Merge pull request #331 from sanger/develop

Develop to master
sanger · Apr 30, 2021 · e48007e · e48007e
2 parents a101812 + 2b5434c
commit e48007e
Show file tree

Hide file tree

Showing 6 changed files with 26 additions and 3 deletions.
diff --git a/.release-version b/.release-version
@@ -1 +1 @@
-1.12.0
+1.13.0
diff --git a/.talismanrc b/.talismanrc
@@ -0,0 +1,3 @@
+fileignoreconfig:
+- filename: Pipfile.lock
+  checksum: 571c95637cfc5da15ed07f99831d6d4b7361b7220a7112a9f70c5370e2696531
diff --git a/crawler/config/centre.py b/crawler/config/centre.py
@@ -102,4 +102,18 @@
         "file_names_to_ignore": [r"^lw-randox-biocentre-box-((\d)|(1\d)|20)-.*$"],
         "biomek_labware_class": BIOMEK_LABWARE_CLASS_KINGFISHER,
     },
+    {
+        "barcode_field": FIELD_RNA_ID,
+        "barcode_regex": CENTRE_REGEX_BARCODE,
+        "name": "Health Services Laboratories",
+        "prefix": "HSLL",
+        "lab_id_default": "HSLL",
+        "backups_folder": f"{CENTRE_DIR_BACKUPS}/HSL",
+        "sftp_file_regex_unconsolidated_surveillance": r"^$",
+        "sftp_file_regex_consolidated_surveillance": r"^HSL\d+\.csv$",
+        "sftp_file_regex_consolidated_eagle": r"^$",
+        "sftp_root_read": "project-heron_hsl",
+        "file_names_to_ignore": [],
+        "biomek_labware_class": BIOMEK_LABWARE_CLASS_KINGFISHER,
+    },
 ]
diff --git a/migrations/back_populate_uuids.py b/migrations/back_populate_uuids.py
@@ -8,6 +8,7 @@
 
 from crawler.constants import (
     COLLECTION_SAMPLES,
+    FIELD_CREATED_AT,
     FIELD_LH_SAMPLE_UUID,
     FIELD_MONGODB_ID,
     FIELD_UPDATED_AT,
@@ -168,7 +169,7 @@ def get_samples(samples_collection: Collection, start_datetime: datetime, end_da
     match = {
         "$match": {
             # Filter by the start and end dates and UUID updated
-            FIELD_UPDATED_AT: {"$gte": start_datetime, "$lte": end_datetime},
+            FIELD_CREATED_AT: {"$gte": start_datetime, "$lte": end_datetime},
             UUID_UPDATED: True,
         }
     }

diff --git a/tests/test_file_processing.py b/tests/test_file_processing.py
@@ -190,6 +190,8 @@ def test_process_files_one_wrong_format(mongo_database, config, testing_files_fo
 AP_CONSOLIDATED_SURVEILLANCE_FILENAME2 = "AP-rna-123456.csv"
 GLASGOW_CONSOLIDATED_SURVEILLANCE_FILENAME1 = "GLA123456a.csv"
 GLASGOW_CONSOLIDATED_SURVEILLANCE_FILENAME2 = "GLS-GP-123456.csv"
+HSLL_CONSOLIDATED_SURVEILLANCE_FILENAME1 = "HSL123456.csv"
+HSLL_CONSOLIDATED_SURVEILLANCE_FILENAME2 = "HSL123456789.csv"
 
 
 @mark.parametrize(
@@ -206,6 +208,9 @@ def test_process_files_one_wrong_format(mongo_database, config, testing_files_fo
         [GLASGOW_CONSOLIDATED_SURVEILLANCE_FILENAME1, 2, True],
         [GLASGOW_CONSOLIDATED_SURVEILLANCE_FILENAME2, 2, True],
         ["GLS-123456.csv", 2, False],
+        [HSLL_CONSOLIDATED_SURVEILLANCE_FILENAME1, 5, True],
+        [HSLL_CONSOLIDATED_SURVEILLANCE_FILENAME2, 5, True],
+        ["HSL32334r.csv", 5, False],
     ],
 )
 def test_can_identify_valid_filename(config, filename, centre_config_index, expected_value):

diff --git a/tests/test_main.py b/tests/test_main.py
@@ -7,7 +7,7 @@
 from crawler.db.mongo import get_mongo_collection
 from crawler.main import run
 
-NUMBER_CENTRES = 6
+NUMBER_CENTRES = 7
 NUMBER_VALID_SAMPLES = 21
 NUMBER_SAMPLES_ON_PARTIAL_IMPORT = 10
 NUMBER_OF_FILES_PROCESSED = 12