Merge branch 'main' into MDE/PKFE-44

Strexas · Oct 2, 2024 · b4bfeb8 · b4bfeb8
2 parents d9e4eac + 925c3df
commit b4bfeb8
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Showing 29 changed files with 6,639 additions and 476 deletions.
diff --git a/api/__init__.py b/api/__init__.py
@@ -32,7 +32,7 @@
 )
 
 # DATA COLLECTION IMPORT
-from .data.collection import (
+from .data.downloading import (
     # Custom exceptions
     BadResponseException,
     DownloadError,
@@ -46,7 +46,7 @@
     download_database_for_eys_gene,
 
     # Functions for storing databases
-    store_database_for_eys_gene
+    download_selected_database_for_eys_gene
 )
 
 # DATA REFACTORING IMPORT

diff --git a/api/data/__init__.py b/api/data/__init__.py
@@ -34,7 +34,7 @@
 )
 
 # DATA COLLECTION IMPORT
-from .collection import (
+from .downloading import (
     # Custom exceptions
     BadResponseException,
     DownloadError,
@@ -46,9 +46,11 @@
     download_lovd_database_for_eys_gene,
     download_genes_lovd,
     download_database_for_eys_gene,
+    download_data_from_gnomad_eys,
 
     # Functions for storing databases
-    store_database_for_eys_gene
+    download_selected_database_for_eys_gene
+
 )
 
 # DATA REFACTORING IMPORT
@@ -58,7 +60,6 @@
     parse_lovd,
     from_clinvar_name_to_cdna_position,
     save_lovd_as_vcf,
-    request_gnomad_api_data,
     merge_gnomad_lovd,
     parse_gnomad,
     set_gnomad_dtypes,

diff --git a/api/data/collection.py b/api/data/collection.py
diff --git a/api/data/constants.py b/api/data/constants.py
@@ -8,6 +8,7 @@
 LOVD_FILE_URL = "https://databases.lovd.nl/shared/download/all/gene/"
 LOVD_FILE_URL_EYS = LOVD_FILE_URL + "EYS"
 STORE_AS_LOVD = "../data/lovd/lovd_data.txt"
+STORE_AS_GNOMAD = "../data/gnomad/gnomad_data.csv"
 
 GNOMAD_URL = "https://gnomad.broadinstitute.org/gene"
 GNOMAD_URL_EYS = "https://gnomad.broadinstitute.org/gene/ENSG00000188107?dataset=gnomad_r4"
@@ -25,6 +26,7 @@
 LOVD_PATH = os.path.join(DATA_PATH, "lovd/")
 GNOMAD_PATH = os.path.join(DATA_PATH, "gnomad/")
 CLINVAR_PATH = os.path.join(DATA_PATH, "clinvar/")
+DEFAULT_SAVE_PATH = os.path.join(DATA_PATH, "merged_data/")
 
 # variable data types
 LOVD_TABLES_DATA_TYPES = {