Merge pull request #293 from CanDIG/daisieh/query-sample

CanDIG · Mar 4, 2024 · b25e0e7 · b25e0e7
2 parents c5f4b33 + 07b09fa
commit b25e0e7
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Showing 2 changed files with 21 additions and 1 deletion.
diff --git a/htsget_server/htsget_openapi.yaml b/htsget_server/htsget_openapi.yaml
@@ -865,6 +865,17 @@ components:
                     description: An array of associated GenomicDrsObjects that describe transcriptome data.
                     items:
                         type: string
+                variants:
+                    type: array
+                    description: An array of associated GenomicDataDrsObjects that describe variant files.
+                    items:
+                        type: string
+                reads:
+                    type: array
+                    description: An array of associated GenomicDataDrsObjects that describe read files.
+                    items:
+                        type: string
+
 
         # ERROR SCHEMAS
         Error:

diff --git a/htsget_server/htsget_operations.py b/htsget_server/htsget_operations.py
@@ -238,7 +238,9 @@ def get_sample(id_=None):
     result = {
         "sample_id": id_,
         "genomes": [],
-        "transcriptomes": []
+        "transcriptomes": [],
+        "variants": [],
+        "reads": []
     }
 
     # Get the SampleDrsObject. It will have a contents array of GenomicContentsObjects > GenomicDrsObjects.
@@ -252,6 +254,13 @@ def get_sample(id_=None):
                     result["genomes"].append(drs_obj["id"])
                 elif drs_obj["description"] == "wts":
                     result["transcriptomes"].append(drs_obj["id"])
+                # check the contents of this genomic drs object and see if it contains variants or reads
+                if "contents" in drs_obj:
+                    for content in drs_obj["contents"]:
+                        if content["id"] == "variant":
+                            result["variants"].append(drs_obj["id"])
+                        elif content["id"] == "read":
+                            result["reads"].append(drs_obj["id"])
         return result, 200
     return {"message": f"Could not find sample {id_}"}, 404