Removed code for downloading resources via schug

CHANGELOG.md

@@ -7,6 +7,8 @@
 - To avoid timeout errors, update genes, transcripts exons only from pre-downloaded files from schug
 - Documentation on how to update genes, transcripts and exons database tables
 - Renamed Pydantic `orm_mode` config param to `model_config`
+### Removed
+- Code for downloading resources from Ensembl using the schug library
 
 ## [3.1]
 ### Changed

src/chanjo2/meta/handle_load_intervals.py

@@ -1,13 +1,9 @@
 import logging
 from typing import Iterator, List, Optional, Union
 
-import requests
-from schug.load.biomart import EnsemblBiomartClient
-from schug.models.common import Build as SchugBuild
 from sqlalchemy.orm import Session
 
 from chanjo2.constants import (
-    ENSEMBL_RESOURCE_CLIENT,
     EXONS_FILE_HEADER,
     GENES_FILE_HEADER,
     TRANSCRIPTS_FILE_HEADER,
@@ -32,17 +28,6 @@
 END_OF_PARSED_FILE: str = "[success]"
 
 
-def read_resource_lines(build: Builds, interval_type: IntervalType) -> Iterator[str]:
-    """Returns lines of a remote Ensembl Biomart resource (genes, transcripts or exons) in a given genome build."""
-
-    shug_client: EnsemblBiomartClient = ENSEMBL_RESOURCE_CLIENT[interval_type](
-        build=SchugBuild(build)
-    )
-    url: str = shug_client.build_url(xml=shug_client.xml)
-    response: requests.models.responses = requests.get(url, stream=True)
-    return response.iter_lines(decode_unicode=True)
-
-
 def _replace_empty_cols(line: str, nr_expected_columns: int) -> List[Union[str, None]]:
     """Split line into columns, replacing empty columns with None values."""
     cols = [

tests/src/chanjo2/endpoints/test_intervals.py

@@ -19,8 +19,6 @@
     BUILD_TRANSCRIPTS_RESOURCE,
 )
 
-MOCKED_FILE_PARSER = "chanjo2.meta.handle_load_intervals.read_resource_lines"
-
 
 @pytest.mark.parametrize("build, path", BUILD_GENES_RESOURCE)
 def test_load_genes(