Merge pull request #176 from 4dn-dcic/ajs_validation_bug_fix

validation error report update
4dn-dcic · Jun 3, 2024 · 1897045 · 1897045
2 parents 0a9596f + a8c636c
commit 1897045
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diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -6,6 +6,14 @@ Submit4DN
 Change Log
 ----------
 
+4.0.3
+=====
+
+`PR 176: bug fix on error reporting <https://github.com/4dn-dcic/Submit4DN/pull/176>`_
+
+* fix of bug introduced by the previous error reporting fix
+* test to cover that case
+
 4.0.2
 =====
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "Submit4DN"
-version = "4.0.2"
+version = "4.0.3"
 description = "Utility package for submitting data to the 4DN Data Portal"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"

diff --git a/tests/test_import_data.py b/tests/test_import_data.py
@@ -280,16 +280,21 @@ def test_combine_set_expsets_with_existing():
 
 
 def test_error_report(connection_mock):
-    # There are 6 errors in the err_dict, 5 of them are legit, 1 is checked against the all aliases list, and excluded
+    # There are 7 errors in the err_dict, 5 of them are legit, 2 are checked against the all aliases list, and excluded
     err_dict = {
                     "title": "Unprocessable Entity",
                     "status": "error",
                     "errors": [
                         {"location": "body",
                          "description": "Test for error with no name"},
-                        {# This one should be excluded from report as this alias is in the sheet alias list
+                        {
+                         # This one should be excluded from report as this alias is in the sheet alias list
                          "name": "Schema: ", "location": "body",
                          "description": "Unable to resolve link: siyuan-wang-lab:region_1MB_TAD_1"},
+                        {
+                         # This also excluded - error format different (includes type name)
+                         "name": "Schema: ", "location": "body",
+                         "description": "Unable to resolve link: /GenomicRegion/siyuan-wang-lab:region_1MB_TAD_1"},
                         {"name": "Schema: ", "location": "body",
                          "description": "Unable to resolve link: siyuan-wang-lab:region_5MB_TAD_2"},
                         {"location": "body", "name": "Schema: genome_location.1",

diff --git a/wranglertools/import_data.py b/wranglertools/import_data.py
@@ -798,6 +798,7 @@ def error_report(error_dic, sheet, all_aliases, connection, error_id=''):
                 elif error_description.endswith(nf_txt):
                     alias_bit = error_description.replace(nf_txt, '').replace("'", '')
                 if alias_bit:
+                    alias_bit = alias_bit.split('/')[-1]
                     not_found = alias_bit.strip()
                 # ignore ones about existing aliases
                 if not_found and not_found in all_aliases: