Merge pull request #334 from uc-cdis/fix/allow-more-data-file-categories

(PXP-7094): fix mapping file for any node category ending in "_file" (e.g. "genomic_data_file")

sheepdog/api.py

@@ -1,5 +1,6 @@
 import os
 import sys
+import logging
 
 from flask import Flask, jsonify
 from psqlgraph import PsqlGraphDriver
@@ -162,6 +163,12 @@ def app_init(app):
 
 
 # Setup logger
+app.logger.setLevel(
+    logging.DEBUG if (os.environ.get("GEN3_DEBUG") == "True") else logging.WARNING
+)
+app.logger.propagate = False
+while app.logger.handlers:
+    app.logger.removeHandler(app.logger.handlers[0])
 app.logger.addHandler(get_handler())
 
 setup_default_handlers(app)

sheepdog/transactions/upload/entity.py

@@ -51,8 +51,6 @@ class UploadEntity(EntityBase):
     session.
     """
 
-    DATA_FILE_CATEGORIES = ["data_file", "metadata_file", "index_file"]
-
     def __init__(self, transaction, config=None):
         """
         Args:

sheepdog/transactions/upload/entity_factory.py

@@ -38,7 +38,13 @@ def create(transaction, doc, config=None):
         node_type = doc.get("type")
         node_category = get_node_category(node_type)
 
-        if node_category in UploadEntity.DATA_FILE_CATEGORIES:
+        if node_category.endswith("_file"):
+            transaction.logger.debug(
+                "Identified %s node as a data file node", node_type
+            )
             return FileUploadEntity(transaction, config)
         else:
+            transaction.logger.debug(
+                "Identified %s node as a non-data file node", node_type
+            )
             return NonFileUploadEntity(transaction, config)