Updated based on builder changes to place encrypted in graph and tidy…

… up from RO-Crate group

pyproject.toml

@@ -7,7 +7,7 @@ readme = "README.md"
 packages = [{include = "src"}]
 
 [tool.poetry.dependencies]
-python = ">=3.11,<3.12"
+python = ">=3.11,<3.12.4"
 passpy = "^1.0.2"
 ldap3 = "^2.9.1"
 python-gnupg = "^0.5.1"
@@ -29,8 +29,9 @@ backoff = "^2.2.1"
 requests = "^2.31.0"
 build = "^1.1.1"
 pydantic-settings = "^2.2.1"
-ro-crate-py = {git = "https://github.com/UoA-eResearch/ro-crate-py.git",  branch = "encrypted-metadata"}
-mytardis-rocrate-builder = {git = "https://github.com/JLoveUOA/mytardis_rocrate_builder"}
+mytardis-rocrate-builder = {git = "https://github.com/JLoveUOA/mytardis_rocrate_builder", branch="optional-identifiers"}
+ro-crate-py = {git = "https://github.com/UoA-eResearch/ro-crate-py.git",  branch = "move-encrypted-into-graph"}
+numpy = "^2.0.0"
 
 [tool.poetry.group.dev.dependencies]
 pylint = "^3.1.0"

src/cli/main.py

@@ -17,6 +17,7 @@
     archive_crate,
     bagit_crate,
     write_crate,
+    bulk_encrypt_file
 )
 from rocrate.rocrate import ROCrate
 from slugify import slugify
@@ -171,6 +172,9 @@ def abi(
 )
 @OPTION_COLLECT_ALL
 @OPTION_CLONE_DIRECTORY
+@click.option(
+    "--bulk_encrypt",type=bool,is_flag=True, default=False, help="Bulk encrypt the entire crate or archive"
+)
 def print_lab(
     input_metadata: Path,
     pubkey_fingerprints: list[str],
@@ -185,6 +189,7 @@ def print_lab(
     collect_all: Optional[bool],
     gpg_binary: Optional[Path],
     duplicate_directory: Optional[bool],
+    bulk_encrypt: Optional[bool]
 ) -> None:
     """
     Create an RO-Crate based on a Print Lab metadata file
@@ -254,7 +259,12 @@ def print_lab(
     )
     if bag_crate:
         bagit_crate(crate_destination, mt_user or "")
-    archive_crate(archive_type, final_output, crate_destination)
+    if bulk_encrypt:
+        archive_crate(archive_type, crate_destination, crate_destination, True)
+        logger.info("Bulk Encrypting RO-Crate")
+        bulk_encrypt_file(gpg_binary=gpg_binary, pubkey_fingerprints=pubkey_fingerprints, data_to_encrypt=crate_destination,output_path=final_output)
+    else:
+        archive_crate(archive_type, final_output, crate_destination, True)
 
 
 @click.command()

src/ingestion_targets/abi_music/abi_json_parser.py

@@ -10,9 +10,9 @@
 
 from mytardis_rocrate_builder.rocrate_builder import ROBuilder
 from mytardis_rocrate_builder.rocrate_dataclasses.data_class_utils import (
-    CrateManifest,
     convert_to_property_value,
 )
+from mytardis_rocrate_builder.rocrate_dataclasses.crate_manifest import CrateManifest
 from mytardis_rocrate_builder.rocrate_dataclasses.rocrate_dataclasses import (
     ContextObject,
     Dataset,

src/ingestion_targets/abi_music/crate_builder.py

@@ -4,7 +4,7 @@
 from pathlib import Path
 from typing import Optional
 
-from mytardis_rocrate_builder.rocrate_dataclasses.data_class_utils import CrateManifest
+from mytardis_rocrate_builder.rocrate_dataclasses.crate_manifest import CrateManifest
 
 import src.ingestion_targets.abi_music.consts as profile_consts
 from src.cli.mytardisconfig import SchemaConfig