Update create data package utility

[r-b-g-b]

Two changes to the d1_util.create_data_packages to let it run correctly. I added some more detail inline in the "Files changed" tab.

[r-b-g-b]

Adding some inline comments to explain the changes!

[r-b-g-b]

Currently, this line results in the error:

TypeError                                 Traceback (most recent call last)
Cell In[62], line 8
      6 for file_path in files_in_group:
      7     print("  File: {}".format(file_path))
----> 8     create_science_object_on_member_node(client, file_path)

File ~/projects/cib-data-infrastructure/.venv/lib/python3.13/site-packages/d1_util/create_data_packages.py:178, in create_science_object_on_member_node(client, file_path)
    174 sci_obj = open(file_path, "rb").read()
    175 sys_meta = generate_system_metadata_for_science_object(
    176     pid, SYSMETA_FORMATID, sci_obj
    177 )
--> 178 client.create(pid, io.StringIO(sci_obj), sys_meta)

TypeError: initial_value must be str or None, not bytes

That makes sense, since the file is opened in "rb" binary mode so needs to be wrapped with BytesIO instead of StringIO (which expects a decoded str).

[r-b-g-b]

As is I get the error:

AttributeError                            Traceback (most recent call last)
Cell In[83], line 1
----> 1 create_package_on_member_node(client, files_in_group)

Cell In[65], line 90, in create_package_on_member_node(client, files_in_group)
     88 package_pid = group_name(files_in_group[0])
     89 pids = [os.path.basename(p) for p in files_in_group]
---> 90 resource_map = create_resource_map_for_pids(package_pid, pids)
     91 sys_meta = generate_system_metadata_for_science_object(
     92     package_pid, RESOURCE_MAP_FORMAT_ID, resource_map
     93 )
     94 client.create(package_pid, io.StringIO(resource_map), sys_meta)

Cell In[65], line 102, in create_resource_map_for_pids(package_pid, pids)
     97 def create_resource_map_for_pids(package_pid, pids):
     98     # Create a resource map generator that will generate resource maps that, by
     99     # default, use the DataONE production environment for resolving the object
    100     # URIs. To use the resource map generator in a test environment, pass the base
    101     # url to the root CN in that environment in the dataone_root parameter.
--> 102     resource_map_generator = d1_common.resource_map.ResourceMapGenerator()
    103     return resource_map_generator.simple_generate_resource_map(
    104         package_pid, pids[0], pids[1:]
    105     )

AttributeError: module 'd1_common.resource_map' has no attribute 'ResourceMapGenerator'

I believe this class has since been removed and its method simple_generate_resource_map replaced with d1_common.resource_map.createSimpleResourceMap.

[r-b-g-b]

If we don't serialize the resource map, we get an error here:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[97], line 1
----> 1 create_package_on_member_node(client, files_in_group)

Cell In[96], line 91, in create_package_on_member_node(client, files_in_group)
     89 pids = [os.path.basename(p) for p in files_in_group]
     90 resource_map = create_resource_map_for_pids(package_pid, pids)
---> 91 sys_meta = generate_system_metadata_for_science_object(
     92     package_pid, RESOURCE_MAP_FORMAT_ID, resource_map
     93 )
     94 client.create(package_pid, io.BytesIO(resource_map), sys_meta)

Cell In[96], line 111, in generate_system_metadata_for_science_object(pid, format_id, science_object)
    109 def generate_system_metadata_for_science_object(pid, format_id, science_object):
    110     size = len(science_object)
--> 111     md5 = hashlib.md5(science_object).hexdigest()
    112     now = d1_common.date_time.utc_now()
    113     sys_meta = generate_sys_meta(pid, format_id, size, md5, now)

TypeError: object supporting the buffer API required

Since the science_object is expected to be a sequence of bytes.