Deprecate etl enrollments

lib/id3c/api/datastore.py

@@ -51,27 +51,6 @@ def login(username: str, password: str) -> DatabaseSession:
         raise AuthenticationRequired() from None
 
 
-@export
-@catch_permission_denied
-def store_enrollment(session: DatabaseSession, document: str) -> None:
-    """
-    Store the given enrollment JSON *document* (a **string**) in the backing
-    database using *session*.
-
-    Raises a :class:`BadRequestDatabaseError` exception if the given *document*
-    isn't valid and a :class:`Forbidden` exception if the database reports a
-    `permission denied` error.
-    """
-    with session, session.cursor() as cursor:
-        try:
-            cursor.execute(
-                "INSERT INTO receiving.enrollment (document) VALUES (%s)",
-                    (document,))
-
-        except (DataError, IntegrityError) as error:
-            raise BadRequestDatabaseError(error) from None
-
-
 @export
 @catch_permission_denied
 def store_presence_absence(session: DatabaseSession, document: str) -> None:

lib/id3c/api/routes.py

@@ -29,28 +29,6 @@ def index():
     return send_file("static/index.html", "text/html; charset=UTF-8")
 
 
-@api_v1.route("/receiving/enrollment", methods = ['POST'])
-@api_unversioned.route("/enrollment", methods = ['POST'])
-@content_types_accepted(["application/json"])
-@check_content_length
-@authenticated_datastore_session_required
-def receive_enrollment(*, session):
-    """
-    Receive a new enrollment document.
-
-    POST /enrollment with a JSON body.  Note that we don't actually need to
-    parse the JSON body.  The body is passed directly to the database which
-    will check its validity.
-    """
-    document = request.get_data(as_text = True)
-
-    LOG.debug(f"Received enrollment")
-
-    datastore.store_enrollment(session, document)
-
-    return "", 204
-
-
 @api_v1.route("/receiving/presence-absence", methods = ['POST'])
 @api_unversioned.route("/presence-absence", methods = ['POST'])
 @content_types_accepted(["application/json"])

lib/id3c/api/static/index.html

@@ -36,10 +36,6 @@ <h2>Status codes</h2>
 
     <h2>Routes</h2>
 
-    <h3 class="code">POST /v1/receiving/enrollment</h3>
-    <p>Stores the request data as an enrollment document in a receiving area of
-    the study database. Accepts any JSON object.
-
     <h3 class="code">POST /v1/receiving/presence-absence</h3>
     <p>Stores the request data as presence/absence calls in a receiving area of
     the study database. Accepts any JSON object.
@@ -113,5 +109,12 @@ <h3 class="code">POST /sequence-read-set</h3>
   ]
 }</pre>
 
+  <h2>Deprecated Routes</h2>
+  <p>
+    These routes are no longer supported.
+  </p>
+
+  <h3 class="code">POST /v1/receiving/enrollment</h3>
+
   </body>
 </html>

lib/id3c/cli/command/etl/__init__.py

@@ -21,10 +21,8 @@ def etl():
 
 # Load all ETL subcommands.
 __all__ = [
-    "enrollments",
     "manifest",
     "presence_absence",
-    "kit",
     "consensus_genome",
     "redcap_det",
     "fhir",