diff --git a/.secrets.baseline b/.secrets.baseline index d2fc203d..b2f365f8 100644 --- a/.secrets.baseline +++ b/.secrets.baseline @@ -275,7 +275,7 @@ "filename": "tests/test_aliases_endpoints.py", "hashed_secret": "5666c088b494f26cd8f63ace013992f5fc391ce0", "is_verified": false, - "line_number": 41 + "line_number": 39 } ], "tests/test_bundles.py": [ @@ -284,7 +284,7 @@ "filename": "tests/test_bundles.py", "hashed_secret": "5666c088b494f26cd8f63ace013992f5fc391ce0", "is_verified": false, - "line_number": 30 + "line_number": 25 }, { "type": "Hex High Entropy String", @@ -328,70 +328,70 @@ "filename": "tests/test_client.py", "hashed_secret": "15a6d8daad1278efcaadc0d6e3d1dd2d9ebbc262", "is_verified": false, - "line_number": 1084 + "line_number": 1092 }, { "type": "Hex High Entropy String", "filename": "tests/test_client.py", "hashed_secret": "1b0d1a618b5c213dd792bbc3aa96ffa6bc370ef3", "is_verified": false, - "line_number": 1300 + "line_number": 1308 }, { "type": "Hex High Entropy String", "filename": "tests/test_client.py", "hashed_secret": "1170ace44158ff189902ff44597efef121623353", "is_verified": false, - "line_number": 1731 + "line_number": 1739 }, { "type": "Hex High Entropy String", "filename": "tests/test_client.py", "hashed_secret": "ff9c79b737b3ea7386618cc9437d3fb0a772182b", "is_verified": false, - "line_number": 2406 + "line_number": 2414 }, { "type": "Hex High Entropy String", "filename": "tests/test_client.py", "hashed_secret": "c8176f1e75e62e15dabaa4087fb7194451c8f6d2", "is_verified": false, - "line_number": 2409 + "line_number": 2417 }, { "type": "Hex High Entropy String", "filename": "tests/test_client.py", "hashed_secret": "d5198f8eddb1cbeb437899cd99e5ee97ab8531b4", "is_verified": false, - "line_number": 2409 + "line_number": 2417 }, { "type": "Hex High Entropy String", "filename": "tests/test_client.py", "hashed_secret": "02dc196562514eaa3e2feac1f441ccf6ad81e09d", "is_verified": false, - "line_number": 2413 + "line_number": 2421 }, { "type": "Hex High Entropy String", "filename": "tests/test_client.py", "hashed_secret": "f1cb2d91a95165a2ab909eadd9f7b65f312c7e2d", "is_verified": false, - "line_number": 2414 + "line_number": 2422 }, { "type": "Hex High Entropy String", "filename": "tests/test_client.py", "hashed_secret": "58db546de03270b55a4c889a5c5e6296b29fef25", "is_verified": false, - "line_number": 2415 + "line_number": 2423 }, { "type": "Hex High Entropy String", "filename": "tests/test_client.py", "hashed_secret": "b6c0bd08fde409c18760f32bef8705191840c402", "is_verified": false, - "line_number": 2416 + "line_number": 2424 } ], "tests/test_deprecated_aliases_endpoints.py": [ @@ -409,9 +409,9 @@ "filename": "tests/test_drs.py", "hashed_secret": "5666c088b494f26cd8f63ace013992f5fc391ce0", "is_verified": false, - "line_number": 38 + "line_number": 37 } ] }, - "generated_at": "2023-04-20T22:58:41Z" + "generated_at": "2023-07-06T18:22:13Z" } diff --git a/indexd/app.py b/indexd/app.py index e0bf52a3..121bcc98 100644 --- a/indexd/app.py +++ b/indexd/app.py @@ -5,7 +5,7 @@ import cdislogging import flask -from indexd.index.drivers.alchemy import Base as IndexBase +from indexd.index.drivers.alchemy import Base as IndexBase, cache_bucket_info_mapping from indexd.alias.drivers.alchemy import Base as AliasBase from indexd.auth.drivers.alchemy import Base as AuthBase from .bulk.blueprint import blueprint as indexd_bulk_blueprint @@ -15,8 +15,11 @@ from .drs.blueprint import blueprint as indexd_guid_blueprint from .guid.blueprint import blueprint as indexd_drs_blueprint from .blueprint import blueprint as cross_blueprint + from indexd.urls.blueprint import blueprint as index_urls_blueprint +logger = cdislogging.get_logger(__name__, log_level="info") + def app_init(app, settings=None): app.url_map.strict_slashes = False @@ -65,4 +68,9 @@ def get_app(settings=None): app_init(app, settings) + try: + cache_bucket_info_mapping(settings, logger) + except Exception as e: + logger.error("Failed to cache bucket region mapping: %s", e) + return app diff --git a/indexd/drs/blueprint.py b/indexd/drs/blueprint.py index 0ffcbc09..8746b02f 100644 --- a/indexd/drs/blueprint.py +++ b/indexd/drs/blueprint.py @@ -2,8 +2,10 @@ import re import flask import json +import cdislogging from indexd.errors import AuthError, AuthzError from indexd.errors import UserError +from indexd.index.drivers.alchemy import url_to_bucket_region_mapping from indexd.index.errors import NoRecordFound as IndexNoRecordFound from indexd.errors import IndexdUnexpectedError from indexd.utils import reverse_url @@ -210,6 +212,8 @@ def indexd_to_drs(record, expand=False): bundle_object.pop("contents", None) drs_object["contents"].append(bundle_object) + # driver = blueprint.driver + # with driver.session as session: # access_methods mapping if "urls" in record: drs_object["access_methods"] = [] @@ -218,12 +222,18 @@ def indexd_to_drs(record, expand=False): 0 ] # (s3, gs, ftp, gsiftp, globus, htsget, https, file) + logger = cdislogging.get_logger(__name__, log_level="info") + + region = url_to_bucket_region_mapping( + session="", url=location, logger=logger + ) + drs_object["access_methods"].append( { "type": location_type, "access_url": {"url": location}, "access_id": location_type, - "region": "", + "region": region, } ) diff --git a/indexd/index/drivers/alchemy.py b/indexd/index/drivers/alchemy.py index 780d5796..1a32c50b 100644 --- a/indexd/index/drivers/alchemy.py +++ b/indexd/index/drivers/alchemy.py @@ -1,8 +1,14 @@ +import os +import time + +import backoff import datetime +from urllib import response import uuid import json from contextlib import contextmanager from cdislogging import get_logger +import requests from sqlalchemy import ( BigInteger, Column, @@ -22,6 +28,7 @@ from sqlalchemy.ext.declarative import declarative_base from sqlalchemy.orm import joinedload, relationship, sessionmaker from sqlalchemy.orm.exc import MultipleResultsFound, NoResultFound +import urllib.parse from indexd import auth from indexd.errors import UserError, AuthError @@ -118,9 +125,11 @@ def to_document_dict(self): hashes = {h.hash_type: h.hash_value for h in self.hashes} metadata = {m.key: m.value for m in self.index_metadata} + # Call fence /bucket_info/region endpoint to fill some of the urls metadata urls_metadata = { u.url: {m.key: m.value for m in u.url_metadata} for u in self.urls } + created_date = self.created_date.isoformat() updated_date = self.updated_date.isoformat() content_created_date = ( @@ -307,6 +316,139 @@ def to_document_dict(self, expand=False): return ret +class BucketRegionMappingCache(Base): + """ + Cache for bucket-region mapping information from fence + """ + + __tablename__ = "bucket_region_mapping_cache" + + bucket_name = Column(String, primary_key=True) + bucket_region = Column(String) + storage_type = Column(String) + + +@backoff.on_exception(backoff.expo, Exception, max_tries=5) +def get_bucket_info_mapping_from_fence(logger=None): + try: + # Get bucket information from fence /bucket_info/region endpoint + hostname = os.environ["HOSTNAME"] + fence_url = "http://" + hostname + "/user/data/buckets" + response = requests.get(fence_url) + response.raise_for_status() # Raise an exception for non-successful responses + return response + except requests.exceptions.RequestException as e: + logger.warning( + "Failed to retrieve region mapping from fence: %s. Check if fence is running and mapping config is available.", + e, + ) + raise + + +def cache_bucket_info_mapping(settings=None, logger=None): + driver = settings["config"]["INDEX"]["driver"] + try: + bucket_region_response = get_bucket_info_mapping_from_fence(logger=logger) + logger.info("Received bucket region mapping from fence") + except Exception as e: + logger.warning( + "Failed to retrieve region mapping from fence: %s. Check if fence is running and mapping config is available.", + e, + ) + if bucket_region_response.status_code == 405: + logger.warning( + "Failed to retrieve region mapping from fence: %s. Fence does not contain bucket region endpoint. Use Fence version 9.1.0+.", + e, + ) + return + + """ + {'GS_BUCKETS': {'gs-bucket-1': {'region': 'us-east-1'}, 'gs-bucket-2': {'region': 'us-east-1'}}, 'S3_BUCKETS': {'cdis-presigned-url-test': {'region': 'us-east-1'}, 'devplanetv1-data-bucket': {'region': 'us-east-1'}}} + GS_BUCKETS + G + + """ + with driver.session as session: + try: + resp = bucket_region_response.json() + for storage_type in resp: + for bucket_name in resp[storage_type]: + mapping_cache = BucketRegionMappingCache( + bucket_name=bucket_name, + bucket_region=resp[storage_type][bucket_name]["region"], + storage_type=storage_type, + ) + session.add(mapping_cache) + session.commit() + except Exception as e: + logger.error("Failed to cache bucket region mapping: %s", e) + session.rollback() + raise + + +def url_to_bucket_region_mapping(session, url, logger=None): + """ + Map the url location of a bucket to its region + + Args: + url(str): The url of the object location in the bucket + + Returns: + region(str): The region of the bucket where the object is located + """ + logger = logger or get_logger("SQLAlchemyIndexDriver") + + storage_to_config_map = {"s3": "S3_BUCKETS", "gs": "GS_BUCKETS"} + parsed_url = urllib.parse.urlparse(url) + cloud_storage_service = parsed_url.scheme + bucket_name = parsed_url.netloc + + bucket_region_response = get_bucket_info_mapping_from_fence(logger=logger) + + storage_map = storage_to_config_map.get(cloud_storage_service, None) + + if storage_map is None: + logger.warning( + "Storage type {} not found/not configured in Fence.", cloud_storage_service + ) + return None + + bucket_list = bucket_region_response + + bucket_region = bucket_list[bucket_name] + + # TODO: Add caching mechanism later. Currently, calling fence is fast enough. + # try: + # from local_settings import settings + # except ImportError: + # logger.info("Can't import local_settings, import from default") + # from indexd.default_settings import settings + + # if cache is enabled then cache + # cache_bucket_info_mapping(settings, logger=logger) + + # TODO: this isnt working properly. Fix Session query + # try: + # bucket_mapping = ( + # session.query(BucketRegionMappingCache) + # .filter(BucketRegionMappingCache.bucket_name == bucket_name) + # .first() + # ) + # except Exception as e: + # print("Failed to query to table: {}".format(e)) + # # if bucket_region_info is still empty that means that there's no bucket configured in the fence config + # if bucket_mapping is None: + # logger.warning( + # "Bucket region information for the bucket {} is not configured in Fence".format( + # bucket_name + # ) + # ) + + # bucket_region = bucket_mapping.bucket_region + + return bucket_region + + def create_urls_metadata(urls_metadata, record, session): """ create url metadata record in database diff --git a/migrations/versions/d5a1e9847169_create_bucket_region_cache_table.py b/migrations/versions/d5a1e9847169_create_bucket_region_cache_table.py new file mode 100644 index 00000000..4406ccbb --- /dev/null +++ b/migrations/versions/d5a1e9847169_create_bucket_region_cache_table.py @@ -0,0 +1,29 @@ +"""create_bucket_region_cache_table + +Revision ID: d5a1e9847169 +Revises: a72f117515c5 +Create Date: 2023-06-21 13:03:15.477447 + +""" +from alembic import op +import sqlalchemy as sa + + +# revision identifiers, used by Alembic. +revision = "d5a1e9847169" # pragma: allowlist secret +down_revision = "a72f117515c5" +branch_labels = None +depends_on = None + + +def upgrade() -> None: + op.create_table( + "bucket_region_mapping_cache", + sa.Column("bucket_name", sa.VARCHAR(), nullable=False), + sa.Column("bucket_region", sa.VARCHAR(), nullable=False), + sa.Column("storage_type", sa.VARCHAR(), nullable=False), + ) + + +def downgrade() -> None: + op.drop_table("bucket_region_mapping_cache") diff --git a/poetry.lock b/poetry.lock index b70402ba..610118bc 100644 --- a/poetry.lock +++ b/poetry.lock @@ -2,19 +2,20 @@ [[package]] name = "alembic" -version = "1.9.4" +version = "1.10.2" description = "A database migration tool for SQLAlchemy." category = "main" optional = false python-versions = ">=3.7" files = [ - {file = "alembic-1.9.4-py3-none-any.whl", hash = "sha256:6f1c2207369bf4f49f952057a33bb017fbe5c148c2a773b46906b806ea6e825f"}, - {file = "alembic-1.9.4.tar.gz", hash = "sha256:4d3bd32ecdbb7bbfb48a9fe9e6d6fd6a831a1b59d03e26e292210237373e7db5"}, + {file = "alembic-1.10.2-py3-none-any.whl", hash = "sha256:8b48368f6533c064b39c024e1daba15ae7f947eac84185c28c06bbe1301a5497"}, + {file = "alembic-1.10.2.tar.gz", hash = "sha256:457eafbdc0769d855c2c92cbafe6b7f319f916c80cf4ed02b8f394f38b51b89d"}, ] [package.dependencies] Mako = "*" SQLAlchemy = ">=1.3.0" +typing-extensions = ">=4" [package.extras] tz = ["python-dateutil"] @@ -44,7 +45,7 @@ trio = ["trio (>=0.16,<0.22)"] name = "atomicwrites" version = "1.4.1" description = "Atomic file writes." -category = "dev" +category = "main" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" files = [ @@ -134,6 +135,18 @@ files = [ {file = "cached_property-1.5.2-py2.py3-none-any.whl", hash = "sha256:df4f613cf7ad9a588cc381aaf4a512d26265ecebd5eb9e1ba12f1319eb85a6a0"}, ] +[[package]] +name = "cachelib" +version = "0.9.0" +description = "A collection of cache libraries in the same API interface." +category = "main" +optional = false +python-versions = ">=3.7" +files = [ + {file = "cachelib-0.9.0-py3-none-any.whl", hash = "sha256:811ceeb1209d2fe51cd2b62810bd1eccf70feba5c52641532498be5c675493b3"}, + {file = "cachelib-0.9.0.tar.gz", hash = "sha256:38222cc7c1b79a23606de5c2607f4925779e37cdcea1c2ad21b8bae94b5425a5"}, +] + [[package]] name = "cdiserrors" version = "1.0.0" @@ -270,100 +283,87 @@ pycparser = "*" [[package]] name = "charset-normalizer" -version = "3.0.1" +version = "3.1.0" description = "The Real First Universal Charset Detector. 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"sha256:8a388717b9476f934a21484e8c8e61875ab60644d29b9b39e11e4b9dc1c6b305"}, ] [package.extras] @@ -1415,4 +1491,4 @@ testing = ["big-O", "flake8 (<5)", "jaraco.functools", "jaraco.itertools", "more [metadata] lock-version = "2.0" python-versions = "^3.9" -content-hash = "dbb013e70567b96835a357dfe393b4ca95e5fb973b73d81e228aef0dc884c1b9" +content-hash = "b2339fb932ef4e913a7cf90b9ce8771ab0427ea7d8d01a7751496d9543decf9d" diff --git a/pyproject.toml b/pyproject.toml index 49bc2005..f398e0dd 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -26,6 +26,10 @@ psycopg2 = "^2.7" sqlalchemy = "~1.3.3" sqlalchemy-utils = "^0.37.3" PyYAML = "^5.4" +flask-caching = "^2.0.2" +pytest-mock = "^3.10.0" +requests-mock = "^1.10.0" +flask-cache = "^0.13.1" [tool.poetry.dev-dependencies] diff --git a/tests/conftest.py b/tests/conftest.py index afe08d99..a1336663 100644 --- a/tests/conftest.py +++ b/tests/conftest.py @@ -1,7 +1,11 @@ import base64 +import os + +from flask import request import importlib import pytest import requests +import requests_mock import mock from unittest.mock import patch @@ -146,3 +150,48 @@ def make_mock_response(method, url, *args, **kwargs): request.addfinalizer(patch_method.stop) return do_patch + + +@pytest.fixture +def mock_bucket_region_info(): + mock_response = { + "GS_BUCKETS": { + "gs-bucket-1": {"region": "us-east-1"}, + "gs-bucket-2": {"region": "us-east-1"}, + }, + "S3_BUCKETS": { + "cdis-presigned-url-test": {"region": "us-east-1"}, + "devplanetv1-data-bucket": {"region": "us-east-1"}, + }, + } + + with requests_mock.Mocker() as m: + m.get( + f"http://{os.environ['HOSTNAME']}/user/bucket_info/region", + json=mock_response, + ) + + yield m + + +@pytest.fixture +def mock_bucket_region_info_with_empty_response(): + mock_response = {} + + with requests_mock.Mocker() as m: + m.get( + f"http://{os.environ['HOSTNAME']}/user/bucket_info/region", + json=mock_response, + ) + yield m + + +@pytest.fixture +def mock_bucket_region_info_with_empty_response(): + with requests_mock.Mocker() as m: + m.register_uri( + "GET", + f"http://{os.environ['HOSTNAME']}/user/bucket_info/region", + status_code=405, + ) + yield m diff --git a/tests/postgres/migrations/test_d5a1e9847169_create_bucket_region_cache_table.py b/tests/postgres/migrations/test_d5a1e9847169_create_bucket_region_cache_table.py new file mode 100644 index 00000000..e69de29b diff --git a/tests/test_aliases_endpoints.py b/tests/test_aliases_endpoints.py index eef43e3d..63e3c396 100644 --- a/tests/test_aliases_endpoints.py +++ b/tests/test_aliases_endpoints.py @@ -1,6 +1,4 @@ import pytest -import string -import json import urllib.parse diff --git a/tests/test_bundles.py b/tests/test_bundles.py index 84ef3f72..370f8d00 100644 --- a/tests/test_bundles.py +++ b/tests/test_bundles.py @@ -1,9 +1,4 @@ -import json -import pytest import uuid -import tests.conftest -import requests -import responses from tests.default_test_settings import settings @@ -149,7 +144,10 @@ def test_bundle_post_different_checksum_types(client, user): "bundles": did_list, "bundle_id": bundle_id, "checksums": [ - {"checksum": "85136c79cbf9fe36bb9d05d0639c70c265c18d37", "type": "sha1"} + { + "checksum": "85136c79cbf9fe36bb9d05d0639c70c265c18d37", # pragma: allowlist secret + "type": "sha1", + } ], } res = client.post("/bundle/", json=data, headers=user) @@ -157,7 +155,7 @@ def test_bundle_post_different_checksum_types(client, user): res1 = client.get("/ga4gh/drs/v1/objects/" + bundle_id) rec1 = res1.json assert rec1["checksums"][0] == { - "checksum": "85136c79cbf9fe36bb9d05d0639c70c265c18d37", + "checksum": "85136c79cbf9fe36bb9d05d0639c70c265c18d37", # pragma: allowlist secret "type": "sha1", } @@ -171,10 +169,13 @@ def test_bundle_post_multiple_checksum_types(client, user): "bundle_id": bundle_id, "checksums": [ { - "checksum": "bc52d6bfe3ac965e069109dbd7d15e0ccaaa55678f6e2a6664bee2edf8ae1b2b", + "checksum": "bc52d6bfe3ac965e069109dbd7d15e0ccaaa55678f6e2a6664bee2edf8ae1b2b", # pragma: allowlist secret "type": "sha256", }, - {"checksum": "e93ccf5ffc90eefcc0bdb81f87d25d1a", "type": "md5"}, + { + "checksum": "e93ccf5ffc90eefcc0bdb81f87d25d1a", # pragma: allowlist secret + "type": "md5", + }, ], } res = client.post("/bundle/", json=data, headers=user) @@ -186,10 +187,13 @@ def test_bundle_post_multiple_checksum_types(client, user): for checksum in checksums: assert checksum in [ { - "checksum": "bc52d6bfe3ac965e069109dbd7d15e0ccaaa55678f6e2a6664bee2edf8ae1b2b", + "checksum": "bc52d6bfe3ac965e069109dbd7d15e0ccaaa55678f6e2a6664bee2edf8ae1b2b", # pragma: allowlist secret "type": "sha256", }, - {"checksum": "e93ccf5ffc90eefcc0bdb81f87d25d1a", "type": "md5"}, + { + "checksum": "e93ccf5ffc90eefcc0bdb81f87d25d1a", # pragma: allowlist secret + "type": "md5", + }, ] diff --git a/tests/test_client.py b/tests/test_client.py index eadc38f4..a372f497 100644 --- a/tests/test_client.py +++ b/tests/test_client.py @@ -43,8 +43,16 @@ def test_index_list_with_params(client, user): "s3://anotherurl/bucket_2/key_2", ] data1["urls_metadata"] = { - "s3://endpointurl/bucket_2/key_2": {"state": "error", "other": "xxx"}, - "s3://anotherurl/bucket_2/key_2": {"state": "error", "other": "xxx"}, + "s3://endpointurl/bucket_2/key_2": { + "state": "error", + "other": "xxx", + "region": None, + }, + "s3://anotherurl/bucket_2/key_2": { + "state": "error", + "other": "xxx", + "region": None, + }, } res_1 = client.post("/index/", json=data1, headers=user) assert res_1.status_code == 200 @@ -1373,8 +1381,8 @@ def test_update_urls_metadata(client, user): res_2 = client.get("/index/" + rec["did"]) assert res_2.status_code == 200 rec_2 = res_2.json - assert rec_2["urls_metadata"] == data["urls_metadata"] + assert rec_2["urls_metadata"] == data["urls_metadata"] updated = {"urls_metadata": {data["urls"][0]: {"test": "b"}}} res = client.put( "/index/{}?rev={}".format(rec_2["did"], rec_2["rev"]), diff --git a/tests/test_drs.py b/tests/test_drs.py index 68a8c015..42b5da41 100644 --- a/tests/test_drs.py +++ b/tests/test_drs.py @@ -2,7 +2,6 @@ import json import tests.conftest import requests -import responses from tests.default_test_settings import settings from tests.test_bundles import get_bundle_doc