Multi study ingest & export (#152)

* create multiple studies

* improve ingest error reporting in the terminal

* cleaned up imports

* updated export test output with accession id nested json

* added try catch & logging function to all attempts at creating models

* updated logger name and fixed classes being passed through to logging

bia-export/bia_export/cli.py

@@ -3,7 +3,9 @@
 from rich.logging import RichHandler
 from typing_extensions import Annotated
 from pathlib import Path
-from .website_conversion import create_study
+from .website_conversion import create_studies
+from typing import List
+import json
 
 logging.basicConfig(
     level="NOTSET", format="%(message)s", datefmt="[%X]", handlers=[RichHandler()]
@@ -15,17 +17,17 @@
 
 @app.command()
 def website_study(
-    accession_id: Annotated[str, typer.Argument(help="Accession ID of the study to export")],
+    accession_id_list: Annotated[List[str], typer.Argument(help="Accession IDs of the studies to export")],
     root_directory: Annotated[Path, typer.Option("--root", "-r", help="If root directory specified then use files there, rather than calling API")] = None,
     output_filename: Annotated[Path, typer.Option("--out_file", "-o",)] = Path("bia-images-export.json")
     ):
 
     abs_root = root_directory.resolve()
-    study = create_study(accession_id, abs_root)
+    studies_map = create_studies(accession_id_list, abs_root)
 
     logging.info(f"Writing study info to {output_filename.absolute()}")
     with open(output_filename, "w") as output:
-        output.write(study.model_dump_json(indent=4)) 
+        output.write(json.dumps(studies_map, indent=4))
 
 
 @app.command()

bia-export/bia_export/website_conversion.py

@@ -56,6 +56,14 @@ def find_associated_objects(
     return linked_object
 
 
+def create_studies(accession_id_list: str, root_directory: Path) -> dict:
+    study_map = {}
+    for accession_id in accession_id_list:
+        study  = create_study(accession_id, root_directory)
+        study_map[accession_id] = study.model_dump(mode='json')
+    return study_map
+
+
 def create_study(accession_id: str, root_directory: Path) -> Study:
 
     if root_directory:
@@ -171,7 +179,7 @@ def process_details_section(
             eid_dict["specimen_growth_protocol"] = process_details_section(
                 root_directory,
                 accession_id,
-                detail_map[BioSample],
+                detail_map[SpecimenGrowthProtocol],
                 association_by_type["specimen"],
             )
             eid_dict["acquisition_process"] = process_details_section(