Merge pull request #43 from alneberg/typofix

Typofix

daily_read/config.py

@@ -22,9 +22,9 @@ def __init__(self, env_file_path):
         self.STATUS_PRIORITY = {
             0: "Pending",
             1: "Samples Received",
-            2: "Reception Control finished",
-            3: "Library QC finished",
+            2: "Reception Control Finished",
+            3: "Library QC Finished",
             4: "All Samples Sequenced",
-            5: "All Raw data Delivered",
+            5: "All Raw Data Delivered",
         }
         self.STATUS_PRIORITY_REV = {v: k for k, v in self.STATUS_PRIORITY.items()}

daily_read/daily_report.py

@@ -15,18 +15,18 @@
 
 
 STATUS_ICONS = {
-    "All Raw data Delivered": "cloud-download",
+    "All Raw Data Delivered": "cloud-download",
     "All Samples Sequenced": "body-text",
-    "Library QC finished": "check2-all",
-    "Reception Control finished": "check2",
+    "Library QC Finished": "check2-all",
+    "Reception Control Finished": "check2",
     "Samples Received": "box-seam",
 }
 
 STATUS_DESCRIPTIONS = {
-    "All Raw data Delivered": "The data has been made available through NGIs delivery system.",
+    "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.",
+    "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.",
     "Pending": "The order has been set up but the samples have not yet been received or registered by NGI.",
 }

tests/conftest.py

@@ -13,7 +13,7 @@
     "orderer": "[email protected]",
     "project_dates": {
         "2023-06-15": ["Samples Received"],
-        "2023-06-28": ["Reception Control finished", "Library QC finished"],
+        "2023-06-28": ["Reception Control Finished", "Library QC Finished"],
     },
     "internal_id": "P123456",
     "internal_name": "D.Dummysson_23_01",
@@ -24,9 +24,9 @@
     "orderer": "[email protected]",
     "project_dates": {
         "2023-06-15": ["Samples Received"],
-        "2023-06-28": ["Reception Control finished", "Library QC finished"],
+        "2023-06-28": ["Reception Control Finished", "Library QC Finished"],
         "2023-07-28": ["All Samples Sequenced"],
-        "2023-07-29": ["All Raw data Delivered"],
+        "2023-07-29": ["All Raw Data Delivered"],
     },
     "internal_id": "P123455",
     "internal_name": "D.Dummysson_23_02",

tests/test_daily_report.py

@@ -22,7 +22,7 @@ def test_write_report_to_out_dir(data_repo_full, mock_project_data_record, creat
 
     assert op.all_orders[0]["identifier"] == order_id
     modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV)
-    assert modified_orders[orderer]["projects"]["Library QC finished"][0] == data_master.data[order_id]
+    assert modified_orders[orderer]["projects"]["Library QC Finished"][0] == data_master.data[order_id]
     pull_date = f"{datetime.datetime.strptime(modified_orders[orderer]['pull_date'], '%Y-%m-%d %H:%M:%S.%f').date()}"
     report_path = os.path.join(config_values.REPORTS_LOCATION, f"{orderer.split('@')[0]}_{pull_date}.html")
 

tests/test_order_portal.py

@@ -22,11 +22,11 @@ def test_get_and_process_orders_open_upload_fail(data_repo_full, mock_project_da
 
     assert op.all_orders[0]["identifier"] == order_id
     modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV)
-    assert modified_orders[orderer]["projects"]["Library QC finished"][0] == data_master.data[order_id]
+    assert modified_orders[orderer]["projects"]["Library QC Finished"][0] == data_master.data[order_id]
     with mock.patch("daily_read.order_portal.requests.post") as mock_post:
         mock_post.return_value.status_code = 404
         uploaded = op.upload_report_to_order_portal(
-            "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC finished"][0], "published"
+            "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC Finished"][0], "published"
         )
         assert not uploaded
         assert f"Report not updated for order with project id: {order_id}\nReason: 404" in caplog.text
@@ -47,11 +47,11 @@ def test_get_and_process_orders_open_and_upload(data_repo_full, mock_project_dat
 
     assert op.all_orders[0]["identifier"] == order_id
     modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV)
-    assert modified_orders[orderer]["projects"]["Library QC finished"][0] == data_master.data[order_id]
+    assert modified_orders[orderer]["projects"]["Library QC Finished"][0] == data_master.data[order_id]
     with mock.patch("daily_read.order_portal.requests.post") as mock_post:
         mock_post.return_value.status_code = 200
         op.upload_report_to_order_portal(
-            "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC finished"][0], "published"
+            "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC Finished"][0], "published"
         )
         url = f"{config_values.ORDER_PORTAL_URL}/api/v1/report"
         indata = dict(
@@ -86,12 +86,12 @@ def test_get_and_process_orders_open_with_report_and_upload(
 
     assert op.all_orders[3]["identifier"] == order_id
     modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV)
-    assert modified_orders[orderer]["projects"]["Library QC finished"][0] == data_master.data[order_id]
+    assert modified_orders[orderer]["projects"]["Library QC Finished"][0] == data_master.data[order_id]
     with mock.patch("daily_read.order_portal.requests.post") as mock_post:
         mock_post.return_value.status_code = 200
         with caplog.at_level(logging.INFO):
             uploaded = op.upload_report_to_order_portal(
-                "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC finished"][0], "published"
+                "<html>test data</html>", modified_orders[orderer]["projects"]["Library QC Finished"][0], "published"
             )
             url = f"{config_values.ORDER_PORTAL_URL}/api/v1/report/{op.all_orders[3]['reports'][0]['iuid']}"
             indata = dict(
@@ -129,11 +129,11 @@ def test_get_and_process_orders_open_to_aborted_with_report_and_upload(
     assert op.all_orders[4]["identifier"] == order_id
     modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV)
 
-    assert modified_orders[orderer]["delete_report_for"]["Library QC finished"][0] == data_master.data[order_id]
+    assert modified_orders[orderer]["delete_report_for"]["Library QC Finished"][0] == data_master.data[order_id]
     with mock.patch("daily_read.order_portal.requests.post") as mock_post:
         mock_post.return_value.status_code = 200
         op.upload_report_to_order_portal(
-            "", modified_orders[orderer]["delete_report_for"]["Library QC finished"][0], "review"
+            "", modified_orders[orderer]["delete_report_for"]["Library QC Finished"][0], "review"
         )
         url = f"{config_values.ORDER_PORTAL_URL}/api/v1/report/{op.all_orders[4]['reports'][0]['iuid']}"
         indata = dict(
@@ -161,7 +161,7 @@ def test_get_and_process_orders_closed(data_repo_full, mock_project_data_record,
 
     assert op.all_orders[1]["identifier"] == order_id
     modified_orders = op.process_orders(config_values.STATUS_PRIORITY_REV)
-    assert modified_orders[orderer]["delete_report_for"]["All Raw data Delivered"][0] == data_master.data[order_id]
+    assert modified_orders[orderer]["delete_report_for"]["All Raw Data Delivered"][0] == data_master.data[order_id]
 
 
 def test_get_and_process_orders_mult_reports(data_repo_full, mock_project_data_record, get_env_file_path):