Mccalluc/consistent arrays

CHANGELOG-consistent-arrays.md

@@ -0,0 +1 @@
+- Update to handle new response structure from portal-vis

context/app/api/client.py

@@ -7,17 +7,18 @@
 import requests
 
 from hubmap_commons.type_client import TypeClient
+from vitessce import VitessceConfig
 
 from .client_utils import files_from_response
 from portal_visualization.builder_factory import get_view_config_builder
-from portal_visualization.builders.base_builders import ConfCells
+from portal_visualization.builders.base_builders import ConfigsCells
 
 Entity = namedtuple('Entity', ['uuid', 'type', 'name'], defaults=['TODO: name'])
 
 
 @dataclass
 class VitessceConfLiftedUUID:
-    vitessce_conf: dict
+    configs_cells: tuple
     vis_lifted_uuid: str
 
 
@@ -151,9 +152,9 @@ def get_files(self, uuids):
             body_json=query)
         return files_from_response(response_json)
 
-    def get_vitessce_conf_cells_and_lifted_uuid(self, entity, marker=None, wrap_error=True):
+    def get_configs_cells_and_lifted_uuid(self, entity, marker=None, wrap_error=True):
         '''
-        Returns a dataclass with vitessce_conf and is_lifted.
+        Returns a dataclass with configs_cells and vis_lifted_uuid.
         '''
         vis_lifted_uuid = None  # default
         image_pyramid_descendants = _get_image_pyramid_descendants(entity)
@@ -167,13 +168,13 @@ def get_vitessce_conf_cells_and_lifted_uuid(self, entity, marker=None, wrap_erro
             # about "files". Bill confirms that when the new structure comes in
             # there will be a period of backward compatibility to allow us to migrate.
             derived_entity['files'] = derived_entity['metadata'].get('files', [])
-            vitessce_conf = self.get_vitessce_conf_cells_and_lifted_uuid(
+            configs_cells = self.get_configs_cells_and_lifted_uuid(
                 derived_entity, marker=marker, wrap_error=wrap_error
-            ).vitessce_conf
+            ).configs_cells
             vis_lifted_uuid = derived_entity['uuid']
 
         elif not entity.get('files') or not entity.get('data_types'):
-            vitessce_conf = ConfCells(None, None)
+            configs_cells = ConfigsCells([], [])
 
         # Otherwise, just try to visualize the data for the entity itself:
         else:
@@ -185,13 +186,13 @@ def get_assay(name):
                     return type_client.getAssayType(name)
                 Builder = get_view_config_builder(entity=entity, get_assay=get_assay)
                 builder = Builder(entity, self.groups_token, current_app.config["ASSETS_ENDPOINT"])
-                vitessce_conf = builder.get_conf_cells(marker=marker)
+                configs_cells = builder.get_configs_cells(marker=marker)
             except Exception as e:
                 if not wrap_error:
                     raise e
                 current_app.logger.error(
                     f'Building vitessce conf threw error: {traceback.format_exc()}')
-                vitessce_conf = ConfCells({
+                configs_cells = ConfigsCells([VitessceConfig.from_dict({
                     'name': 'Error',
                     'version': '1.0.4',
                     'datasets': [],
@@ -203,10 +204,10 @@ def get_assay(name):
                         },
                         'x': 0, 'y': 0, 'w': 12, 'h': 1
                     }],
-                }, None)
+                })], [])
 
         return VitessceConfLiftedUUID(
-            vitessce_conf=vitessce_conf,
+            configs_cells=configs_cells,
             vis_lifted_uuid=vis_lifted_uuid)
 
 

context/app/api/mock_client.py

@@ -2,7 +2,7 @@
 
 from datauri import DataURI
 
-from portal_visualization.builders.base_builders import ConfCells
+from portal_visualization.builders.base_builders import ConfigsCells
 from .client import ApiClient
 
 
@@ -19,7 +19,7 @@ def get_entity(self, uuid=None, hbm_id=None):
         }
 
     def get_vitessce_conf_cells(self, entity):
-        return ConfCells(_get_mock_vitessce_conf(), None)
+        return ConfigsCells(_get_mock_vitessce_conf(), None)
 
 
 def _get_mock_vitessce_conf():

context/app/routes_browse.py

@@ -57,11 +57,13 @@ def details(type, uuid):
     marker = request.args.get('marker')
 
     if type == 'dataset':
-        conf_cells_uuid = client.get_vitessce_conf_cells_and_lifted_uuid(entity, marker=marker)
+        configs_cells_uuid = client.get_configs_cells_and_lifted_uuid(entity, marker=marker)
         flask_data.update({
-            'vitessce_conf': conf_cells_uuid.vitessce_conf.conf,
-            'has_notebook': conf_cells_uuid.vitessce_conf.cells is not None,
-            'vis_lifted_uuid': conf_cells_uuid.vis_lifted_uuid
+            'vitessce_conf_list': [
+                config.to_dict() for config in
+                configs_cells_uuid.configs_cells.configs],
+            'has_notebook': len(configs_cells_uuid.configs_cells.cells) > 0,
+            'vis_lifted_uuid': configs_cells_uuid.vis_lifted_uuid
         })
 
     template = 'base-pages/react-content.html'
@@ -89,9 +91,9 @@ def details_vitessce(type, uuid):
         abort(404)
     client = get_client()
     entity = client.get_entity(uuid)
-    vitessce_conf = client.get_vitessce_conf_cells_and_lifted_uuid(entity).vitessce_conf
+    configs_cells = client.get_configs_cells_and_lifted_uuid(entity).configs_cells
     # Returns a JSON null if there is no visualization.
-    response = jsonify(vitessce_conf.conf)
+    response = jsonify([config.to_dict() for config in configs_cells.configs])
     response.headers.add("Access-Control-Allow-Origin", "*")
     return response
 

context/app/routes_file_based.py

@@ -28,7 +28,7 @@ def preview_details_view(name):
             'created_by_user_displayname': preview_metadata['created_by_user_displayname'],
             'created_by_user_email': preview_metadata['created_by_user_email'],
         },
-        'vitessce_conf': preview_metadata.get('vitessce_conf')
+        'vitessce_conf_list': [preview_metadata.get('vitessce_conf')]
     }
     return render_template(
         'base-pages/react-content.html',

context/app/routes_notebooks.py

@@ -96,10 +96,8 @@ def details_notebook(type, uuid, create_workspace):
     client = get_client()
     entity = client.get_entity(uuid)
     workspace_name = f"{entity['hubmap_id']} Workspace" if create_workspace else None
-    vitessce_conf = client.get_vitessce_conf_cells_and_lifted_uuid(entity).vitessce_conf
-    if (vitessce_conf is None
-            or vitessce_conf.conf is None
-            or vitessce_conf.cells is None):
+    configs_cells = client.get_configs_cells_and_lifted_uuid(entity).configs_cells
+    if (len(configs_cells.configs) == 0 or len(configs_cells.cells) == 0):
         abort(404)
 
     hubmap_id = entity['hubmap_id']
@@ -114,7 +112,7 @@ def details_notebook(type, uuid, create_workspace):
             '!pip uninstall community flask albumentations -y '
             '# Preinstalled on Colab; Causes version conflicts.\n'
             f'!pip install vitessce[all]=={vitessce.__version__}'),
-        *vitessce_conf.cells
+        *configs_cells.cells
     ]
 
     return _nb_response_from_objs(hubmap_id, cells, workspace_name=workspace_name, uuids=[uuid])

context/app/static/js/components/Routes/Routes.jsx

@@ -37,7 +37,7 @@ const WorkspacePleaseWait = lazy(() => import('js/pages/WorkspacePleaseWait'));
 function Routes({ flaskData }) {
   const {
     entity,
-    vitessce_conf,
+    vitessce_conf_list,
     title,
     publications,
     markdown,
@@ -66,14 +66,14 @@ function Routes({ flaskData }) {
   if (urlPath.startsWith('/browse/donor/')) {
     return (
       <Route>
-        <Donor assayMetadata={entity} vitData={vitessce_conf} />
+        <Donor assayMetadata={entity} vitData={vitessce_conf_list} />
       </Route>
     );
   }
   if (urlPath.startsWith('/browse/sample/')) {
     return (
       <Route>
-        <Sample assayMetadata={entity} vitData={vitessce_conf} />
+        <Sample assayMetadata={entity} vitData={vitessce_conf_list} />
       </Route>
     );
   }
@@ -83,7 +83,7 @@ function Routes({ flaskData }) {
       <Route>
         <Dataset
           assayMetadata={entity}
-          vitData={vitessce_conf}
+          vitData={vitessce_conf_list}
           hasNotebook={has_notebook}
           visLiftedUUID={vis_lifted_uuid}
         />
@@ -166,7 +166,7 @@ function Routes({ flaskData }) {
   if (urlPath.startsWith('/preview')) {
     return (
       <Route>
-        <Preview title={title} vitData={vitessce_conf} assayMetadata={entity} markdown={markdown} />
+        <Preview title={title} vitData={vitessce_conf_list} assayMetadata={entity} markdown={markdown} />
       </Route>
     );
   }
@@ -287,7 +287,7 @@ Routes.propTypes = {
     publications: PropTypes.object,
     entity: PropTypes.object,
     entities: PropTypes.array,
-    vitessce_conf: PropTypes.oneOfType([PropTypes.object, PropTypes.arrayOf(PropTypes.object)]),
+    vitessce_conf_list: PropTypes.arrayOf(PropTypes.object),
     markdown: PropTypes.string,
     collection: PropTypes.object,
     errorCode: PropTypes.number,

context/app/static/js/components/detailPage/visualization/Visualization/hooks.js

@@ -7,7 +7,7 @@ export function useVitessceConfig({ vitData, setVitessceState, setVitessceErrors
 
   useEffect(() => {
     function setVitessceDefaults(vData) {
-      setVitessceState(Array.isArray(vData) ? vData[0] : vData);
+      setVitessceState(vData.length === 1 ? vData[0] : vData);
       setVitessceSelection(0);
       setVitessceConfig(vData);
     }
@@ -31,11 +31,11 @@ export function useVitessceConfig({ vitData, setVitessceState, setVitessceErrors
       let initializedVitDataFromUrl = vitData;
       let initialSelectionFromUrl;
       // If these is a url conf and the we have a multidataset, use the url conf to find the initial selection of the multi-dataset.
-      if (Array.isArray(vitData)) {
+      if (vitData.length > 1) {
         initialSelectionFromUrl = Math.max(0, vitData.map(({ name }) => name).indexOf(vitessceURLConf?.name));
         initializedVitDataFromUrl[initialSelectionFromUrl] = vitessceURLConf || vitData[initialSelectionFromUrl];
       } else {
-        initializedVitDataFromUrl = vitessceURLConf || vitData;
+        initializedVitDataFromUrl = vitessceURLConf || vitData[0];
       }
       setVitessceState(initializedVitDataFromUrl[initialSelectionFromUrl]);
       setVitessceSelection(initialSelectionFromUrl);

etc/qa/find-vis-bugs.py

@@ -73,10 +73,10 @@ def get_errors(override_uuids):
         warn(f'{i}/{len(uuids)} ({len(errors)} errors): Checking {uuid} ...')
         try:
             before_conf = perf_counter()
-            conf_uuid = client.get_vitessce_conf_cells_and_lifted_uuid(dataset, wrap_error=False)
+            configs_cells_uuid = client.get_configs_cells_and_lifted_uuid(dataset, wrap_error=False)
             warn(
-                f'\tVis: {conf_uuid.vitessce_conf.conf is not None}; '
-                f'Lifted: {conf_uuid.vis_lifted_uuid} ')
+                f'\tVis: {len(configs_cells_uuid.configs_cells.configs) > 0}; '
+                f'Lifted: {configs_cells_uuid.vis_lifted_uuid} ')
             waiting_for_conf += perf_counter() - before_conf
         except Exception as e:
             warn(f'\tERROR: {e}')