Merge pull request #131 from Clinical-Genomics/update_submission_schema

Update submission schema to the latest

CHANGELOG.md

@@ -1,5 +1,9 @@
 
 ## [unreleased]
+### Changed
+- Updated API submission schema to the latest available on `ncbi/clinvar` GitHub pages
+- Modified the json submission example to use one from the ClinVar GitHib repo (`sample_clinical_significance_hgvs_submission.json`)
+- Removed the example of an old json submission (before 2022-11-21) 
 ### Fixed
 - Updated setuptools to v.71 to fix a security issue
 - Updated issue templates

preClinVar/demo/__init__.py

@@ -22,5 +22,5 @@
 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 = str(files(BASE_PATH).joinpath(subm_json))
+clinsig_subm_json = "sample_clinical_significance_hgvs_submission.json"
+subm_json_path = str(files(BASE_PATH).joinpath(clinsig_subm_json))

preClinVar/demo/sample_clinical_significance_hgvs_submission.json

@@ -0,0 +1,52 @@
+{
+  "clinvarSubmissionReleaseStatus": "hold until published",
+  "assertionCriteria":{
+          "db": "PubMed",
+          "id":  "25741868"
+  },
+  "clinvarSubmission":[{
+  "recordStatus": "novel",
+    "clinicalSignificance": {
+         "clinicalSignificanceDescription": "Pathogenic",
+         "dateLastEvaluated": "2018-04-28",
+         "comment": "This comment explains the rationale for classifying this PDE6B variant as pathogenic for Retinitis pigmentosa-40.",
+         "citation":  [{
+                "db": "PubMed",
+                "id": "PMID:11295882"
+
+            },
+            {
+                "db": "PubMed",
+                "id": "PMID:1363786"
+
+            },
+            {
+                "url": "https://yourdatabaselink.org"
+            }],
+  "modeOfInheritance":"Autosomal dominant inheritance"
+         },
+      "observedIn":[ {
+            "alleleOrigin": "germline",
+            "affectedStatus": "yes",
+             "collectionMethod": "clinical testing",
+             "numberOfIndividuals": 1
+        }],
+   "variantSet": {
+       "variant": [{
+         "hgvs":"NM_000283.3:c.3645A>T",
+         "gene":[ {
+             "id":2
+       }]
+   }]},
+   "conditionSet": {
+       "condition": [{
+            "db": "OMIM",
+            "id": "613801"
+         }]
+
+   }
+
+
+}
+]
+}