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reformat repo #77

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Apr 3, 2024
Merged

reformat repo #77

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20 changes: 7 additions & 13 deletions bento_beacon/app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,21 +26,14 @@

# find path for beacon-v2 spec
app_parent_dir = os.path.dirname(app.root_path)
beacon_request_spec_uri = urlunsplit(
("file", app_parent_dir, REQUEST_SPEC_RELATIVE_PATH, "", ""))
app.config.from_mapping(
BEACON_REQUEST_SPEC_URI=beacon_request_spec_uri
)
beacon_request_spec_uri = urlunsplit(("file", app_parent_dir, REQUEST_SPEC_RELATIVE_PATH, "", ""))
app.config.from_mapping(BEACON_REQUEST_SPEC_URI=beacon_request_spec_uri)

app.config.from_object(Config)

# all logs are printed in dev mode regardless of level
logging.basicConfig(
level=logging.INFO,
format="%(asctime)s [%(levelname)s] %(message)s",
handlers=[
logging.StreamHandler()
]
level=logging.INFO, format="%(asctime)s [%(levelname)s] %(message)s", handlers=[logging.StreamHandler()]
)

# attach authz middleware to the Flask app
Expand Down Expand Up @@ -72,7 +65,7 @@
count_threshold = None
retries = 0
max_retries = current_app.config["MAX_RETRIES_FOR_CENSORSHIP_PARAMS"]
for tries in range(max_retries+1):
for tries in range(max_retries + 1):
current_app.logger.info(f"calling katsu for censorship parameters (try={tries})")
try:
max_filters, count_threshold = katsu_censorship_settings()
Expand All @@ -83,14 +76,15 @@
# swallow exception and continue retries
current_app.logger.error(f"error calling katsu for censorship settings: {e}")

sleep(5 + 5*tries)
sleep(5 + 5 * tries)

# either params retrieved or we hit max retries
if max_filters is None or count_threshold is None:
current_app.logger.error("unable to retrieve censorship settings from katsu")
else:
current_app.logger.info(
f"retrieved censorship params: max_filter {max_filters}, count_threshold: {count_threshold}")
f"retrieved censorship params: max_filter {max_filters}, count_threshold: {count_threshold}"
)

# save even if None
set_censorship_settings(max_filters, count_threshold)
Expand Down
2 changes: 1 addition & 1 deletion bento_beacon/authz/middleware.py
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Original file line number Diff line number Diff line change
Expand Up @@ -15,7 +15,7 @@
Config.AUTHZ_URL,
enabled=Config.AUTHZ_ENABLED,
beacon_meta_callback=middleware_meta_callback,
debug_mode=Config.BENTO_DEBUG
debug_mode=Config.BENTO_DEBUG,
)


Expand Down
110 changes: 52 additions & 58 deletions bento_beacon/config_files/config.py
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Original file line number Diff line number Diff line change
Expand Up @@ -17,13 +17,16 @@ class Config:
"biosamples": "count",
"cohorts": "record",
"datasets": "record",
"info": "record"
"info": "record",
}

DEFAULT_PAGINATION_PAGE_SIZE = 10

BENTO_DEBUG = os.environ.get("BENTO_DEBUG", os.environ.get(
"FLASK_DEBUG", "false")).strip().lower() in ('true', '1', 't')
BENTO_DEBUG = os.environ.get("BENTO_DEBUG", os.environ.get("FLASK_DEBUG", "false")).strip().lower() in (
"true",
"1",
"t",
)

BENTO_DOMAIN = os.environ.get("BENTOV2_DOMAIN")
BEACON_BASE_URL = os.environ.get("BEACON_BASE_URL")
Expand All @@ -33,7 +36,7 @@ class Config:
BEACON_ID = ".".join(reversed(BENTO_DOMAIN.split("."))) + ".beacon"

BEACON_NAME = os.environ.get("BENTO_PUBLIC_CLIENT_NAME", "Bento") + " Beacon"
BEACON_UI_ENABLED = os.environ.get("BENTO_BEACON_UI_ENABLED").strip().lower() in ('true', '1', 't')
BEACON_UI_ENABLED = os.environ.get("BENTO_BEACON_UI_ENABLED").strip().lower() in ("true", "1", "t")
BEACON_UI_URL = BENTO_PUBLIC_URL + "/#/en/beacon"

ENTRY_TYPES_DETAILS = {
Expand All @@ -44,10 +47,10 @@ class Config:
"defaultSchema": {
"id": "ga4gh-beacon-biosample-v2.0.0",
"name": "Default schema for biosamples",
"referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/biosamples/defaultSchema.json",
"schemaVersion": "v2.0.0"
"referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/biosamples/defaultSchema.json",
"schemaVersion": "v2.0.0",
},
"partOfSpecification": "Beacon v2.0.0"
"partOfSpecification": "Beacon v2.0.0",
},
"cohorts": {
"entryType": "cohort",
Expand All @@ -56,84 +59,80 @@ class Config:
"defaultSchema": {
"id": "ga4gh-beacon-cohort-v2.0.0",
"name": "Default schema for cohorts",
"referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/cohorts/defaultSchema.json",
"schemaVersion": "v2.0.0"
"referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/cohorts/defaultSchema.json",
"schemaVersion": "v2.0.0",
},
"partOfSpecification": "Beacon v2.0.0"

"partOfSpecification": "Beacon v2.0.0",
},
"datasets": {
"entryType": "dataset",
"name": "Dataset",
"ontologyTermForThisType": {"id": "NCIT:C47824", "label": "Data set"},
"ontologyTermForThisType": {"id": "NCIT:C47824", "label": "Data set"},
"defaultSchema": {
"id": "ga4gh-beacon-dataset-v2.0.0",
"name": "Default schema for datasets",
"referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/datasets/defaultSchema.json",
"schemaVersion": "v2.0.0"
"referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/datasets/defaultSchema.json",
"schemaVersion": "v2.0.0",
},
"partOfSpecification": "Beacon v2.0.0"

"partOfSpecification": "Beacon v2.0.0",
},
"individuals": {
"entryType": "individual",
"name": "Individual",
"ontologyTermForThisType": {"id": "NCIT:C25190", "label": "Person"},
"ontologyTermForThisType": {"id": "NCIT:C25190", "label": "Person"},
"defaultSchema": {
"id": "phenopacket-v2",
"name": "phenopacket v2",
"referenceToSchemaDefinition": f"{BEACON_BASE_URL}/individual_schema",
"schemaVersion": "v2.0.0"
"referenceToSchemaDefinition": f"{BEACON_BASE_URL}/individual_schema",
"schemaVersion": "v2.0.0",
},
"partOfSpecification": "Phenopacket v1"
"partOfSpecification": "Phenopacket v1",
},
"variants": {
"entryType": "genomicVariation",
"name": "Genomic Variant",
"ontologyTermForThisType": {"id": "ENSGLOSSARY:0000092", "label": "Variant"},
"ontologyTermForThisType": {"id": "ENSGLOSSARY:0000092", "label": "Variant"},
"defaultSchema": {
"id": "ga4gh-beacon-variant-v2.0.0",
"name": "Default schema for a genomic variation",
"referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json",
"schemaVersion": "v2.0.0"
"referenceToSchemaDefinition": f"{GA4GH_BEACON_REPO_URL}/main/models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json",
"schemaVersion": "v2.0.0",
},
"partOfSpecification": "Beacon v2.0.0"

}
"partOfSpecification": "Beacon v2.0.0",
},
}

INFO_ENDPOINTS_SCHEMAS = {
"/": {
"/": {
"entityType": "info",
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconInfoResponse.json"
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconInfoResponse.json",
},
"/configuration": {
"entityType": "configuration",
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconConfigurationResponse.json"
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconConfigurationResponse.json",
},
"/entry_types": {
"entityType": "entryType",
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconEntryTypesResponse.json"
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconEntryTypesResponse.json",
},
"/filtering_terms": {
"entityType": "filteringTerm",
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconFilteringTermsResponse.json"
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconFilteringTermsResponse.json",
},
"/info": {
"entityType": "info",
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconInfoResponse.json"
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconInfoResponse.json",
},
"/map": {
"entityType": "map",
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconMapResponse.json"
"schema": f"{GA4GH_BEACON_REPO_URL}/main/framework/json/responses/beaconMapResponse.json",
},
"/overview": {}
"/overview": {},
}
# -------------------
# katsu
# -------------------
# katsu

KATSU_BASE_URL = os.environ.get(
"KATSU_BASE_URL")
KATSU_BASE_URL = os.environ.get("KATSU_BASE_URL")
KATSU_BIOSAMPLES_ENDPOINT = "/api/biosamples"
KATSU_INDIVIDUALS_ENDPOINT = "/api/individuals"
KATSU_BATCH_INDIVIDUALS_ENDPOINT = "/api/batch/individuals"
Expand All @@ -152,45 +151,40 @@ class Config:
KATSU_PUBLIC_OVERVIEW = "/api/public_overview"
KATSU_TIMEOUT = int(os.environ.get("BEACON_KATSU_TIMEOUT", 180))

MAP_EXTRA_PROPERTIES_TO_INFO = os.environ.get(
"MAP_EXTRA_PROPERTIES_TO_INFO", True)
MAP_EXTRA_PROPERTIES_TO_INFO = os.environ.get("MAP_EXTRA_PROPERTIES_TO_INFO", True)

PHENOPACKETS_SCHEMA_REFERENCE = {
"entityType": "individual",
"schema": "phenopackets v1"
}
PHENOPACKETS_SCHEMA_REFERENCE = {"entityType": "individual", "schema": "phenopackets v1"}

MAX_RETRIES_FOR_CENSORSHIP_PARAMS = 2
# -------------------
# gohan
# -------------------
# gohan

GOHAN_BASE_URL = os.environ.get("GOHAN_BASE_URL")
GOHAN_SEARCH_ENDPOINT = "/variants/get/by/variantId"
GOHAN_COUNT_ENDPOINT = "/variants/count/by/variantId"
GOHAN_OVERVIEW_ENDPOINT = "/variants/overview"
GOHAN_TIMEOUT = int(os.environ.get("BEACON_GOHAN_TIMEOUT", 60))

# -------------------
# drs
# -------------------
# drs

DRS_URL = os.environ.get("DRS_URL")

# -------------------
# authorization
# -------------------
# authorization

AUTHZ_URL: str = os.environ.get("BENTO_AUTHZ_SERVICE_URL", "")
AUTHZ_ENABLED: bool = os.environ.get("AUTHZ_ENABLED", "true").strip().lower() in ("true", "1", "yes")

# -------------------
# handle injected config files
# a) obtain reference to the expected configuration files' location by
# using the programmable env variable `CONFIG_ABSOLUTE_PATH` if it exists, or
# b) default to using "this file's directory" as the reference to where
# configuration files are expected to be located
# -------------------
# handle injected config files
# a) obtain reference to the expected configuration files' location by
# using the programmable env variable `CONFIG_ABSOLUTE_PATH` if it exists, or
# b) default to using "this file's directory" as the reference to where
# configuration files are expected to be located
def retrieve_config_json(filename):
# TODO: abstract out CONFIG_PATH if needed
config_path = os.environ.get(
"CONFIG_ABSOLUTE_PATH", os.path.dirname(os.path.abspath(__file__)))
config_path = os.environ.get("CONFIG_ABSOLUTE_PATH", os.path.dirname(os.path.abspath(__file__)))
print(f"Searching for file {filename} in {config_path}")
file_path = os.path.join(config_path, filename)
try:
Expand Down
10 changes: 5 additions & 5 deletions bento_beacon/endpoints/biosamples.py
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Expand Up @@ -5,26 +5,26 @@
biosamples = Blueprint("biosamples", __name__)


@biosamples.route("/biosamples", methods=['GET', 'POST'])
@biosamples.route("/biosamples", methods=["GET", "POST"])
def get_biosamples(): # TODO: authz
raise NotImplemented()


@biosamples.route("/biosamples/<id>", methods=['GET', 'POST'])
@biosamples.route("/biosamples/<id>", methods=["GET", "POST"])
def get_katsu_biosamples_by_id(id): # TODO: authz
raise NotImplemented()


@biosamples.route("/biosamples/<id>/g_variants", methods=['GET', 'POST'])
@biosamples.route("/biosamples/<id>/g_variants", methods=["GET", "POST"])
def variants_by_biosample(id): # TODO: authz
raise NotImplemented()


@biosamples.route("/biosamples/<id>/analyses", methods=['GET', 'POST'])
@biosamples.route("/biosamples/<id>/analyses", methods=["GET", "POST"])
def analyses_by_biosample(id): # TODO: authz
raise NotImplemented()


@biosamples.route("/biosamples/<id>/runs", methods=['GET', 'POST'])
@biosamples.route("/biosamples/<id>/runs", methods=["GET", "POST"])
def runs_by_biosample(id): # TODO: authz
raise NotImplemented()
4 changes: 2 additions & 2 deletions bento_beacon/endpoints/cohorts.py
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Expand Up @@ -5,14 +5,14 @@
cohorts = Blueprint("cohorts", __name__)


@cohorts.route("/cohorts", methods=['GET', 'POST'])
@cohorts.route("/cohorts", methods=["GET", "POST"])
@authz_middleware.deco_public_endpoint
def get_cohorts():
cohorts = current_app.config["BEACON_COHORT"]
return beacon_collections_response({"collections": cohorts})


@cohorts.route("/cohorts/<id>", methods=['GET', 'POST'])
@cohorts.route("/cohorts/<id>", methods=["GET", "POST"])
@authz_middleware.deco_public_endpoint
def get_cohort_by_id(id):
cohorts = current_app.config["BEACON_COHORT"]
Expand Down
4 changes: 2 additions & 2 deletions bento_beacon/endpoints/datasets.py
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Expand Up @@ -7,15 +7,15 @@
datasets = Blueprint("datasets", __name__)


@datasets.route("/datasets", methods=['GET', 'POST'])
@datasets.route("/datasets", methods=["GET", "POST"])
@authz_middleware.deco_public_endpoint # TODO: authz - more flexibility in what is visible (?)
def get_datasets():
k_datasets = katsu_datasets()
datasets_beacon_format = list(map(katsu_to_beacon_dataset_mapping, k_datasets))
return beacon_collections_response({"collections": datasets_beacon_format})


@datasets.route("/datasets/<id>", methods=['GET', 'POST'])
@datasets.route("/datasets/<id>", methods=["GET", "POST"])
@authz_middleware.deco_public_endpoint # TODO: authz - more flexibility in what is visible (?)
def get_datasets_by_id(id):
k_dataset = katsu_datasets(id)
Expand Down
15 changes: 6 additions & 9 deletions bento_beacon/endpoints/individuals.py
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Expand Up @@ -4,10 +4,7 @@
)
from flask import Blueprint
from functools import reduce
from ..authz.middleware import (
authz_middleware,
check_permission
)
from ..authz.middleware import authz_middleware, check_permission
from ..utils.beacon_request import (
query_parameters_from_request,
summary_stats_requested,
Expand All @@ -18,13 +15,13 @@
add_overview_stats_to_response,
zero_count_response,
build_query_response,
beacon_result_set_response
beacon_result_set_response,
)
from ..utils.katsu_utils import (
katsu_filters_and_sample_ids_query,
katsu_total_individuals_count,
search_from_config,
phenopackets_for_ids
phenopackets_for_ids,
)
from ..utils.search import biosample_id_search
from ..utils.handover_utils import handover_for_ids
Expand All @@ -33,7 +30,7 @@
individuals = Blueprint("individuals", __name__)


@individuals.route("/individuals", methods=['GET', 'POST'])
@individuals.route("/individuals", methods=["GET", "POST"])
def get_individuals():
variants_query, phenopacket_filters, experiment_filters, config_filters = query_parameters_from_request()

Expand Down Expand Up @@ -124,7 +121,7 @@ def individuals_full_results(ids):


# forbidden / unauthorized if no permissions
@individuals.route("/individuals/<id>", methods=['GET', 'POST'])
@individuals.route("/individuals/<id>", methods=["GET", "POST"])
@authz_middleware.deco_require_permissions_on_resource({P_QUERY_DATA})
def individual_by_id(id):
result_sets, numTotalResults = individuals_full_results([id])
Expand All @@ -133,7 +130,7 @@ def individual_by_id(id):
# only authorized users will get 404 here, so this can't be used to probe ids
if not result_sets:
raise NotFoundException()

return beacon_result_set_response(result_sets, numTotalResults)


Expand Down
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