last valid bugfix/resuable migration tweak (#134)

* last valid bugfix/resuable migration tweak * proper markdown file casing
smart-on-fhir · Oct 25, 2024 · e90c6fa · e90c6fa
1 parent bd98255
commit e90c6fa
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Showing 4 changed files with 23 additions and 20 deletions.
diff --git a/scripts/migrations/MAINTAINER.md b/scripts/migrations/MAINTAINER.md
@@ -0,0 +1,4 @@
+As of this writing, migration #3 is safe to run any time you need 
+to regenerate the table column type data/data package cache (i.e. 
+if things are deleted, or in response to bugs in this process).
+You should run the appropriate crawler first.
diff --git a/scripts/migrations/migration.003.data_packages.py b/scripts/migrations/migration.003.data_packages.py
@@ -108,8 +108,6 @@ def get_s3_json_as_dict(bucket, key: str):
     """reads a json object as dict (typically metadata in this case)"""
     s3_client = boto3.client("s3")
     bytes_buffer = io.BytesIO()
-    print(bucket)
-    print(key)
     s3_client.download_fileobj(
         Bucket=bucket,
         Key=key,
@@ -136,23 +134,24 @@ def cache_api_data(s3_bucket_name: str, db: str) -> None:
     )
     dp_details = []
     for dp in list(data_packages):
-        dp_detail = {
-            "study": dp.split("__", 1)[0],
-            "name": dp.split("__", 1)[1],
-        }
         try:
-            versions = column_types[dp_detail["study"]][dp_detail["name"]]
-            for version in versions:
-                dp_details.append(
-                    {
-                        **dp_detail,
-                        **versions[version],
-                        "version": version,
-                        "id": dp + "__" + version,
-                    }
-                )
-        except KeyError:
+            study, name, version = dp.split("__")
+        except ValueError:
+            print("invalid name: ", dp)
             continue
+        try:
+            matching_col_types = column_types[study][name]
+            dp_details.append(
+                {
+                    "study": study,
+                    "name": name,
+                    "version": version,
+                    **matching_col_types[dp],
+                    "id": dp,
+                }
+            )
+        except KeyError as e:
+            print("invalid key: ", e)
     s3_client.put_object(
         Bucket=s3_bucket_name,
         Key=f"{BucketPath.CACHE.value}/{JsonFilename.DATA_PACKAGES.value}.json",

diff --git a/src/handlers/dashboard/get_csv.py b/src/handlers/dashboard/get_csv.py
@@ -82,7 +82,7 @@ def get_csv_list_handler(event, context):
     del context
     s3_bucket_name = os.environ.get("BUCKET_NAME")
     s3_client = boto3.client("s3")
-    if event["path"].startswith("/last_valid"):
+    if event["path"].startswith("/last-valid"):
         key_prefix = "last_valid"
         url_prefix = "last_valid"
     elif event["path"].startswith("/aggregates"):

diff --git a/tests/dashboard/test_get_csv.py b/tests/dashboard/test_get_csv.py
@@ -125,7 +125,7 @@ def test_get_csv(mock_bucket, params, status, expected):
             does_not_raise(),
         ),
         (
-            "/last_valid",
+            "/last-valid",
             200,
             [
                 "last_valid/study/encounter/princeton_plainsboro_teaching_hospital/099/study__encounter__aggregate.csv"
@@ -138,7 +138,7 @@ def test_get_csv(mock_bucket, params, status, expected):
 @mock.patch.dict(os.environ, mock_utils.MOCK_ENV)
 def test_get_csv_list(mock_bucket, path, status, expected, raises):
     with raises:
-        if path.startswith("/last_valid"):
+        if path.startswith("/last-valid"):
             _mock_last_valid()
         event = {"path": path}
         res = get_csv.get_csv_list_handler(event, {})