From 02db1b0b39ad62b296ed2e9b0f10c704277ef332 Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Mon, 30 Oct 2023 17:06:30 +0100 Subject: [PATCH] lint --- bbconf/__init__.py | 1 - bbconf/bbconf.py | 22 +++++++++++++++++----- bbconf/const.py | 2 ++ interactive_testing.py | 6 +++++- tests/test_bbconf.py | 27 +++++++++++++++++++++------ 5 files changed, 45 insertions(+), 13 deletions(-) diff --git a/bbconf/__init__.py b/bbconf/__init__.py index e7ad25b..153392c 100644 --- a/bbconf/__init__.py +++ b/bbconf/__init__.py @@ -3,4 +3,3 @@ from bbconf.const import * __all__ = ["BedBaseConf", "get_bedbase_cfg"] - diff --git a/bbconf/bbconf.py b/bbconf/bbconf.py index b8ee8ff..cb2645e 100644 --- a/bbconf/bbconf.py +++ b/bbconf/bbconf.py @@ -39,6 +39,7 @@ DEFAULT_HF_MODEL, DEFAULT_VEC2VEC_MODEL, DEFAULT_REGION2_VEC_MODEL, + DRS_ACCESS_URL, ) from bbconf.exceptions import MissingConfigDataError, BedBaseConfError from bbconf.helpers import raise_missing_key, get_bedbase_cfg @@ -52,8 +53,6 @@ _LOGGER = getLogger(__name__) -DRS_ACCESS_URL = "{server_url}/objects/{object_id}/access/{access_id}" - class BedBaseConf: """ @@ -596,7 +595,13 @@ def get_prefixed_uri(self, postfix: str, remote_class: str = "http") -> str: """ return os.path.join(self.prefix(remote_class), postfix) - def get_bed_drs_metadata(object_id: str) -> dict: + def get_bed_drs_metadata(self, object_id: str) -> dict: + """ + + + :param object_id: + :return: + """ bed_metadata = self.bed.retrieve(object_id) drs_dict = { "id": object_id, @@ -606,7 +611,7 @@ def get_bed_drs_metadata(object_id: str) -> dict: "access_methods": [], } # add access method for each remote class - for access_id in keys(self.config[CFG_REMOTE_KEY]): + for access_id in self.config[CFG_REMOTE_KEY].keys(): access_dict = { "type": "https", "access_id": access_id, @@ -622,7 +627,14 @@ def get_bed_drs_metadata(object_id: str) -> dict: drs_dict["access_methods"].append(access_dict) return drs_dict - def get_bed_url(object_id: str, access_id: str) -> str: + def get_bed_url(self, object_id: str, access_id: str) -> str: + """ + + + :param object_id: + :param access_id: + :return: + """ access_url = DRS_ACCESS_URL.format( server_url=self.config["access_methods"][access_id]["server_url"], object_id=object_id, diff --git a/bbconf/const.py b/bbconf/const.py index 8eba947..dd33feb 100644 --- a/bbconf/const.py +++ b/bbconf/const.py @@ -95,3 +95,5 @@ DEFAULT_HF_MODEL = "sentence-transformers/all-MiniLM-L12-v2" DEFAULT_VEC2VEC_MODEL = "databio/v2v-ChIP-atlas-hg38-ATAC" DEFAULT_REGION2_VEC_MODEL = "databio/r2v-ChIP-atlas-hg38" + +DRS_ACCESS_URL = "{server_url}/objects/{object_id}/access/{access_id}" diff --git a/interactive_testing.py b/interactive_testing.py index d9c3134..af3b934 100644 --- a/interactive_testing.py +++ b/interactive_testing.py @@ -7,10 +7,13 @@ import logging import sys + def set_up_interactive_logger(package=None) -> logging.Logger: """Set up a logger for interactive testing""" _LOGGER = logging.getLogger(package) - formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') + formatter = logging.Formatter( + "%(asctime)s - %(name)s - %(levelname)s - %(message)s" + ) stream = logging.StreamHandler(sys.stdout) stream.setFormatter(formatter) stream.setLevel(logging.DEBUG) @@ -18,6 +21,7 @@ def set_up_interactive_logger(package=None) -> logging.Logger: _LOGGER.setLevel(logging.DEBUG) return _LOGGER + _LOGGER = set_up_interactive_logger() _LOGGER.debug("Test log message") diff --git a/tests/test_bbconf.py b/tests/test_bbconf.py index 244d697..463a602 100644 --- a/tests/test_bbconf.py +++ b/tests/test_bbconf.py @@ -6,7 +6,7 @@ from bbconf import BedBaseConf, get_bedbase_cfg from bbconf.exceptions import * -from sqlmodel import Session, SQLModel, create_engine +from sqlmodel import SQLModel, create_engine from sqlmodel.main import default_registry @@ -74,7 +74,9 @@ def test_reporting_relationships(self, cfg_pth, test_data_bed, test_data_bedset) bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth)) bbc.bed.report(record_identifier="bed1", values=test_data_bed) bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset) - bbc.report_relationship(bedfile_record_id="bed1", bedset_record_id="bedset1") + bbc.report_relationship( + bedfile_record_id="bed1", bedset_record_id="bedset1" + ) def test_cant_remove_record_if_in_reltable( self, cfg_pth, test_data_bed, test_data_bedset @@ -83,7 +85,9 @@ def test_cant_remove_record_if_in_reltable( bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth)) bbc.bed.report(record_identifier="bed1", values=test_data_bed) bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset) - bbc.report_relationship(bedfile_record_id="bed1", bedset_record_id="bedset1") + bbc.report_relationship( + bedfile_record_id="bed1", bedset_record_id="bedset1" + ) with pytest.raises(IntegrityError): bbc.bed.remove(record_identifier="bed1") with pytest.raises(IntegrityError): @@ -94,7 +98,9 @@ def test_select(self, cfg_pth, test_data_bed, test_data_bedset): bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth)) bbc.bed.report(record_identifier="bed1", values=test_data_bed) bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset) - bbc.report_relationship(bedfile_record_id="bed1", bedset_record_id="bedset1") + bbc.report_relationship( + bedfile_record_id="bed1", bedset_record_id="bedset1" + ) unique_bedfiles = bbc.select_unique(table_name="bedfile__sample") assert unique_bedfiles[0].record_identifier == "bed1" @@ -108,8 +114,13 @@ def test_removal(self, cfg_pth, test_data_bed, test_data_bedset): bbc = BedBaseConf(get_bedbase_cfg(cfg=cfg_pth)) bbc.bed.report(record_identifier="bed1", values=test_data_bed) bbc.bedset.report(record_identifier="bedset1", values=test_data_bedset) - bbc.report_relationship(bedfile_record_id="bed1", bedset_record_id="bedset1",) - bbc.remove_relationship(bedset_record_id="bedset1", bedfile_record_id=["bed1"]) + bbc.report_relationship( + bedfile_record_id="bed1", + bedset_record_id="bedset1", + ) + bbc.remove_relationship( + bedset_record_id="bedset1", bedfile_record_id=["bed1"] + ) ori_cnt = bbc.bed.record_count bbc.bed.remove(record_identifier="bed1") assert ori_cnt - 1 == bbc.bed.record_count @@ -125,3 +136,7 @@ def test_config_variables_are_set(self, cfg_pth, test_data_bed, test_data_bedset assert bbc.config["qdrant"]["host"] == "localhost" assert bbc.config["path"]["region2vec"] is not None assert bbc.config["database"]["host"] in ["localhost", "127.0.0.1"] + + def test_get_bed_drs_metadata(self): + # TODO: add test + assert True