From 2048c16ffaf3767f286cd1808044ed25ab5b8842 Mon Sep 17 00:00:00 2001
From: MarvinDo <qarst@gmx.de>
Date: Fri, 26 Jul 2024 09:42:23 +0200
Subject: [PATCH] added specific variants reannotate & improved heredicare job

---
 .../annotation_jobs/heredicare_job.py         | 23 +++++++++----------
 .../templates/user/admin_dashboard.html       |  7 ++++++
 .../user/variant_import_summary.html          |  2 +-
 .../webapp/user/user_routes.py                |  9 +++++---
 4 files changed, 25 insertions(+), 16 deletions(-)

diff --git a/src/annotation_service/annotation_jobs/heredicare_job.py b/src/annotation_service/annotation_jobs/heredicare_job.py
index 5a81f468..2b91aa4a 100644
--- a/src/annotation_service/annotation_jobs/heredicare_job.py
+++ b/src/annotation_service/annotation_jobs/heredicare_job.py
@@ -98,21 +98,20 @@ def annotate_heredicare(self, variant_id, conn):
                         err_msg += "The date could not be saved in the database. Format should be dd.mm.yyyy, but was: " + str(classification_date)
                         status_code = 1
 
-                heredicare_annotation_id = None
                 if status_code == 0:
                     heredicare_annotation_id = conn.insert_update_heredicare_annotation(variant_id, vid, n_fam, n_pat, consensus_class, classification_date, comment, lr_cooc, lr_coseg, lr_family)
 
-                for key in heredicare_variant:
-                    if key.startswith("PATH_Z"):
-                        zid = int(key[6:])
-                        heredicare_center_classification_raw = heredicare_variant[key]
-                        if heredicare_center_classification_raw is not None and heredicare_variant[key] == "-1":
-                            heredicare_center_classification_raw = None
-                        classification, comment = self.preprocess_heredicare_center_classification(heredicare_center_classification_raw)
-                        if classification is not None:
-                            conn.insert_update_heredicare_center_classification(heredicare_annotation_id, zid, classification, comment)
-                        else:
-                            conn.delete_heredicare_center_classification(heredicare_annotation_id, zid)
+                    for key in heredicare_variant:
+                        if key.startswith("PATH_Z"):
+                            zid = int(key[6:])
+                            heredicare_center_classification_raw = heredicare_variant[key]
+                            if heredicare_center_classification_raw is not None and heredicare_variant[key] == "-1":
+                                heredicare_center_classification_raw = None
+                            classification, comment = self.preprocess_heredicare_center_classification(heredicare_center_classification_raw)
+                            if classification is not None:
+                                conn.insert_update_heredicare_center_classification(heredicare_annotation_id, zid, classification, comment)
+                            else:
+                                conn.delete_heredicare_center_classification(heredicare_annotation_id, zid)
 
         return status_code, err_msg
 
diff --git a/src/frontend_celery/webapp/templates/user/admin_dashboard.html b/src/frontend_celery/webapp/templates/user/admin_dashboard.html
index d3d9d324..1708baaf 100644
--- a/src/frontend_celery/webapp/templates/user/admin_dashboard.html
+++ b/src/frontend_celery/webapp/templates/user/admin_dashboard.html
@@ -150,6 +150,13 @@ <h4>Warnings</h4>
                         <button type="button" class="btn btn-outline-primary reannotate_variants_button" data-bs-toggle="modal" data-bs-target="#reannotate-variants-modal" modal_text="ALL VARIANTS MISSING AN ANNOTATION" value="unannotated">unannotated variants</button>
                     </span>
                 </div>
+                <div class="form-group d-flex sst">
+                    <span class="d-inline-block" tabindex="0" data-bs-toggle="tooltip" title="Pressing this button requests an annotation of specific variants in HerediVar. Please specify HerediVar variant_ids.">
+                        <button type="button" class="btn btn-outline-primary reannotate_variants_button width_small" data-bs-toggle="modal" data-bs-target="#reannotate-variants-modal" modal_text="SPECIFIC VARIANTS" value="specific">specific variants</button>
+                    </span>
+                    <input class="form-control" type="text" name="specific_variants" placeholder="variant_id_1;variant_id_2;...">
+                </div>
+                
             </form>
         </div>
 
diff --git a/src/frontend_celery/webapp/templates/user/variant_import_summary.html b/src/frontend_celery/webapp/templates/user/variant_import_summary.html
index a1a2d36d..512559a2 100644
--- a/src/frontend_celery/webapp/templates/user/variant_import_summary.html
+++ b/src/frontend_celery/webapp/templates/user/variant_import_summary.html
@@ -96,7 +96,7 @@ <h4 class="card-subcaption">Status details</h4>
 
             <p class="card-text">
 
-
+                <div>Refresh page so see changes</div>
                 <div>
 
                     <div id="tabnav-head" class="row align-items-end  nsl nsr">
diff --git a/src/frontend_celery/webapp/user/user_routes.py b/src/frontend_celery/webapp/user/user_routes.py
index f21caeaf..6e9b4a88 100644
--- a/src/frontend_celery/webapp/user/user_routes.py
+++ b/src/frontend_celery/webapp/user/user_routes.py
@@ -257,6 +257,9 @@ def admin_dashboard():
                 variant_ids = annotation_stati['aborted']
             elif reannotate_which == 'unannotated':
                 variant_ids = annotation_stati['unannotated']
+            elif reannotate_which == 'specific':
+                raw = request.form.get('specific_variants', '')
+                variant_ids = search_utils.preprocess_query(raw, pattern = "\d+")
 
             tasks.annotate_all_variants.apply_async(args=[variant_ids, selected_job_config, session['user']['user_id'], session['user']['roles']])
             current_app.logger.info(session['user']['preferred_username'] + " issued a reannotation of " + reannotate_which + " variants") 
@@ -411,21 +414,21 @@ def extract_stati_vis(request_args, allowed_stati):
     raw = request_args.getlist('status')#
     raw = ';'.join(raw)
     regex_inner = '|'.join(allowed_stati)
-    processed = preprocess_query(raw, r'(' + regex_inner + r')?')
+    processed = search_utils.preprocess_query(raw, r'(' + regex_inner + r')?')
     if processed is None:
         flash("You have an error in your status queries. Results are not filtered by stati.", "alert-danger")
     return processed
 
 def extract_comments_vis(request_args):
     raw = request_args.get('comment', '')
-    processed = preprocess_query(raw, pattern=r".*", seps = "[;]", remove_whitespace = False)
+    processed = search_utils.preprocess_query(raw, pattern=r".*", seps = "[;]", remove_whitespace = False)
     if processed is None:
         flash("You have an error in your comment query(s). Results are not filtered by comment.", "alert-danger")
     return processed
 
 def extract_vids_vids(request_args):
     raw = request_args.get('vid', '')
-    processed = preprocess_query(raw, pattern=r"\d+")
+    processed = search_utils.preprocess_query(raw, pattern=r"\d+")
     if processed is None:
         flash("You have an error in your VID query(s). Results are not filtered by VIDs.", "alert-danger")
     return processed