lint

databio · Oct 30, 2023 · 02db1b0 · 02db1b0
1 parent 252e592
commit 02db1b0
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Showing 5 changed files with 45 additions and 13 deletions.
diff --git 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
@@ -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
@@ -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
@@ -7,17 +7,21 @@
 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)
     _LOGGER.addHandler(stream)
     _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
@@ -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
Original file line number	Diff line number	Diff line change
Expand Up		@@ -3,4 +3,3 @@
		from bbconf.const import *

		__all__ = ["BedBaseConf", "get_bedbase_cfg"]