25189645180

Committed 30 Apr 2026 09:13PM UTC coverage: 87.432% (+0.08%) from 87.353%

Build # 25189645180

Build Type

Pull #441

github

Committed by

web-flow

Commit Message

Merge 73bd004c0 into f8372f13b

Pull Request Pull Request #441: Feat/drs 1.5

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3075 of 3517 relevant lines covered (87.43%)

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91.67

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
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}

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

uc-cdis / indexd / 25189645180

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