Merge pull request #44 from bento-platform/develop

Version 0.10.0

MANIFEST.in

@@ -1,2 +1,2 @@
-include chord_lib/schemas/*.json
-include chord_lib/package.cfg
+include bento_lib/schemas/*.json
+include bento_lib/package.cfg

README.md

@@ -1,10 +1,10 @@
-# CHORD Library (for Python CHORD microservices)
+# Bento Library (for Python Bento microservices)
 
-![Build Status](https://api.travis-ci.org/c3g/chord_lib.svg?branch=master)
-[![codecov](https://codecov.io/gh/c3g/chord_lib/branch/master/graph/badge.svg)](https://codecov.io/gh/c3g/chord_lib)
-[![PyPI version](https://badge.fury.io/py/chord-lib.svg)](https://badge.fury.io/py/chord-lib)
+![Build Status](https://api.travis-ci.org/bento-platform/bento_lib.svg?branch=master)
+[![codecov](https://codecov.io/gh/bento-platform/bento_lib/branch/master/graph/badge.svg)](https://codecov.io/gh/bento-platform/bento_lib)
+[![PyPI version](https://badge.fury.io/py/bento-lib.svg)](https://badge.fury.io/py/bento-lib)
 
-Common utilities and helpers for CHORD services.
+Common utilities and helpers for Bento platform services.
 
 
 ## Running Tests
@@ -22,7 +22,7 @@ python3 -m tox
   * [ ] All tests pass and test coverage has not been reduced
 
   * [ ] Package version has been updated (following semver) in 
-    `chord_lib/package.cfg`
+    `bento_lib/package.cfg`
 
   * [ ] The latest changes have been merged from the `develop` branch into the
     `master` branch
@@ -46,7 +46,7 @@ git pull
 source env/bin/activate
 
 # Remove existing build files
-rm -rf build/ dist/ chord_lib.egg-info/
+rm -rf build/ dist/ bento_lib.egg-info/
 
 # Build the new package
 python3 setup.py sdist bdist_wheel
@@ -64,58 +64,58 @@ twine upload dist/*
 ### `auth`
 
 `auth` provides Python service decorators and Django / DRF backends for dealing
-with the CHORD container authentication headers (derived from
+with the Bento container authentication headers (derived from
 `lua-resty-openidc`, set by the internal container NGINX instance.)
 
 ### `events`
 
-`events` facilitates JSON-serialized message-passing between CHORD
+`events` facilitates JSON-serialized message-passing between Bento
 microservices. Serialized objects can be at most 512 MB.
 
 Events should have a lower-case type which is type-insensitively unique and
 adequately describes the associated data.
 
-All CHORD channels are prefixed with `chord.`.
+All Bento channels are prefixed with `bento.`.
 
 ### `ingestion`
 
 `ingestion` contains common code used for handling ingestion routines in
-different CHORD data services.
+different Bento data services.
 
 ### `schemas`
 
 `schemas` contains common JSON schemas which may be useful to a variety of
-different CHORD services.
+different Bento services.
 
-`schemas.chord` contains CHORD-specific schemas, and `schemas.ga4gh` contains
+`schemas.bento` contains Bento-specific schemas, and `schemas.ga4gh` contains
 GA4GH-standardized schemas (possibly not exactly to spec.)
 
 ### `search`
 
 `search` contains definitions, validators, and transformations for the query
-syntax for CHORD, as well as a transpiler to the `psycopg2` PostgreSQL IR.
+syntax for Bento, as well as a transpiler to the `psycopg2` PostgreSQL IR.
 
-The query syntax for CHORD takes advantage of JSON schemas augmented with
+The query syntax for Bento 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
+`search.data_structure` contains code for evaluating a Bento 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
+`search.postgres` contains a "transpiler" from the Bento 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
+`search.queries` provides definitions for the Bento query AST and some helper
 methods for creating and processing ASTs.
 
 ### `utils`
 
-`utils` contains miscellaneous utilities commonly required by CHORD services.
+`utils` contains miscellaneous utilities commonly required by Bento services.
 
 ### `workflows`
 

chord_lib/auth/django_remote_user.py → bento_lib/auth/django_remote_user.py

@@ -2,26 +2,26 @@
 from django.contrib.auth.middleware import RemoteUserMiddleware
 from rest_framework.authentication import RemoteUserAuthentication
 
-from chord_lib.auth.headers import DJANGO_USER_HEADER, DJANGO_USER_ROLE_HEADER
-from chord_lib.auth.roles import ROLE_OWNER, ROLE_USER
+from bento_lib.auth.headers import DJANGO_USER_HEADER, DJANGO_USER_ROLE_HEADER
+from bento_lib.auth.roles import ROLE_OWNER, ROLE_USER
 
 
 __all__ = [
-    "CHORDRemoteUserAuthentication",
-    "CHORDRemoteUserBackend",
-    "CHORDRemoteUserMiddleware",
+    "BentoRemoteUserAuthentication",
+    "BentoRemoteUserBackend",
+    "BentoRemoteUserMiddleware",
 ]
 
 
-class CHORDRemoteUserAuthentication(RemoteUserAuthentication):
+class BentoRemoteUserAuthentication(RemoteUserAuthentication):
     header = DJANGO_USER_HEADER
 
 
-class CHORDRemoteUserMiddleware(RemoteUserMiddleware):
+class BentoRemoteUserMiddleware(RemoteUserMiddleware):
     header = DJANGO_USER_HEADER
 
 
-class CHORDRemoteUserBackend(RemoteUserBackend):
+class BentoRemoteUserBackend(RemoteUserBackend):
     # noinspection PyMethodMayBeStatic
     def configure_user(self, request, user):
         is_owner = request.META.get(DJANGO_USER_ROLE_HEADER, ROLE_USER) == ROLE_OWNER

chord_lib/auth/flask_decorators.py → bento_lib/auth/flask_decorators.py

@@ -4,9 +4,9 @@
 from functools import wraps
 from typing import Union
 
-from chord_lib.auth.headers import CHORD_USER_HEADER, CHORD_USER_ROLE_HEADER
-from chord_lib.auth.roles import ROLE_OWNER, ROLE_USER
-from chord_lib.responses.flask_errors import flask_forbidden_error
+from bento_lib.auth.headers import BENTO_USER_HEADER, BENTO_USER_ROLE_HEADER
+from bento_lib.auth.roles import ROLE_OWNER, ROLE_USER
+from bento_lib.responses.flask_errors import flask_forbidden_error
 
 
 __all__ = [
@@ -17,16 +17,16 @@
 
 
 # TODO: Centralize this
-CHORD_DEBUG = os.environ.get("CHORD_DEBUG", "true").lower() == "true"
-CHORD_PERMISSIONS = os.environ.get("CHORD_PERMISSIONS", str(not CHORD_DEBUG)).lower() == "true"
+BENTO_DEBUG = os.environ.get("CHORD_DEBUG", "true").lower() == "true"
+BENTO_PERMISSIONS = os.environ.get("CHORD_PERMISSIONS", str(not BENTO_DEBUG)).lower() == "true"
 
 
 def _check_roles(headers, roles: Union[set, dict]):
     method_roles = roles if not isinstance(roles, dict) else roles.get(request.method, set())
     return (
-        not CHORD_PERMISSIONS or
+        not BENTO_PERMISSIONS or
         len(method_roles) == 0 or
-        (CHORD_USER_HEADER in headers and headers.get(CHORD_USER_ROLE_HEADER, "") in method_roles)
+        (BENTO_USER_HEADER in headers and headers.get(BENTO_USER_ROLE_HEADER, "") in method_roles)
     )
 
 

bento_lib/auth/headers.py

@@ -0,0 +1,18 @@
+__all__ = [
+    "BENTO_USER_HEADER",
+    "BENTO_USER_ROLE_HEADER",
+
+    "DJANGO_USER_HEADER",
+    "DJANGO_USER_ROLE_HEADER",
+]
+
+
+def _to_django_header(header: str):
+    return f"HTTP_{header.replace('-', '_').upper()}"
+
+
+BENTO_USER_HEADER = "X-User"
+BENTO_USER_ROLE_HEADER = "X-User-Role"
+
+DJANGO_USER_HEADER = _to_django_header(BENTO_USER_HEADER)
+DJANGO_USER_ROLE_HEADER = _to_django_header(BENTO_USER_ROLE_HEADER)

chord_lib/events/__init__.py → bento_lib/events/__init__.py

@@ -18,11 +18,11 @@
 ]
 
 
-ALL_SERVICE_EVENTS = "chord.service.*"
-ALL_DATA_TYPE_EVENTS = "chord.data_type.*"
+ALL_SERVICE_EVENTS = "bento.service.*"
+ALL_DATA_TYPE_EVENTS = "bento.data_type.*"
 
-_SERVICE_CHANNEL_TPL = "chord.service.{}"
-_DATA_TYPE_CHANNEL_TPL = "chord.data_type.{}"
+_SERVICE_CHANNEL_TPL = "bento.service.{}"
+_DATA_TYPE_CHANNEL_TPL = "bento.data_type.{}"
 
 
 # Types

chord_lib/package.cfg → bento_lib/package.cfg

@@ -1,5 +1,5 @@
 [package]
-name = chord_lib
-version = 0.9.0
+name = bento_lib
+version = 0.10.0
 authors = David Lougheed
 author_emails = [email protected]

chord_lib/responses/errors.py → bento_lib/responses/errors.py

@@ -22,12 +22,12 @@ def _error_message(message):
 
 def http_error(code: int, *errors):
     if code not in HTTP_STATUS_CODES:
-        print(f"[CHORD Lib] Error: Could not find code {code} in valid HTTP status codes.")
+        print(f"[Bento Lib] Error: Could not find code {code} in valid HTTP status codes.")
         code = 500
         errors = (*errors, f"An invalid status code of {code} was specified by the service.")
 
     if code < 400:
-        print(f"[CHORD Lib] Error: Code {code} is not an HTTP error code.")
+        print(f"[Bento Lib] Error: Code {code} is not an HTTP error code.")
         code = 500
         errors = (*errors, f"A non-error status code of {code} was specified by the service.")
 

chord_lib/responses/flask_errors.py → bento_lib/responses/flask_errors.py

@@ -5,7 +5,7 @@
 from functools import partial
 from typing import Callable
 
-from chord_lib.responses import errors
+from bento_lib.responses import errors
 
 
 __all__ = [
@@ -24,7 +24,7 @@
 ]
 
 
-def flask_error_wrap_with_traceback(fn: Callable, service_name="CHORD Service") -> Callable:
+def flask_error_wrap_with_traceback(fn: Callable, service_name="Bento Service") -> Callable:
     """
     Function to wrap flask_* error creators with something that supports the application.register_error_handler method,
     while also printing a traceback.

bento_lib/schemas/__init__.py

@@ -0,0 +1,4 @@
+from . import bento
+from . import ga4gh
+
+__all__ = ["bento", "ga4gh"]

bento_lib/schemas/bento.py

@@ -0,0 +1,13 @@
+from ._utils import load_json_schema
+
+
+__all__ = [
+    "BENTO_INGEST_SCHEMA",
+    "BENTO_DATA_USE_SCHEMA",
+]
+
+
+# TODO: Refactor this schema and semi-combine with workflow schema
+BENTO_INGEST_SCHEMA = load_json_schema("bento_ingest.schema.json")
+
+BENTO_DATA_USE_SCHEMA = load_json_schema("bento_data_use.schema.json")

chord_lib/schemas/chord_data_use.schema.json → bento_lib/schemas/bento_data_use.schema.json

@@ -1,7 +1,7 @@
 {
-  "$id": "https://raw.githubusercontent.com/c3g/chord_lib/master/chord_lib/schemas/chord_data_use.schema.json",
+  "$id": "https://raw.githubusercontent.com/bento-platform/bento_lib/master/bento_lib/schemas/bento_data_use.schema.json",
   "$schema": "http://json-schema.org/draft-07/schema#",
-  "title": "CHORD Data Use File",
+  "title": "Bento Data Use File",
   "description": "Schema defining data usage conditions from the GA4GH DUO ontology.",
   "type": "object",
   "properties": {

chord_lib/schemas/ga4gh_service_info.schema.json → bento_lib/schemas/ga4gh_service_info.schema.json

@@ -1,5 +1,5 @@
 {
-  "$id": "https://raw.githubusercontent.com/c3g/chord_lib/master/chord_lib/schemas/ga4gh_service_info.schema.json",
+  "$id": "https://raw.githubusercontent.com/bento-platform/bento_lib/master/bento_lib/schemas/ga4gh_service_info.schema.json",
   "$schema": "http://json-schema.org/draft-07/schema#",
   "type": "object",
   "properties": {

bento_lib/search/_types.py

@@ -0,0 +1,5 @@
+from typing import Dict
+
+__all__ = ["JSONSchema"]
+
+JSONSchema = Dict