Ejl/fix date consistency

README.md

@@ -164,3 +164,12 @@ make clean && make run
 
 Consult `docs/`.
 
+
+# Troubleshooting possible development errors
+
+## bifrost_db container ERROR: child process failed, exited with 1
+When running make run. If the bifrost conainer keeps failing with an error message saying "ERROR: child process failed, exited with 1". Look for if "Error creating journal directory".
+One way to get around this error is by running `make run` with sudo privilidges:
+```shell
+sudo make run
+```

bifrost/bifrost_queue_broker/common/database.py

@@ -1,7 +1,7 @@
 import os, sys
 import binascii
 import logging
-import datetime
+from datetime import datetime
 
 from typing import Dict, Literal, Tuple, overload
 
@@ -173,9 +173,9 @@ def encrypt_dict(encryption_client: ClientEncryption, val, filter_list=None):
 def coerce_date(dayfirst):
     def parse_value(v):
         try:
-            if isinstance(v, datetime.datetime):
-                return v.isoformat()
-            return parser.parse(v, dayfirst=dayfirst).isoformat() if v else None
+            if isinstance(v, datetime):
+                return v
+            return parser.parse(v, dayfirst=dayfirst) if v else None
         except:
             return None
     return parse_value

docker-compose.local.yml

@@ -16,7 +16,9 @@ services:
       - "bifrost_db"
 
   sap_broker_queue:
-    image: sekvensanalyseplatform/sap-queue-broker:437
+    build:
+      context: ./bifrost/bifrost_queue_broker
+      dockerfile: Dockerfile
     depends_on:
       - "sap_api"
       - "bifrost_db"

sap_tbr_integration/DG.SAP.TBRIntegration/tbr.generated.jsonl

@@ -1,3 +1,3 @@
-{"isolate_id":"2010F00006","institution":"SSI","date_received":"1945-12-13T12:05:56.143Z","run_id":"culpa tempor","provided_species":"culpa officia sint id","primary_isolate":false,"date_run":"1978-01-12T02:11:46.207Z","project_number":-27841476.650654063,"project_title":"nisi officia","date_sample":"1973-11-09T21:59:05.017Z","public":"amet ut eu sit deserunt","cpr_nr":"2902007734","gender":"K","name":"Elliot Rosenbaum","age":53,"travel":"et occaecat Lorem adipisicing","travel_country":"Guernsey","date_received_kma":"1947-08-02T21:01:12.522Z","kma":"ul","region":"sint cupidatat veniam","fud_number":"nostrud occaecat","cluster_id":"cillum nostrud cupidatat non officia","epi_export":"consequat enim exercitation"}
-{"isolate_id":"2010F00048","institution":"SSI","date_received":"1994-11-20T22:49:04.27Z","run_id":"laboris tempor","provided_species":"eu culpa exercitation","primary_isolate":true,"date_run":"1945-01-15T16:52:56.924Z","project_number":-33496873.684678532,"project_title":"labore","date_sample":"2003-11-26T18:48:06.257Z","public":"dolore aute consectetur","cpr_nr":"0000000002","gender":"M","name":"Adaline Waelchi","age":0,"travel":"Duis","travel_country":"Serbia","date_received_kma":"1971-03-15T05:10:15.052Z","kma":"ea","region":"cupidatat ex","fud_number":"non","cluster_id":"tempor i","epi_export":"dolor aute"}
-{"isolate_id":"2009T00243","institution":"SSI","date_received":"1987-05-15T16:41:34.514Z","run_id":"in Excepteur nostrud proident","provided_species":"aute minim","primary_isolate":false,"date_run":"1980-01-04T05:31:12.256Z","project_number":12997890.419586033,"project_title":"consectetur esse","date_sample":"1946-03-26T02:37:54.67Z","public":"pariatur","cpr_nr":"0000000001","gender":"K","name":"Brendon Ledner","age":6,"travel":"incididunt est veniam","travel_country":"Ethiopia","date_received_kma":"1987-07-10T12:45:08.443Z","kma":"nostrud aliquip velit dolor Lore","region":"sint et","fud_number":"enim nulla ut","cluster_id":"do Ut incididunt magna nisi","epi_export":"laboris mollit"}
+{"isolate_id":"2010F00006","institution":"SSI","ssi_date":"1945-12-13T12:05:56.143Z","run_id":"culpa tempor","provided_species":"culpa officia sint id","primary_isolate":false,"date_run":"1978-01-12T02:11:46.207Z","project_number":-27841476.650654063,"project_title":"nisi officia","test_date":"1973-11-09T21:59:05.017Z","public":"amet ut eu sit deserunt","cpr_nr":"2902007734","gender":"K","name":"Elliot Rosenbaum","age":53,"travel":"et occaecat Lorem adipisicing","travel_country":"Guernsey","kma_date":"1947-08-02T21:01:12.522Z","kma_name":"ul","region":"sint cupidatat veniam","fud_number":"nostrud occaecat","cluster_id":"cillum nostrud cupidatat non officia","epi_export":"consequat enim exercitation"}
+{"isolate_id":"2010F00048","institution":"SSI","ssi_date":"1994-11-20T22:49:04.27Z","run_id":"laboris tempor","provided_species":"eu culpa exercitation","primary_isolate":true,"date_run":"1945-01-15T16:52:56.924Z","project_number":-33496873.684678532,"project_title":"labore","test_date":"2003-11-26T18:48:06.257Z","public":"dolore aute consectetur","cpr_nr":"0000000002","gender":"M","name":"Adaline Waelchi","age":0,"travel":"Duis","travel_country":"Serbia","kma_date":"1971-03-15T05:10:15.052Z","kma_name":"ea","region":"cupidatat ex","fud_number":"non","cluster_id":"tempor i","epi_export":"dolor aute"}
+{"isolate_id":"2009T00243","institution":"SSI","ssi_date":"1987-05-15T16:41:34.514Z","run_id":"in Excepteur nostrud proident","provided_species":"aute minim","primary_isolate":false,"date_run":"1980-01-04T05:31:12.256Z","project_number":12997890.419586033,"project_title":"consectetur esse","test_date":"1946-03-26T02:37:54.67Z","public":"pariatur","cpr_nr":"0000000001","gender":"K","name":"Brendon Ledner","age":6,"travel":"incididunt est veniam","travel_country":"Ethiopia","kma_date":"1987-07-10T12:45:08.443Z","kma_name":"nostrud aliquip velit dolor Lore","region":"sint et","fud_number":"enim nulla ut","cluster_id":"do Ut incididunt magna nisi","epi_export":"laboris mollit"}

web/src/SAP/common/database.py

@@ -1,7 +1,7 @@
 import os, sys
 import binascii
 import logging
-import datetime
+from datetime import datetime
 
 from typing import Dict, Literal, Tuple, overload
 
@@ -173,9 +173,9 @@ def encrypt_dict(encryption_client: ClientEncryption, val, filter_list=None):
 def coerce_date(dayfirst):
     def parse_value(v):
         try:
-            if isinstance(v, datetime.datetime):
-                return v.isoformat()
-            return parser.parse(v, dayfirst=dayfirst).isoformat() if v else None
+            if isinstance(v, datetime):
+                return v
+            return parser.parse(v, dayfirst=dayfirst) if v else None
         except:
             return None
     return parse_value