fix tombstone ingest and add tombstone UI (#1378)

DesignSafe-CI · Jul 29, 2024 · ab6dc48 · ab6dc48
1 parent 3db894e
commit ab6dc48
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Showing 9 changed files with 96 additions and 22 deletions.
diff --git a/client/modules/_hooks/src/datafiles/projects/types.ts b/client/modules/_hooks/src/datafiles/projects/types.ts
@@ -76,6 +76,8 @@ export type TBaseProjectValue = {
 
   title: string;
   description: string;
+  tombstone?: boolean;
+  tombstoneMessage?: string;
   users: TProjectUser[];
   dataTypes?: TDropdownValue[];
   authors: TProjectUser[];
@@ -100,6 +102,8 @@ export type TBaseProjectValue = {
 
 export type TEntityValue = {
   title: string;
+  tombstone?: boolean;
+  tombstoneMessage?: string;
   description?: string;
   dataCollectors?: TProjectUser[];
   projectId?: string;

diff --git a/client/modules/_hooks/src/datafiles/publications/useDataciteEvents.ts b/client/modules/_hooks/src/datafiles/publications/useDataciteEvents.ts
@@ -39,5 +39,6 @@ export function useDataciteEvents(doi: string, enabled: boolean = true) {
       return getDataciteEvents({ doi, signal });
     },
     enabled: enabled && !!doi,
+    retry: false,
   });
 }
diff --git a/client/modules/_hooks/src/datafiles/publications/useDataciteMetrics.ts b/client/modules/_hooks/src/datafiles/publications/useDataciteMetrics.ts
@@ -41,5 +41,6 @@ export function useDataciteMetrics(doi: string, enabled: boolean = true) {
       return getDataciteMetrics({ doi, signal });
     },
     enabled: enabled && !!doi,
+    retry: false,
   });
 }
diff --git a/client/modules/datafiles/src/projects/PublishedEntityDetails.tsx b/client/modules/datafiles/src/projects/PublishedEntityDetails.tsx
@@ -7,6 +7,7 @@ import {
   LicenseDisplay,
   UsernamePopover,
 } from './BaseProjectDetails';
+import { Alert } from 'antd';
 
 export const PublishedEntityDetails: React.FC<{
   entityValue: TEntityValue;
@@ -15,6 +16,25 @@ export const PublishedEntityDetails: React.FC<{
 }> = ({ entityValue, publicationDate, license }) => {
   return (
     <section style={{ marginBottom: '20px' }}>
+      {entityValue.tombstone && (
+        <Alert
+          showIcon
+          style={{ marginBottom: '12px' }}
+          type="warning"
+          message={
+            <strong>The following Dataset does not exist anymore</strong>
+          }
+          description={
+            <div>
+              The Dataset with DOI:{' '}
+              <a href={`https://doi.org/${entityValue.dois?.[0]}`}>
+                {entityValue.dois?.[0]}
+              </a>{' '}
+              was incomplete and removed. The metadata is still available.
+            </div>
+          }
+        />
+      )}
       <table
         style={{ width: '100%', marginBottom: '20px', borderSpacing: '200px' }}
       >

diff --git a/client/src/datafiles/layouts/published/PublishedDetailLayout.tsx b/client/src/datafiles/layouts/published/PublishedDetailLayout.tsx
@@ -117,27 +117,47 @@ export const PublishedDetailLayout: React.FC = () => {
       </div>
 
       {data.baseProject.projectType === 'other' && (
-        <section
-          style={{
-            backgroundColor: '#eef9fc',
-            padding: '10px 20px',
-            margin: '10px 0px',
-          }}
-        >
-          <strong>Cite This Data:</strong>
+        <>
+          {data.baseProject.tombstone && (
+            <Alert
+              showIcon
+              type="warning"
+              message={
+                <strong>The following Dataset does not exist anymore</strong>
+              }
+              description={
+                <div>
+                  The Dataset with DOI:{' '}
+                  <a href={`https://doi.org/${data.baseProject.dois[0]}`}>
+                    {data.baseProject.dois[0]}
+                  </a>{' '}
+                  was incomplete and removed. The metadata is still available.
+                </div>
+              }
+            />
+          )}
+          <section
+            style={{
+              backgroundColor: '#eef9fc',
+              padding: '10px 20px',
+              margin: '10px 0px',
+            }}
+          >
+            <strong>Cite This Data:</strong>
 
-          <PublishedCitation
-            projectId={projectId}
-            entityUuid={data.tree.children[0].uuid}
-          />
-          <br />
-          <div>
-            <DownloadCitation
+            <PublishedCitation
               projectId={projectId}
               entityUuid={data.tree.children[0].uuid}
             />
-          </div>
-        </section>
+            <br />
+            <div>
+              <DownloadCitation
+                projectId={projectId}
+                entityUuid={data.tree.children[0].uuid}
+              />
+            </div>
+          </section>
+        </>
       )}
       <BaseProjectDetails
         projectValue={data?.baseProject}

diff --git a/designsafe/apps/api/projects_v2/migration_utils/file_obj_ingest.py b/designsafe/apps/api/projects_v2/migration_utils/file_obj_ingest.py
@@ -1,14 +1,15 @@
 """Utilities to update the database with existing project file associations"""
 
 import json
+import os
 from typing import Iterator
 import requests
 from urllib3.util import Retry
 from requests import Session
 from requests.exceptions import RetryError
 from requests.adapters import HTTPAdapter
 from django.conf import settings
-from designsafe.apps.api.agave import service_account
+from designsafe.apps.api.agave import get_service_account_client_v2 as service_account
 from designsafe.apps.api.projects_v2.schema_models._field_models import FileObj
 from designsafe.apps.api.projects_v2.models.project_metadata import ProjectMetadata
 from designsafe.apps.api.projects_v2.operations.project_meta_operations import (
@@ -98,7 +99,7 @@ def get_files_for_entity(
                 file_meta = resp.json()["result"][0]
                 entity_file_objs.append(
                     FileObj(
-                        name=file_meta["name"],
+                        name=os.path.basename(file_meta["path"]),
                         system=file_meta["system"],
                         path=file_meta["path"],
                         type=file_meta["type"],

diff --git a/designsafe/apps/api/projects_v2/migration_utils/project_db_ingest.py b/designsafe/apps/api/projects_v2/migration_utils/project_db_ingest.py
@@ -212,13 +212,33 @@ def ingest_publications():
 def ingest_tombstones():
     """Ingest Elasticsearch tombstones into the db"""
 
+    tombstone_ids = [
+        "PRJ-1945",
+        "PRJ-1895",
+        "PRJ-2329",
+        "PRJ-2016",
+        "PRJ-2227",
+        "PRJ-2420",
+        "PRJ-3815",
+        "PRJ-3908",
+        "PRJ-4151",
+        "PRJ-4014",
+    ]
     all_pubs = (
-        IndexedPublication.search().filter(Q("term", status="tombstone")).execute().hits
+        IndexedPublication.search()
+        .filter(
+            Q("term", status="tombstone")
+            | Q("terms", **{"projectId._exact": tombstone_ids})
+        )
+        .execute()
+        .hits
     )
     print(all_pubs)
     for pub in all_pubs:
         try:
             pub_graph = combine_pub_versions(pub["projectId"])
+            for published_entity_node_id in pub_graph.successors("NODE_ROOT"):
+                pub_graph.nodes[published_entity_node_id]["value"]["tombstone"] = True
             latest_version: int = IndexedPublication.max_revision(pub["projectId"]) or 1
             pub_base = next(
                 (

diff --git a/designsafe/apps/api/projects_v2/migration_utils/publication_transforms.py b/designsafe/apps/api/projects_v2/migration_utils/publication_transforms.py
@@ -76,6 +76,9 @@ def convert_v2_user(user):
         role = "team_member"
         username = user["name"]
 
+    if not user.get("fname"):
+        user = {**user, **get_user_info(user["name"], role)}
+
     return {
         "fname": user["fname"],
         "lname": user["lname"],

diff --git a/designsafe/apps/api/publications_v2/views.py b/designsafe/apps/api/publications_v2/views.py
@@ -170,13 +170,17 @@ def get(self, request: HttpRequest):
         if has_query:
             hits, total = handle_search(query_opts, offset, limit)
             publications_query = (
-                Publication.objects.filter(project_id__in=hits)
+                Publication.objects.filter(project_id__in=hits, is_published=True)
                 .defer("tree")
                 .order_by("-created")
             )
             publications = publications_query
         else:
-            publications_query = Publication.objects.defer("tree").order_by("-created")
+            publications_query = (
+                Publication.objects.filter(is_published=True)
+                .defer("tree")
+                .order_by("-created")
+            )
             total = publications_query.count()
             publications = publications_query[offset : offset + limit]
         result = [