From 561cd9971905a799fe26d94f9959d23ded7111f7 Mon Sep 17 00:00:00 2001
From: Sergey Golitsynskiy <sgolitsynskiy@gmail.com>
Date: Mon, 1 Feb 2021 22:05:06 -0500
Subject: [PATCH] Improve error handling; modify exception

ReferenceDataError is more appropriate than MissingDataError
---
 lib/galaxy/exceptions/__init__.py      |  4 ++--
 lib/galaxy/exceptions/error_codes.json |  4 ++--
 lib/galaxy/visualization/genomes.py    | 13 ++++++++-----
 3 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/lib/galaxy/exceptions/__init__.py b/lib/galaxy/exceptions/__init__.py
index 34c02448e14..c79d1f9c8c6 100644
--- a/lib/galaxy/exceptions/__init__.py
+++ b/lib/galaxy/exceptions/__init__.py
@@ -221,9 +221,9 @@ class InvalidFileFormatError(MessageException):
     err_code = error_codes_by_name['INVALID_FILE_FORMAT']
 
 
-class MissingDataError(MessageException):
+class ReferenceDataError(MessageException):
     status_code = 500
-    err_code = error_codes_by_name['MISSING_DATA_ERROR']
+    err_code = error_codes_by_name['REFERENCE_DATA_ERROR']
 
 
 # non-web exceptions
diff --git a/lib/galaxy/exceptions/error_codes.json b/lib/galaxy/exceptions/error_codes.json
index 054f8ee999c..4a746065df1 100644
--- a/lib/galaxy/exceptions/error_codes.json
+++ b/lib/galaxy/exceptions/error_codes.json
@@ -160,9 +160,9 @@
     "message": "File format not supported for this operation."
    },
    {
-    "name": "MISSING_DATA_ERROR",
+    "name": "REFERENCE_DATA_ERROR",
     "code": 500006,
-    "message": "Data required for program execution is missing."
+    "message": "Reference data required for program execution failed to load."
    },
    {
     "name": "NOT_IMPLEMENTED",
diff --git a/lib/galaxy/visualization/genomes.py b/lib/galaxy/visualization/genomes.py
index b342c78ad9a..1da998bb0df 100644
--- a/lib/galaxy/visualization/genomes.py
+++ b/lib/galaxy/visualization/genomes.py
@@ -7,7 +7,7 @@ from json import loads
 from bx.seq.twobit import TwoBitFile
 
 from galaxy.exceptions import (
-    MissingDataError,
+    ReferenceDataError,
     ObjectNotFound,
 )
 from galaxy.util.bunch import Bunch
@@ -92,7 +92,7 @@ class Genome:
         """
         # if there's no len_file, there's nothing to return
         if not self.len_file:
-            raise MissingDataError(f'len_file not set for {self.key}')
+            raise ReferenceDataError(f'len_file not set for {self.key}')
 
         def check_int(s):
             if s.isdigit():
@@ -375,7 +375,7 @@ class Genomes:
             dbkey_user = trans.user
 
         if not self.has_reference_data(dbkey, dbkey_user):
-            return None
+            raise ReferenceDataError(f"No reference data for {dbkey}")
 
         #
         # Get twobit file with reference data.
@@ -395,6 +395,9 @@ class Genomes:
                 twobit_dataset = fasta_dataset.get_converted_dataset(trans, 'twobit')
                 twobit_file_name = twobit_dataset.file_name
 
+        return self._get_reference_data()
+
+    def _get_reference_data():
         # Read and return reference data.
         try:
             with open(twobit_file_name, 'rb') as f:
@@ -402,5 +405,5 @@ class Genomes:
                 if chrom in twobit:
                     seq_data = twobit[chrom].get(int(low), int(high))
                     return GenomeRegion(chrom=chrom, start=low, end=high, sequence=seq_data)
-        except OSError:
-            return None
+        except OSError as e:
+            raise e()