Bug fixes (#70)

* Adding test data * Refactoring results count, updated examples guide * merge master * Added updated s3 ownershipt controls * capture granularity from query params * Bug fix: indexer * Update read me
aehrc · Apr 27, 2023 · 10f40b0 · 10f40b0
1 parent ada3e2e
commit 10f40b0
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Showing 4 changed files with 32 additions and 3 deletions.
diff --git a/examples/test-data/GUIDE.md b/examples/test-data/GUIDE.md
@@ -16,11 +16,11 @@ Now edit the `submission.json` file such that they match the S3 URI of the `vcf.
 
 You can submit the data in two ways.
 
-### Submission as request body
+### Option 1: Submission as request body
 
 You can simply copy the edited JSON content in to the API gateway `/submit_dataset` POST endpoint. If you're using a REST client make sure you add authorization headers before you make the request. For example, Postman supports Authorization type AWS Signature and there you can enter AWS Keys.
 
-### Submission as an S3 payload
+### Option 2: Submission as an S3 payload
 
 Alternatively, you can upload edited `submission.json` file to an S3 location accessible from deployment. Then you can use the file's S3 URI as follows in the API Gateway or in your REST client.
 

diff --git a/lambda/indexer/lambda_function.py b/lambda/indexer/lambda_function.py
@@ -146,7 +146,7 @@ def threaded_request_ontoserver(term, url):
                                 "compose": {
                                     "include": [
                                         {
-                                            "system": data["baseUri"],
+                                            "system": "http://snomed.info/sct",
                                             "filter": [
                                                 {
                                                     "property": "concept",

diff --git a/s3.tf b/s3.tf
@@ -7,7 +7,16 @@ resource "aws_s3_bucket" "variants-bucket" {
   tags          = var.common-tags
 }
 
+resource "aws_s3_bucket_ownership_controls" "variants_bucket_ownership_controls" {
+  bucket = aws_s3_bucket.variants-bucket.id
+  rule {
+    object_ownership = "BucketOwnerPreferred"
+  }
+}
+
 resource "aws_s3_bucket_acl" "variants_bucket_acl" {
+  depends_on = [aws_s3_bucket_ownership_controls.variants_bucket_ownership_controls]
+
   bucket = aws_s3_bucket.variants-bucket.id
   acl    = "private"
 }
@@ -38,7 +47,16 @@ resource "aws_s3_bucket" "metadata-bucket" {
   tags          = var.common-tags
 }
 
+resource "aws_s3_bucket_ownership_controls" "metadata_bucket_ownership_controls" {
+  bucket = aws_s3_bucket.metadata-bucket.id
+  rule {
+    object_ownership = "BucketOwnerPreferred"
+  }
+}
+
 resource "aws_s3_bucket_acl" "metadata" {
+  depends_on = [aws_s3_bucket_ownership_controls.metadata_bucket_ownership_controls]
+
   bucket = aws_s3_bucket.metadata-bucket.id
   acl    = "private"
 }
@@ -82,7 +100,16 @@ resource "aws_s3_bucket" "lambda-layers-bucket" {
   tags          = var.common-tags
 }
 
+resource "aws_s3_bucket_ownership_controls" "lambda_layers_bucket_ownership_controls" {
+  bucket = aws_s3_bucket.lambda-layers-bucket.id
+  rule {
+    object_ownership = "BucketOwnerPreferred"
+  }
+}
+
 resource "aws_s3_bucket_acl" "lambda-layers" {
+  depends_on = [aws_s3_bucket_ownership_controls.lambda_layers_bucket_ownership_controls]
+
   bucket = aws_s3_bucket.lambda-layers-bucket.id
   acl    = "private"
 }
diff --git a/shared_resources/python-modules/python/shared/apiutils/requests.py b/shared_resources/python-modules/python/shared/apiutils/requests.py
@@ -155,6 +155,8 @@ def from_request(self, query_params) -> Self:
                 self.query.pagination.limit = int(v)
             elif k == "includeResultsetResponses":
                 self.query.include_resultset_responses = IncludeResultsetResponses(v)
+            elif k == "requestedGranularity":
+                self.query.requested_granularity = Granularity(v)
             else:
                 req_params_dict[k] = v
         if len(req_params_dict):