Merge branch 'main' into multiple_conditions_explanation

CHANGELOG.md

@@ -1,10 +1,13 @@
 ## [unreleased]
 ### Changed
 - Updated version of external images in GitHub actions
+- Updated API submission schema to the latest
+- Dmo variant to take care of "Somatic mutation" no longer available among Mode of inheritance choices
 - Parse `conditionSet.MultipleConditionExplanation` value from `Explanation for multiple conditions` column of variants file
 ### Fixed
 - Bump certifi from 2022.12.7 to 2023.7.22
-- Description of the response returned by dry run endpoint in README file 
+- Description of the response returned by dry run endpoint in README file
+- Migrate from deprecated `pkg_resources` lib to `importlib_resources`
 
 ## [2.3.1]
 ### Fixed

preClinVar/demo/Variant_sv_range_coords.csv

@@ -1,2 +1,2 @@
 "##Local ID","Linking ID","Chromosome","Reference allele","Alternate allele","Variant type","Copy number","Reference copy number","Outer start","Inner start","Inner stop","Outer stop","Condition ID type","Condition ID value","Clinical significance","Date last evaluated","Mode of inheritance"
-"77d69d4d78a8e272365bdabe4f607327","77d69d4d78a8e272365bdabe4f607327","15","TAAGAATGTTGTGGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAA","T","Deletion","1","2","66633800","66633900","66634100","66634200","HPO","HP:0001298;HP:0001250","Likely pathogenic","2022-12-07","Somatic mutation"
+"77d69d4d78a8e272365bdabe4f607327","77d69d4d78a8e272365bdabe4f607327","15","TAAGAATGTTGTGGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAGATCGAGACCATCCCGGCTAACACGGTGAAACCCCGTCTCTACTAAAAATACAAAAAATTAGCCGGGCGTAGTGGCGGGCGCCTGTAGTCCCAGCTACTTGGGAGGCTGAGGCAGGAGAATGGCGTGAACCCGGGAGGCGGAGCTTGCAGTGAGCCGAGATCCCGCCACTGCACTCCAGCCTGGGCGACAGAGCGAGACTCCGTCTCAAAAAAAAAAAAAAAAAAAAAAAAAAAA","T","Deletion","1","2","66633800","66633900","66634100","66634200","HPO","HP:0001298;HP:0001250","Likely pathogenic","2022-12-07","Unknown mechanism"

preClinVar/demo/__init__.py

@@ -1,4 +1,6 @@
-import pkg_resources
+from importlib_resources import files
+
+BASE_PATH = "preClinVar.demo"
 
 ###### .csv files ######
 casedata_old_csv = "CaseData_before_221121.csv"
@@ -11,27 +13,14 @@
 casedata_sv_csv = "CaseData_sv.csv"
 
 ###### Path to .csv files ######
-casedata_old_csv_path = pkg_resources.resource_filename(
-    "preClinVar", "/".join(["demo", casedata_old_csv])
-)
-variants_old_csv_path = pkg_resources.resource_filename(
-    "preClinVar", "/".join(["demo", variants_old_csv])
-)
-casedata_snv_csv_path = pkg_resources.resource_filename(
-    "preClinVar", "/".join(["demo", casedata_snv_csv])
-)
-casedata_sv_csv_path = pkg_resources.resource_filename(
-    "preClinVar", "/".join(["demo", casedata_sv_csv])
-)
-variants_hgvs_csv_path = pkg_resources.resource_filename(
-    "preClinVar", "/".join(["demo", variants_hgvs_csv])
-)
-variants_sv_breakpoints_csv_path = pkg_resources.resource_filename(
-    "preClinVar", "/".join(["demo", variants_sv_breakpoints_csv])
-)
-variants_sv_range_coords_csv_path = pkg_resources.resource_filename(
-    "preClinVar", "/".join(["demo", variants_sv_range_coords_csv])
-)
+casedata_old_csv_path = str(files(BASE_PATH).joinpath(casedata_old_csv))
+variants_old_csv_path = str(files(BASE_PATH).joinpath(variants_old_csv))
+casedata_snv_csv_path = str(files(BASE_PATH).joinpath(casedata_snv_csv))
+casedata_sv_csv_path = str(files(BASE_PATH).joinpath(casedata_sv_csv))
+variants_hgvs_csv_path = str(files(BASE_PATH).joinpath(variants_hgvs_csv))
+variants_sv_breakpoints_csv_path = str(files(BASE_PATH).joinpath(variants_sv_breakpoints_csv))
+variants_sv_range_coords_csv_path = str(files(BASE_PATH).joinpath(variants_sv_range_coords_csv))
+
 ###### Example of a json file submission ######
 subm_json = "submission.json"
-subm_json_path = pkg_resources.resource_filename("preClinVar", "/".join(["demo", subm_json]))
+subm_json_path = str(files(BASE_PATH).joinpath(subm_json))

preClinVar/resources/__init__.py

@@ -1,10 +1,10 @@
-import pkg_resources
+from importlib_resources import files
+
+BASE_PATH = "preClinVar.resources"
 
 ###### submission schema json file ######
 
 subm_schema = "submission_schema.json"
 
 ###### Path to submission schema file ######
-subm_schema_path = pkg_resources.resource_filename(
-    "preClinVar", "/".join(["resources", subm_schema])
-)
+subm_schema_path = str(files(BASE_PATH).joinpath(subm_schema))