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https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Template fixes: get current FormDefinition when inheriting templates, and use filter then retrieving FormDeinition for library templates. A few other miscellaneous bug fixes as well. Functional tests should now pass.
This commit is contained in:
Greg Von Kuster
@@ -693,7 +693,10 @@ class Library( object ):
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return None, inherited
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def get_template_widgets( self, trans, get_contents=True ):
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# See if we have any associated templates - the returned value for
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# inherited is not applicable at the library level
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# inherited is not applicable at the library level. The get_contents
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# param is passed by callers that are inheriting a template - these
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# are usually new library datsets for which we want to include template
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# fields on the upload form.
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info_association, inherited = self.get_info_association()
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if info_association:
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template = info_association.template
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@@ -738,10 +741,16 @@ class LibraryFolder( object ):
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return self.library_root[0].get_info_association( inherited=True )
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return None, inherited
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def get_template_widgets( self, trans, get_contents=True ):
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# See if we have any associated templates
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# See if we have any associated templates. The get_contents
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# param is passed by callers that are inheriting a template - these
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# are usually new library datsets for which we want to include template
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# fields on the upload form.
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info_association, inherited = self.get_info_association()
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if info_association:
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template = info_association.template
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if inherited:
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template = info_association.template.current.latest_form
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else:
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template = info_association.template
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# See if we have any field contents, but only if the info_association was
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# not inherited ( we do not want to display the inherited contents ).
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if not inherited and get_contents:
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@@ -881,10 +890,16 @@ class LibraryDatasetDatasetAssociation( DatasetInstance ):
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return None, inherited
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return self.library_dataset.folder.get_info_association( inherited=True )
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def get_template_widgets( self, trans, get_contents=True ):
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# See if we have any associated templates
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# See if we have any associated templatesThe get_contents
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# param is passed by callers that are inheriting a template - these
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# are usually new library datsets for which we want to include template
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# fields on the upload form.
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info_association, inherited = self.get_info_association()
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if info_association:
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template = info_association.template
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if inherited:
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template = info_association.template.current.latest_form
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else:
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template = info_association.template
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# See if we have any field contents, but only if the info_association was
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# not inherited ( we do not want to display the inherited contents ).
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if not inherited and get_contents:
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@@ -717,11 +717,21 @@ class Library( BaseController ):
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if trans.app.security_agent.can_add_library_item( user, roles, folder ) or \
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( replace_dataset and trans.app.security_agent.can_modify_library_item( user, roles, replace_dataset ) ):
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if params.get( 'new_dataset_button', False ):
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# See if we have any inherited templates, but do not inherit contents.
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info_association, inherited = folder.get_info_association( inherited=True )
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if info_association:
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template_id = str( info_association.template.id )
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widgets = folder.get_template_widgets( trans, get_contents=False )
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else:
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template_id = None
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widgets = []
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upload_option = params.get( 'upload_option', 'upload_file' )
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created_ldda_ids = trans.webapp.controllers[ 'library_dataset' ].upload_dataset( trans,
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controller='library',
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library_id=library_id,
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folder_id=folder_id,
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template_id=template_id,
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widgets=widgets,
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replace_dataset=replace_dataset,
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**kwd )
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if created_ldda_ids:
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@@ -1049,6 +1059,17 @@ class Library( BaseController ):
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library_item_desc = 'library'
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response_action = 'browse_library'
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response_id = library_id
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forms = get_all_forms( trans,
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filter=dict( deleted=False ),
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form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE )
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if not forms:
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msg = "There are no forms on which to base the template, so create a form and "
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msg += "try again to add the information template to the %s." % library_item_desc
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trans.response.send_redirect( web.url_for( controller='forms',
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action='new',
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new=True,
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msg=msg,
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messagetype='done' ) )
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if params.get( 'add', False ):
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if params.get( 'add_info_template_button', False ):
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form = trans.app.model.FormDefinition.get( int( kwd[ 'form_id' ] ) )
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@@ -1068,14 +1089,13 @@ class Library( BaseController ):
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id=response_id,
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msg=msg,
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message_type='done' ) )
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return trans.fill_template( '/library/select_info_template.mako',
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return trans.fill_template( '/admin/library/select_info_template.mako',
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library_item_name=library_item.name,
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library_item_desc=library_item_desc,
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library_id=library_id,
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folder_id=folder_id,
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ldda_id=ldda_id,
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forms=get_all_forms( trans, filter=dict(deleted=False),
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form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE ),
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forms=forms,
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msg=msg,
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messagetype=messagetype )
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@web.expose
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@@ -429,11 +429,21 @@ class LibraryAdmin( BaseController ):
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ldatatypes = [ dtype_name for dtype_name, dtype_value in trans.app.datatypes_registry.datatypes_by_extension.iteritems() if dtype_value.allow_datatype_change ]
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ldatatypes.sort()
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if params.get( 'new_dataset_button', False ):
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# See if we have any inherited templates, but do not inherit contents.
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info_association, inherited = folder.get_info_association( inherited=True )
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if info_association:
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template_id = str( info_association.template.id )
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widgets = folder.get_template_widgets( trans, get_contents=False )
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else:
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template_id = None
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widgets = []
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upload_option = params.get( 'upload_option', 'upload_file' )
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created_ldda_ids = trans.webapp.controllers[ 'library_dataset' ].upload_dataset( trans,
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controller='library_admin',
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library_id=library_id,
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folder_id=folder_id,
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template_id=template_id,
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widgets=widgets,
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replace_dataset=replace_dataset,
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**kwd )
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if created_ldda_ids:
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@@ -915,7 +925,9 @@ class LibraryAdmin( BaseController ):
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library_item_desc = 'library'
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response_action = 'browse_library'
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response_id = library_id
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forms = get_all_forms( trans, filter=dict(deleted=False) )
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forms = get_all_forms( trans,
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filter=dict( deleted=False ),
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form_type=trans.app.model.FormDefinition.types.LIBRARY_INFO_TEMPLATE )
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if not forms:
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msg = "There are no forms on which to base the template, so create a form and "
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msg += "try again to add the information template to the %s." % library_item_desc
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@@ -203,16 +203,20 @@ class UploadLibraryDataset( BaseController ):
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err_redirect = False
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# See if we have any template field contents
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template_field_contents = []
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template = None
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template_id = params.get( 'template_id', None )
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folder = trans.app.model.LibraryFolder.get( folder_id )
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info_association, inherited = folder.get_info_association()
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if info_association:
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template = info_association.template
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# We are inheriting the folder's info_association, so we did not
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# receive any inherited contents, but we may have redirected here
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# after the user entered template contents ( due to errors ).
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if template_id:
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template = trans.app.model.FormDefinition.get( template_id )
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for field_index in range( len( template.fields ) ):
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field_name = 'field_%i' % field_index
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if params.get( field_name, False ):
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field_value = util.restore_text( params.get( field_name, '' ) )
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template_field_contents.append( field_value )
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else:
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template = None
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if upload_option == 'upload_file' and data_file == '' and url_paste == '':
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msg = 'Select a file, enter a URL or enter text'
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err_redirect = True
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@@ -226,15 +226,15 @@ class RowCounter( object ):
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<h2>Data Library “${library.name}”</h2>
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<%
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can_add = trans.app.security_agent.can_add_library_item( user, roles, library )
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can_modify = trans.app.security_agent.can_modify_library_item( user, roles, library )
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can_manage = trans.app.security_agent.can_manage_library_item( user, roles, library )
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can_add = trans.app.security_agent.can_add_library_item( user, roles, library )
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can_modify = trans.app.security_agent.can_modify_library_item( user, roles, library )
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can_manage = trans.app.security_agent.can_manage_library_item( user, roles, library )
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%>
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<ul class="manage-table-actions">
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%if can_add and not_deleted:
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%if can_add:
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<li>
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<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this library</span></a>
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<a class="action-button" href="${h.url_for( controller='library', action='library_dataset_dataset_association', library_id=library.id, folder_id=library.root_folder.id )}"><span>Add datasets to this data library</span></a>
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</li>
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<li>
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<a class="action-button" href="${h.url_for( controller='library', action='folder', new=True, id=library.root_folder.id, library_id=library.id )}">Add a folder to this library</a>
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@@ -246,7 +246,7 @@ can_manage = trans.app.security_agent.can_manage_library_item( user, roles, libr
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<li><a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a></li>
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%endif
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%if can_add and forms and not library.info_association:
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<a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this library</a>
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<a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, add=True )}">Add an information template to this data library</a>
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%endif
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%if can_manage:
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<li><a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a></li>
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@@ -169,9 +169,18 @@
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</div>
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</div>
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<div style="clear: both"></div>
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<% folder = trans.app.model.LibraryFolder.get( folder_id ) %>
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%if upload_option == 'upload_file' and widgets:
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${render_template_info( folder, library_id, widgets )}
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%if widgets:
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<p/>
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%for i, field in enumerate( widgets ):
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<div class="form-row">
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<label>${field[ 'label' ]}</label>
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${field[ 'widget' ].get_html()}
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<div class="toolParamHelp" style="clear: both;">
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${field[ 'helptext' ]}
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</div>
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<div style="clear: both"></div>
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</div>
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%endfor
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%endif
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<div class="form-row">
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<input type="submit" class="primary-button" name="new_dataset_button" value="Upload to library"/>
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@@ -488,7 +488,7 @@ class TestSecurityAndLibraries( TwillTestCase ):
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.order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) \
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.all()
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for fdc in fdcs:
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if form_name == fdc.latest_form.name:
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if form_name == fdc.latest_form.name and form_type == fdc.latest_form.type:
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form_one = fdc.latest_form
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break
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assert form_one is not None, 'Problem retrieving form named (%s) from the database' % form_name
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