enh: simplify by using class variable in place of string

Use class variable for defining the default download hierarchy template.
This simplifies updating the default template, improves readability and
will allow for specifying alternative preset templates more easily.

Author: fedorov

idc_index/index.py

@@ -4,7 +4,6 @@
 
 import logging
 import os
-import re
 import shutil
 import subprocess
 import tempfile
@@ -27,6 +26,10 @@
 
 
 class IDCClient:
+    DOWNLOAD_HIERARCHY_DEFAULT = (
+        "%collection_id/%PatientID/%StudyInstanceUID/%Modality_%SeriesInstanceUID"
+    )
+
     def __init__(self):
         file_path = idc_index_data.IDC_INDEX_PARQUET_FILEPATH
 
@@ -487,7 +490,7 @@ def _validate_update_manifest_and_get_download_size(
             validate_manifest (bool, optional): If True, validates the manifest for any errors. Defaults to True.
             show_progress_bar (bool, optional): If True, tracks the progress of download
             use_s5cmd_sync (bool, optional): If True, will use s5cmd sync operation instead of cp when downloadDirectory is not empty; this can significantly improve the download speed if the content is partially downloaded
-            dirTemplate (str): A template string for the directory path. Must start with %. Defaults to %collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID. It can contain attributes (PatientID, collection_id, Modality, StudyInstanceUID, SeriesInstanceUID) wrapped in '%'. Special characters can be used as connectors: '-' (hyphen), '/' (slash for subdirectories), '_' (underscore). Can be disabled by None.
+            dirTemplate (str): A template string for the directory path. Must start with %. Defaults to index.DOWNLOAD_HIERARCHY_DEFAULT. It can contain attributes (PatientID, collection_id, Modality, StudyInstanceUID, SeriesInstanceUID) wrapped in '%'. Special characters can be used as connectors: '-' (hyphen), '/' (slash for subdirectories), '_' (underscore). Can be disabled by None.
 
         Returns:
             total_size (float): The total size of all series in the manifest file.
@@ -709,7 +712,7 @@ def _generate_sql_concat_for_building_directory(dirTemplate, downloadDir):
         # CONCAT command may contain empty strings, and they are not harmless -
         # duckdb does not like them!
         # NB: double-quotes are not allowed by duckdb!
-        concat_command = "CONCAT('" + concat_command + "')"
+        concat_command = f"CONCAT('{downloadDir}/','" + concat_command + "')"
         concat_command = concat_command.replace(",''", "")
         concat_command = concat_command.replace("'',", "")
         concat_command = concat_command.replace(",'',", "")
@@ -791,7 +794,7 @@ def _parse_s5cmd_sync_output_and_generate_synced_manifest(
         Args:
             output (str): The output of s5cmd sync --dry-run command.
             downloadDir (str): The directory to download the files to.
-            dirTemplate (str): A template string for the directory path. Defaults to %collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID. It can contain attributes (PatientID, collection_id, Modality, StudyInstanceUID, SeriesInstanceUID) wrapped in '%'. Special characters can be used as connectors: '-' (hyphen), '/' (slash for subdirectories), '_' (underscore). Can be disabled by None.
+            dirTemplate (str): A template string for the directory path.
 
         Returns:
             Path: The path to the generated synced manifest file.
@@ -904,7 +907,7 @@ def _s5cmd_run(
             quiet (bool, optional): If True, suppresses the stdout and stderr of the s5cmd command.
             show_progress_bar (bool, optional): If True, tracks the progress of download
             use_s5cmd_sync (bool, optional): If True, will use s5cmd sync operation instead of cp when downloadDirectory is not empty; this can significantly improve the download speed if the content is partially downloaded
-            dirTemplate (str): A template string for the directory path. Defaults to %collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID. It can contain attributes (PatientID, collection_id, Modality, StudyInstanceUID, SeriesInstanceUID) wrapped in '%'. Special characters can be used as connectors: '-' (hyphen), '/' (slash for subdirectories), '_' (underscore). Can be disabled by None.
+            dirTemplate (str): A template string for the directory path.
 
         Raises:
             subprocess.CalledProcessError: If the s5cmd command fails.
@@ -1079,7 +1082,7 @@ def download_from_manifest(
         validate_manifest: bool = True,
         show_progress_bar: bool = True,
         use_s5cmd_sync: bool = False,
-        dirTemplate="%collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID",
+        dirTemplate=DOWNLOAD_HIERARCHY_DEFAULT,
     ) -> None:
         """
         Download the manifest file. In a series of steps, the manifest file
@@ -1094,7 +1097,7 @@ def download_from_manifest(
             validate_manifest (bool, optional): If True, validates the manifest for any errors. Defaults to True.
             show_progress_bar (bool, optional): If True, tracks the progress of download
             use_s5cmd_sync (bool, optional): If True, will use s5cmd sync operation instead of cp when downloadDirectory is not empty; this can significantly improve the download speed if the content is partially downloaded
-            dirTemplate (str): A template string for the directory path. Defaults to %collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID. It can contain attributes (PatientID, collection_id, Modality, StudyInstanceUID, SeriesInstanceUID) wrapped in '%'. Special characters can be used as connectors: '-' (hyphen), '/' (slash for subdirectories), '_' (underscore). Can be disabled by None.
+            dirTemplate (str): A template string for the directory path. Defaults to index.DOWNLOAD_HIERARCHY_DEFAULT set to %collection_id/%PatientID/%StudyInstanceUID/%Modality_%SeriesInstanceUID. It can contain attributes (PatientID, collection_id, Modality, StudyInstanceUID, SeriesInstanceUID) prefixed by '%'. The following special characters can be used as connectors: '-' (hyphen), '/' (slash for subdirectories), '_' (underscore). When set to None all files will be downloaded to the download directory with no subdirectories.
 
         Raises:
             ValueError: If the download directory does not exist.
@@ -1144,8 +1147,7 @@ def download_from_selection(
         quiet=True,
         show_progress_bar=True,
         use_s5cmd_sync=False,
-        # TODO: replace with class variables, have more than one preset
-        dirTemplate="%collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID",
+        dirTemplate=DOWNLOAD_HIERARCHY_DEFAULT,
     ):
         """Download the files corresponding to the selection. The filtering will be applied in sequence (but does it matter?) by first selecting the collection(s), followed by
         patient(s), study(studies) and series. If no filtering is applied, all the files will be downloaded.
@@ -1290,7 +1292,7 @@ def download_dicom_series(
         quiet=True,
         show_progress_bar=True,
         use_s5cmd_sync=False,
-        dirTemplate="%collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID",
+        dirTemplate=DOWNLOAD_HIERARCHY_DEFAULT,
     ) -> None:
         """
         Download the files corresponding to the seriesInstanceUID to the specified directory.
@@ -1328,7 +1330,7 @@ def download_dicom_studies(
         quiet=True,
         show_progress_bar=True,
         use_s5cmd_sync=False,
-        dirTemplate="%collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID",
+        dirTemplate=DOWNLOAD_HIERARCHY_DEFAULT,
     ) -> None:
         """
         Download the files corresponding to the studyInstanceUID to the specified directory.
@@ -1366,7 +1368,7 @@ def download_dicom_patients(
         quiet=True,
         show_progress_bar=True,
         use_s5cmd_sync=False,
-        dirTemplate="%collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID",
+        dirTemplate=DOWNLOAD_HIERARCHY_DEFAULT,
     ) -> None:
         """
         Download the files corresponding to the studyInstanceUID to the specified directory.
@@ -1404,7 +1406,7 @@ def download_collection(
         quiet=True,
         show_progress_bar=True,
         use_s5cmd_sync=False,
-        dirTemplate="%collection_id/%PatientID/%Modality/%StudyInstanceUID/%SeriesInstanceUID",
+        dirTemplate=DOWNLOAD_HIERARCHY_DEFAULT,
     ) -> None:
         """
         Download the files corresponding to the studyInstanceUID to the specified directory.