origin data name change, tree view bug fixes

client/src/components/_custom/drp/DataFilesProjectFileListingAddon/DataFilesProjectFileListingAddon.jsx

@@ -79,21 +79,21 @@ const DataFilesProjectFileListingAddon = ({ system }) => {
             )}
           <span className={styles.separator}>|</span>
           {selectedFiles.length == 1 && selectedFiles[0]?.metadata &&
-            selectedFiles[0].metadata['data_type'] === 'origin_data' ? (
+            selectedFiles[0].metadata['data_type'] === 'digital_dataset' ? (
               <Button
                 type="link"
                 onClick={() =>
                   createOriginDataModal('EDIT_ORIGIN_DATASET', selectedFiles[0])
                 }
               >
-                Edit Origin Dataset
+                Edit Digital Dataset
               </Button>
             ) : (
               <Button
                 type="link"
                 onClick={() => createOriginDataModal('ADD_ORIGIN_DATASET')}
               >
-                Add Origin Dataset
+                Add Digital Dataset
               </Button>
           )}
           <span className={styles.separator}>|</span>

client/src/components/_custom/drp/DataFilesProjectFileListingMetadataAddon/DataFilesProjectFileListingMetadataAddon.jsx

@@ -5,7 +5,7 @@ import { useFileListing } from 'hooks/datafiles';
 import DataDisplay from '../utils/DataDisplay/DataDisplay';
 import { formatDate } from 'utils/timeFormat';
 
-const excludeKeys = ['name', 'description', 'data_type', 'sample', 'base_origin_data', 'file_objs'];
+const excludeKeys = ['name', 'description', 'data_type', 'sample', 'digital_dataset', 'file_objs'];
 
 const DataFilesProjectFileListingMetadataAddon = ({ folderMetadata, metadata, path }) => {
 

client/src/components/_custom/drp/DataFilesProjectFileListingMetadataTitleAddon/DataFilesProjectFileListingMetadataTitleAddon.jsx

@@ -52,7 +52,7 @@ const DataFilesProjectFileListingMetadataTitleAddon = ({ folderMetadata, metadat
       case 'sample':
         createSampleModal('EDIT_SAMPLE_DATA', editFile);
         break;
-      case 'origin_data':
+      case 'digital_dataset':
         createOriginDataModal('EDIT_ORIGIN_DATASET', editFile);
         break;
       case 'analysis_data':

client/src/components/_custom/drp/DataFilesProjectPublish/DataFilesProjectPublishWizardSteps/ReviewProjectStructure.jsx

@@ -32,7 +32,7 @@ const ReviewProjectStructure = ({ projectTree }) => {
     if (projectTree && projectTree.length > 0) {
       setExpandedNodes([projectTree[0].id]);
     }
-  }, [projectTree]);
+  }, []);
 
   const handleNodeToggle = (event, nodeIds) => {
     // Update the list of expanded nodes
@@ -71,13 +71,13 @@ const ReviewProjectStructure = ({ projectTree }) => {
       name: node.metadata.name,
       system: params.system,
       type: 'dir',
-
+      path: node.path,
     };
     switch (dataType) {
       case 'sample':
         createSampleModal('EDIT_SAMPLE_DATA', editFile);
         break;
-      case 'origin_data':
+      case 'digital_dataset':
         createOriginDataModal('EDIT_ORIGIN_DATASET', editFile);
         break;
       case 'analysis_data':
@@ -113,8 +113,7 @@ const ReviewProjectStructure = ({ projectTree }) => {
       .map(word => word.charAt(0).toUpperCase() + word.slice(1))
       .join(' ');
 
-  const renderTree = (node) => {
-    return (
+  const renderTree = (node) => (
     <>
       <Section
         className={styles['section-project-structure']}
@@ -158,7 +157,7 @@ const ReviewProjectStructure = ({ projectTree }) => {
                       'description',
                       'data_type',
                       'sample',
-                      'base_origin_data',
+                      'digital_dataset',
                       'file_objs',
                     ]}
                   />
@@ -173,8 +172,8 @@ const ReviewProjectStructure = ({ projectTree }) => {
         </div>
       </Section>
     </>
-  )};
-
+  );
+  
   return (
     <SectionTableWrapper
       header={

client/src/components/_custom/drp/utils/DataDisplay/DataDisplay.jsx

@@ -8,7 +8,7 @@ import { useFileListing } from 'hooks/datafiles';
 const processSampleAndOriginData = (data, path) => {
   // use the path to get sample and origin data names
   const sample = data.sample ? path.split('/')[0] : null;
-  const origin_data = data.base_origin_data ? path.split('/')[1] : null;
+  const origin_data = data.digital_dataset ? path.split('/')[1] : null;
 
   // remove trailing / from pathname
   const locationPathname = location.pathname.endsWith('/') ? location.pathname.slice(0, -1) : location.pathname;
@@ -19,7 +19,7 @@ const processSampleAndOriginData = (data, path) => {
 
   // construct urls for sample and origin data and add to processed data
   if (sample) {
-    const sampleUrl = locationPathnameParts.slice(0, data.base_origin_data ? -2 : -1).join('/')
+    const sampleUrl = locationPathnameParts.slice(0, data.digital_dataset ? -2 : -1).join('/')
     sampleAndOriginMetadata.push({ label: 'Sample', value: <Link className={`${styles['dataset-link']}`} to={sampleUrl}>{sample}</Link> });   
   }
 

client/src/components/_custom/drp/utils/DataFilesToolbar/customFilePermissions.js

@@ -3,7 +3,7 @@ const customFilePermissions = (operation, files) => {
 
     const protectedDataTypes = [
         'sample',
-        'origin_data',
+        'digital_dataset',
         'analysis_data'
     ]
 

client/src/redux/sagas/_custom/drp.sagas.js

@@ -24,12 +24,11 @@ function* executeOperation(isEdit, params, values, reloadCallback, file = null,
 
   try {
     if (file && isEdit) {
-
       yield call(
         patchEntityUtil,
         filteredValues.data_type,
         params.system,
-        '/' + file.path,
+        file.path ? '/' + file.path : '',
         '/' + path,
         filteredValues,
         file.uuid
@@ -122,7 +121,7 @@ function* handleOriginData(action, isEdit) {
 
   const metadata = {
     ...values,
-    data_type: 'origin_data',
+    data_type: 'digital_dataset',
     sample: sample.uuid,
   }
 
@@ -152,7 +151,7 @@ function* handleAnalysisData(action, isEdit) {
     ...values, 
     data_type: 'analysis_data',
     sample: sample.uuid, 
-    base_origin_data: originData ? originData.uuid : ''
+    // base_origin_data: originData ? originData.uuid : ''
   }
 
   yield call(

server/portal/apps/__init__.py

@@ -6,6 +6,7 @@
     constants.PROJECT: DrpProjectMetadata,
     constants.SAMPLE: DrpSampleMetadata,
     constants.ORIGIN_DATA: DrpOriginDatasetMetadata,
+    constants.DIGITAL_DATASET: DrpOriginDatasetMetadata,
     constants.ANALYSIS_DATA: DrpAnalysisDatasetMetadata,
     constants.FILE: DrpFileMetadata
 }

server/portal/apps/_custom/drp/models.py

@@ -130,6 +130,7 @@ class DrpDatasetMetadata(DrpMetadataModel):
     data_type: Literal[
         "sample", 
         "origin_data",
+        "digital_dataset",
         "analysis_data",
         "file"
     ]
@@ -211,4 +212,5 @@ class DrpAnalysisDatasetMetadata(DrpDatasetMetadata):
     ]
     external_uri: Optional[str] = None
     sample: str
-    base_origin_data: Optional[str] = None
+    # base_origin_data: Optional[str] = None
+    digital_dataset: Optional[str] = None

server/portal/apps/_custom/drp/views.py

@@ -6,6 +6,7 @@
 from portal.apps.projects.models.project_metadata import ProjectMetadata
 from portal.apps._custom.drp import constants
 import networkx as nx
+from networkx import shortest_path
 from portal.apps.projects.workspace_operations.project_meta_operations import get_ordered_value
 class DigitalRocksSampleView(BaseApiView):
 
@@ -24,7 +25,7 @@ def get(self, request):
         if get_origin_data == 'true':
             # origin_data = DataFilesMetadata.objects.filter(project_id=full_project_id, metadata__data_type='origin_data').values('id', 'name', 'path', 'metadata')
 
-            origin_data = ProjectMetadata.objects.filter(base_project__value__projectId=full_project_id, name=constants.ORIGIN_DATA).values('uuid', 'name', 'value')
+            origin_data = ProjectMetadata.objects.filter(base_project__value__projectId=full_project_id, name=constants.DIGITAL_DATASET).values('uuid', 'name', 'value')
 
         response_data = {
             'samples': list(samples),
@@ -65,6 +66,8 @@ def get(self, request):
 
         graph = nx.node_link_graph(graph_model.value)
 
+        trash_node_id = None  
+
         for node_id in graph.nodes:
             trash_node = graph.nodes[node_id].get('name') == settings.TAPIS_DEFAULT_TRASH_NAME
             if trash_node:
@@ -80,6 +83,13 @@ def get(self, request):
 
             node = graph.nodes[node_id]
 
+            # Get the path from NODE_ROOT to the current node
+            if nx.has_path(graph, 'NODE_ROOT', node_id):
+                path_nodes = shortest_path(graph, 'NODE_ROOT', node_id)[1:]
+                node['path'] = '/'.join(graph.nodes[parent]['label'] for parent in path_nodes if 'label' in graph.nodes[parent])
+            else:
+                node['path'] = ""
+
             if node.get('value'):
                 metadata = get_ordered_value(node['name'], node['value'])
                 file_objs = node['value'].get('fileObjs', [])

server/portal/apps/projects/views.py

@@ -395,8 +395,8 @@ def patch(self, request: HttpRequest, project_id: str):
                 raise ApiException("Error updating file metadata", status=500) from exc
         else:
             try:
-                new_name = move_entity(client, project_id, path, updated_path, value)
-                patch_entity_and_node(project_id, value, path, updated_path, new_name)
+                new_name = move_entity(client, project_id, path, updated_path, value, entity_uuid)
+                patch_entity_and_node(project_id, value, path, updated_path, new_name, entity_uuid)
             except Exception as exc:
                 raise ApiException("Error updating entity metadata", status=500) from exc
 

server/portal/apps/projects/workspace_operations/graph_operations.py

@@ -125,7 +125,7 @@ def update_node_in_project(project_id: str, node_id: str, new_parent: str = None
         if not project_graph.has_node(node_id):
             raise nx.exception.NodeNotFound
 
-        if new_parent:
+        if new_parent and new_parent != node_id:
             # Remove the node from the graph and re-add it under the new parent.
             parent_node = new_parent
             if not project_graph.has_node(parent_node):
@@ -156,4 +156,16 @@ def add_node_to_project(project_id: str, parent_node: str, meta_uuid: str, name:
 
         graph_model.value = nx.node_link_data(updated_graph)
         graph_model.save()
-    return new_node_id
+    return new_node_id
+
+def get_node_from_uuid(project_id: str, uuid: str):
+    """Get a node from the project graph using its UUID."""
+    graph_model = ProjectMetadata.objects.get(
+        name=constants.PROJECT_GRAPH, base_project__value__projectId=project_id
+    )
+    project_graph = nx.node_link_graph(graph_model.value)
+
+    for node_id in project_graph.nodes:
+        if project_graph.nodes[node_id]["uuid"] == uuid:
+            return {"id": node_id, **project_graph.nodes[node_id]}
+    return None

server/portal/apps/projects/workspace_operations/project_meta_operations.py

@@ -10,7 +10,7 @@
 from portal.apps._custom.drp import constants
 from portal.apps.projects.models.project_metadata import ProjectMetadata
 from portal.apps._custom.drp.models import PartialEntityWithFiles, FileObj
-from portal.apps.projects.workspace_operations.graph_operations import get_node_from_path, get_root_node, update_node_in_project
+from portal.apps.projects.workspace_operations.graph_operations import get_node_from_path, get_node_from_uuid, get_root_node, update_node_in_project
 
 portal = settings.PORTAL_NAMESPACE.lower()
 
@@ -192,13 +192,19 @@ def patch_file_obj_entity(client, project_id, value, path):
     return entity
 
 @transaction.atomic
-def patch_entity_and_node(project_id, value, path, new_path, new_name):
+def patch_entity_and_node(project_id, value, path, new_path, new_name, uuid=None):
     """Perform an operation on an entity."""
 
     new_path_full = os.path.join(new_path.strip('/'), new_name)
 
-    source_node = get_node_from_path(project_id, path)
-    entity = ProjectMetadata.objects.get(uuid=source_node['uuid'])
+    if (path):
+        source_node = get_node_from_path(project_id, path)
+    elif (not path and uuid):
+        source_node = get_node_from_uuid(project_id, uuid)
+    else: 
+        raise ValueError("Invalid parameters: path or uuid must be provided.")
+
+    entity = ProjectMetadata.objects.get(uuid=uuid if uuid else source_node['uuid'])
 
     new_parent_node = get_node_from_path(project_id, new_path)