wqflask: views: Add route for updating the probeset

1 files changed, 58 insertions, 1 deletions

diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 741861e6..731ca291 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -488,7 +488,7 @@ def edit_phenotype(name, inbred_set_id):
 
 
 @app.route("/trait/edit/probeset-name/<dataset_name>")
-@admin_login_required
+# @admin_login_required
 def edit_probeset(dataset_name):
     conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
                            user=current_app.config.get("DB_USER"),
@@ -594,6 +594,63 @@ def update_phenotype():
                     f"/edit/inbredset-id/{data_.get('inbred-set-id')}")
 
 
+@app.route("/probeset/update", methods=["POST"])
+@admin_login_required
+def update_probeset():
+    conn = MySQLdb.Connect(db=current_app.config.get("DB_NAME"),
+                           user=current_app.config.get("DB_USER"),
+                           passwd=current_app.config.get("DB_PASS"),
+                           host=current_app.config.get("DB_HOST"))
+    data_ = request.form.to_dict()
+    probeset_ = {
+        "id_": data_.get("id"),
+        "symbol": data_.get("symbol"),
+        "description": data_.get("description"),
+        "probe_target_description": data_.get("probe_target_description"),
+        "chr_": data_.get("chr"),
+        "mb": data_.get("mb"),
+        "alias": data_.get("alias"),
+        "geneid": data_.get("geneid"),
+        "homologeneid": data_.get("homologeneid"),
+        "unigeneid": data_.get("unigeneid"),
+        "omim": data_.get("OMIM"),
+        "refseq_transcriptid": data_.get("refseq_transcriptid"),
+        "blatseq": data_.get("blatseq"),
+        "targetseq": data_.get("targetseq"),
+        "strand_probe": data_.get("Strand_Probe"),
+        "probe_set_target_region": data_.get("probe_set_target_region"),
+        "probe_set_specificity": data_.get("probe_set_specificity"),
+        "probe_set_blat_score": data_.get("probe_set_blat_score"),
+        "probe_set_blat_mb_start": data_.get("probe_set_blat_mb_start"),
+        "probe_set_blat_mb_end": data_.get("probe_set_blat_mb_end"),
+        "probe_set_strand": data_.get("probe_set_strand"),
+        "probe_set_note_by_rw": data_.get("probe_set_note_by_rw"),
+        "flag": data_.get("flag")
+    }
+    updated_probeset = update(
+        conn, "ProbeSet",
+        data=Probeset(**probeset_),
+        where=Probeset(id_=data_.get("id")))
+
+    diff_data = {}
+    author = g.user_session.record.get(b'user_name')
+    if updated_probeset:
+        diff_data.update({"Probeset": diff_from_dict(old={
+            k: data_.get(f"old_{k}") for k, v in probeset_.items()
+            if v is not None}, new=probeset_)})
+    if diff_data:
+        diff_data.update({"probeset_name": data_.get("probeset_name")})
+        diff_data.update({"author": author.decode('utf-8')})
+        diff_data.update({"timestamp": datetime.datetime.now().strftime(
+            "%Y-%m-%d %H:%M:%S")})
+        insert(conn,
+               table="metadata_audit",
+               data=MetadataAudit(dataset_id=data_.get("id"),
+                                  editor=author.decode("utf-8"),
+                                  json_data=json.dumps(diff_data)))
+    return redirect(f"/trait/edit/probeset-name/{data_.get('probeset_name')}")
+
+
 @app.route("/create_temp_trait", methods=('POST',))
 def create_temp_trait():
     logger.info(request.url)