Merge pull request #303 from smart-on-fhir/mikix/better-ls-error

Print better error "bad label studio config" message and update black

.github/workflows/ci.yaml

@@ -107,7 +107,7 @@ jobs:
         # black is synced with the .pre-commit-hooks version
         run: |
           python -m pip install --upgrade pip
-          pip install bandit[toml] pycodestyle pylint black==23.11.0
+          pip install bandit[toml] pycodestyle pylint 'black >= 24, < 25'
 
       - name: Run pycodestyle
         # E203: pycodestyle is a little too rigid about slices & whitespace

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 repos:
   - repo: https://github.com/psf/black
     # this version is synced with the black mentioned in .github/workflows/ci.yml
-    rev: 23.11.0
+    rev: 24.3.0
     hooks:
       - id: black
         entry: bash -c 'black "$@"; git add -u' --

cumulus_etl/errors.py

@@ -3,6 +3,8 @@
 import sys
 from typing import NoReturn
 
+import rich.console
+
 
 # Error return codes, mostly just distinguished for the benefit of tests.
 # These start at 10 just to leave some room for future use.
@@ -56,5 +58,5 @@ class FatalError(Exception):
 
 def fatal(message: str, status: int) -> NoReturn:
     """Convenience method to exit the program with a user-friendly error message a test-friendly status code"""
-    print(message, file=sys.stderr)
+    rich.console.Console(stderr=True).print(message, style="bold red", highlight=False)
     sys.exit(status)  # raises a SystemExit exception

cumulus_etl/loaders/i2b2/external_mappings.py

@@ -1,6 +1,5 @@
 """Mappings of various external coding systems to the concepts they represent"""
 
-
 # PHIN VADS 1000-9, Race & Ethnicity - CDC
 # https://phinvads.cdc.gov/vads/ViewCodeSystemConcept.action?oid=2.16.840.1.113883.6.238&code=1000-9
 # https://hl7.org/fhir/us/core/StructureDefinition-us-core-race.html

cumulus_etl/upload_notes/labelstudio.py

@@ -92,7 +92,14 @@ def _get_labels_config(self) -> tuple[str, dict]:
                 return k, v
 
         errors.fatal(
-            "Could not find a Labels or Choices config in the Label Studio project.", errors.LABEL_STUDIO_CONFIG_INVALID
+            "Could not find a Labels or Choices config in the Label Studio project.\n"
+            "Add one in your project’s Settings → Labeling Interface page.\n"
+            "If you want a basic dynamic config, use this:\n"
+            "<View>\n"
+            '  <Labels name="label" toName="text" value="$label"/>\n'
+            '  <Text name="text" value="$text"/>\n'
+            "</View>",
+            errors.LABEL_STUDIO_CONFIG_INVALID,
         )
 
     def _format_task_for_note(self, note: LabelStudioNote) -> dict:

pyproject.toml

@@ -75,6 +75,6 @@ tests = [
     "time-machine",
 ]
 dev = [
-    "black == 23.11.0",
+    "black >= 24, < 25",
     "pre-commit"
 ]

tests/i2b2/test_i2b2_oracle_extract.py

@@ -1,4 +1,5 @@
 """Tests for oracle extraction"""
+
 import os
 from unittest import mock
 

tests/test_common.py

@@ -1,4 +1,5 @@
 """Tests for common.py"""
+
 import contextlib
 import itertools
 import tempfile