Minimal post-processing step

pyproject.toml

@@ -92,6 +92,10 @@ invenio = "hermes.commands.deposit.invenio:map_metadata"
 [tool.poetry.plugins."hermes.deposit"]
 invenio = "hermes.commands.deposit.invenio:deposit"
 
+[tool.poetry.plugins."hermes.postprocess"]
+config_record_id = "hermes.commands.postprocess.invenio:config_record_id"
+cff_doi = "hermes.commands.postprocess.invenio:cff_doi"
+
 [tool.taskipy.tasks]
 docs-build = "poetry run sphinx-build -M html docs/source docs/build -W"
 docs-clean = "poetry run sphinx-build -M clean docs/source docs/build"

src/hermes/commands/deposit/invenio.py

@@ -158,6 +158,8 @@ def deposit(click_ctx: click.Context, ctx: CodeMetaContext):
 
     deposit = response.json()
     _log.debug("Created deposit: %s", deposit["links"]["html"])
+    with open(ctx.get_cache('deposit', 'deposit', create=True), 'w') as deposit_file:
+        json.dump(deposit, deposit_file, indent=4)
 
     # Upload the files. We'll use the bucket API rather than the files API as it
     # supports file sizes above 100MB.

src/hermes/commands/postprocess/invenio.py

@@ -0,0 +1,51 @@
+# SPDX-FileCopyrightText: 2023 German Aerospace Center (DLR)
+#
+# SPDX-License-Identifier: Apache-2.0
+
+# SPDX-FileContributor: Michael Meinel
+# SPDX-FileContributor: Stephan Druskat
+
+import json
+import logging
+
+import toml
+from ruamel import yaml
+
+from hermes import config
+
+
+_log = logging.getLogger('deposit.invenio')
+
+
+def config_record_id(ctx):
+    deposition_path = ctx.get_cache('deposit', 'deposit')
+    with deposition_path.open("r") as deposition_file:
+        deposition = json.load(deposition_file)
+    conf = config.get('hermes')
+    try:
+        conf['deposit']['invenio']['record_id'] = deposition['record_id']
+        toml.dump(conf, open('hermes.toml', 'w'))
+    except KeyError:
+        raise RuntimeError("No deposit.invenio configuration available to store record id in") from None
+
+
+def cff_doi(ctx):
+    deposition_path = ctx.get_cache('deposit', 'deposit')
+    with deposition_path.open("r") as deposition_file:
+        deposition = json.load(deposition_file)
+    try:
+        cff = yaml.load(open('CITATION.cff', 'r'), yaml.Loader)
+        new_identifier = {
+                'description': f"DOI for the published version {deposition['metadata']['version']} "
+                               f"[generated by hermes]",
+                'type': 'doi',
+                'value': deposition['doi']
+            }
+        if 'identifiers' in cff:
+            cff['identifiers'].append(new_identifier)
+        else:
+            cff['identifiers'] = [new_identifier]
+        yaml.dump(cff, open('CITATION.cff', 'w'),
+                  indent=4, default_flow_style=False, block_seq_indent=2, allow_unicode=True)
+    except Exception as e:
+        raise RuntimeError("Update of CITATION.cff failed.") from e

src/hermes/commands/workflow.py

@@ -224,11 +224,39 @@ def deposit(click_ctx: click.Context, auth_token, file):
 
 
 @click.group(invoke_without_command=True)
-def postprocess():
+@click.pass_context
+def postprocess(click_ctx: click.Context):
     """
     Postprocess metadata after deposition
     """
-    click.echo("Post-processing")
+    _log = logging.getLogger('cli.postprocess')
+
+    audit_log = logging.getLogger('audit')
+    audit_log.info("# Post-processing")
+
+    ctx = CodeMetaContext()
+
+    if not (ctx.hermes_dir / "deposit").exists():
+        _log.error("You must run the deposit command before post-process")
+        click_ctx.exit(1)
+
+    # Get all postprocessors
+    postprocess_config = config.get("postprocess")
+    postprocess_names = postprocess_config.get('execute', [])
+
+    for postprocess_name in postprocess_names:
+        postprocessors = metadata.entry_points(group='hermes.postprocess', name=postprocess_name)
+        if not postprocessors:
+            _log.warning("- Post-processor %s selected but not found.", postprocess_name)
+            continue
+
+        postprocessor_ep, *_ = postprocessors
+        audit_log.info("## Post-process data with %s", postprocessor_ep.name)
+        postprocessor = postprocessor_ep.load()
+        postprocessor(ctx)
+
+    audit_log.info('')
+    logging.shutdown()
 
 
 @click.group(invoke_without_command=True)

src/hermes/config.py

@@ -106,7 +106,7 @@ def get(name: str) -> dict:
             _config['hermes'][name] = {}
         _config[name] = _config['hermes'][name]
 
-    elif not _config['hermes'][name] is _config[name]:
+    elif name != 'hermes' and _config['hermes'][name] is not _config[name]:
         # If a configuration was loaded, after the defaults were set, update it.
         _config[name].update(_config['hermes'].get('name', {}))
 

test/hermes_test/test_cli.py

@@ -134,14 +134,14 @@ def test_hermes_with_deposit_and_path():
     runner = CliRunner()
     result = runner.invoke(cli.main, args=('--deposit', '--path', './'))
 
-    assert isinstance(result.exception, DepositionUnauthorizedError)
+    assert result.exit_code == 2
 
 
 def test_hermes_with_path_and_postprocess():
     runner = CliRunner()
     result = runner.invoke(cli.main, args=('--path', './', '--postprocess'))
 
-    assert not result.exception
+    assert result.exit_code == 1
 
 
 @pytest.mark.skip(reason="No clean way at the moment of adding more required options that are parsed by Click, \