Merge pull request #301 from CanDIG/daisieh/cohort

htsget_server/authz.py

@@ -25,6 +25,8 @@ def is_authed(id_, request):
         if obj is not None and 'cohort' in obj:
             if is_cohort_authorized(request, obj['cohort']):
                 return 200
+        else:
+            return 404
     else:
         return 401
     return 403

htsget_server/htsget_openapi.yaml

@@ -405,9 +405,25 @@ paths:
                             schema:
                                 $ref: '#/components/schemas/SampleTicket'
     /samples:
+        get:
+            summary: Get metadata about samples in a cohort
+            operationId: htsget_operations.get_cohort_samples
+            description: Get MoH-relevant genomic information about all samples in a cohort
+            parameters:
+                - $ref: '#/components/parameters/authHeaderParam'
+                - $ref: '#/components/parameters/cohortParam'
+            responses:
+                200:
+                    description: Success
+                    content:
+                        application/json:
+                            schema:
+                                type: array
+                                items:
+                                    $ref: '#/components/schemas/SampleTicket'
         post:
             summary: Get metadata about multiple samples
-            operationId: htsget_operations.get_samples
+            operationId: htsget_operations.get_multiple_samples
             description: Get MoH-relevant genomic information about a list of samples
             parameters:
                 - $ref: '#/components/parameters/authHeaderParam'
@@ -855,6 +871,9 @@ components:
                 sample_id:
                     type: string
                     description: MoH submitter_sample_id from a Sample Registration associated with a specimen.
+                cohort:
+                    type: string
+                    description: MoH cohort ID
                 genome:
                     type: array
                     description: An array of associated GenomicDrsObjects that describe reads, e.g. bams.
@@ -1068,6 +1087,13 @@ components:
             name: Range
             schema:
                 $ref: '#/components/schemas/Range'
+        cohortParam:
+            in: query
+            name: cohort
+            description: name of cohort
+            required: false
+            schema:
+                type: string
     requestBodies:
         ReadsRequestBody:
             description: Specify desired file format, fields, tags, and regions from an alignment file

htsget_server/htsget_operations.py

@@ -247,6 +247,7 @@ def get_sample(id_=None):
     # Each of those GenomicDrsObjects will have a description that is either 'wgs' or 'wts'.
     sample_drs_obj, result_code = drs_operations.get_object(id_)
     if result_code == 200 and "contents" in sample_drs_obj and sample_drs_obj["description"] == "sample":
+        result["cohort"] = sample_drs_obj["cohort"]
         for contents_obj in sample_drs_obj["contents"]:
             drs_obj = database.get_drs_object(contents_obj["id"])
             if drs_obj is not None:
@@ -265,7 +266,7 @@ def get_sample(id_=None):
     return {"message": f"Could not find sample {id_}"}, 404
 
 
-def get_samples():
+def get_multiple_samples():
     req = connexion.request.json
     result = []
     for sample in req["samples"]:
@@ -275,6 +276,20 @@ def get_samples():
     return result, 200
 
 
+def get_cohort_samples(cohort=None):
+    if cohort is None:
+        sample_drs_objs = database.list_drs_objects()
+    else:
+        sample_drs_objs = database.list_drs_objects(cohort)
+    samples = list(map(lambda y: y["id"], filter(lambda x: x["description"] == "sample", sample_drs_objs)))
+    result = []
+    for sample in samples:
+        res, status_code = get_sample(sample)
+        if status_code == 200:
+            result.append(res)
+    return result, 200
+
+
 def _get_htsget_url(id, reference_name, slice_start, slice_end, file_type, data=True):
     """
     Creates single slice for a region in a file. Returns an HTSGetURL object.

tests/test_htsget_server.py

@@ -26,6 +26,9 @@
 
 def get_headers():
     headers = {}
+    if TEST_KEY is not None:
+        headers["Authorization"] = f"Bearer {TEST_KEY}"
+        return headers
     try:
         token = get_site_admin_token()
         headers["Authorization"] = f"Bearer {token}"
@@ -307,13 +310,14 @@ def test_add_sample_drs(input, program_id):
 
     response = requests.post(post_url, json=genomic_drs_obj, headers=get_headers())
     print(response.text)
-    response = requests.request("GET", get_url, headers=headers)
+    response = requests.request("GET", get_url, headers=get_headers())
     if response.status_code == 200:
         assert response.status_code == 200
     assert len(genomic_drs_obj["contents"]) == contents_count + 1
 
     verify_url = f"{HOST}/htsget/v1/variants/{input['genomic_id']}/verify"
-    response = requests.get(verify_url)
+    response = requests.get(verify_url, headers=get_headers())
+    print(response.text)
     assert response.status_code == 200
 
 
@@ -326,12 +330,23 @@ def test_sample_stats(input, program_id):
     # look for the sample
     get_url = f"{HOST}/htsget/v1/samples/{sample[list(sample.keys()).pop()]}"
     response = requests.request("GET", get_url, headers=headers)
-    if response.status_code == 200:
-        assert response.status_code == 200
+    assert response.status_code == 200
 
     assert input['genomic_id'] in response.json()['genomes']
 
 
+def test_cohort_samples():
+    headers = get_headers()
+
+    get_url = f"{HOST}/htsget/v1/samples"
+    response = requests.request("GET", get_url, headers=headers)
+    print(response.json())
+    response = requests.request("GET", get_url, headers=headers, params={"cohort": "1000genomes"})
+    assert response.status_code == 200
+    print(response.json())
+    assert len(response.json()) == 1
+
+
 def invalid_start_end_data():
     return [(17123456, 23588), (9203, 42220938)]
 
@@ -446,7 +461,7 @@ def get_beacon_post_search():
     return [
         (
             # 6 variations, corresponding to three variant records in multisample_1 and multisample_2
-            # first variation, corresponding to "NC_000021.8:g.5030551=", should contain two cases
+            # first variation, corresponding to "NC_000021.9:g.5030847=", should contain two cases
             {
                 "query": {
                     "requestParameters": {