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src/wags_tails/chembl.py

@@ -3,7 +3,6 @@
 import re
 import tarfile
 from pathlib import Path
-from typing import Optional
 
 import requests
 
@@ -14,17 +13,8 @@
 class ChemblData(DataSource):
     """Provide access to ChEMBL database."""
 
-    def __init__(self, data_dir: Optional[Path] = None, silent: bool = False) -> None:
-        """Set common class parameters.
-
-        :param data_dir: direct location to store data files in, if specified. See
-            ``get_data_dir()`` in the ``storage_utils`` module for further configuration
-            details.
-        :param silent: if True, don't print any info/updates to console
-        """
-        self._src_name = "chembl"
-        self._filetype = "db"
-        super().__init__(data_dir, silent)
+    _src_name = "chembl"
+    _filetype = "db"
 
     @staticmethod
     def _get_latest_version() -> str:

src/wags_tails/do.py

@@ -3,7 +3,6 @@
 import tarfile
 from datetime import datetime
 from pathlib import Path
-from typing import Optional
 
 import requests
 
@@ -15,18 +14,9 @@
 class DoData(GitHubDataSource):
     """Provide access to human disease ontology data."""
 
-    def __init__(self, data_dir: Optional[Path] = None, silent: bool = False) -> None:
-        """Set common class parameters.
-
-        :param data_dir: direct location to store data files in, if specified. See
-            ``get_data_dir()`` in the ``storage_utils`` module for further configuration
-            details.
-        :param silent: if True, don't print any info/updates to console
-        """
-        self._src_name = "do"
-        self._filetype = "owl"
-        self._repo = "DiseaseOntology/HumanDiseaseOntology"
-        super().__init__(data_dir, silent)
+    _src_name = "do"
+    _filetype = "owl"
+    _repo = "DiseaseOntology/HumanDiseaseOntology"
 
     @staticmethod
     def _asset_handler(dl_path: Path, outfile_path: Path) -> None:

src/wags_tails/mondo.py

@@ -2,7 +2,7 @@
 import logging
 from datetime import datetime
 from pathlib import Path
-from typing import Optional, Tuple
+from typing import Tuple
 
 import requests
 
@@ -17,17 +17,9 @@
 class MondoData(GitHubDataSource):
     """Provide access to Mondo disease ontology data."""
 
-    def __init__(self, data_dir: Optional[Path] = None, silent: bool = False) -> None:
-        """Set common class parameters.
-
-        :param data_dir: direct location to store data files in, if specified. See
-            ``get_data_dir()`` in the ``storage_utils`` module for further configuration
-            details.
-        :param silent: if True, don't print any info/updates to console
-        """
-        self._src_name = "mondo"
-        self._repo = "monarch-initiative/mondo"
-        super().__init__(data_dir, silent)
+    _src_name = "mondo"
+    _filetype = "owl"
+    _repo = "monarch-initiative/mondo"
 
     @staticmethod
     def _get_latest_version() -> Tuple[str, str]:

src/wags_tails/ncit.py

@@ -1,7 +1,6 @@
 """Provide source fetching for NCI Thesaurus."""
 import re
 from pathlib import Path
-from typing import Optional
 
 import requests
 
@@ -12,17 +11,8 @@
 class NcitData(DataSource):
     """Provide access to NCI Thesaurus database."""
 
-    def __init__(self, data_dir: Optional[Path] = None, silent: bool = False) -> None:
-        """Set common class parameters.
-
-        :param data_dir: direct location to store data files in, if specified. See
-            ``get_data_dir()`` in the ``storage_utils`` module for further configuration
-            details.
-        :param silent: if True, don't print any info/updates to console
-        """
-        self._src_name = "ncit"
-        self._filetype = "owl"
-        super().__init__(data_dir, silent)
+    _src_name = "ncit"
+    _filetype = "owl"
 
     @staticmethod
     def _get_latest_version() -> str:

src/wags_tails/oncotree.py

@@ -1,34 +1,19 @@
 """Provide access to Oncotree data."""
-import logging
 from datetime import datetime
 from pathlib import Path
-from typing import Optional
 
 import requests
 
 from .base_source import DataSource, RemoteDataError
 from .utils.downloads import download_http
 from .utils.versioning import DATE_VERSION_PATTERN
 
-_logger = logging.getLogger(__name__)
-
 
 class OncoTreeData(DataSource):
     """Provide access to OncoTree data."""
 
-    def __init__(self, data_dir: Optional[Path] = None, silent: bool = False) -> None:
-        """Set common class parameters.
-
-        :param data_dir: direct location to store data files in. If not provided, tries
-            to find a "oncotree" subdirectory within the path at environment variable
-            $WAGS_TAILS_DIR, or within a "wags_tails" subdirectory under environment
-            variables $XDG_DATA_HOME or $XDG_DATA_DIRS, or finally, at
-            ``~/.local/share/``
-        :param silent: if True, don't print any info/updates to console
-        """
-        self._src_name = "oncotree"
-        self._filetype = "json"
-        super().__init__(data_dir, silent)
+    _src_name = "oncotree"
+    _filetype = "json"
 
     def _get_latest_version(self) -> str:
         """Retrieve latest version value

src/wags_tails/utils/downloads.py

@@ -17,8 +17,8 @@ def handle_zip(dl_path: Path, outfile_path: Path) -> None:
     """Provide simple callback function to extract the largest file within a given
     zipfile and save it within the appropriate data directory.
 
-    :param Path dl_path: path to temp data file
-    :param Path outfile_path: path to save file within
+    :param dl_path: path to temp data file
+    :param outfile_path: path to save file within
     """
     with zipfile.ZipFile(dl_path, "r") as zip_ref:
         if len(zip_ref.filelist) > 1:
@@ -46,6 +46,7 @@ def download_http(
     :param headers: Any needed HTTP headers to include in request
     :param handler: provide if downloaded file requires additional action, e.g.
         it's a zip file.
+    :param tqdm_params: Optional TQDM configuration.
     """
     if not tqdm_params:
         tqdm_params = {}
@@ -60,12 +61,12 @@ def download_http(
         total_size = int(r.headers.get("content-length", 0))
         with open(dl_path, "wb") as h:
             if not tqdm_params["disable"]:
-                if "apiKey" in url:
+                if "apiKey" in url:  # don't print RxNorm API key
                     pattern = r"&apiKey=.{8}-.{4}-.{4}-.{4}-.{12}"
                     print_url = re.sub(pattern, "", os.path.basename(url))
-                    print(f"Downloading {print_url}")
+                    print(f"Downloading {print_url}...")
                 else:
-                    print(f"Downloading {os.path.basename(url)}")
+                    print(f"Downloading {os.path.basename(url)}...")
             with tqdm(
                 total=total_size,
                 **tqdm_params,