Merge pull request #1322 from microbiomedata/884-sortable-submissions-list

884 sortable submissions list

Author: marySalvi

nmdc_server/api.py

@@ -633,8 +633,10 @@ async def list_submissions(
     db: Session = Depends(get_db),
     user: models.User = Depends(get_current_user),
     pagination: Pagination = Depends(),
+    column_sort: str = "created",
+    sort_order: str = "desc",
 ):
-    query = crud.get_submissions_for_user(db, user)
+    query = crud.get_submissions_for_user(db, user, column_sort, sort_order)
     return pagination.response(query)
 
 
@@ -671,6 +673,8 @@ async def get_submission(
             created=submission.created,
             author=schemas.User(**submission.author.__dict__),
             permission_level=permission_level,
+            templates=submission.templates,
+            study_name=submission.study_name,
         )
         if submission.locked_by is not None:
             submission_metadata_schema.locked_by = schemas.User(**submission.locked_by.__dict__)
@@ -938,8 +942,14 @@ async def submit_metadata(
     db: Session = Depends(get_db),
     user: models.User = Depends(get_current_user),
 ):
-    submission = SubmissionMetadata(**body.dict(), author_orcid=user.orcid)
+    submission = SubmissionMetadata(
+        **body.dict(),
+        author_orcid=user.orcid,
+    )
     submission.author_id = user.id
+    submission.study_name = body.metadata_submission.studyForm.studyName
+    submission.templates = body.metadata_submission.templates
+
     db.add(submission)
     db.commit()
     owner_role = SubmissionRole(

nmdc_server/crud.py

@@ -629,10 +629,18 @@ def can_edit_entire_submission(db: Session, submission_id: str, user_orcid: str)
     return (role and models.SubmissionEditorRole(role.role) in contributors_edit_roles) is True
 
 
-def get_submissions_for_user(db: Session, user: models.User):
+def get_submissions_for_user(db: Session, user: models.User, column_sort: str, order: str):
     """Return all submissions that a user has permission to view."""
-    all_submissions = db.query(models.SubmissionMetadata).order_by(
-        models.SubmissionMetadata.created.desc()
+    column = (
+        models.User.name
+        if column_sort == "author.name"
+        else getattr(models.SubmissionMetadata, column_sort)
+    )
+
+    all_submissions = (
+        db.query(models.SubmissionMetadata)
+        .join(models.User, models.SubmissionMetadata.author_id == models.User.id)
+        .order_by(column.asc() if order == "asc" else column.desc())
     )
 
     if user.is_admin:

nmdc_server/fakes.py

@@ -345,6 +345,8 @@ class Meta:
     author = SubFactory(UserFactory)
     author_orcid = Faker("pystr")
     status = "In Progress"
+    study_name = Faker("word")
+    templates = Faker("pylist", nb_elements=2, value_types=[str])
     created = datetime.utcnow()
     # TODO specify all fields!
     metadata_submission = {

nmdc_server/migrations/versions/0ff690fb929d_add_study_name_and_template_columns_to_.py

@@ -0,0 +1,65 @@
+"""Add study_name and template columns to submission_metadata
+
+Revision ID: 0ff690fb929d
+Revises: c0b36f8dc4b8
+Create Date: 2024-08-01 16:01:05.023371
+
+"""
+
+from typing import Optional
+
+import sqlalchemy as sa
+from alembic import op
+from sqlalchemy.dialects.postgresql import JSONB
+from sqlalchemy.sql import column, table
+
+# revision identifiers, used by Alembic.
+revision: str = "0ff690fb929d"
+down_revision: Optional[str] = "c0b36f8dc4b8"
+branch_labels: Optional[str] = None
+depends_on: Optional[str] = None
+
+
+def upgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.add_column("submission_metadata", sa.Column("study_name", sa.String(), nullable=True))
+    op.add_column(
+        "submission_metadata",
+        sa.Column("templates", JSONB(astext_type=sa.Text()), nullable=True),  # type:ignore
+    )
+    submission_metadata = table(
+        "submission_metadata",
+        column("id", sa.String),
+        column("metadata_submission", JSONB),
+        column("study_name", sa.String),
+        column("templates", JSONB),
+    )
+
+    connection = op.get_bind()
+    submissions = connection.execute(
+        sa.select([submission_metadata.c.id, submission_metadata.c.metadata_submission])
+    )
+
+    for submission in submissions:
+        study_name = submission.metadata_submission["studyForm"].get("studyName")
+        templates = submission.metadata_submission.get("templates")
+        if study_name:
+            connection.execute(
+                submission_metadata.update()
+                .where(submission_metadata.c.id == submission.id)
+                .values(study_name=study_name)
+            )
+        if templates:
+            connection.execute(
+                submission_metadata.update()
+                .where(submission_metadata.c.id == submission.id)
+                .values(templates=templates)
+            )
+    # ### end Alembic commands ###
+
+
+def downgrade():
+    # ### commands auto generated by Alembic - please adjust! ###
+    op.drop_column("submission_metadata", "templates")
+    op.drop_column("submission_metadata", "study_name")
+    # ### end Alembic commands ###

nmdc_server/models.py

@@ -851,6 +851,8 @@ class SubmissionMetadata(Base):
     status = Column(String, nullable=False, default="in-progress")
     metadata_submission = Column(JSONB, nullable=False)
     author_id = Column(UUID(as_uuid=True), ForeignKey(User.id))
+    study_name = Column(String, nullable=True)
+    templates = Column(JSONB, nullable=True)
 
     # The client which initially created the submission. A null value indicates it was created by
     # an "unregistered" client. This could be legitimate usage, but it should be monitored.

nmdc_server/schemas_submission.py

@@ -111,6 +111,8 @@ class SubmissionMetadataSchema(SubmissionMetadataSchemaCreate):
     created: datetime
     status: str
     author: schemas.User
+    templates: List[str]
+    study_name: Optional[str]
 
     lock_updated: Optional[datetime]
     locked_by: Optional[schemas.User]

web/src/data/api.ts

@@ -338,6 +338,8 @@ export interface BulkDownload {
 export interface SearchParams {
   offset?: number;
   limit?: number;
+  sortColumn?: string;
+  sortOrder?: string;
   conditions: Condition[];
   data_object_filter?: DataObjectFilter[];
 }

web/src/use/usePaginatedResults.ts

@@ -17,6 +17,8 @@ export default function usePaginatedResult<T>(
     results: { count: 0, results: [] } as SearchResponse<T>,
     offset: 0,
     limit, // same as pageSize
+    sortColumn: '',
+    sortOrder: 'desc',
     pageSync: 1,
   });
   const { error, loading, request } = useRequest();
@@ -33,6 +35,8 @@ export default function usePaginatedResult<T>(
       data.results = await func({
         limit: data.limit,
         offset: data.offset,
+        sortColumn: data.sortColumn,
+        sortOrder: data.sortOrder,
         conditions: conditions.value,
         data_object_filter: dataObjectFilter?.value,
       });
@@ -66,12 +70,19 @@ export default function usePaginatedResult<T>(
     debouncedFetchResults();
   }
 
+  function setSortOptions(columnSort: string, sortOrder: string) {
+    data.sortColumn = columnSort;
+    data.sortOrder = sortOrder;
+    debouncedFetchResults();
+  }
+
   return {
     data,
     error,
     loading,
     page,
     setPage,
     setItemsPerPage,
+    setSortOptions,
   };
 }

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

@@ -1,8 +1,8 @@
 <script lang="ts">
 import {
-  defineComponent, ref, watch,
+  defineComponent, ref, watch, Ref,
 } from '@vue/composition-api';
-import { DataTableHeader } from 'vuetify';
+import { DataOptions, DataTableHeader } from 'vuetify';
 import { useRouter } from '@/use/useRouter';
 import usePaginatedResults from '@/use/usePaginatedResults';
 import {
@@ -19,28 +19,23 @@ import ContactCard from '@/views/SubmissionPortal/Components/ContactCard.vue';
 const headers: DataTableHeader[] = [
   {
     text: 'Study Name',
-    value: 'metadata_submission.studyForm.studyName',
-    sortable: false,
+    value: 'study_name',
   },
   {
     text: 'Author',
     value: 'author.name',
-    sortable: false,
   },
   {
     text: 'Template',
-    value: 'metadata_submission.templates',
-    sortable: false,
+    value: 'templates',
   },
   {
     text: 'Status',
     value: 'status',
-    sortable: false,
   },
   {
     text: 'Created',
     value: 'created',
-    sortable: false,
   },
   {
     text: '',
@@ -57,9 +52,15 @@ export default defineComponent({
   setup() {
     const router = useRouter();
     const itemsPerPage = 10;
-    const options = ref({
+    const options: Ref<DataOptions> = ref<DataOptions>({
       page: 1,
       itemsPerPage,
+      sortBy: ['created'],
+      sortDesc: [true],
+      groupBy: [],
+      groupDesc: [],
+      multiSort: false,
+      mustSort: false,
     });
 
     function getStatus(item: api.MetadataSubmissionRecord) {
@@ -80,7 +81,11 @@ export default defineComponent({
     }
 
     const submission = usePaginatedResults(ref([]), api.listRecords, ref([]), itemsPerPage);
-    watch(options, () => submission.setPage(options.value.page), { deep: true });
+    watch(options, () => {
+      submission.setPage(options.value.page);
+      const sortOrder = options.value.sortDesc[0] ? 'desc' : 'asc';
+      submission.setSortOptions(options.value.sortBy[0], sortOrder);
+    }, { deep: true });
 
     return {
       HARMONIZER_TEMPLATES,
@@ -173,7 +178,7 @@ export default defineComponent({
               :authenticated="true"
             />
           </template>
-          <template #[`item.metadata_submission.templates`]="{ item }">
+          <template #[`item.templates`]="{ item }">
             {{ item.metadata_submission.templates.map((template) => HARMONIZER_TEMPLATES[template].displayName).join(' + ') }}
           </template>
           <template #[`item.created`]="{ item }">

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

@@ -47,6 +47,8 @@ interface MetadataSubmissionRecord {
   lock_updated: string;
   permission_level: string | null;
   source_client: 'submission_portal' | 'field_notes' | null;
+  study_name: string;
+  templates: string[];
 }
 
 interface PaginatedResponse<T> {
@@ -87,6 +89,8 @@ async function listRecords(params: SearchParams) {
     params: {
       limit: params.limit,
       offset: params.offset,
+      column_sort: params.sortColumn,
+      sort_order: params.sortOrder,
     },
   });
   return resp.data;