Continue to send full submission records in existing list endpoint; add new endpoint for slim records

Author: pkalita-lbl

nmdc_server/api.py

@@ -1055,26 +1055,48 @@ async def get_metadata_submissions_report(
     return response
 
 
-@router.get(
-    "/metadata_submission",
-    tags=["metadata_submission"],
-    responses=login_required_responses,
-    response_model=query.Paginated[schemas_submission.SubmissionMetadataSchemaListItem],
-)
-async def list_submissions(
+async def get_paginated_submission_list(
     db: Session = Depends(get_db),
     user: models.User = Depends(get_current_user),
     pagination: Pagination = Depends(),
     column_sort: str = "created",
     sort_order: str = "desc",
     is_test_submission_filter: Optional[bool] = None,
 ):
+    """
+    Dependency function for getting a list of submissions with pagination, sorting, and filtering
+    applied.
+    """
     query = crud.get_submissions_for_user(
         db, user, column_sort, sort_order, is_test_submission_filter
     )
     return pagination.response(query)
 
 
+# The following two endpoints perform the same underlying query, but only differ in the
+# response model they return.
+@router.get(
+    "/metadata_submission",
+    tags=["metadata_submission"],
+    responses=login_required_responses,
+    response_model=query.Paginated[schemas_submission.SubmissionMetadataSchema],
+)
+async def list_submissions(submissions=Depends(get_paginated_submission_list)):
+    """Return a paginated list of submissions in full detail."""
+    return submissions
+
+
+@router.get(
+    "/metadata_submission/slim",
+    tags=["metadata_submission"],
+    responses=login_required_responses,
+    response_model=query.Paginated[schemas_submission.SubmissionMetadataSchemaSlim],
+)
+async def list_submissions_slim(submissions=Depends(get_paginated_submission_list)):
+    """Return a paginated list of submissions in slim format."""
+    return submissions
+
+
 @router.get(
     "/metadata_submission/{id}",
     tags=["metadata_submission"],
@@ -1228,10 +1250,7 @@ def create_github_issue(submission: schemas_submission.SubmissionMetadataSchema,
     data_generated = "Yes" if multiomics_form.dataGenerated else "No"
     omics_processing_types = ", ".join(multiomics_form.omicsProcessingTypes)
     sample_types = ", ".join(submission.metadata_submission.templates)
-    sample_data = submission.metadata_submission.sampleData
-    num_samples = 0
-    for key in sample_data:
-        num_samples = max(num_samples, len(sample_data[key]))
+    num_samples = submission.sample_count
 
     # some variable data to supply depending on if data has been generated or not
     id_dict = {

nmdc_server/models.py

@@ -944,6 +944,21 @@ class SubmissionImagesObject(Base):
     ),
 )
 
+# TODO: It would be nice if this could be derived from the schema
+ENVIRONMENTAL_DATA_SLOTS = [
+    "air_data",
+    "built_env_data",
+    "host_associated_data",
+    "hcr_cores_data",
+    "hcr_fluids_swabs_data",
+    "biofilm_data",
+    "misc_envs_data",
+    "plant_associated_data",
+    "sediment_data",
+    "soil_data",
+    "water_data",
+]
+
 
 class SubmissionMetadata(Base):
     __tablename__ = "submission_metadata"
@@ -1038,14 +1053,28 @@ def owners(self) -> list[str]:
         ]
 
     @property
-    def study_images_total_size(self):
+    def study_images_total_size(self) -> int:
         """Calculate the total size of all study images associated with this submission."""
         return (
             sum(image.size for image in self.study_images)  # type: ignore
             if self.study_images
             else 0
         )
 
+    @property
+    def sample_count(self) -> int:
+        if not self.metadata_submission or not isinstance(self.metadata_submission, dict):
+            return 0
+        sample_data = self.metadata_submission.get("sampleData", {})
+        if not sample_data:
+            return 0
+        count = 0
+        for slot in sample_data:
+            if slot in ENVIRONMENTAL_DATA_SLOTS:
+                samples = sample_data.get(slot, [])
+                count += len(samples)
+        return count
+
 
 class SubmissionRole(Base):
     __tablename__ = "submission_role"

nmdc_server/schemas_submission.py

@@ -135,7 +135,7 @@ class SubmissionMetadataSchemaPatch(BaseModel):
     field_notes_metadata: Optional[Dict[str, Any]] = None
 
 
-class SubmissionMetadataSchemaListItem(BaseModel):
+class SubmissionMetadataSchemaSlim(BaseModel):
     id: UUID
     author: schemas.User
     study_name: Optional[str] = None
@@ -144,6 +144,7 @@ class SubmissionMetadataSchemaListItem(BaseModel):
     date_last_modified: datetime
     created: datetime
     is_test_submission: bool = False
+    sample_count: int = 0
 
 
 class SubmissionImagesObject(BaseModel):
@@ -154,7 +155,7 @@ class SubmissionImagesObject(BaseModel):
     content_type: str
 
 
-class SubmissionMetadataSchema(SubmissionMetadataSchemaListItem, SubmissionMetadataSchemaCreate):
+class SubmissionMetadataSchema(SubmissionMetadataSchemaSlim, SubmissionMetadataSchemaCreate):
     model_config = ConfigDict(from_attributes=True)
 
     author_orcid: str

web/src/views/SubmissionPortal/Components/SubmissionList.vue

@@ -16,7 +16,12 @@ import IntroBlurb from '@/views/SubmissionPortal/Components/IntroBlurb.vue';
 import ContactCard from '@/views/SubmissionPortal/Components/ContactCard.vue';
 import { SearchParams } from '@/data/api';
 import { deleteSubmission } from '../store/api';
-import { HARMONIZER_TEMPLATES, MetadataSubmissionRecord, PaginatedResponse } from '@/views/SubmissionPortal/types';
+import {
+  HARMONIZER_TEMPLATES,
+  MetadataSubmissionRecord,
+  MetadataSubmissionRecordSlim,
+  PaginatedResponse,
+} from '@/views/SubmissionPortal/types';
 
 const headers: DataTableHeader[] = [
   {
@@ -65,14 +70,14 @@ export default defineComponent({
       mustSort: false,
     });
     const isDeleteDialogOpen = ref(false);
-    const deleteDialogSubmission = ref<MetadataSubmissionRecord | null>(null);
+    const deleteDialogSubmission = ref<MetadataSubmissionRecordSlim | null>(null);
     const isTestFilter = ref(null);
     const testFilterValues = [
       { text: 'Show all submissions', val: null },
       { text: 'Show only test submissions', val: true },
       { text: 'Hide test submissions', val: false }];
 
-    async function getSubmissions(params: SearchParams): Promise<PaginatedResponse<MetadataSubmissionRecord>> {
+    async function getSubmissions(params: SearchParams): Promise<PaginatedResponse<MetadataSubmissionRecordSlim>> {
       return api.listRecords(params, isTestFilter.value);
     }
 
@@ -106,14 +111,14 @@ export default defineComponent({
       submission.setSortOptions(options.value.sortBy[0], sortOrder);
     }, { deep: true });
 
-    function handleOpenDeleteDialog(item: MetadataSubmissionRecord | null) {
+    function handleOpenDeleteDialog(item: MetadataSubmissionRecordSlim | null) {
       deleteDialogSubmission.value = item;
       if (deleteDialogSubmission) {
         isDeleteDialogOpen.value = true;
       }
     }
 
-    async function handleDelete(item: MetadataSubmissionRecord | null) {
+    async function handleDelete(item: MetadataSubmissionRecordSlim | null) {
       if (!item) {
         return;
       }

web/src/views/SubmissionPortal/store/api.ts

@@ -4,6 +4,7 @@ import {
   LockOperationResult,
   MetadataSubmission,
   MetadataSubmissionRecord,
+  MetadataSubmissionRecordSlim,
   MetadataSuggestion,
   MetadataSuggestionRequest,
   NmdcAddress,
@@ -47,27 +48,20 @@ async function updateRecord(id: string, record: Partial<MetadataSubmission>, sta
   return { data: resp.data, httpStatus: resp.status };
 }
 
-async function listRecords(params: SearchParams, isTestFilter: boolean | null) {
+async function listRecords(searchParams: SearchParams, isTestFilter: boolean | null) {
+  const params: Record<string, any> = {
+    limit: searchParams.limit,
+    offset: searchParams.offset,
+    column_sort: searchParams.sortColumn,
+    sort_order: searchParams.sortOrder,
+  };
   if (isTestFilter !== null) {
-    const resp = await client.get<PaginatedResponse<MetadataSubmissionRecord>>('metadata_submission', {
-      params: {
-        limit: params.limit,
-        offset: params.offset,
-        column_sort: params.sortColumn,
-        sort_order: params.sortOrder,
-        is_test_submission_filter: isTestFilter,
-      },
-    });
-    return resp.data;
+    params.is_test_submission_filter = isTestFilter;
   }
-  const resp = await client.get<PaginatedResponse<MetadataSubmissionRecord>>('metadata_submission', {
-    params: {
-      limit: params.limit,
-      offset: params.offset,
-      column_sort: params.sortColumn,
-      sort_order: params.sortOrder,
-    },
-  });
+  const resp = await client.get<PaginatedResponse<MetadataSubmissionRecordSlim>>(
+    'metadata_submission/slim',
+    { params },
+  );
   return resp.data;
 }
 

web/src/views/SubmissionPortal/types.ts

@@ -231,20 +231,25 @@ export interface MetadataSubmission {
   sampleData: Record<string, any[]>;
 }
 
-export interface MetadataSubmissionRecord {
+export interface MetadataSubmissionRecordSlim {
   id: string;
-  author_orcid: string;
+  author: User;
+  study_name: string;
+  templates: string[];
+  status: string;
+  date_last_modified: string;
   created: string;
+  is_test_submission: boolean;
+  sample_count: number;
+}
+
+export interface MetadataSubmissionRecord extends MetadataSubmissionRecordSlim {
+  author_orcid: string;
   metadata_submission: MetadataSubmission;
-  status: string;
   locked_by: User;
   lock_updated: string;
   permission_level: string | null;
   source_client: 'submission_portal' | 'field_notes' | 'nmdc_edge' | null;
-  study_name: string;
-  templates: string[];
-  is_test_submission: boolean;
-  date_last_modified: string;
 }
 
 export interface PaginatedResponse<T> {