Merge pull request #27 from c3g/develop

Version 0.3.0

README.md

@@ -16,6 +16,12 @@ python3 -m pytest --cov=chord_lib --cov-branch
 
 ## Modules
 
+### `auth`
+
+`auth` provides Python service decorators and Django / DRF backends for dealing
+with the CHORD container authentication headers (derived from
+`lua-resty-openidc`, set by the internal container NGINX instance.)
+
 ### `events`
 
 `events` facilitates JSON-serialized message-passing between CHORD
@@ -44,6 +50,24 @@ GA4GH-standardized schemas (possibly not exactly to spec.)
 `search` contains definitions, validators, and transformations for the query
 syntax for CHORD, as well as a transpiler to the `psycopg2` PostgreSQL IR.
 
+The query syntax for CHORD takes advantage of JSON schemas augmented with
+additional properties about the field's accessibility and, in the case of
+Postgres, how the field maps to a table column (or JSON column sub-field.)
+
+`search.data_structure` contains code for evaluating a CHORD query against a
+Python data structure.
+
+`search.operations` contains constants representing valid search operations one
+can allow against particular fields from within an augmented JSON schema.
+
+`search.postgres` contains a "transpiler" from the CHORD query syntax to the
+`psycopg2`-provided
+[intermediate representation (IR)](https://www.psycopg.org/docs/sql.html) for
+PostgreSQL, allowing safe queries against a Postgres database.
+
+`search.queries` provides definitions for the CHORD query AST and some helper
+methods for creating and processing ASTs.
+
 ### `utils`
 
 `utils` contains miscellaneous utilities commonly required by CHORD services.

chord_lib/responses/flask_errors.py

@@ -1,9 +1,17 @@
+import sys
+import traceback
+
 from flask import jsonify
 from functools import partial
+from typing import Callable
+
 from .errors import *
 
 
 __all__ = [
+    "flask_error_wrap_with_traceback",
+    "flask_error_wrap",
+
     "flask_error",
 
     "flask_bad_request_error",
@@ -16,11 +24,36 @@
 ]
 
 
+def flask_error_wrap_with_traceback(fn: Callable, service_name="CHORD Service") -> Callable:
+    """
+    Function to wrap flask_* error creators with something that supports the application.register_error_handler method,
+    while also printing a traceback.
+    :param fn: The flask error-generating function to wrap
+    :param service_name: The name of the service (for logging purposes)
+    :return: The wrapped function
+    """
+    # TODO: pass exception?
+    def handle_error(_e):
+        print(f"[{service_name}] Encountered error:", file=sys.stderr)
+        traceback.print_exc()
+        return fn()
+    return handle_error
+
+
+def flask_error_wrap(fn: Callable) -> Callable:
+    """
+    Function to wrap flask_* error creators with something that supports the application.register_error_handler method.
+    :param fn: The flask error-generating function to wrap
+    :return: The wrapped function
+    """
+    return lambda _e: fn()
+
+
 def flask_error(code: int, *errors):
     return jsonify(http_error(code, *errors)), code
 
 
-def _flask_error(code: int):
+def _flask_error(code: int) -> Callable:
     return partial(flask_error, code)