Merge pull request #7 from ssi-dk/hotfixfeedback

fix AB#430

reporter/assets/custom.css

@@ -848,4 +848,8 @@ td.center {
 
 .unset-width-table {
   width: unset;
+}
+
+.qc-feedback {
+  color: rgb(179, 204, 193);
 }

reporter/components/admin.py

@@ -15,15 +15,17 @@ def html_qc_expert_form():
                                     id="feedback-button"), className="three columns")
             ], className="row"),
             html.Div([
-                html.Details([
-                    html.Summary("How it works (click to show)"),
-                    html.P("""If you want to send a sample to resequence,
-                    go to the sample card and select "Resequence" in 
-                    the Suplying Lab Feedback section. The admin will get
-                    an email with the change. You can also "Accept" samples
-                    with the "Supplying lab" warning and their data will
-                    be used in the future to adjust QC thresholds.""")
-                ])
+                html.Div(
+                    html.Details([
+                        html.Summary("How it works (click to show)"),
+                        html.P("""If you want to send a sample to resequence,
+                        go to the sample card and select "Resequence" in 
+                        the Suplying Lab Feedback section. The admin will get
+                        an email with the change. You can also "Accept" samples
+                        with the "Supplying lab" warning and their data will
+                        be used in the future to adjust QC thresholds.""")
+                ]), className="six columns"),
+                html.Div(id="qc-feedback", className="six columns qc-feedback")
             ], className="row mb-1")
 
         ])

reporter/components/import_data.py

@@ -164,14 +164,15 @@ def get_last_runs(run, n):
 def post_stamps(stamplist):
     for pair in stamplist:
         sample_id, stamp = pair
-        sample_db = mongo_interface.get_samples([sample_id])[0]
+        sample_db = mongo_interface.get_samples([ObjectId(sample_id)])[0]
         stamps = sample_db.get("stamps", {})
         stamp_list = stamps.get("stamp_list", [])
         stamp_list.append(stamp)
         stamps["stamp_list"] = stamp_list
         stamps[stamp["name"]] = stamp
         sample_db["stamps"] = stamps
         mongo_interface.save_sample(sample_db)
+    return "Feedback saved"
 
 def get_run(run_name):
     return mongo_interface.get_run(run_name)
@@ -191,7 +192,7 @@ def email_stamps(stamplist):
         sample_id, stamp = stamp_pair
         user = stamp["user"]
         new_status = stamp["value"]
-        sample = mongo_interface.get_samples([sample_id])[0]
+        sample = mongo_interface.get_samples([ObjectId(sample_id)])[0]
         if sample is not None:
             sample_name = sample["name"]
         else:

reporter/components/mongo_interface.py

@@ -483,21 +483,21 @@ def get_sample_QC_status(last_runs):
                         if qc_val == "N/A" and (not "reads" in sample_db or not "R1" in sample_db["reads"]):
                             qc_val = "CF(LF)"
                         expert_check = False
-                        if "ssi_expert_check" in stamps and "value" in stamps["ssi_expert_check"]:
-                            qc_val = stamps["ssi_expert_check"]["value"]
+                        if "supplying_lab_check" in stamps and "value" in stamps["supplying_lab_check"]:
+                            qc_val = stamps["supplying_lab_check"]["value"]
                             expert_check = True
 
-                    if qc_val == "fail:supplying lab":
-                        qc_val = "SL"
-                    elif (qc_val == "fail:core facility" or
-                            qc_val == "fail:resequence"):
-                        qc_val = "CF"
-                    elif qc_val == "pass:OK":
-                        qc_val = "OK"
-
-                    if expert_check:
-                        qc_val += "*"
-                    sample_dict[run["name"]] = qc_val
+                        if qc_val == "fail:supplying lab":
+                            qc_val = "SL"
+                        elif (qc_val == "fail:core facility" or
+                                qc_val == "fail:resequence"):
+                            qc_val = "CF"
+                        elif qc_val == "pass:OK" or qc_val == "pass:accepted":
+                            qc_val = "OK"
+
+                        if expert_check:
+                            qc_val += "*"
+                        sample_dict[run["name"]] = qc_val
         samples_runs_qc[name] = sample_dict
     return samples_runs_qc
 

reporter/reporter.py

@@ -1100,7 +1100,7 @@ def display_confirm_feedback(button):
 
 
 @app.callback(
-    Output("placeholder0", "children"),
+    Output("qc-feedback", "children"),
     [Input("qc-confirm", "submit_n_clicks")],
     [State("qc-user-1", "value")] + [State("sample-radio-{}".format(n), "value")
                                      for n in range(PAGESIZE)]
@@ -1122,6 +1122,7 @@ def print_radio(n_clicks_timestamp, user, *args):
         if len(stamplist) > 0:
             import_data.email_stamps(stamplist)
             import_data.post_stamps(stamplist)
+            return "Feedback saved"
     return []
 
 

reporter/run_checker.py

@@ -301,7 +301,7 @@ def update_run_report(store, n_intervals):
                 qc_val = "CF"
             elif qc_val == "CF(LF)":
                 statusname = "status--1"
-            elif qc_val == "pass:OK":
+            elif qc_val == "pass:OK" or qc_val == "pass:accepted":
                 statusname = "status-ok"
                 qc_val = "OK"
 
@@ -358,6 +358,7 @@ def update_run_report(store, n_intervals):
                     className = "0"
                     title = "Not Run"
                     status = p_runs[last_runs[index]["name"]]
+                    print(name, status)
                     if status.startswith("OK"):
                         className = "ok"
                         title = "OK"