_folder_ids, parent=None, row_counter=None, root_folder=False )"> diff -r 9d615c906e6c -r 8cbdd73ab68c templates/library/new_dataset.mako --- a/templates/library/new_dataset.mako Fri Sep 18 22:41:11 2009 -0400 +++ b/templates/library/new_dataset.mako Sat Sep 19 00:25:14 2009 -0400 @@ -170,7 +170,7 @@ </div> <div style="clear: both"></div> <% folder = trans.app.model.LibraryFolder.get( folder_id ) %> - %if widgets: + %if upload_option == 'upload_file' and widgets: ${render_template_info( folder, library_id, widgets )} %endif <div class="form-row"> diff -r 9d615c906e6c -r 8cbdd73ab68c test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Sep 18 22:41:11 2009 -0400 +++ b/test/base/twilltestcase.py Sat Sep 19 00:25:14 2009 -0400 @@ -980,8 +980,6 @@ different scope in the tool) cannot be properly tested when they both exist at the same time. """ - # TODO: RC: enhance this so that all supported field types can be passed in - # and tested. If nothing is passed, all fields are TextField. self.home() self.visit_url( "%s/forms/new" % self.url ) self.check_page_for_string( 'Create a new form definition' ) @@ -1253,21 +1251,13 @@ self.check_page_for_string( check_str ) self.home() def add_library_dataset( self, filename, library_id, folder_id, folder_name, file_format='auto', - dbkey='hg18', roles=[], message='', root=False, check_template_str1='', check_template_str2='', - check_template_str3='' ): + dbkey='hg18', roles=[], message='', root=False, template_field_name1='', template_field_contents1='' ): """Add a dataset to a folder""" filename = self.get_filename( filename ) self.home() self.visit_url( "%s/library_admin/library_dataset_dataset_association?upload_option=upload_file&library_id=%s&folder_id=%s&message=%s" % \ ( self.url, library_id, folder_id, message ) ) self.check_page_for_string( 'Upload files' ) - # If we've been sent some template labels, make sure they are included in the upload form - if check_template_str1: - self.check_page_for_string( check_template_str1 ) - if check_template_str2: - self.check_page_for_string( check_template_str2 ) - if check_template_str3: - self.check_page_for_string( check_template_str3 ) tc.fv( "1", "folder_id", folder_id ) tc.formfile( "1", "file_data", filename ) tc.fv( "1", "file_format", file_format ) @@ -1275,6 +1265,9 @@ tc.fv( "1", "message", message.replace( '+', ' ' ) ) for role_id in roles: tc.fv( "1", "roles", role_id ) # form field 7 is the select list named out_groups, note the buttons... + # Add template field contents, if any... + if template_field_name1: + tc.fv( "1", template_field_name1, template_field_contents1 ) tc.submit( "new_dataset_button" ) if root: check_str = "Added 1 datasets to the library '%s' ( each is selected )." % folder_name @@ -1347,7 +1340,7 @@ self.check_page_for_string( check_str ) self.home() def upload_new_dataset_version( self, filename, library_id, folder_id, folder_name, library_dataset_id, ldda_name, file_format='auto', - dbkey='hg18', message='', check_template_str1='', check_template_str2='', check_template_str3='' ): + dbkey='hg18', message='', template_field_name1='', template_field_contents1='' ): """Upload new version(s) of a dataset""" self.home() filename = self.get_filename( filename ) @@ -1356,40 +1349,32 @@ self.check_page_for_string( 'Upload files' ) self.check_page_for_string( 'You are currently selecting a new file to replace' ) self.check_page_for_string( ldda_name ) - # If we've been sent some template labels, make sure they are included in the upload form - if check_template_str1: - self.check_page_for_string( check_template_str1 ) - if check_template_str2: - self.check_page_for_string( check_template_str2 ) - if check_template_str3: - self.check_page_for_string( check_template_str3 ) tc.formfile( "1", "file_data", filename ) tc.fv( "1", "file_format", file_format ) tc.fv( "1", "dbkey", dbkey ) tc.fv( "1", "message", message.replace( '+', ' ' ) ) + # Add template field contents, if any... + if template_field_name1: + tc.fv( "1", template_field_name1, template_field_contents1 ) tc.submit( "new_dataset_button" ) check_str = "Added 1 dataset versions to the library dataset '%s' in the folder '%s'." % ( ldda_name, folder_name ) self.check_page_for_string( check_str ) self.home() def upload_new_dataset_versions( self, library_id, folder_id, folder_name, library_dataset_id, ldda_name, file_format='auto', - dbkey='hg18', message='', check_template_str1='', check_template_str2='', check_template_str3='' ): + dbkey='hg18', message='', template_field_name1='', template_field_contents1='' ): """Upload new version(s) of a dataset using a directory of files""" self.home() self.visit_url( "%s/library_admin/library_dataset_dataset_association?upload_option=upload_directory&library_id=%s&folder_id=%s&replace_id=%s" \ % ( self.url, library_id, folder_id, library_dataset_id ) ) self.check_page_for_string( 'Upload a directory of files' ) self.check_page_for_string( 'You are currently selecting a new file to replace' ) - # If we've been sent some template labels, make sure they are included in the upload form - if check_template_str1: - self.check_page_for_string( check_template_str1 ) - if check_template_str2: - self.check_page_for_string( check_template_str2 ) - if check_template_str3: - self.check_page_for_string( check_template_str3 ) tc.fv( "1", "file_format", file_format ) tc.fv( "1", "dbkey", dbkey ) tc.fv( "1", "message", message.replace( '+', ' ' ) ) tc.fv( "1", "server_dir", "library" ) + # Add template field contents, if any... + if template_field_name1: + tc.fv( "1", template_field_name1, template_field_contents1 ) tc.submit( "new_dataset_button" ) check_str = "Added 3 dataset versions to the library dataset '%s' in the folder '%s'." % ( ldda_name, folder_name ) self.check_page_for_string( check_str ) @@ -1406,19 +1391,12 @@ self.check_page_for_string( check_str ) self.home() def add_dir_of_files_from_admin_view( self, library_id, folder_id, file_format='auto', dbkey='hg18', roles_tuple=[], - message='', check_str_after_submit='', check_str1='', check_str2='', check_str3='' ): + message='', check_str_after_submit='', template_field_name1='', template_field_contents1='' ): """Add a directory of datasets to a folder""" # roles is a list of tuples: [ ( role_id, role_description ) ] self.home() self.visit_url( "%s/library_admin/library_dataset_dataset_association?upload_option=upload_directory&library_id=%s&folder_id=%s" % ( self.url, library_id, folder_id ) ) self.check_page_for_string( 'Upload a directory of files' ) - # If we've been sent some template labels, make sure they are included in the upload form - if check_str1: - self.check_page_for_string( check_str1 ) - if check_str2: - self.check_page_for_string( check_str2 ) - if check_str3: - self.check_page_for_string( check_str3 ) tc.fv( "1", "folder_id", folder_id ) tc.fv( "1", "file_format", file_format ) tc.fv( "1", "dbkey", dbkey ) @@ -1426,24 +1404,20 @@ tc.fv( "1", "server_dir", "library" ) for role_tuple in roles_tuple: tc.fv( "1", "roles", role_tuple[1] ) # role_tuple[1] is the role name + # Add template field contents, if any... + if template_field_name1: + tc.fv( "1", template_field_name1, template_field_contents1 ) tc.submit( "new_dataset_button" ) if check_str_after_submit: self.check_page_for_string( check_str_after_submit ) self.home() def add_dir_of_files_from_libraries_view( self, library_id, folder_id, selected_dir, file_format='auto', dbkey='hg18', roles_tuple=[], - message='', check_str_after_submit='', check_str1='', check_str2='', check_str3='' ): + message='', check_str_after_submit='', template_field_name1='', template_field_contents1='' ): """Add a directory of datasets to a folder""" # roles is a list of tuples: [ ( role_id, role_description ) ] self.home() self.visit_url( "%s/library/library_dataset_dataset_association?upload_option=upload_directory&library_id=%s&folder_id=%s" % ( self.url, library_id, folder_id ) ) self.check_page_for_string( 'Upload a directory of files' ) - # If we've been sent some template labels, make sure they are included in the upload form - if check_str1: - self.check_page_for_string( check_str1 ) - if check_str2: - self.check_page_for_string( check_str2 ) - if check_str3: - self.check_page_for_string( check_str3 ) tc.fv( "1", "folder_id", folder_id ) tc.fv( "1", "file_format", file_format ) tc.fv( "1", "dbkey", dbkey ) @@ -1451,6 +1425,9 @@ tc.fv( "1", "server_dir", selected_dir ) for role_tuple in roles_tuple: tc.fv( "1", "roles", role_tuple[1] ) # role_tuple[1] is the role name + # Add template field contents, if any... + if template_field_name1: + tc.fv( "1", template_field_name1, template_field_contents1 ) tc.submit( "new_dataset_button" ) if check_str_after_submit: self.check_page_for_string( check_str_after_submit ) diff -r 9d615c906e6c -r 8cbdd73ab68c test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Fri Sep 18 22:41:11 2009 -0400 +++ b/test/functional/test_forms_and_requests.py Sat Sep 19 00:25:14 2009 -0400 @@ -41,7 +41,7 @@ global form_one_name name = form_one_name desc = "This is Form One's description" - formtype = 'Sequencing Request Form' + formtype = galaxy.model.FormDefinition.types.REQUEST self.create_form( name=name, desc=desc, formtype=formtype ) self.home() self.visit_page( 'forms/manage' ) diff -r 9d615c906e6c -r 8cbdd73ab68c test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Fri Sep 18 22:41:11 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Sat Sep 19 00:25:14 2009 -0400 @@ -475,15 +475,23 @@ library_one.refresh() self.rename_library( str( library_one.id ), library_one.name, name=name, description=description ) library_one.refresh() - """ - def test_075_library_template_features( self ): - Testing adding a template to a library, along with template features on the admin side + def test_075_library_template_features( self ): + """Testing adding a template to a library, then filling in the contents""" # Make sure a form exists - self.create_form( name='Form One', description='This is Form One' ) - current_form = galaxy.model.FormDefinitionCurrent.filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ - .order_by( desc( galaxy.model.FormDefinitionCurrent.table.c.create_time ) ).first() + form_name = 'Library template Form One' + form_desc = 'This is Form One' + form_type = galaxy.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE + self.create_form( name=form_name, desc=form_desc, formtype=form_type ) global form_one - form_one = current_form.latest_form + form_one = None + fdcs = galaxy.model.FormDefinitionCurrent.filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ + .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) \ + .all() + for fdc in fdcs: + if form_name == fdc.latest_form.name: + form_one = fdc.latest_form + break + assert form_one is not None, 'Problem retrieving form named (%s) from the database' % form_name # Add a new information template to the library template_name = 'Library Template 1' self.add_library_info_template( str( library_one.id ), @@ -491,32 +499,46 @@ str( form_one.id ), form_one.name ) # Make sure the template fields are displayed on the library information page - self.home() + field_dict = form_one.fields[ 0 ] + global form_one_field_label + form_one_field_label = '%s' % str( field_dict.get( 'label', 'Field 0' ) ) + global form_one_field_help + form_one_field_help = '%s' % str( field_dict.get( 'helptext', 'Field 0 help' ) ) + global form_one_field_required + form_one_field_required = '%s' % str( field_dict.get( 'required', 'optional' ) ).capitalize() + # Add information to the library using the template + global form_one_field_name + form_one_field_name = 'field_0' + contents = '%s library contents' % form_one_field_label self.visit_url( '%s/library_admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - num_fields = len( form_one.fields ) - for index in range( num_fields ): - label_check_str = form_one.fields[ index ][ 'label' ] - help_check_str = form_one.fields[ index ][ 'helptext' ] - required_check_str = form_one.fields[ index ][ 'required' ].capitalize() - self.check_page_for_string( label_check_str ) - self.check_page_for_string( help_check_str ) - self.check_page_for_string( required_check_str ) - # Add information to the library using the template - for index in range( num_fields ): - field_name = 'field_%i' % index - contents = '%s contents' % form_one.fields[ index ][ 'label' ] - # There are 2 forms on this page and the template is the 2nd form - tc.fv( '2', field_name, contents ) + # There are 2 forms on this page and the template is the 2nd form + tc.fv( '2', form_one_field_name, contents ) tc.submit( 'edit_info_button' ) - self.check_page_for_string ( 'The information has been updated.' ) - self.home() - # TODO: add more testing for full feature coverage - """ - def test_080_add_public_dataset_to_root_folder( self ): - """Testing adding a public dataset to the root folder""" + # For some reason, the following check: + # self.check_page_for_string ( 'The information has been updated.' ) + # ...throws the following exception - I have not idea why! + # self.check_page_for_string ( 'The information has been updated.' ) + # TypeError: 'str' object is not callable + # The work-around is to not make ANY self.check_page_for_string() calls until the next method + def test_080_edit_template_contents_admin_view( self ): + """Test editing template contents on the admin side""" + # First make sure the templlate contents from the previous method were correctly saved + contents = '%s library contents' % form_one_field_label + contents_edited = contents + ' edited' + self.visit_url( '%s/library_admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( contents ) + # Edit the contents and then save them + tc.fv( '2', form_one_field_name, contents_edited ) + tc.submit( 'edit_info_button' ) + self.check_page_for_string( 'The information has been updated.' ) + self.check_page_for_string( contents_edited ) + def test_085_add_public_dataset_to_root_folder( self ): + """Testing adding a public dataset to the root folder, making sure library template is inherited""" actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] actions.sort() message = 'Testing adding a public dataset to the root folder' + # The form_one template should be inherited to the library dataset upload form. + template_contents = "%s contents for root folder 1.bed" % form_one_field_label self.add_library_dataset( '1.bed', str( library_one.id ), str( library_one.root_folder.id ), @@ -524,7 +546,9 @@ file_format='bed', dbkey='hg18', message=message.replace( ' ', '+' ), - root=True ) + root=True, + template_field_name1=form_one_field_name, + template_field_contents1=template_contents ) global ldda_one ldda_one = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -550,17 +574,11 @@ if not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: raise AssertionError( 'The DatasetPermissions.action for dataset id %d is "%s", but it should be "manage permissions"' \ % ( ldda_one.dataset.id, dp.action ) ) - ## TODO: temporarily eliminating templates until we have the new forms features done - # Make sure the library template was inherited by the ldda - """ + # Make sure the library template contents were correctly saved self.home() self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - """ + self.check_page_for_string( template_contents ) # Make sure other users can access the dataset from the Libraries view self.logout() self.login( email=regular_user2.email ) @@ -570,23 +588,6 @@ self.logout() self.login( email=admin_user.email ) self.home() - """ - ## TODO: temporarily eliminating templates until we have the new forms features done - def test_085_editing_dataset_information( self ): - Testing editing dataset template element information - # Need the current library_item_info_element.id - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - global ldda_one_ele_2_field_name - ldda_one_ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) - ele_2_contents = 'pipe' - global ldda_one_ele_1_field_name - ldda_one_ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) - ele_1_contents = 'blown' - self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), - ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents ) - self.home() - """ def test_090_add_new_folder_to_root_folder( self ): """Testing adding a folder to a library root folder""" root_folder = library_one.root_folder @@ -602,42 +603,25 @@ self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) self.check_page_for_string( description ) - ## TODO: temporarily eliminating templates until we have the new forms features done - # Make sure the library template is inherited - """ self.home() self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - """ - self.home() - """ - ## TODO: temporarily eliminating templates until we have the new forms features done - def test_095_add_folder_template( self ): - Testing adding a new folder template to a folder - # Add a new information template to the folder - template_name = 'Folder Template 1' - ele_name_0 = 'Fu' - ele_help_0 = 'This is the Fu component'.replace( ' ', '+' ) - ele_name_1 = 'Bar' - ele_help_1 = 'This is the Bar component'.replace( ' ', '+' ) - self.home() - self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_one.id ), folder_one.name, - name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, - ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) - self.home() - self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) - self.check_page_for_string( ele_name_0 ) - check_str = ele_help_0.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - self.check_page_for_string( ele_name_1 ) - check_str = ele_help_1.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - self.home() - """ - def test_100_add_subfolder_to_folder( self ): + # Make sure the template was inherited + self.check_page_for_string( form_one_field_name ) + # Make sure the template contents were NOT inherited + contents = '%s library contents' % form_one_field_label + try: + self.check_page_for_string( contents ) + raise AssertionError, "Library level template contents were displayed in the folders inherited template fields" + except: + pass + # Add contents to the inherited template + template_contents = "%s contents for Folder One" % form_one_field_label + # There are 2 forms on this page and the template is the 2nd form + tc.fv( '2', form_one_field_name, template_contents ) + tc.submit( 'edit_info_button' ) + self.check_page_for_string( 'The information has been updated.' ) + self.check_page_for_string( template_contents ) + def test_095_add_subfolder_to_folder( self ): """Testing adding a folder to a library folder""" name = "Folder One's Subfolder" description = "This is the Folder One's subfolder" @@ -651,101 +635,25 @@ self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) self.check_page_for_string( description ) - ## TODO: temporarily eliminating templates until we have the new forms features done - # Make sure the parent folder's template is inherited self.home() - """ - self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) - self.check_page_for_string( 'Fu' ) - self.check_page_for_string( 'This is the Fu component' ) - self.check_page_for_string( 'Bar' ) - self.check_page_for_string( 'This is the Bar component' ) - # Make sure the library template is not inherited + self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( subfolder_one.id ), str( library_one.id ) ) ) + # Make sure the template was inherited + self.check_page_for_string( form_one_field_name ) + # Make sure the template contents were NOT inherited + contents = "%s contents for Folder One" % form_one_field_label try: - self.check_page_for_string( 'wind' ) - raise AssertionError( 'Library template inherited by folder when it should not have been.' ) + self.check_page_for_string( contents ) + raise AssertionError, "Parent folder level template contents were displayed in the sub-folders inherited template fields" except: pass - self.home() - """ - ## TODO: temporarily eliminating templates until we have the new forms features done - """ - def test_105_add_template_element( self ): - Testing adding a new element to an existing library template - library_one_template.refresh() - element_ids = [] - for ele in library_one_template.elements: - element_ids.append( ele.id ) - element_ids.sort() - - name = 'Library Template 1 renamed' - ele_field_name_1 = "element_name_%s" % element_ids[0] - ele_name_1 = 'wind' - ele_field_desc_1 = "element_description_%s" % element_ids[0] - ele_desc_1 = 'This is the wind component' - ele_field_name_2 = "element_name_%s" % element_ids[1] - ele_name_2 = 'bag' - ele_field_desc_2 = "element_description_%s" % element_ids[1] - ele_desc_2 = 'This is the bag component' - new_ele_name = 'Fubar' - new_ele_desc = 'This is the Fubar component' - self.add_library_info_template_element( str( library_one.id ), - str( library_one_template.id ), - library_one_template.name, - ele_field_name_1, - ele_name_1, - ele_field_desc_1, - ele_desc_1, - ele_field_name_2, - ele_name_2, - ele_field_desc_2, - ele_desc_2, - new_ele_name=new_ele_name, - new_ele_desc=new_ele_desc ) - # Make sure the new template element shows up on the existing library info page - self.home() - self.visit_url( '%s/library_admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( library_one.name ) - self.check_page_for_string( library_one.description ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'hello' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'world' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - # Make sure the new template element does not show up on existing info pages for folder_one since it has its own template - self.home() - self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) - self.check_page_for_string( 'Fu' ) - self.check_page_for_string( 'This is the Fu component' ) - self.check_page_for_string( 'Bar' ) - self.check_page_for_string( 'This is the Bar component' ) - try: - self.check_page_for_string( 'Fubar' ) - raise AssertionError( 'Changed library template inherited by folder "%s" when folder had an associated template of its own' ) - except: - pass - # Make sure the new template element shows up on existing info pages for ldda_one since it is contained in the root folder - self.home() - self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_one.id ) ) ) - # Visiting the above page will have resulted in the creation of a new LibraryItemInfoElement, so we'll retrieve it - # for later use - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - global ldda_one_ele_3_field_name - ldda_one_ele_3_field_name = "info_element_%s" % str( last_library_item_info_element.id ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - self.home() - """ - def test_110_add_2nd_new_folder_to_root_folder( self ): + # Add contents to the inherited template + template_contents = "%s contents for Folder One's Subfolder" % form_one_field_label + # There are 2 forms on this page and the template is the 2nd form + tc.fv( '2', form_one_field_name, template_contents ) + tc.submit( 'edit_info_button' ) + self.check_page_for_string( 'The information has been updated.' ) + self.check_page_for_string( template_contents ) + def test_100_add_2nd_new_folder_to_root_folder( self ): """Testing adding a 2nd folder to a library root folder""" root_folder = library_one.root_folder name = "Folder Two" @@ -760,24 +668,24 @@ self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) self.check_page_for_string( description ) - ## TODO: temporarily eliminating templates until we have the new forms features done - # Make sure the changed library template is inherited to the new folder - """ self.home() - self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - """ - self.home() - def test_115_add_public_dataset_to_root_folders_2nd_subfolder( self ): + self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( subfolder_one.id ), str( library_one.id ) ) ) + # Make sure the template was inherited + self.check_page_for_string( form_one_field_name ) + # Make sure the template contents were NOT inherited + contents = '%s library contents' % form_one_field_label + try: + self.check_page_for_string( contents ) + raise AssertionError, "Parent folder level template contents were displayed in the sub-folders inherited template fields" + except: + pass + def test_105_add_public_dataset_to_root_folders_2nd_subfolder( self ): """Testing adding a public dataset to the root folder's 2nd sub-folder""" actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] actions.sort() message = "Testing adding a public dataset to the folder named %s" % folder_two.name + # The form_one template should be inherited to the library dataset upload form. + template_contents = "%s contents for %s 2.bed" % ( form_one_field_label, folder_two.name ) self.add_library_dataset( '2.bed', str( library_one.id ), str( folder_two.id ), @@ -785,7 +693,9 @@ file_format='bed', dbkey='hg18', message=message.replace( ' ', '+' ), - root=False ) + root=False, + template_field_name1=form_one_field_name, + template_field_contents1=template_contents ) global ldda_two ldda_two = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -795,64 +705,18 @@ self.check_page_for_string( "2.bed" ) self.check_page_for_string( message ) self.check_page_for_string( admin_user.email ) - ## TODO: temporarily eliminating templates until we have the new forms features done - """ - def test_120_add_template_to_root_folders_2nd_subfolder( self ): - Testing adding a template to the root folder's 2nd sub-folder - # Before adding the folder template, the inherited library template should be displayed - self.home() - self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - self.home() - # Add a new folde template - template_name = 'Folder 2 Template' - ele_name_0 = 'kill' - ele_help_0 = 'This is the kill component'.replace( ' ', '+' ) - ele_name_1 = 'bill' - ele_help_1 = 'This is the bill component'.replace( ' ', '+' ) - self.home() - self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_two.id ), folder_two.name, - name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, - ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) - # Make sure the new template id displayed on the folder information page - self.home() - self.visit_url( '%s/library_admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) ) - self.check_page_for_string( ele_name_0 ) - check_str = ele_help_0.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - self.check_page_for_string( ele_name_1 ) - check_str = ele_help_1.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - # The library dataset ldda_two had previously inherited the library template prior to the new folder template - # being introduced, so the library template should still be displayed on the ldda information page - self.home() - self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - # Make sure the new folder template is not displayed - try: - self.check_page_for_string( 'kill' ) - raise AssertionError( 'New folder template elements incorrectly included in information page for ldda "%s"' % ldda_two.name ) - except: - pass - self.home() - """ - def test_125_add_2nd_public_dataset_to_root_folders_2nd_subfolder( self ): + # Make sure the library template contents were correctly saved + self.home() + self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) + self.check_page_for_string( template_contents ) + def test_110_add_2nd_public_dataset_to_root_folders_2nd_subfolder( self ): """Testing adding a 2nd public dataset to the root folder's 2nd sub-folder""" actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] actions.sort() message = "Testing adding a 2nd public dataset to the folder named %s" % folder_two.name + # The form_one template should be inherited to the library dataset upload form. + template_contents = "%s contents for %s 3.bed" % ( form_one_field_label, folder_two.name ) self.add_library_dataset( '3.bed', str( library_one.id ), str( folder_two.id ), @@ -860,7 +724,9 @@ file_format='bed', dbkey='hg18', message=message.replace( ' ', '+' ), - root=False ) + root=False, + template_field_name1=form_one_field_name, + template_field_contents1=template_contents ) global ldda_three ldda_three = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -870,26 +736,12 @@ self.check_page_for_string( "3.bed" ) self.check_page_for_string( message ) self.check_page_for_string( admin_user.email ) - ## TODO: temporarily eliminating templates until we have the new forms features done - """ - def test_130_editing_dataset_information_with_new_folder_template( self ): - Testing editing dataset template element information with new inherited folder template - # Need the current library_item_info_element.id - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - # Make sure the changed inherited template is included in the ldda information - ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) - ele_2_contents = 'II' - ele_2_help = 'This is the bill component' - ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) - ele_1_contents = 'Volume' - ele_1_help = 'This is the kill component' - self.edit_ldda_template_element_info( str( library_one.id ), str( folder_two.id ), str( ldda_three.id ), - ldda_three.name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents, - ele_1_help=ele_1_help, ele_2_help=ele_2_help ) - self.home() - """ - def test_135_add_dataset_with_private_role_restriction_to_folder( self ): + # Make sure the library template contents were correctly saved + self.home() + self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_three.id ) ) ) + self.check_page_for_string( template_contents ) + def test_115_add_dataset_with_private_role_restriction_to_folder( self ): """Testing adding a dataset with a private role restriction to a folder""" # Add a dataset restricted by the following: # DATASET_MANAGE_PERMISSIONS = "test(a)bx.psu.edu" via DefaultUserPermissions @@ -905,10 +757,8 @@ # setting is useless if test(a)bx.psu.edu is not an admin. This should be corrected, # by displaying a warning message on the permissions form. message ='This is a test of the fourth dataset uploaded' - ele_name_0 = 'Fu' - ele_name_1 = 'Bar' - ## TODO: temporarily eliminating templates until we have the new forms features done - """ + # The form_one template should be inherited to the library dataset upload form. + template_contents = "%s contents for %s 4.bed" % ( form_one_field_label, folder_one.name ) self.add_library_dataset( '4.bed', str( library_one.id ), str( folder_one.id ), @@ -918,18 +768,8 @@ roles=[ str( regular_user1_private_role.id ) ], message=message.replace( ' ', '+' ), root=False, - check_template_str1=ele_name_0, - check_template_str2=ele_name_1 ) - """ - self.add_library_dataset( '4.bed', - str( library_one.id ), - str( folder_one.id ), - folder_one.name, - file_format='bed', - dbkey='hg18', - roles=[ str( regular_user1_private_role.id ) ], - message=message.replace( ' ', '+' ), - root=False ) + template_field_name1=form_one_field_name, + template_field_contents1=template_contents ) global ldda_four ldda_four = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -940,7 +780,12 @@ self.check_page_for_string( message ) self.check_page_for_string( admin_user.email ) self.home() - def test_140_accessing_dataset_with_private_role_restriction( self ): + # Make sure the library template contents were correctly saved + self.home() + self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_four.id ) ) ) + self.check_page_for_string( template_contents ) + def test_120_accessing_dataset_with_private_role_restriction( self ): """Testing accessing a dataset with a private role restriction""" # admin_user should not be able to see 2.bed from the analysis view's access libraries self.home() @@ -998,7 +843,7 @@ self.logout() self.login( email=admin_user.email ) self.home() - def test_145_change_dataset_access_permission( self ): + def test_125_change_dataset_access_permission( self ): """Testing changing the access permission on a dataset with a private role restriction""" # We need admin_user to be able to access 2.bed permissions_in = [ k for k, v in galaxy.model.Dataset.permitted_actions.items() ] + \ @@ -1012,41 +857,15 @@ self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( ldda_four.name ) self.home() - ## TODO: temporarily eliminating templates until we have the new forms features done - """ - def test_150_editing_restricted_datasets_information( self ): - Testing editing a restricted library dataset's template element information - ele_1_contents = '' - ele_2_contents = '' - ele_3_contents = 'Adding Fubar text' - self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), - ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents, - ele_1_help='This is the wind component'.replace( ' ', '+' ), - ele_2_help='This is the bag component'.replace( ' ', '+' ), - ele_3_field_name=ldda_one_ele_3_field_name, ele_3_contents=ele_3_contents.replace( ' ', '+' ) ) - # Check the updated information from the libraries view - self.home() - self.visit_url( '%s/library/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s' \ - % ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) ) - self.check_page_for_string( ele_3_contents ) - try: - self.check_page_for_string( 'blown' ) - raise AssertionError( 'Element contents were not correctly eliminated when the information was edited for ldda %s' % ldda_one.name) - except: - pass - self.home() - """ - def test_155_add_dataset_with_role_associated_with_group_and_users( self ): + def test_130_add_dataset_with_role_associated_with_group_and_users( self ): """Testing adding a dataset with a role that is associated with a group and users""" self.login( email='test(a)bx.psu.edu' ) # Add a dataset restricted by role_two, which is currently associated as follows: # groups: group_two # users: test(a)bx.psu.edu, test1(a)bx.psu.edu via group_two message = 'Testing adding a dataset with a role that is associated with a group and users' - ele_name_0 = 'Fu' - ele_name_1 = 'Bar' - ## TODO: temporarily eliminating templates until we have the new forms features done - """ + # The form_one template should be inherited to the library dataset upload form. + template_contents = "%s contents for %s 5.bed" % ( form_one_field_label, folder_one.name ) self.add_library_dataset( '5.bed', str( library_one.id ), str( folder_one.id ), @@ -1056,18 +875,8 @@ roles=[ str( role_two.id ) ], message=message.replace( ' ', '+' ), root=False, - check_template_str1=ele_name_0, - check_template_str2=ele_name_1 ) - """ - self.add_library_dataset( '5.bed', - str( library_one.id ), - str( folder_one.id ), - folder_one.name, - file_format='bed', - dbkey='hg17', - roles=[ str( role_two.id ) ], - message=message.replace( ' ', '+' ), - root=False ) + template_field_name1=form_one_field_name, + template_field_contents1=template_contents ) global ldda_five ldda_five = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -1078,7 +887,12 @@ self.check_page_for_string( message ) self.check_page_for_string( admin_user.email ) self.home() - def test_160_accessing_dataset_with_role_associated_with_group_and_users( self ): + # Make sure the library template contents were correctly saved + self.home() + self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_five.id ) ) ) + self.check_page_for_string( template_contents ) + def test_135_accessing_dataset_with_role_associated_with_group_and_users( self ): """Testing accessing a dataset with a role that is associated with a group and users""" # admin_user should be able to see 5.bed since she is associated with role_two self.home() @@ -1152,7 +966,7 @@ pass self.logout() self.login( email='test(a)bx.psu.edu' ) - def test_165_copy_dataset_from_history_to_subfolder( self ): + def test_140_copy_dataset_from_history_to_subfolder( self ): """Testing copying a dataset from the current history to a subfolder""" self.new_history() self.upload_file( "6.bed" ) @@ -1173,18 +987,19 @@ ldda_six = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() assert ldda_six is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six from the database' + self.home() # Make sure the correct template was inherited - ## TODO: temporarily eliminating templates until we have the new forms features done - self.home() - """ - self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) ) - self.check_page_for_string( 'Fu' ) - self.check_page_for_string( 'This is the Fu component' ) - self.check_page_for_string( 'Bar' ) - self.check_page_for_string( 'This is the Bar component' ) - """ - def test_170_editing_dataset_attribute_info( self ): + self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' \ + % ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) ) + self.check_page_for_string( form_one_field_name ) + # Make sure the template contents were NOT inherited + contents = "%s contents for Folder One's Subfolder" % form_one_field_label + try: + self.check_page_for_string( contents ) + raise AssertionError, "Parent folder template contents were displayed in the sub-folders inherited template fields" + except: + pass + def test_145_editing_dataset_attribute_info( self ): """Testing editing a datasets attribute information""" new_ldda_name = '6.bed ( version 1 )' self.edit_ldda_attribute_info( str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ), ldda_six.name, new_ldda_name ) @@ -1193,11 +1008,21 @@ self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( ldda_six.name ) self.home() - def test_175_uploading_new_dataset_version( self ): + # Make sure the template contents were NOT inherited + self.visit_url( '%s/library/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s' \ + % ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) ) + self.check_page_for_string( form_one_field_name ) + contents = "%s contents for Folder One's Subfolder" % form_one_field_label + try: + self.check_page_for_string( contents ) + raise AssertionError, "Parent folder template contents were displayed in the sub-folders inherited template fields" + except: + pass + def test_150_uploading_new_dataset_version( self ): """Testing uploading a new version of a dataset""" message = 'Testing uploading a new version of a dataset' - ## TODO: temporarily eliminating templates until we have the new forms features done - """ + # The form_one template should be inherited to the library dataset upload form. + template_contents = "%s contents for %s new version of 6.bed" % ( form_one_field_label, folder_one.name ) self.upload_new_dataset_version( '6.bed', str( library_one.id ), str( subfolder_one.id ), @@ -1207,39 +1032,31 @@ file_format='auto', dbkey='hg18', message=message.replace( ' ', '+' ), - check_template_str1='Fu', - check_template_str2='Bar' ) - """ - self.upload_new_dataset_version( '6.bed', - str( library_one.id ), - str( subfolder_one.id ), - str( subfolder_one.name ), - str( ldda_six.library_dataset.id ), - ldda_six.name, - file_format='auto', - dbkey='hg18', - message=message.replace( ' ', '+' ) ) + template_field_name1=form_one_field_name, + template_field_contents1=template_contents ) global ldda_six_version_two ldda_six_version_two = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() assert ldda_six_version_two is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six_version_two from the database' self.home() - self.visit_url( "%s/library_admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \ + self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_two.id ) ) ) self.check_page_for_string( 'This is the latest version of this library dataset' ) # Make sure the correct template was inherited - ## TODO: temporarily eliminating templates until we have the new forms features done - """ - self.check_page_for_string( 'Fu' ) - self.check_page_for_string( 'This is the Fu component' ) - self.check_page_for_string( 'Bar' ) - self.check_page_for_string( 'This is the Bar component' ) - check_str = 'Expired versions of %s' % ldda_six_version_two.name - self.check_page_for_string( check_str ) - self.check_page_for_string( ldda_six.name ) - """ - self.home() - # Make sure th permissions are the same + self.check_page_for_string( template_contents ) + # Make sure it does not include any inherited contents + contents = "%s contents for Folder One's Subfolder" % form_one_field_label + try: + self.check_page_for_string( contents ) + raise AssertionError, "Parent folder template contents were displayed in the sub-folders inherited template fields" + except: + pass + # There are 4 forms on this page and the template is the 4th form + tc.fv( '4', form_one_field_name, template_contents ) + tc.submit( 'edit_info_button' ) + self.check_page_for_string( 'The information has been updated.' ) + self.check_page_for_string( template_contents ) + # Make sure the permissions are the same ldda_six.refresh() if len( ldda_six.actions ) != len( ldda_six_version_two.actions ): raise AssertionError( 'ldda "%s" actions "%s" != ldda "%s" actions "%s"' \ @@ -1256,47 +1073,55 @@ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) ) self.check_page_for_string( 'This is an expired version of this library dataset' ) self.home() - def test_180_uploading_new_dataset_versions( self ): + # Make sure ldda_six is no longer displayed in the library + self.visit_url( '%s/library_admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) + try: + self.check_page_for_string( ldda_six.name ) + raise AssertionError, "Old version of library dataset %s is displayed in library" % ldda_six.name + except: + pass + self.home() + def test_155_uploading_new_dataset_versions( self ): """Testing uploading new versions of a dataset using a directory of files""" message = 'Testing uploading new versions of a dataset using a directory of files' + # The form_one template should be inherited to the library dataset upload form. + template_contents = "%s contents for %s 5th new version of 6.bed" % ( form_one_field_label, folder_one.name ) ldda_six_version_two.refresh() - ## TODO: temporarily eliminating templates until we have the new forms features done - """ - self.upload_new_dataset_versions( str( library_one.id ), - str( subfolder_one.id ), - str( subfolder_one.name ), - str( ldda_six_version_two.library_dataset.id ), - ldda_six_version_two.name, - file_format='auto', - dbkey='hg18', - message=message.replace( ' ', '+' ), - check_template_str1='Fu', - check_template_str2='Bar' ) - """ - self.upload_new_dataset_versions( str( library_one.id ), - str( subfolder_one.id ), - str( subfolder_one.name ), - str( ldda_six_version_two.library_dataset.id ), - ldda_six_version_two.name, - file_format='auto', - dbkey='hg18', - message=message.replace( ' ', '+' ) ) + self.upload_new_dataset_version( '6.bed', + str( library_one.id ), + str( subfolder_one.id ), + str( subfolder_one.name ), + str( ldda_six_version_two.library_dataset.id ), + ldda_six_version_two.name, + file_format='auto', + dbkey='hg18', + message=message.replace( ' ', '+' ), + template_field_name1=form_one_field_name, + template_field_contents1=template_contents ) global ldda_six_version_five ldda_six_version_five = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() assert ldda_six_version_five is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six_version_five from the database' self.home() - self.visit_url( "%s/library_admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \ + self.visit_url( "%s/library_admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_five.id ) ) ) self.check_page_for_string( 'This is the latest version of this library dataset' ) # Make sure the correct template was inherited - ## TODO: temporarily eliminating templates until we have the new forms features done - """ - self.check_page_for_string( 'Fu' ) - self.check_page_for_string( 'This is the Fu component' ) - self.check_page_for_string( 'Bar' ) - self.check_page_for_string( 'This is the Bar component' ) - """ + self.check_page_for_string( template_contents ) + # Make sure it does not include any inherited contents + contents = "%s contents for Folder One's Subfolder" % form_one_field_label + try: + self.check_page_for_string( contents ) + raise AssertionError, "Parent folder template contents were displayed in the sub-folders inherited template fields" + except: + pass + # There are 4 forms on this page and the template is the 4th form + tc.fv( '4', form_one_field_name, template_contents ) + tc.submit( 'edit_info_button' ) + self.check_page_for_string( 'The information has been updated.' ) + self.check_page_for_string( template_contents ) + self.visit_url( "%s/library_admin/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_five.id ) ) ) check_str = 'Expired versions of %s' % ldda_six_version_five.name self.check_page_for_string( check_str ) self.check_page_for_string( ldda_six.name ) @@ -1318,32 +1143,24 @@ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_two.id ) ) ) self.check_page_for_string( 'This is an expired version of this library dataset' ) self.home() - def test_185_upload_directory_of_files_from_admin_view( self ): + def test_160_upload_directory_of_files_from_admin_view( self ): """Testing uploading a directory of files to a root folder from the Admin view""" message = 'This is a test for uploading a directory of files' + template_contents = "%s contents for directory of 3 datasets in %s" % ( form_one_field_label, folder_one.name ) roles_tuple = [ ( str( role_one.id ), role_one.name ) ] check_str = "Added 3 datasets to the library '%s' ( each is selected )." % library_one.root_folder.name - ## TODO: temporarily eliminating templates until we have the new forms features done - """ - self.add_dir_of_files_from_admin_view( str( library_one.id ), - str( library_one.root_folder.id ), - roles_tuple=roles_tuple, - message=message.replace( '+', ' ' ), - check_str=check_str, - check_template_str1='wind', - check_template_str2='bag', - check_template_str3='Fubar' ) - """ self.add_dir_of_files_from_admin_view( str( library_one.id ), str( library_one.root_folder.id ), roles_tuple=roles_tuple, - message=message.replace( '+', ' ' ) ) + message=message.replace( '+', ' ' ), + template_field_name1=form_one_field_name, + template_field_contents1=template_contents ) self.home() self.visit_page( 'library_admin/browse_library?id=%s' % ( str( library_one.id ) ) ) self.check_page_for_string( admin_user.email ) self.check_page_for_string( message ) self.home() - def test_190_change_permissions_on_datasets_uploaded_from_library_dir( self ): + def test_165_change_permissions_on_datasets_uploaded_from_library_dir( self ): """Testing changing the permissions on datasets uploaded from a directory""" # It would be nice if twill functioned such that the above test resulted in a # form with the uploaded datasets selected, but it does not ( they're not checked ), @@ -1451,7 +1268,7 @@ pass check_edit_page2( latest_3_lddas ) self.home() - def test_195_upload_directory_of_files_from_libraries_view( self ): + def test_170_upload_directory_of_files_from_libraries_view( self ): """Testing uploading a directory of files to a root folder from the Data Libraries view""" # admin_user will not have the option sto upload a directory of files from the # Libraries view since a sub-directory named the same as their email is not contained @@ -1483,7 +1300,6 @@ str( library_one.root_folder.id ), 'run1', check_str_after_submit=check_str_after_submit, - check_str1=check_str1, message=message.replace( '+', ' ' ) ) self.home() self.visit_page( 'library/browse_library?id=%s' % ( str( library_one.id ) ) ) @@ -1492,7 +1308,8 @@ self.home() self.logout() self.login( email=admin_user.email ) - def test_200_mark_group_deleted( self ): + + def test_175_mark_group_deleted( self ): """Testing marking a group as deleted""" self.home() self.visit_url( '%s/admin/groups' % self.url ) @@ -1506,13 +1323,13 @@ raise AssertionError( '%s incorrectly lost all members when it was marked as deleted.' % group_two.name ) if not group_two.roles: raise AssertionError( '%s incorrectly lost all role associations when it was marked as deleted.' % group_two.name ) - def test_205_undelete_group( self ): + def test_180_undelete_group( self ): """Testing undeleting a deleted group""" self.undelete_group( str( group_two.id ), group_two.name ) group_two.refresh() if group_two.deleted: raise AssertionError( '%s was not correctly marked as not deleted.' % group_two.name ) - def test_210_mark_role_deleted( self ): + def test_185_mark_role_deleted( self ): """Testing marking a role as deleted""" self.home() self.visit_url( '%s/admin/roles' % self.url ) @@ -1526,10 +1343,10 @@ raise AssertionError( '%s incorrectly lost all user associations when it was marked as deleted.' % role_two.name ) if not role_two.groups: raise AssertionError( '%s incorrectly lost all group associations when it was marked as deleted.' % role_two.name ) - def test_215_undelete_role( self ): + def test_190_undelete_role( self ): """Testing undeleting a deleted role""" self.undelete_role( str( role_two.id ), role_two.name ) - def test_220_mark_dataset_deleted( self ): + def test_195_mark_dataset_deleted( self ): """Testing marking a library dataset as deleted""" self.home() self.delete_library_item( str( library_one.id ), str( ldda_two.library_dataset.id ), ldda_two.name, library_item_type='library_dataset' ) @@ -1542,13 +1359,13 @@ except: pass self.home() - def test_225_display_deleted_dataset( self ): + def test_200_display_deleted_dataset( self ): """Testing displaying deleted dataset""" self.home() self.visit_url( "%s/library_admin/browse_library?id=%s&show_deleted=True" % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( ldda_two.name ) self.home() - def test_230_hide_deleted_dataset( self ): + def test_205_hide_deleted_dataset( self ): """Testing hiding deleted dataset""" self.home() self.visit_url( "%s/library_admin/browse_library?id=%s&show_deleted=False" % ( self.url, str( library_one.id ) ) ) @@ -1558,7 +1375,7 @@ except: pass self.home() - def test_235_mark_folder_deleted( self ): + def test_210_mark_folder_deleted( self ): """Testing marking a library folder as deleted""" self.home() self.delete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' ) @@ -1570,7 +1387,7 @@ except: pass self.home() - def test_240_mark_folder_undeleted( self ): + def test_215_mark_folder_undeleted( self ): """Testing marking a library folder as undeleted""" self.home() self.undelete_library_item( str( library_one.id ), str( folder_two.id ), folder_two.name, library_item_type='folder' ) @@ -1585,7 +1402,7 @@ except: pass self.home() - def test_245_mark_library_deleted( self ): + def test_220_mark_library_deleted( self ): """Testing marking a library as deleted""" self.home() # First mark folder_two as deleted to further test state saving when we undelete the library @@ -1595,7 +1412,7 @@ self.visit_page( 'library_admin/deleted_libraries' ) self.check_page_for_string( library_one.name ) self.home() - def test_240_mark_library_undeleted( self ): + def test_225_mark_library_undeleted( self ): """Testing marking a library as undeleted""" self.home() self.undelete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' ) @@ -1609,7 +1426,7 @@ except: pass self.home() - def test_250_purge_user( self ): + def test_230_purge_user( self ): """Testing purging a user account""" self.mark_user_deleted( user_id=self.security.encode_id( regular_user3.id ), email=regular_user3.email ) regular_user3.refresh() @@ -1641,7 +1458,7 @@ role = galaxy.model.Role.get( ura.role_id ) if role.type != 'private': raise AssertionError( 'UserRoleAssociations for user %s are not related with the private role.' % regular_user3.email ) - def test_255_manually_unpurge_user( self ): + def test_235_manually_unpurge_user( self ): """Testing manually un-purging a user account""" # Reset the user for later test runs. The user's private Role and DefaultUserPermissions for that role # should have been preserved, so all we need to do is reset purged and deleted. @@ -1649,7 +1466,7 @@ regular_user3.purged = False regular_user3.deleted = False regular_user3.flush() - def test_260_purge_group( self ): + def test_240_purge_group( self ): """Testing purging a group""" group_id = str( group_two.id ) self.mark_group_deleted( group_id, group_two.name ) @@ -1664,7 +1481,7 @@ raise AssertionError( "Purging the group did not delete the GroupRoleAssociations for group_id '%s'" % group_id ) # Undelete the group for later test runs self.undelete_group( group_id, group_two.name ) - def test_265_purge_role( self ): + def test_245_purge_role( self ): """Testing purging a role""" role_id = str( role_two.id ) self.mark_role_deleted( role_id, role_two.name ) @@ -1689,14 +1506,14 @@ dp = galaxy.model.DatasetPermissions.filter( galaxy.model.DatasetPermissions.table.c.role_id == role_id ).all() if dp: raise AssertionError( "Purging the role did not delete the DatasetPermissionss for role_id '%s'" % role_id ) - def test_270_manually_unpurge_role( self ): + def test_250_manually_unpurge_role( self ): """Testing manually un-purging a role""" # Manually unpurge, then undelete the role for later test runs # TODO: If we decide to implement the GUI feature for un-purging a role, replace this with a method call role_two.purged = False role_two.flush() self.undelete_role( str( role_two.id ), role_two.name ) - def test_275_purge_library( self ): + def test_255_purge_library( self ): """Testing purging a library""" self.home() self.delete_library_item( str( library_one.id ), str( library_one.id ), library_one.name, library_item_type='library' ) @@ -1732,7 +1549,7 @@ raise AssertionError( 'The library_dataset id %s named "%s" has not been marked as deleted.' % \ ( str( library_dataset.id ), library_dataset.name ) ) check_folder( library_one.root_folder ) - def test_280_reset_data_for_later_test_runs( self ): + def test_260_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" ################## # Eliminate all non-private roles

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[hg] galaxy 2723: Commenting out functional test for fastx_colla...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/5e78a1fd1351 changeset: 2723:5e78a1fd1351 user: guru date: Fri Sep 18 15:48:06 2009 -0400 description: Commenting out functional test for fastx_collapser tool as the order of sequences in the output seems to differ between 32 bit and 64 bit machines. 1 file(s) affected in this change: tools/fastx_toolkit/fastx_collapser.xml diffs (19 lines): diff -r 6ed5f088a2ad -r 5e78a1fd1351 tools/fastx_toolkit/fastx_collapser.xml --- a/tools/fastx_toolkit/fastx_collapser.xml Fri Sep 18 15:28:18 2009 -0400 +++ b/tools/fastx_toolkit/fastx_collapser.xml Fri Sep 18 15:48:06 2009 -0400 @@ -6,13 +6,14 @@ <param format="fastqsolexa,fasta" name="input" type="data" label="Library to collapse" /> </inputs> +  <outputs> <data format="fasta" name="output" metadata_source="input" /> </outputs>

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[hg] galaxy 2725: Backed out changeset 4e93d6c5665b
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/cb9b12f8e127 changeset: 2725:cb9b12f8e127 user: James Taylor <james(a)jamestaylor.org> date: Fri Sep 18 16:07:17 2009 -0400 description: Backed out changeset 4e93d6c5665b 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r 4e93d6c5665b -r cb9b12f8e127 eggs.ini --- a/eggs.ini Fri Sep 18 15:59:19 2009 -0400 +++ b/eggs.ini Fri Sep 18 16:07:17 2009 -0400 @@ -57,12 +57,12 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r405b4a48b824 +bx_python = _dev_r4bf1f32e6b76 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://bitbucket.org/james_taylor/bx-python/get/405b4a48b824.gz +bx_python = http://bitbucket.org/james_taylor/bx-python/get/4bf1f32e6b76.bz2 Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz

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[hg] galaxy 2727: Comment out references to track store from app.py
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/71dbd24649e4 changeset: 2727:71dbd24649e4 user: James Taylor <james(a)jamestaylor.org> date: Fri Sep 18 21:04:58 2009 -0400 description: Comment out references to track store from app.py 1 file(s) affected in this change: lib/galaxy/app.py diffs (21 lines): diff -r 891e1e2a407d -r 71dbd24649e4 lib/galaxy/app.py --- a/lib/galaxy/app.py Fri Sep 18 16:09:14 2009 -0400 +++ b/lib/galaxy/app.py Fri Sep 18 21:04:58 2009 -0400 @@ -1,7 +1,7 @@ import sys, os, atexit from galaxy import config, jobs, util, tools, web -from galaxy.tracks import store +## from galaxy.tracks import store from galaxy.web import security import galaxy.model import galaxy.datatypes.registry @@ -69,7 +69,7 @@ self.job_queue = self.job_manager.job_queue self.job_stop_queue = self.job_manager.job_stop_queue # Track Store - self.track_store = store.TrackStoreManager( self.config.track_store_path ) + ## self.track_store = store.TrackStoreManager( self.config.track_store_path ) def shutdown( self ): self.job_manager.shutdown()

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[hg] galaxy 2728: minor track typos
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9d615c906e6c changeset: 2728:9d615c906e6c user: Kanwei Li <kanwei(a)gmail.com> date: Fri Sep 18 22:41:11 2009 -0400 description: minor track typos 1 file(s) affected in this change: lib/galaxy/web/controllers/tracks.py diffs (30 lines): diff -r 71dbd24649e4 -r 9d615c906e6c lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Fri Sep 18 21:04:58 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Fri Sep 18 22:41:11 2009 -0400 @@ -4,7 +4,7 @@ Track browsers are currently transient -- nothing is stored to the database when a browser is created. Building a browser consists of selecting a set of datasets associated with the same dbkey to display. Once selected, jobs -are started to create any neccesary indexes in the background, and the user +are started to create any necessary indexes in the background, and the user is redirected to the browser interface, which loads the appropriate datasets. Problems @@ -105,7 +105,7 @@ dbkey = dataset.dbkey chrom_lengths = self._chroms( trans, dbkey ) if chrom_lengths is None: - error( "No chromosome lengths file found for '%s'" ) + error( "No chromosome lengths file found for '%s'" % dataset.name ) return trans.fill_template( 'tracks/browser.mako', dataset_ids=dataset_ids, tracks=tracks, @@ -186,7 +186,7 @@ return dataset # See if we can convert the dataset if type not in dataset.get_converter_types(): - log.debug( "Converstion from '%s' to '%d' not possible", dataset.extension, type ) + log.debug( "Conversion from '%s' to '%d' not possible", dataset.extension, type ) return None # See if converted dataset already exists converted_datasets = dataset.get_converted_files_by_type( type )

1 0

[hg] galaxy 2726: Allow array_tree.py to still load with older b...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/891e1e2a407d changeset: 2726:891e1e2a407d user: James Taylor <james(a)jamestaylor.org> date: Fri Sep 18 16:09:14 2009 -0400 description: Allow array_tree.py to still load with older bx (but track browser won't work) 1 file(s) affected in this change: lib/galaxy/visualization/tracks/data/array_tree.py diffs (15 lines): diff -r cb9b12f8e127 -r 891e1e2a407d lib/galaxy/visualization/tracks/data/array_tree.py --- a/lib/galaxy/visualization/tracks/data/array_tree.py Fri Sep 18 16:07:17 2009 -0400 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Fri Sep 18 16:09:14 2009 -0400 @@ -3,7 +3,10 @@ """ import pkg_resources; pkg_resources.require( "bx-python" ) -from bx.arrays.array_tree import FileArrayTreeDict +try: + from bx.arrays.array_tree import FileArrayTreeDict +except: + pass from math import floor, ceil, log # Maybe this should be included in the datatype itself, so users can add their

1 0

[hg] galaxy 2724: Update bx egg
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4e93d6c5665b changeset: 2724:4e93d6c5665b user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Sep 18 15:59:19 2009 -0400 description: Update bx egg 1 file(s) affected in this change: eggs.ini diffs (18 lines): diff -r 5e78a1fd1351 -r 4e93d6c5665b eggs.ini --- a/eggs.ini Fri Sep 18 15:48:06 2009 -0400 +++ b/eggs.ini Fri Sep 18 15:59:19 2009 -0400 @@ -57,12 +57,12 @@ MySQL_python = _5.0.67_static python_lzo = _static flup = .dev_r2311 -bx_python = _dev_r4bf1f32e6b76 +bx_python = _dev_r405b4a48b824 nose = .dev_r101 ; source location, necessary for scrambling [source] -bx_python = http://bitbucket.org/james_taylor/bx-python/get/4bf1f32e6b76.bz2 +bx_python = http://bitbucket.org/james_taylor/bx-python/get/405b4a48b824.gz Cheetah = http://voxel.dl.sourceforge.net/sourceforge/cheetahtemplate/Cheetah-1.0.tar… DRMAA_python = http://gridengine.sunsource.net/files/documents/7/36/DRMAA-python-0.2.tar.gz MySQL_python = http://superb-west.dl.sourceforge.net/sourceforge/mysql-python/MySQL-python… http://downloads.mysql.com/archives/mysql-5.0/mysql-5.0.67.tar.gz

1 0

[hg] galaxy 2721: More work on server side for tracks. Now uses ...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/bed484895e2d changeset: 2721:bed484895e2d user: James Taylor <james(a)jamestaylor.org> date: Fri Sep 18 15:15:39 2009 -0400 description: More work on server side for tracks. Now uses converters instead of indexers. A wiggle to array_tree converter is provided. Still need to purge indexer stuff. This will not work without new bx egg (or likely at all) 12 file(s) affected in this change: datatypes_conf.xml.sample lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml lib/galaxy/tracks/__init__.py lib/galaxy/tracks/messages.py lib/galaxy/tracks/store.py lib/galaxy/visualization/__init__.py lib/galaxy/visualization/tracks/__init__.py lib/galaxy/visualization/tracks/data/__init__.py lib/galaxy/visualization/tracks/data/array_tree.py lib/galaxy/web/controllers/tracks.py static/scripts/trackster.js diffs (626 lines): diff -r 3f3712d36034 -r bed484895e2d datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Fri Sep 18 15:18:57 2009 -0400 +++ b/datatypes_conf.xml.sample Fri Sep 18 15:15:39 2009 -0400 @@ -58,8 +58,9 @@ <datatype extension="blastxml" type="galaxy.datatypes.xml:BlastXml" display_in_upload="true"/> <datatype extension="txtseq.zip" type="galaxy.datatypes.images:Txtseq" mimetype="application/zip" display_in_upload="true"/> <datatype extension="wig" type="galaxy.datatypes.interval:Wiggle" display_in_upload="true"> - <indexer file="wiggle.xml" /> + <converter file="wiggle_to_array_tree_converter.xml" target_datatype="array_tree"/> </datatype> + <datatype extension="array_tree" type="galaxy.datatypes.data:Data" />  <datatype extension="acedb" type="galaxy.datatypes.data:Text"/> <datatype extension="asn1" type="galaxy.datatypes.data:Text"/> diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,29 @@ +#!/usr/bin/env python + +from __future__ import division + +import sys + +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.arrays.array_tree import * +from bx.arrays.wiggle import IntervalReader + +def main(): + + input_fname = sys.argv[1] + out_fname = sys.argv[2] + + reader = IntervalReader( open( input_fname ) ) + + # Fill array from wiggle + d = array_tree_dict_from_wiggle_reader( reader, {} ) + + for value in d.itervalues(): + value.root.build_summary() + + f = open( out_fname, "w" ) + FileArrayTreeDict.dict_to_file( d, f ) + f.close() + +if __name__ == "__main__": + main() \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.xml Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,14 @@ +<tool id="INDEXER_Wiggle_0" name="Index Wiggle for Track Viewer"> +  + <command interpreter="python">wiggle_to_array_tree_converter.py $input $output</command> + <inputs> + <page> + <param format="wiggle" name="input" type="data" label="Choose wiggle"/> + </page> + </inputs> + <outputs> + <data format="array_tree" name="output"/> + </outputs> + <help> + </help> +</tool> \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/tracks/messages.py --- a/lib/galaxy/tracks/messages.py Fri Sep 18 15:18:57 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,4 +0,0 @@ -PENDING = "pending" -NO_DATA = "no data" -NO_CHROMOSOME = "no chromosome" -DATA = "data" diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/tracks/store.py --- a/lib/galaxy/tracks/store.py Fri Sep 18 15:18:57 2009 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,87 +0,0 @@ -import os -import re -from string import Template -from galaxy.util import sanitize_text - -# extra mappings/escape to keep users from traversing around the -# filesystem and wreaking havoc -extra_mappings = { r"/": "__fs__", r"^manifest.tab$": "__manifest.tab__" } - -def sanitize_name( name ): - name = sanitize_text( name ) - for key, value in extra_mappings.items(): - name = re.sub( key, value, name ) - return name - -class TemplateSubber( object ): - def __init__(self, obj): - self.obj = obj - def get( self, key, default=None ): - return getattr(self.obj, key, default) - def __getitem__(self, key): - return self.get(key) - -class TrackStoreManager( object ): - def __init__(self, path=""): - self.path = path - - def get( self, dataset ): - s = Template(self.path) - return TrackStore( path=s.substitute(TemplateSubber(dataset)) ) - -class TrackStore( object ): - MANIFEST_NAME = "manifest.tab" - - def __init__(self, path=""): - self.path = path - - def get_manifest( self ): - if not self.exists: raise self.DoesNotExist("TrackStore at %s does not exist." % self.path) - manifest_path = os.path.join( self.path, self.MANIFEST_NAME ) - if os.path.exists( manifest_path ): - manifest = {} - for line in open( manifest_path ): - line = line.rstrip("\n\r") - fields = line.split("\t") - manifest[fields[0]] = fields[1:] - return manifest - else: - raise self.DoesNotExist( "Manifest for TrackStore object could not be found." ) - - def get(self, chrom="chr1", resolution=None, **kwargs): - if not self.exists: raise self.DoesNotExist("TrackStore at %s does not exist." % self.path) - object_path = self._get_object_path( chrom, resolution ) - if os.path.exists( object_path ): - return open( object_path, "rb" ) - else: - try: - return kwargs['default'] - except KeyError: - raise self.DoesNotExist("TrackStore object at %s does not exist." % object_path ) - - def set(self, chrom="chr1", resolution=None, data=None): - if not self.exists: self._build_path( self.path ) - if not data: return - object_path = self._get_object_path( chrom, resolution ) - fd = open( object_path, "wb" ) - fd.write( data ) - fd.close() - - def _get_object_path( self, chrom, resolution ): - object_name = sanitize_name(chrom) - if resolution: object_name += "_%d" % resolution - return os.path.join( self.path, object_name ) - - def _build_path( self, path ): - try: - os.mkdir( path ) - except OSError: - self._build_path( os.path.dirname( path ) ) - os.mkdir( path ) - - @property - def exists(self): - return os.path.exists( self.path ) - - class DoesNotExist( Exception ): - pass diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/visualization/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/visualization/__init__.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,3 @@ +""" +Package for Galaxy visulization plugins. +""" \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/visualization/tracks/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/visualization/tracks/__init__.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,3 @@ +""" +Package for track style visulization using the trackster UI. +""" \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/visualization/tracks/data/__init__.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/visualization/tracks/data/__init__.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,3 @@ +""" +Package for track data providers +""" \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/visualization/tracks/data/array_tree.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Fri Sep 18 15:15:39 2009 -0400 @@ -0,0 +1,50 @@ +""" +Array tree data provider for Galaxy track browser. +""" + +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.arrays.array_tree import FileArrayTreeDict +from math import floor, ceil, log + +# Maybe this should be included in the datatype itself, so users can add their +# own types to the browser as long as they return the right format of data? + +# FIXME: Assuming block size is always 1000 for the moment +BLOCK_SIZE = 1000 + +class ArrayTreeDataProvider( object ): + def __init__( self, dataset ): + self.dataset = dataset + def get_data( self, chrom, start, end ): + start = int( start ) + end = int( end ) + level = int( ceil( log( end - start, BLOCK_SIZE ) ) ) - 1 + print "!!!!", start, end, level + # Open the file + print self.dataset.file_name + d = FileArrayTreeDict( open( self.dataset.file_name ) ) + # Get the right chromosome + try: + chrom_array_tree = d[chrom] + except KeyError: + return None + # Is the requested level valid? + assert 0 <= level <= chrom_array_tree.levels + # Calculate the actual start/range/step of the block we're getting + size = BLOCK_SIZE ** (level+1) + block_start = ( start // BLOCK_SIZE ) * BLOCK_SIZE + block_step = size // BLOCK_SIZE + indexes = range( block_start, block_start + size, block_step ) + # Return either data point or a summary depending on the level + if level > 0: + s = chrom_array_tree.get_summary( start, level ) + if s is not None: + return zip( indexes, map( float, s.sums / s.counts ) ) + else: + return None + else: + v = chrom_array_tree.get_leaf( start ) + if v is not None: + return zip( indexes, map( float, v ) ) + else: + return None \ No newline at end of file diff -r 3f3712d36034 -r bed484895e2d lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Fri Sep 18 15:18:57 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Fri Sep 18 15:15:39 2009 -0400 @@ -9,18 +9,44 @@ Problems -------- - - Assumes that the only indexing type in Galaxy is for this particular - application. Thus, datatypes can only have one indexer, and the presence - of an indexer results in assuming that datatype can be displayed as a track. - + - Only line tracks supported + - Resolutions are a bit wonky + - Must have a LEN file, not currently able to infer from data (not sure we + need to support that, but need to make user defined build support better) """ import math -from galaxy.tracks import messages from galaxy.util.json import to_json_string from galaxy.web.base.controller import * from galaxy.web.framework import simplejson +from galaxy.util.bunch import Bunch + +from galaxy.visualization.tracks.data.array_tree import ArrayTreeDataProvider + +# Message strings returned to browser +messages = Bunch( + PENDING = "pending", + NO_DATA = "no data", + NO_CHROMOSOME = "no chromosome", + DATA = "data" +) + +# Dataset type required for each track type. This needs to be more flexible, +# there might be mutliple types of indexes that suffice for a given track type. +track_type_to_dataset_type = { + "line": "array_tree" +} + +# Mapping from dataset type to a class that can fetch data from a file of that +# type. This also needs to be more flexible. +dataset_type_to_data_provider = { + "array_tree": ArrayTreeDataProvider +} + +# FIXME: hardcoding this for now, but it should be derived from the available +# converters +browsable_types = set( ["wig" ] ) class TracksController( BaseController ): """ @@ -41,24 +67,26 @@ session = trans.sa_session # If the user clicked the submit button explicately, try to build the browser if browse and dataset_ids: + if not isinstance( dataset_ids, list ): + dataset_ids = [ dataset_ids ] dataset_ids = ",".join( map( str, dataset_ids ) ) trans.response.send_redirect( web.url_for( controller='tracks', action='browser', chrom="", dataset_ids=dataset_ids ) ) - return - # Determine the set of all dbkeys that are used in the current history - dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] - dbkey_set = set( dbkeys ) - # If a dbkey argument was not provided, or is no longer valid, default - # to the first one - if dbkey is None or dbkey not in dbkey_set: - dbkey = dbkeys[0] - # Find all datasets in the current history that are of that dbkey and - # have an indexer. - datasets = {} - for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ): - if dataset.metadata.dbkey == dbkey and trans.app.datatypes_registry.get_indexers_by_datatype( dataset.extension ): - datasets[dataset.id] = dataset.name - # Render the template - return trans.fill_template( "tracks/new_browser.mako", dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) + else: + # Determine the set of all dbkeys that are used in the current history + dbkeys = [ d.metadata.dbkey for d in trans.get_history().datasets if not d.deleted ] + dbkey_set = set( dbkeys ) + # If a dbkey argument was not provided, or is no longer valid, default + # to the first one + if dbkey is None or dbkey not in dbkey_set: + dbkey = dbkeys[0] + # Find all datasets in the current history that are of that dbkey + # and can be displayed + datasets = {} + for dataset in session.query( model.HistoryDatasetAssociation ).filter_by( deleted=False, history_id=trans.history.id ): + if dataset.metadata.dbkey == dbkey and dataset.extension in browsable_types: + datasets[dataset.id] = dataset.name + # Render the template + return trans.fill_template( "tracks/new_browser.mako", dbkey=dbkey, dbkey_set=dbkey_set, datasets=datasets ) @web.expose def browser(self, trans, dataset_ids, chrom=""): @@ -75,13 +103,15 @@ "id": dataset.id } ) dbkey = dataset.dbkey - LEN = self._chroms(trans, dbkey ).get(chrom,0) + chrom_lengths = self._chroms( trans, dbkey ) + if chrom_lengths is None: + error( "No chromosome lengths file found for '%s'" ) return trans.fill_template( 'tracks/browser.mako', dataset_ids=dataset_ids, tracks=tracks, chrom=chrom, dbkey=dbkey, - LEN=LEN ) + LEN=chrom_lengths.get( chrom, 0 ) ) @web.json def chroms(self, trans, dbkey=None ): @@ -91,85 +121,86 @@ """ Called by the browser to get a list of valid chromosomes and lengths """ + # If there is any dataset in the history of extension `len`, this will + # use it db_manifest = trans.db_dataset_for( dbkey ) if not db_manifest: db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey ) else: db_manifest = db_manifest.file_name manifest = {} - if os.path.exists( db_manifest ): - for line in open( db_manifest ): - if line.startswith("#"): continue - line = line.rstrip("\r\n") - fields = line.split("\t") - manifest[fields[0]] = int(fields[1]) - else: - # try to fake a manifest by reading track stores - datasets = trans.app.model.HistoryDatasetAssociation.filter_by(deleted=False, history_id=trans.history.id).all() - for dataset in datasets: - if not dataset.metadata.dbkey == dbkey: continue - track_store = trans.app.track_store.get( dataset ) - if track_store.exists: - try: - for chrom, fields in track_store.get_manifest().items(): - manifest[chrom] = max(manifest.get(chrom, 0), int(fields[0])) - except track_store.DoesNotExist: - pass + if not os.path.exists( db_manifest ): + return None + for line in open( db_manifest ): + if line.startswith("#"): continue + line = line.rstrip("\r\n") + fields = line.split("\t") + manifest[fields[0]] = int(fields[1]) return manifest - - @web.json - def data( self, trans, dataset_id, chrom="", low="", high="" ): + + @web.json + def data( self, trans, dataset_id, track_type, chrom, low, high ): """ Called by the browser to request a block of data """ + # Load the requested dataset dataset = trans.app.model.HistoryDatasetAssociation.get( dataset_id ) - if not dataset: return messages.NO_DATA + # No dataset for that id + if not dataset: + return messages.NO_DATA + # Dataset is in error state, can't display if dataset.state == trans.app.model.Job.states.ERROR: return messages.NO_DATA - if not dataset.state == trans.app.model.Job.states.OK: + # Dataset is still being generated + if dataset.state != trans.app.model.Job.states.OK: return messages.PENDING - track_store = trans.app.track_store.get( dataset ) - if not track_store.exists: - # Test if we can make a track - indexers = trans.app.datatypes_registry.get_indexers_by_datatype( dataset.extension ) - if indexers: - tool = indexers[0] # They are sorted by class chain so use the top one - # If we can, return pending and launch job - job = trans.app.model.Job() - job.session_id = trans.get_galaxy_session().id - job.history_id = trans.history.id - job.tool_id = tool.id - job.tool_version = "1.0.0" - job.add_input_dataset( "input_dataset", dataset ) - job.add_parameter( "input_dataset", to_json_string( dataset.id ) ) - # This is odd - # job.add_output_dataset( "input_dataset", dataset ) - # create store path, this is rather unclear? - track_store.set() - job.add_parameter( "store_path", to_json_string( track_store.path ) ) - job.flush() - trans.app.job_manager.job_queue.put( job.id, tool ) - return messages.PENDING - else: - return messages.NO_DATA - else: - # Data for that chromosome or resolution does not exist? - # HACK: we're "pending" because the store exists without a manifest - try: - track_store.get_manifest() - except track_store.DoesNotExist: - return messages.PENDING - if chrom and low and high: - low = math.floor(float(low)) - high = math.ceil(float(high)) - resolution = dataset.datatype.get_track_resolution( dataset, low, high ) - try: - data = track_store.get( chrom, resolution ) - except track_store.DoesNotExist: - return messages.NO_DATA - window = dataset.datatype.get_track_window( dataset, data, low, high ) - glob = {"data":window, "type":dataset.datatype.get_track_type()}; - if resolution: glob["resolution"] = resolution - return window - else: - return messages.DATA + # Determine what to return based on the type of track being drawn. + converted_dataset_type = track_type_to_dataset_type[track_type] + converted_dataset = self.__dataset_as_type( trans, dataset, converted_dataset_type ) + # If at this point we still don't have an `array_tree_dataset`, there + # is now way we can display this data as an array tree + if converted_dataset is None: + return messages.NO_DATA + # Need to check states again for the converted version + if converted_dataset.state == model.Dataset.states.ERROR: + return messages.NO_DATA + if converted_dataset.state != model.Dataset.states.OK: + return messages.PENDING + # We have a dataset in the right format that is ready to use, wrap in + # a data provider that knows how to access it + data_provider = dataset_type_to_data_provider[ converted_dataset_type ]( converted_dataset ) + # Get the requested chunk of data + data = data_provider.get_data( chrom, low, high ) + # Pack into a dictionary and return + return data + + def __dataset_as_type( self, trans, dataset, type ): + """ + Given a dataset, try to find a way to adapt it to a different type. If the + dataset is already of that type it is returned, if it can be converted a + converted dataset (possibly new) is returned, if it cannot be converted, + None is returned. + """ + # Already of correct type + if dataset.extension == type: + return dataset + # See if we can convert the dataset + if type not in dataset.get_converter_types(): + log.debug( "Converstion from '%s' to '%d' not possible", dataset.extension, type ) + return None + # See if converted dataset already exists + converted_datasets = dataset.get_converted_files_by_type( type ) + if converted_datasets: + for d in converted_datasets: + if d and d.state != 'error': + return d + # Conversion is possible but doesn't exist yet, run converter here + # FIXME: this is largely duplicated from DefaultToolAction + assoc = model.ImplicitlyConvertedDatasetAssociation( parent = dataset, file_type = type, metadata_safe = False ) + new_dataset = dataset.datatype.convert_dataset( trans, dataset, type, return_output = True, visible = False ).values()[0] + new_dataset.hid = dataset.hid # Hrrmmm.... + new_dataset.name = dataset.name + new_dataset.flush() + assoc.dataset = new_dataset + assoc.flush() + return new_dataset diff -r 3f3712d36034 -r bed484895e2d static/scripts/trackster.js --- a/static/scripts/trackster.js Fri Sep 18 15:18:57 2009 -0400 +++ b/static/scripts/trackster.js Fri Sep 18 15:15:39 2009 -0400 @@ -1,4 +1,8 @@ var DENSITY = 1000; + +var BLOCK_SIZE = 1000; + +var log = function( x, b ) { return Math.log( x ) / Math.log( b ) } var View = function( chr, length, low, high ) { this.chr = chr; @@ -83,9 +87,12 @@ high = this.view.high, range = high - low; - var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); + var resolution = Math.pow( BLOCK_SIZE, Math.floor( log( range, BLOCK_SIZE ) ) ); + // Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); + + console//.log( "resolution:", resolution ); resolution = Math.max( resolution, 1 ); - resolution = Math.min( resolution, 100000 ); + resolution = Math.min( resolution, 1000000 ); var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); @@ -155,7 +162,7 @@ // use closure to preserve this and parameters for getJSON var fetcher = function (ref) { return function () { - $.getJSON( TRACKSTER_DATA_URL + ref.type, { chrom: ref.view.chr, low: low, high: high, dataset_id: ref.track.dataset_id }, function ( data ) { + $.getJSON( TRACKSTER_DATA_URL, { track_type: ref.type, chrom: ref.view.chr, low: low, high: high, dataset_id: ref.track.dataset_id }, function ( data ) { if( data == "pending" ) { setTimeout( fetcher, 5000 ); } else { @@ -175,7 +182,7 @@ Track.call( this, name, view, parent_element ); this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; - this.cache = new DataCache( "", this, view ); + this.cache = new DataCache( "line", this, view ); }; $.extend( LineTrack.prototype, TiledTrack.prototype, { make_container: function () { @@ -209,35 +216,37 @@ var canvas = element; canvas.get(0).width = canvas.width(); canvas.get(0).height = canvas.height(); - var ctx = canvas.get(0).getContext("2d"); - var in_path = false; - ctx.beginPath(); - var data = chunk.values; - for ( var i = 0; i < data.length - 1; i++ ) { - var x1 = data[i][0] - tile_low; - var y1 = data[i][1]; - var x2 = data[i+1][0] - tile_low; - var y2 = data[i+1][1]; - console.log( x1, y1, x2, y2 ); - // Missing data causes us to stop drawing - if ( isNaN( y1 ) || isNaN( y2 ) ) { - in_path = false; - } else { - // Translate - x1 = x1 * w_scale; - x2 = x2 * w_scale; - y1 = h_scale - y1 * ( h_scale ); - y2 = h_scale - y2 * ( h_scale ); - if ( in_path ) { - ctx.lineTo( x1, y1, x2, y2 ); - } else { - ctx.moveTo( x1, y1, x2, y2 ); - in_path = true; - } - } - } - ctx.stroke(); - return element; + var data = chunk.values; + if ( data ) { + var ctx = canvas.get(0).getContext("2d"); + var in_path = false; + ctx.beginPath(); + // console.log( "Drawing tile" ); + for ( var i = 0; i < data.length - 1; i++ ) { + var x1 = data[i][0] - tile_low; + var y1 = data[i][1]; + var x2 = data[i+1][0] - tile_low; + var y2 = data[i+1][1]; + // Missing data causes us to stop drawing + if ( isNaN( y1 ) || isNaN( y2 ) ) { + in_path = false; + } else { + // Translate + x1 = x1 * w_scale; + x2 = x2 * w_scale; + y1 = h_scale - y1 * ( h_scale ); + y2 = h_scale - y2 * ( h_scale ); + if ( in_path ) { + ctx.lineTo( x1, y1, x2, y2 ); + } else { + ctx.moveTo( x1, y1, x2, y2 ); + in_path = true; + } + } + } + ctx.stroke(); + } + return element; } });

1 0

[hg] galaxy 2722: Fixed a bug in fasta_formatter tool test case, ...
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/6ed5f088a2ad changeset: 2722:6ed5f088a2ad user: guru date: Fri Sep 18 15:28:18 2009 -0400 description: Fixed a bug in fasta_formatter tool test case, which was causing the functional tests to fail. 1 file(s) affected in this change: tools/fastx_toolkit/fasta_formatter.xml diffs (12 lines): diff -r bed484895e2d -r 6ed5f088a2ad tools/fastx_toolkit/fasta_formatter.xml --- a/tools/fastx_toolkit/fasta_formatter.xml Fri Sep 18 15:15:39 2009 -0400 +++ b/tools/fastx_toolkit/fasta_formatter.xml Fri Sep 18 15:28:18 2009 -0400 @@ -21,7 +21,7 @@  <param name="input" value="fasta_formatter1.fasta" /> <param name="width" value="0" /> - <output name="output" file="fastx_formatter1.out" /> + <output name="output" file="fasta_formatter1.out" /> </test> <test>

1 0

[hg] galaxy 2720: Galaxy AMQP Listener, first pass
by Greg Von Kuster 21 Sep '09

21 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3f3712d36034 changeset: 2720:3f3712d36034 user: rc date: Fri Sep 18 15:18:57 2009 -0400 description: Galaxy AMQP Listener, first pass Added a check for testing completed requests in Requests functional tests 7 file(s) affected in this change: lib/galaxy/web/controllers/requests_admin.py lib/galaxy/web/framework/helpers/grids.py run_galaxy_listener.sh scripts/galaxy_messaging/amqp_consumer.py scripts/galaxy_messaging/galaxydb_interface.py test/functional/test_forms_and_requests.py universe_wsgi.ini.sample diffs (300 lines): diff -r 7f18940a4821 -r 3f3712d36034 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Fri Sep 18 14:21:59 2009 -0400 +++ b/lib/galaxy/web/controllers/requests_admin.py Fri Sep 18 15:18:57 2009 -0400 @@ -98,7 +98,6 @@ else: self.request_grid.default_filter = dict(state=kwargs['show_filter'], deleted=False) self.request_grid.show_filter = kwargs.get('show_filter', trans.app.model.Request.states.SUBMITTED) - self.__update_request_state(trans) # Render the list view return self.request_grid( trans, **kwargs ) @web.expose @@ -980,12 +979,6 @@ request_id=request.id, msg='Bar codes has been saved for this request', messagetype='done')) - - def __update_request_state(self, trans): - requests = trans.app.model.Request.query.filter_by(deleted=False, - state=trans.app.model.Request.states.SUBMITTED) - for request in requests: - self.__set_request_state(request) def __set_request_state(self, request): # check if all the samples of the current request are in the final state diff -r 7f18940a4821 -r 3f3712d36034 lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Fri Sep 18 14:21:59 2009 -0400 +++ b/lib/galaxy/web/framework/helpers/grids.py Fri Sep 18 15:18:57 2009 -0400 @@ -121,7 +121,7 @@ return None def build_initial_query( self, session ): return session.query( self.model_class ) - def apply_default_filter( self, trans, query ): + def apply_default_filter( self, trans, query, **kwargs): return query class GridColumn( object ): diff -r 7f18940a4821 -r 3f3712d36034 run_galaxy_listener.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/run_galaxy_listener.sh Fri Sep 18 15:18:57 2009 -0400 @@ -0,0 +1,3 @@ +#!/bin/sh + +python scripts/galaxy_messaging/amqp_consumer.py \ No newline at end of file diff -r 7f18940a4821 -r 3f3712d36034 scripts/galaxy_messaging/amqp_consumer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/amqp_consumer.py Fri Sep 18 15:18:57 2009 -0400 @@ -0,0 +1,68 @@ +from amqplib import client_0_8 as amqp +import ConfigParser +import sys +import optparse +import xml.dom.minidom +from galaxydb_interface import GalaxyDbInterface + +galaxy_config_file = 'universe_wsgi.ini' +global dbconnstr + +def get_value(dom, tag_name): + ''' + This method extracts the tag value from the xml message + ''' + nodelist = dom.getElementsByTagName(tag_name)[0].childNodes + rc = "" + for node in nodelist: + if node.nodeType == node.TEXT_NODE: + rc = rc + node.data + return rc + +def recv_callback(msg): + #print 'Received: ' + msg.body + ' from channel #' + str(msg.channel.channel_id) + dom = xml.dom.minidom.parseString(msg.body) + barcode = get_value(dom, 'barcode') + state = get_value(dom, 'state') + print barcode, state + # update the galaxy db + galaxy = GalaxyDbInterface(dbconnstr) + sample_id = galaxy.get_sample_id(field_name='bar_code', value=barcode) + if sample_id == -1: + print 'Invalid barcode.' + return + galaxy.change_state(sample_id, state) + +def main(): + config = ConfigParser.ConfigParser() + config.read(galaxy_config_file) + global dbconnstr + dbconnstr = config.get("app:main", "database_connection") + amqp_config = {} + for option in config.options("galaxy:amqp"): + amqp_config[option] = config.get("galaxy:amqp", option) + print amqp_config + conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], + userid=amqp_config['userid'], + password=amqp_config['password'], + virtual_host=amqp_config['virtual_host'], + insist=False) + chan = conn.channel() + chan.queue_declare(queue=amqp_config['queue'], durable=True, exclusive=True, auto_delete=False) + chan.exchange_declare(exchange=amqp_config['exchange'], type="direct", durable=True, auto_delete=False,) + chan.queue_bind(queue=amqp_config['queue'], + exchange=amqp_config['exchange'], + routing_key=amqp_config['routing_key']) + + chan.basic_consume(queue=amqp_config['queue'], + no_ack=True, + callback=recv_callback, + consumer_tag="testtag") + while True: + chan.wait() + chan.basic_cancel("testtag") + chan.close() + conn.close() + +if __name__ == '__main__': + main() \ No newline at end of file diff -r 7f18940a4821 -r 3f3712d36034 scripts/galaxy_messaging/galaxydb_interface.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/galaxy_messaging/galaxydb_interface.py Fri Sep 18 15:18:57 2009 -0400 @@ -0,0 +1,141 @@ +#/usr/bin/python + +from sqlalchemy import * +from sqlalchemy.orm import sessionmaker +from datetime import datetime, timedelta +import sys +import optparse +import os +import time +import logging + +logging.basicConfig(level=logging.DEBUG) +log = logging.getLogger( 'GalaxyDbInterface' ) + +class GalaxyDbInterface(object): + + def __init__(self, dbstr): + self.dbstr = dbstr + self.db_engine = create_engine(self.dbstr) +# self.db_engine.echo = True + self.metadata = MetaData(self.db_engine) + self.session = sessionmaker(bind=self.db_engine) + self.event_table = Table('sample_event', self.metadata, autoload=True ) + self.sample_table = Table('sample', self.metadata, autoload=True ) + self.request_table = Table('request', self.metadata, autoload=True ) + self.state_table = Table('sample_state', self.metadata, autoload=True ) + + def get_sample_id(self, field_name='bar_code', value=None): + if not value: + return -1 + sample_id = -1 + if field_name =='name': + stmt = select(columns=[self.sample_table.c.id], + whereclause=self.sample_table.c.name==value) + result = stmt.execute() + sample_id = result.fetchone()[0] + elif field_name == 'bar_code': + stmt = select(columns=[self.sample_table.c.id], + whereclause=self.sample_table.c.bar_code==value) + result = stmt.execute() + x = result.fetchone() + if x: + sample_id = x[0] + log.debug('Sample ID: %i' % sample_id) + return sample_id + log.warning('This sample %s %s does not belong to any sample in the database.' % (field_name, value)) + return -1 + + def current_state(self, sample_id): + ''' + This method returns the current state of the sample for the given sample_id + ''' + stmt = select(columns=[self.event_table.c.sample_state_id], + whereclause=self.event_table.c.sample_id==sample_id, + order_by=self.event_table.c.update_time.desc()) + result = stmt.execute() + all_states = result.fetchall() + current_state_id = all_states[0][0] + return current_state_id + + def all_possible_states(self, sample_id): + subsubquery = select(columns=[self.sample_table.c.request_id], + whereclause=self.sample_table.c.id==sample_id) + self.request_id = subsubquery.execute().fetchall()[0][0] + log.debug('REQUESTID: %i' % self.request_id) + subquery = select(columns=[self.request_table.c.request_type_id], + whereclause=self.request_table.c.id==self.request_id) + request_type_id = subquery.execute().fetchall()[0][0] + log.debug('REQUESTTYPEID: %i' % request_type_id) + query = select(columns=[self.state_table.c.id, self.state_table.c.name], + whereclause=self.state_table.c.request_type_id==request_type_id, + order_by=self.state_table.c.id.asc()) + states = query.execute().fetchall() + log.debug('POSSIBLESTATES: '+ str(states)) + return states + + def change_state(self, sample_id, new_state=None): + ''' + This method changes the state of the sample to the the 'new_state' + ''' + if not new_state: + return + new_state_id = -1 + # find the state_id for this new state in the list of possible states + possible_states = self.all_possible_states(sample_id) + for state_id, state_name in possible_states: + if new_state == state_name: + new_state_id = state_id + if new_state_id == -1: + return + log.debug('Updating sample_id %i state to %s' % (sample_id, new_state)) + d = timedelta(hours=4) + i = self.event_table.insert() + i.execute(update_time=datetime.now()+d, + create_time=datetime.now()+d, + sample_id=sample_id, + sample_state_id=int(new_state_id), + comment='bar code scanner') + # if all the samples for this request are in the final state + # then change the request state to 'Complete' + result = select(columns=[self.sample_table.c.id], + whereclause=self.sample_table.c.request_id==self.request_id).execute() + sample_id_list = result.fetchall() + request_complete = True + for sid in sample_id_list: + current_state_id = self.current_state(sid[0]) + if current_state_id != possible_states[-1][0]: + request_complete = False + break + if request_complete: + request_state = 'Complete' + else: + request_state = 'Submitted' + log.debug('Updating request_id %i state to "%s"' % (self.request_id, request_state)) + d = timedelta(hours=4) + i = self.request_table.update(whereclause=self.request_table.c.id==self.request_id, + values={self.request_table.c.state: request_state}) + i.execute() + + + +if __name__ == '__main__': + print '''This file should not be run directly. To start the Galaxy AMQP Listener: + %sh run_galaxy_listener.sh''' +# dbstr = 'postgres://postgres:postgres@localhost/galaxy_ft' +# +# parser = optparse.OptionParser() +# parser.add_option('-n', '--name', help='name of the sample field', dest='name', \ +# action='store', default='bar_code') +# parser.add_option('-v', '--value', help='value of the sample field', dest='value', \ +# action='store') +# parser.add_option('-s', '--state', help='new state of the sample', dest='state', \ +# action='store') +# (opts, args) = parser.parse_args() +# +# gs = GalaxyDbInterface(dbstr) +# sample_id = gs.get_sample_id(field_name=opts.name, value=opts.value) +# gs.change_state(sample_id, opts.state) + + + diff -r 7f18940a4821 -r 3f3712d36034 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Fri Sep 18 14:21:59 2009 -0400 +++ b/test/functional/test_forms_and_requests.py Fri Sep 18 15:18:57 2009 -0400 @@ -247,6 +247,8 @@ self.home() request_one.refresh() # check if the request's state is now set to 'complete' + self.visit_url('%s/requests_admin/list?show_filter=Complete' % self.url) + self.check_page_for_string( request_one.name ) assert request_one.state is not request_one.states.COMPLETE, "The state of the request '%s' should be set to '%s'" % ( request_one.name, request_one.states.COMPLETE ) # def test_40_admin_create_request_on_behalf_of_regular_user( self ): # """Testing creating and submitting a request as an admin on behalf of a regular user""" diff -r 7f18940a4821 -r 3f3712d36034 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Fri Sep 18 14:21:59 2009 -0400 +++ b/universe_wsgi.ini.sample Fri Sep 18 15:18:57 2009 -0400 @@ -240,3 +240,22 @@ ucsc_table_direct_archaea1 = local:/// ucsc_table_direct_test1 = local:/// upload1 = local:/// + + +# Galaxy Message Queue +# Galaxy uses AMQ protocol to receive messages from external sources like +# bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. +# For Galaxy to receive messages from a message queue the RabbitMQ server has +# to be set up with a user account and other parameters listed below. The 'host' +# and 'port' fields should point to where the RabbitMQ server is running. + +#[galaxy:amqp] +#host = 127.0.0.1 +#port = 5672 +#userid = galaxy +#password = galaxy +#virtual_host = galaxy_messaging_engine +#queue = galaxy_queue +#exchange = galaxy_exchange +#routing_key = bar_code_scanner +

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