28181841506

Committed 25 Jun 2026 03:36PM UTC coverage: 87.405% (+0.003%) from 87.402%

Build # 28181841506

Build Type

push

github

Committed by

web-flow

Commit Message

Merge pull request #441 from uc-cdis/feat/drs-1.5

Feat/drs 1.5

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3220 of 3684 relevant lines covered (87.4%)

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92.86

indexd/default_settings.py

from .index.drivers.alchemy import SQLAlchemyIndexDriver
from .alias.drivers.alchemy import SQLAlchemyAliasDriver
from .auth.drivers.alchemy import SQLAlchemyAuthDriver
from .index.drivers.single_table_alchemy import SingleTableSQLAlchemyIndexDriver
import json
from os import environ
import json


CONFIG = {}

CONFIG["JSONIFY_PRETTYPRINT_REGULAR"] = False
AUTO_MIGRATE = True
# Key to lock the database during migrations
CONFIG["DB_MIGRATION_POSTGRES_LOCK_KEY"] = 100

USE_SINGLE_TABLE = False

# - DEFAULT_PREFIX: prefix to be prepended.
# - PREPEND_PREFIX: the prefix is preprended to the generated GUID when a
#   new record is created WITHOUT a provided GUID.
# - ADD_PREFIX_ALIAS: aliases are created for new records - "<PREFIX><GUID>".
# Do NOT set both ADD_PREFIX_ALIAS and PREPEND_PREFIX to True, or aliases
# will be created as "<PREFIX><PREFIX><GUID>".
if USE_SINGLE_TABLE is True:
    CONFIG["INDEX"] = {
        "driver": SingleTableSQLAlchemyIndexDriver(
            "postgresql://postgres:postgres@localhost:5432/indexd_tests",  # pragma: allowlist secret
            echo=True,
            index_config={
                "DEFAULT_PREFIX": "testprefix/",
                "PREPEND_PREFIX": True,
                "ADD_PREFIX_ALIAS": False,
            },
        )
    }
else:
    CONFIG["INDEX"] = {
        "driver": SQLAlchemyIndexDriver(
            "postgresql://postgres:postgres@localhost:5432/indexd_tests",  # pragma: allowlist secret
            echo=True,
            index_config={
                "DEFAULT_PREFIX": "testprefix/",
                "PREPEND_PREFIX": True,
                "ADD_PREFIX_ALIAS": False,
            },
        )
    }

CONFIG["ALIAS"] = {
    "driver": SQLAlchemyAliasDriver(
        "postgresql://postgres:postgres@localhost:5432/indexd_tests",  # pragma: allowlist secret
        echo=True,
    )
}


CONFIG["DIST"] = [
    {
        "name": "Other IndexD",
        "host": "https://indexd.example.io/index/",
        "hints": [".*ROCKS.*"],
        "type": "indexd",
    },
    {"name": "DX DOI", "host": "https://doi.org/", "hints": ["10\..*"], "type": "doi"},
    {
        "name": "DOS System",
        "host": "https://example.com/api/ga4gh/dos/v1/",
        "hints": [],
        "type": "dos",
    },
]

# Maximum number of objects in a single bulk DRS request.
# Used in GET /service-info response and enforced by bulk endpoints.
CONFIG["MAX_BULK_REQUEST_LENGTH"] = 100

CONFIG["DRS_SERVICE_INFO"] = {
    "name": "DRS System",
    "type": {
        "group": "org.ga4gh",
        "artifact": "drs",
        "version": "1.5.0",
    },
    "version": "1.5.0",
    "id": "com.example",
    "organization": {
        "name": "CTDS",
        "url": "http://example.com/",
    },
}

cloud_provider_map = environ.get("CLOUD_PROVIDER_MAP", None)
if cloud_provider_map:
    CONFIG["CLOUD_PROVIDER_MAP"] = json.loads(cloud_provider_map)
else:
    CONFIG["CLOUD_PROVIDER_MAP"] = {
        "s3": "aws",
        "gs": "gcp",
        "az": "azure",
    }

AUTH = SQLAlchemyAuthDriver(
    "postgresql://postgres:postgres@localhost:5432/indexd_tests"  # pragma: allowlist secret
)

settings = {"config": CONFIG, "auth": AUTH, "use_single_table": USE_SINGLE_TABLE}

CONFIG["DRS_AUTHORIZATION_METADATA"] = {
    "/gen3/programs/a/projects/b": {
        "supported_types": ["BearerAuth", "PassportAuth"],
        "passport_auth_issuers": ["https://ras/foo/bar"],
        "bearer_auth_issuers": ["https://gen3.datacommons.io"],
    }
}

CONFIG["DEFAULT_BEARER_ISSUER"] = "https://gen3.datacommons.io"
CONFIG["DEFAULT_PASSPORT_ISSUER"] = "test_passport_default"

1	from .index.drivers.alchemy import SQLAlchemyIndexDriver	1✔
2	from .alias.drivers.alchemy import SQLAlchemyAliasDriver	1✔
3	from .auth.drivers.alchemy import SQLAlchemyAuthDriver	1✔
4	from .index.drivers.single_table_alchemy import SingleTableSQLAlchemyIndexDriver	1✔
5	import json	1✔
6	from os import environ	1✔
7	import json	1✔
8
9
10	CONFIG = {}	1✔
11
12	CONFIG["JSONIFY_PRETTYPRINT_REGULAR"] = False	1✔
13	AUTO_MIGRATE = True	1✔
14	# Key to lock the database during migrations
15	CONFIG["DB_MIGRATION_POSTGRES_LOCK_KEY"] = 100	1✔
16
17	USE_SINGLE_TABLE = False	1✔
18
19	# - DEFAULT_PREFIX: prefix to be prepended.
20	# - PREPEND_PREFIX: the prefix is preprended to the generated GUID when a
21	# new record is created WITHOUT a provided GUID.
22	# - ADD_PREFIX_ALIAS: aliases are created for new records - "<PREFIX><GUID>".
23	# Do NOT set both ADD_PREFIX_ALIAS and PREPEND_PREFIX to True, or aliases
24	# will be created as "<PREFIX><PREFIX><GUID>".
25	if USE_SINGLE_TABLE is True:	1✔
26	CONFIG["INDEX"] = {	×
27	"driver": SingleTableSQLAlchemyIndexDriver(
28	"postgresql://postgres:postgres@localhost:5432/indexd_tests", # pragma: allowlist secret
29	echo=True,
30	index_config={
31	"DEFAULT_PREFIX": "testprefix/",
32	"PREPEND_PREFIX": True,
33	"ADD_PREFIX_ALIAS": False,
34	},
35	)
36	}
37	else:
38	CONFIG["INDEX"] = {	1✔
39	"driver": SQLAlchemyIndexDriver(
40	"postgresql://postgres:postgres@localhost:5432/indexd_tests", # pragma: allowlist secret
41	echo=True,
42	index_config={
43	"DEFAULT_PREFIX": "testprefix/",
44	"PREPEND_PREFIX": True,
45	"ADD_PREFIX_ALIAS": False,
46	},
47	)
48	}
49
50	CONFIG["ALIAS"] = {	1✔
51	"driver": SQLAlchemyAliasDriver(
52	"postgresql://postgres:postgres@localhost:5432/indexd_tests", # pragma: allowlist secret
53	echo=True,
54	)
55	}
56
57
58	CONFIG["DIST"] = [	1✔
59	{
60	"name": "Other IndexD",
61	"host": "https://indexd.example.io/index/",
62	"hints": [".ROCKS."],
63	"type": "indexd",
64	},
65	{"name": "DX DOI", "host": "https://doi.org/", "hints": ["10\..*"], "type": "doi"},
66	{
67	"name": "DOS System",
68	"host": "https://example.com/api/ga4gh/dos/v1/",
69	"hints": [],
70	"type": "dos",
71	},
72	]
73
74	# Maximum number of objects in a single bulk DRS request.
75	# Used in GET /service-info response and enforced by bulk endpoints.
76	CONFIG["MAX_BULK_REQUEST_LENGTH"] = 100	1✔
77
78	CONFIG["DRS_SERVICE_INFO"] = {	1✔
79	"name": "DRS System",
80	"type": {
81	"group": "org.ga4gh",
82	"artifact": "drs",
83	"version": "1.5.0",
84	},
85	"version": "1.5.0",
86	"id": "com.example",
87	"organization": {
88	"name": "CTDS",
89	"url": "http://example.com/",
90	},
91	}
92
93	cloud_provider_map = environ.get("CLOUD_PROVIDER_MAP", None)	1✔
94	if cloud_provider_map:	1✔
95	CONFIG["CLOUD_PROVIDER_MAP"] = json.loads(cloud_provider_map)	×
96	else:
97	CONFIG["CLOUD_PROVIDER_MAP"] = {	1✔
98	"s3": "aws",
99	"gs": "gcp",
100	"az": "azure",
101	}
102
103	AUTH = SQLAlchemyAuthDriver(	1✔
104	"postgresql://postgres:postgres@localhost:5432/indexd_tests" # pragma: allowlist secret
105	)
106
107	settings = {"config": CONFIG, "auth": AUTH, "use_single_table": USE_SINGLE_TABLE}	1✔
108
109	CONFIG["DRS_AUTHORIZATION_METADATA"] = {	1✔
110	"/gen3/programs/a/projects/b": {
111	"supported_types": ["BearerAuth", "PassportAuth"],
112	"passport_auth_issuers": ["https://ras/foo/bar"],
113	"bearer_auth_issuers": ["https://gen3.datacommons.io"],
114	}
115	}
116
117	CONFIG["DEFAULT_BEARER_ISSUER"] = "https://gen3.datacommons.io"	1✔
118	CONFIG["DEFAULT_PASSPORT_ISSUER"] = "test_passport_default"	1✔

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