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synced 2026-09-24 16:30:27 +08:00
In library uploads, allow inheriting the existing datasets metadata when replacing. Allow setting library metadata when adding datasets from a history.
This commit is contained in:
Daniel Blankenberg
@@ -1582,6 +1582,9 @@ class LibraryDatasetDatasetInfoAssociation( object ):
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self.library_dataset_dataset_association = library_dataset_dataset_association
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self.template = form_definition
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self.info = info
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@property
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def inheritable( self ):
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return True #always allow inheriting, used for replacement
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class ValidationError( object ):
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def __init__( self, message=None, err_type=None, attributes=None ):
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@@ -746,12 +746,20 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
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roles = params.get( 'roles', '' )
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is_admin = trans.user_is_admin() and cntrller in ( 'library_admin', 'api' )
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current_user_roles = trans.get_current_user_roles()
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widgets = []
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widget_fields_have_contents = False
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info_association, inherited = None, None
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template_id = "None"
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if replace_id not in [ '', None, 'None' ]:
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replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) )
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self._check_access( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted )
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self._check_modify( trans, cntrller, is_admin, replace_dataset, current_user_roles, use_panels, library_id, show_deleted )
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library = replace_dataset.folder.parent_library
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folder = replace_dataset.folder
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info_association, inherited = replace_dataset.library_dataset_dataset_association.get_info_association()
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if info_association and ( not( inherited ) or info_association.inheritable ):
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widgets = replace_dataset.library_dataset_dataset_association.get_template_widgets( trans )
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widget_fields_have_contents = self.widget_fields_have_contents( widgets )
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# The name is stored - by the time the new ldda is created, replace_dataset.name
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# will point to the new ldda, not the one it's replacing.
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replace_dataset_name = replace_dataset.name
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@@ -793,7 +801,8 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
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status='error' ) )
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else:
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# See if we have any inherited templates.
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info_association, inherited = folder.get_info_association( inherited=True )
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if not info_association:
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info_association, inherited = folder.get_info_association( inherited=True )
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if info_association and info_association.inheritable:
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template_id = str( info_association.template.id )
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widgets = folder.get_template_widgets( trans, get_contents=True )
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@@ -836,9 +845,6 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
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else:
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processed_widgets.append( widget_dict )
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widgets = processed_widgets
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else:
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template_id = 'None'
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widgets = []
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created_outputs_dict = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans,
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cntrller=cntrller,
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library_id=trans.security.encode_id( library.id ),
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@@ -910,13 +916,15 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
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# attribute of the html input file type field is typically ignored by browsers as a security precaution.
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# See if we have any inherited templates.
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info_association, inherited = folder.get_info_association( inherited=True )
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if info_association and info_association.inheritable:
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widgets = folder.get_template_widgets( trans, get_contents=True )
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if not info_association:
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info_association, inherited = folder.get_info_association( inherited=True )
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if info_association and info_association.inheritable:
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widgets = folder.get_template_widgets( trans, get_contents=True )
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if info_association:
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# Retain contents of widget fields when form was submitted via refresh_on_change.
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widgets = self.populate_widgets_from_kwd( trans, widgets, **kwd )
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else:
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widgets = []
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template_id = str( info_association.template.id )
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# Send list of data formats to the upload form so the "extension" select list can be populated dynamically
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file_formats = trans.app.datatypes_registry.upload_file_formats
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# Send list of genome builds to the form so the "dbkey" select list can be populated dynamically
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@@ -956,6 +964,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
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roles_select_list=roles_select_list,
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history=history,
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widgets=widgets,
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template_id=template_id,
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space_to_tab=space_to_tab,
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link_data_only=link_data_only,
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show_deleted=show_deleted,
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@@ -1185,6 +1194,10 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
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roles = params.get( 'roles', '' )
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is_admin = trans.user_is_admin() and cntrller in ( 'library_admin', 'api' )
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current_user_roles = trans.get_current_user_roles()
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widgets = []
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widget_fields_have_contents = False
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info_association, inherited = None, None
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template_id = "None"
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if replace_id not in [ None, 'None' ]:
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try:
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replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( trans.security.decode_id( replace_id ) )
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@@ -1195,6 +1208,11 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
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library = replace_dataset.folder.parent_library
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folder = replace_dataset.folder
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last_used_build = replace_dataset.library_dataset_dataset_association.dbkey
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info_association, inherited = replace_dataset.library_dataset_dataset_association.get_info_association()
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if info_association and ( not( inherited ) or info_association.inheritable ):
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widgets = replace_dataset.library_dataset_dataset_association.get_template_widgets( trans )
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widget_fields_have_contents = self.widget_fields_have_contents( widgets )
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template_id = str( info_association.template.id )
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else:
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folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( trans.security.decode_id( folder_id ) )
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self._check_access( trans, cntrller, is_admin, folder, current_user_roles, use_panels, library_id, show_deleted )
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@@ -1241,6 +1259,20 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
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# LDDA and LibraryDataset.
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trans.app.security_agent.copy_library_permissions( trans, folder, ldda )
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trans.app.security_agent.copy_library_permissions( trans, folder, ldda.library_dataset )
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else:
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library_bunch = upload_common.handle_library_params( trans, params, folder_id, replace_dataset )
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if library_bunch.template and library_bunch.template_field_contents:
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# Since information templates are inherited, the template fields can be displayed on the upload form.
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# If the user has added field contents, we'll need to create a new form_values and info_association
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# for the new library_dataset_dataset_association object.
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# Create a new FormValues object, using the template we previously retrieved
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form_values = trans.app.model.FormValues( library_bunch.template, library_bunch.template_field_contents )
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trans.sa_session.add( form_values )
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trans.sa_session.flush()
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# Create a new info_association between the current ldda and form_values
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info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( ldda, library_bunch.template, form_values )
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trans.sa_session.add( info_association )
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trans.sa_session.flush()
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# Make sure to apply any defined dataset permissions, allowing the permissions inherited from the folder to
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# over-ride the same permissions on the dataset, if they exist.
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dataset_permissions_dict = trans.app.security_agent.get_permissions( hda.dataset )
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@@ -1330,6 +1362,7 @@ class LibraryCommon( BaseUIController, UsesFormDefinitions ):
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roles_select_list=roles_select_list,
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history=history,
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widgets=widgets,
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template_id=template_id,
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space_to_tab=space_to_tab,
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link_data_only=link_data_only,
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show_deleted=show_deleted,
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@@ -363,12 +363,6 @@
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<div style="clear: both"></div>
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</div>
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%endif
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## Render hidden template fields so the contents will be associated with the dataset
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%if widgets:
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%for i, field in enumerate( widgets ):
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${render_template_field( field, render_as_hidden=True )}
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%endfor
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%endif
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%for hda in history.visible_datasets:
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<% encoded_id = trans.security.encode_id( hda.id ) %>
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<div class="form-row">
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@@ -376,6 +370,24 @@
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<label for="hist_${encoded_id}" style="display: inline;font-weight:normal;">${hda.hid}: ${hda.name}</label>
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</div>
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%endfor
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%if widgets:
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<input type="hidden" name="template_id" value="${template_id}"/>
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%for i, field in enumerate( widgets ):
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<div class="form-row">
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<label>${field[ 'label' ]}</label>
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<div class="form-row-input">
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${field[ 'widget' ].get_html()}
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</div>
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<div class="toolParamHelp" style="clear: both;">
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%if field[ 'helptext' ]:
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${field[ 'helptext' ]}<br/>
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%endif
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*Inherited template field
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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" name="add_history_datasets_to_library_button" value="Import to library"/>
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</div>
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