added retry all from search button to import summary page

src/common/db_IO.py

@@ -1964,16 +1964,21 @@ def get_imported_variants_page(self, comments, stati, vids, import_queue_id, pag
         new_constraints = "import_queue_id = %s"
         postfix = self.add_constraints_to_command(postfix, new_constraints)
         actual_information += (import_queue_id, )
-        command = prefix + postfix + " ORDER BY requested_at DESC LIMIT %s, %s"
-        page_size = int(page_size)
-        page = int(page)
-        offset = (page - 1) * page_size
-        actual_information += (offset, page_size)
-        print(command % actual_information)
+        command = prefix + postfix + " ORDER BY requested_at DESC"
+        if page_size != "all":
+            command += " LIMIT %s, %s"
+            page_size = int(page_size)
+            page = int(page)
+            offset = (page - 1) * page_size
+            actual_information += (offset, page_size)
+        #print(command % actual_information)
         self.cursor.execute(command, actual_information)
         raw_results = self.cursor.fetchall()
         result = [self.convert_raw_import_variant_request(raw_result) for raw_result in raw_results]
 
+        if page_size == "all":
+            return result, len(result)
+
         # get total number
         prefix = "SELECT COUNT(id) FROM import_variant_queue"
         command = prefix + postfix

src/common/paths.py

@@ -43,7 +43,7 @@ def joinpaths(path, *paths):
     ngs_bits_path = joinpaths(toolsdir, "ngs-bits/bin")
     htslib_path = joinpaths(toolsdir, "htslib")
     automatic_classification_path = joinpaths(toolsdir, "herediclass")
-    automatic_classification_config_path = os.path.join(automatic_classification_path, "config_pejaver_mult_strength_production.yaml") # config_production.yaml
+    automatic_classification_config_path = os.path.join(automatic_classification_path, "config_pejaver_mult_strength_production.yaml") # "config_production.yaml"
     samtools_path = joinpaths(toolsdir, "samtools/samtools")
 
     # data

src/frontend_celery/webapp/templates/user/variant_import_summary.html

@@ -194,6 +194,7 @@ <h4 class="card-subcaption">Status details</h4>
                                     <td><div class="Nellipsis" data-bs-toggle="tooltip" data-bs-title="{{ entry.message }}">{{ entry.message }}</div></td>
                                     <td>
                                         <form action="{{url_for('user.variant_import_summary', import_queue_id=import_queue_id, **request.args)}}" method="post">
+                                            <input class="visually-hidden" name="action" value="retry_one" type="text">
                                             <input class="visually-hidden" name="import_variant_queue_id" type="text" value="{{entry.id}}">
                                             <button class="btn btn-outline-primary" type="submit">Retry</button>
                                         </form>
@@ -203,8 +204,18 @@ <h4 class="card-subcaption">Status details</h4>
                             </tbody>
                         </table>
                     </div>
-
-                    <div id="tabnav-bottom" class="ssb">{{ pagination.links }}</div>
+
+                    <div class="d-flex">
+                        <div id="tabnav-bottom" class="ssb">{{ pagination.links }}</div>
+                        <div class="flex-grow-1"></div>
+                        <div>
+                            <form action="{{url_for('user.variant_import_summary', import_queue_id = import_queue_id, **request.args)}}" method="post">
+                                <input class="visually-hidden" name="action" value="retry_search" type="text">
+                                <button class="btn btn-outline-primary" type="submit">Retry all</button>
+                            </form>
+                        </div>
+                    </div>
+
 
                 </div>
 

src/frontend_celery/webapp/user/user_routes.py

@@ -367,16 +367,28 @@ def variant_import_summary(import_queue_id):
     import_request = conn.get_import_request(import_queue_id)
     require_set(import_request)
 
-    if request.method == 'POST':
-        import_variant_queue_id = request.form.get('import_variant_queue_id')
-        require_valid(import_variant_queue_id, 'import_variant_queue', conn)
+    static_information = get_static_vis_information(conn)
 
-        tasks.retry_variant_import(import_variant_queue_id, session['user']['user_id'], session['user']['roles'], conn)
-        vid = conn.get_vid_from_import_variant_queue(import_variant_queue_id)
-        flash("Successfully requested reimport of vid " + str(vid) + ". It is processed in the background. If this page does not show a pending variant refresh to view changes.", "alert-success")
-        return redirect(url_for('user.variant_import_summary', import_queue_id = import_queue_id, **request.args))
+    if request.method == 'POST':
+        action = request.form.get('action')
+        require_set(action)
+        if action == "retry_one":
+            import_variant_queue_id = request.form.get('import_variant_queue_id')
+            require_valid(import_variant_queue_id, 'import_variant_queue', conn)
+
+            tasks.retry_variant_import(import_variant_queue_id, session['user']['user_id'], session['user']['roles'], conn)
+            vid = conn.get_vid_from_import_variant_queue(import_variant_queue_id)
+            flash("Successfully requested reimport of vid " + str(vid) + ". It is processed in the background. If this page does not show a pending variant refresh to view changes.", "alert-success")
+            return redirect(url_for('user.variant_import_summary', import_queue_id = import_queue_id, **request.args))
+        if action == "retry_search":
+            imported_variants, total, page, page_size = get_vis_page(request.args, import_queue_id, static_information, conn, paginate = False)
+            for imported_variant in imported_variants:
+                import_variant_queue_id = imported_variant.id
+                tasks.retry_variant_import(import_variant_queue_id, session['user']['user_id'], session['user']['roles'], conn)
+            flash("Successfully requested reimport of " + str(len(imported_variants)) + " VIDs. If this page does not show a pending variant refresh to view changes.", "alert-success")
+            return redirect(url_for('user.variant_import_summary', import_queue_id = import_queue_id, **request.args))
 
-    static_information = get_static_vis_information(conn)
+
     imported_variants, total, page, page_size = get_vis_page(request.args, import_queue_id, static_information, conn)
     pagination = Pagination(page=page, per_page=page_size, total=total, css_framework='bootstrap5')
 
@@ -396,9 +408,11 @@ def get_static_vis_information(conn: Connection):
     result["allowed_stati"] = conn.get_enumtypes("import_variant_queue", "status")
     return result
 
-def get_vis_page(request_args, import_queue_id, static_information, conn: Connection):
+def get_vis_page(request_args, import_queue_id, static_information, conn: Connection, paginate = True):
     page = request.args.get('page', static_information["default_page"])
-    page_size = request.args.get('page_size', static_information["default_page_size"])
+    page_size = "all"
+    if paginate:
+        page_size = request.args.get('page_size', static_information["default_page_size"])
 
     comments = extract_comments_vis(request_args)
     stati = extract_stati_vis(request_args, static_information["allowed_stati"])