Merge pull request #90 from guzman-raphael/disable-deep-dependency

Disable deep dependency and update NGINX image

Author: Synicix

CHANGELOG.md

@@ -2,12 +2,12 @@
 
 Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) convention.
 
-## [Unreleased]
+## [0.1.0b0] - 2021-02-26
 
-## Security
+### Security
 - Documentation with detail regarding warning on bearer token. (#83) PR #88
 
-## Fixed
+### Fixed
 - Incorrect virtual module reference of `schema_virtual_module` in table metadata. (#85) PR #88
 
 ### Added
@@ -20,6 +20,8 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 - Replaced `DJConnector.snake_to_camel_case` usage with `datajoint.utils.to_camel_case`. PR #88
 - Default behavior for `/delete_tuple` now deletes without cascading. (#86) PR #88
 - Consolidated `pytest` fixtures into `__init__.py` to facilitate reuse. PR #88
+- Modify dependency check to not perform deep check and use accessible fk relations only. (#89) PR #90
+- Update nginx image to pull from datajoint organization. (#80) PR #90
 
 ### Removed
 - Docker `base` environment to simplify dependencies. PR #79
@@ -34,5 +36,5 @@ Observes [Semantic Versioning](https://semver.org/spec/v2.0.0.html) standard and
 - Support for DataJoint attribute types: `varchar`, `int`, `float`, `datetime`, `date`, `time`, `decimal`, `uuid`.
 - Check dependency utility to determine child table references.
 
-[Unreleased]: https://github.com/datajoint/pharus/compare/0.1.0a5...HEAD
+[0.1.0b0]: https://github.com/datajoint/pharus/compare/0.1.0a5...0.1.0b0
 [0.1.0a5]: https://github.com/datajoint/pharus/releases/tag/0.1.0a5

docker-compose-deploy.yaml

@@ -1,5 +1,5 @@
-# PHARUS_VERSION=0.1.0a5 docker-compose -f docker-compose-deploy.yaml pull
-# PHARUS_VERSION=0.1.0a5 docker-compose -f docker-compose-deploy.yaml up -d
+# PHARUS_VERSION=0.1.0b0 docker-compose -f docker-compose-deploy.yaml pull
+# PHARUS_VERSION=0.1.0b0 docker-compose -f docker-compose-deploy.yaml up -d
 #
 # Intended for production deployment.
 # Note: You must run both commands above for minimal outage
@@ -20,7 +20,7 @@ services:
     #   - PHARUS_PREFIX=/
   fakeservices.datajoint.io:
     <<: *net
-    image: raphaelguzman/nginx:v0.0.15
+    image: datajoint/nginx:v0.0.15
     environment:
       - ADD_pharus_TYPE=REST
       - ADD_pharus_ENDPOINT=pharus:5000

docker-compose-dev.yaml

@@ -23,7 +23,7 @@ services:
     command: pharus
   fakeservices.datajoint.io:
     <<: *net
-    image: raphaelguzman/nginx:v0.0.15
+    image: datajoint/nginx:v0.0.15
     environment:
       - ADD_pharus_TYPE=REST
       - ADD_pharus_ENDPOINT=pharus:5000

pharus/interface.py

@@ -4,14 +4,10 @@
 import datetime
 import numpy as np
 from functools import reduce
-from datajoint.errors import AccessError
-import re
 from .error import InvalidDeleteRequest, InvalidRestriction, UnsupportedTableType
 
 DAY = 24 * 60 * 60
 DEFAULT_FETCH_LIMIT = 1000  # Stop gap measure to deal with super large tables
-TABLE_INFO_REGEX = re.compile(
-    r'.*?FROM\s+`(?P<schema>\w+)`.*?name\s*?=\s*?"(?P<table>.*?)".*?')
 
 
 class DJConnector():
@@ -312,16 +308,6 @@ def record_dependency(jwt_payload: dict, schema_name: str, table_name: str,
         dependencies = [dict(schema=descendant.database, table=descendant.table_name,
                              accessible=True, count=len(descendant & primary_restriction))
                         for descendant in table().descendants(as_objects=True)]
-        # Determine first issue regarding access
-        # Start transaction, try to delete, catch first occurrence, rollback
-        virtual_module.schema.connection.start_transaction()
-        try:
-            (table & primary_restriction).delete(safemode=False, transaction=False)
-        except AccessError as errors:
-            dependencies = dependencies + [dict(TABLE_INFO_REGEX.match(
-                errors.args[2]).groupdict(), accessible=False)]
-        finally:
-            virtual_module.schema.connection.cancel_transaction()
         return dependencies
 
     @staticmethod

pharus/version.py

@@ -1,2 +1,2 @@
 """Package metadata."""
-__version__ = '0.1.0a5'
+__version__ = '0.1.0b0'

tests/test_dependencies.py

@@ -3,38 +3,6 @@
 from . import SCHEMA_PREFIX, client, token, group1_token, connection, schemas_simple
 
 
-def test_dependencies_underprivileged(group1_token, client, schemas_simple):
-    schema_name = f'{SCHEMA_PREFIX}group1_simple'
-    table_name = 'TableA'
-    restriction = b64encode(dumps(dict(a_id=0)).encode('utf-8')).decode('utf-8')
-    REST_dependencies = client.get(
-        f"""/record/dependency?schemaName={
-            schema_name}&tableName={table_name}&restriction={restriction}""",
-        headers=dict(Authorization=f'Bearer {group1_token}')).json['dependencies']
-    REST_records = client.post('/fetch_tuples',
-                               headers=dict(Authorization=f'Bearer {group1_token}'),
-                               json=dict(schemaName=schema_name,
-                                         tableName=table_name)).json['tuples']
-    assert len(REST_records) == 2
-    assert len(REST_dependencies) == 4
-    table_a = [el for el in REST_dependencies
-               if (el['schema'] == f'{SCHEMA_PREFIX}group1_simple' and
-                   'table_a' in el['table'])][0]
-    assert table_a['accessible'] and table_a['count'] == 1
-    table_b = [el for el in REST_dependencies
-               if (el['schema'] == f'{SCHEMA_PREFIX}group1_simple' and
-                   'table_b' in el['table'])][0]
-    assert table_b['accessible'] and table_b['count'] == 2
-    table_c = [el for el in REST_dependencies
-               if (el['schema'] == f'{SCHEMA_PREFIX}group1_simple' and
-                   'table_c' in el['table'])][0]
-    assert table_c['accessible'] and table_c['count'] == 3
-    diff_table_b = [el for el in REST_dependencies
-                    if (el['schema'] == f'{SCHEMA_PREFIX}group2_simple' and
-                        'diff_table_b' in el['table'])][0]
-    assert not diff_table_b['accessible']
-
-
 def test_dependencies_admin(token, client, schemas_simple):
     schema_name = f'{SCHEMA_PREFIX}group1_simple'
     table_name = 'TableA'