Show pending projects in the report

daily_read/config.py

@@ -20,7 +20,7 @@ def __init__(self, env_file_path):
         self.FETCH_FROM_SNPSEQ = os.getenv("DAILY_READ_FETCH_FROM_SNPSEQ")
         self.FETCH_FROM_UGC = os.getenv("DAILY_READ_FETCH_FROM_UGC")
         self.STATUS_PRIORITY = {
-            0: "None",
+            0: "Pending",
             1: "Samples Received",
             2: "Reception Control finished",
             3: "Library QC finished",

daily_read/daily_report.py

@@ -23,11 +23,12 @@
 }
 
 STATUS_DESCRIPTIONS = {
-    "All Raw data Delivered": "The data has been made available through NGIs delivery system",
-    "All Samples Sequenced": "Sequencing (including potential resequencing) of all samples has been finished",
+    "All Raw data Delivered": "The data has been made available through NGIs delivery system.",
+    "All Samples Sequenced": "Sequencing (including potential resequencing) of all samples has been finished.",
     "Library QC finished": "Library QC is a quality control of the sequencing library produced either by NGI or supplied by you, depending on the type of project.",
     "Reception Control finished": "Reception Control consists of NGI staff measuring e.g. concentration and volume for the samples received.",
-    "Samples Received": "The samples have been received and registered at NGI",
+    "Samples Received": "The samples have been received and registered at NGI.",
+    "Pending": "The order has been set up but the samples have not yet been received by NGI.",
 }
 
 PORTAL_URL = "https://ngisweden.scilifelab.se/orders"

daily_read/ngi_data.py

@@ -278,7 +278,8 @@ def __init__(
             else:
                 self.status = latest_statuses[0]
         else:
-            log.info(f"No project dates found for {project_id}")
+            log.info(f"No project dates found for {project_id}, so setting its status to Pending")
+            self.status = "Pending"
 
     @property
     def internal_id_or_portal_id(self):

daily_read/templates/daily_report.html.j2

@@ -148,7 +148,7 @@
           </div>
         </div>
       </div>
-      {% if data["projects"]|length == 1 and None in data["projects"] %}
+      {% if data["projects"]|length == 0 %}
       <div class="row justify-content-center p-5 m-3">
         <div class="col-auto">No recorded activity at the time of report generation!</div>
       </div>

tests/test_ngi_data.py

@@ -229,7 +229,8 @@ def test_get_data_with_no_project_dates(data_repo_full, mocked_statusdb_conn_row
             data_master.get_data("NGI123459")
             assert len(data_master.data.keys()) == 1
             assert "NGI123459" in data_master.data
-            assert "No project dates found for NGI123459" in caplog.text
+            assert "No project dates found for NGI123459, so setting its status to Pending" in caplog.text
+            assert data_master.data["NGI123459"].status == "Pending"
 
 
 def test_skip_order_with_no_year(data_repo_full, mocked_statusdb_conn_rows, caplog, get_env_file_path):