Merge pull request #253 from softwarepub/feature/244-fixes-for-081

Fixes from the first release

.github/workflows/hermes-zenodo.yml

@@ -42,7 +42,7 @@ jobs:
  - uses: actions/setup-python@v4
  with:
  python-version: '3.10'
- - run: pip install hermes
+ - run: pip install hermes hermes-plugin-python
  - run: hermes harvest
  - run: hermes process
  - run: hermes curate

.gitignore

@@ -23,3 +23,4 @@ dist/
 
 # HERMES workflow specifics
 .hermes/
+hermes.log

CITATION.cff

@@ -14,7 +14,7 @@ title: hermes
 message: >-
  If you use this software, please cite it using the
  metadata from this file.
-version: 0.8.1b1
+version: 0.8.1
 license: "Apache-2.0"
 abstract: "Tool to automate software publication. Not stable yet."
 type: software

hermes.toml

@@ -3,10 +3,7 @@
 # SPDX-License-Identifier: CC0-1.0
 
 [harvest]
-sources = [ "cff" ] # ordered priority (first one is most important)
-
-[harvest.cff]
-enable_validation = false
+sources = [ "cff", "toml" ] # ordered priority (first one is most important)
 
 [deposit]
 target = "invenio_rdm"

pyproject.toml

@@ -9,7 +9,7 @@
 [tool.poetry]
 # Reference at https://python-poetry.org/docs/pyproject/
 name = "hermes"
-version = "0.1.0"
+version = "0.8.1"
 description = "Workflow to publish research software with rich metadata"
 homepage = "https://software-metadata.pub"
 license = "Apache-2.0"
@@ -20,6 +20,7 @@ authors = [
  "Jeffrey Kelling <j.kelling@hzdr.de>",
  "Oliver Knodel <o.knodel@hzdr.de>",
  "David Pape <d.pape@hzdr.de>",
+ "Sophie Kernchen <sohpie.kernchen@dlr.de>",
 ]
 
 readme = "README.md"

src/hermes/commands/base.py

@@ -43,6 +43,7 @@ def __init__(self, parser: argparse.ArgumentParser):
  self.settings = None
 
  self.log = logging.getLogger(f"hermes.{self.command_name}")
+ self.errors = []
 
  def init_plugins(self):
  """Collect and initialize the plugins available for the HERMES command."""

src/hermes/commands/cli.py

@@ -9,7 +9,9 @@
 This module provides the main entry point for the HERMES command line application.
 """
 import argparse
+import sys
 
+from hermes import logger
 from hermes.commands import HermesHelpCommand, HermesCleanCommand, HermesHarvestCommand, HermesProcessCommand, \
  HermesCurateCommand, HermesDepositCommand, HermesPostprocessCommand
 from hermes.commands.base import HermesCommand
@@ -56,6 +58,28 @@ def main() -> None:
  # Actually parse the command line, configure it and execute the selected sub-command.
  args = parser.parse_args()
 
- args.command.load_settings(args)
- args.command.patch_settings(args)
- args.command(args)
+ logger.init_logging()
+ log = logger.getLogger("hermes.cli")
+ log.debug("Running hermes with the following command line arguments: %s", args)
+
+ try:
+ log.debug("Loading settings...")
+ args.command.load_settings(args)
+
+ log.debug("Update settings from command line...")
+ args.command.patch_settings(args)
+
+ log.info("Run subcommand %s", args.command.command_name)
+ args.command(args)
+ except Exception as e:
+ log.error("An error occurred during execution of %s", args.command.command_name)
+ log.debug("Original exception was: %s", e)
+
+ sys.exit(2)
+
+ if args.command.errors:
+ for e in args.command.errors:
+ log.error(e)
+ sys.exit(1)
+
+ sys.exit(0)

src/hermes/commands/deposit/base.py

@@ -120,7 +120,6 @@ def init_command_parser(self, command_parser: argparse.ArgumentParser) -> None:
  def __call__(self, args: argparse.Namespace) -> None:
  self.args = args
  plugin_name = self.settings.target
- print(self.args)
 
  ctx = CodeMetaContext()
  codemeta_file = ctx.get_cache("curate", ctx.hermes_name)
@@ -135,11 +134,13 @@ def __call__(self, args: argparse.Namespace) -> None:
  try:
  plugin_func = self.plugins[plugin_name](self, ctx)
 
- except KeyError:
+ except KeyError as e:
  self.log.error("Plugin '%s' not found.", plugin_name)
+ self.errors.append(e)
 
  try:
  plugin_func(self)
 
  except HermesValidationError as e:
  self.log.error("Error while executing %s: %s", plugin_name, e)
+ self.errors.append(e)

src/hermes/commands/deposit/invenio.py

@@ -105,7 +105,7 @@ class InvenioResolver:
  invenio_client_class = InvenioClient
 
  def __init__(self, client=None):
- self.client = client or self.invenio_client_class()
+ self.client = client or self.invenio_client_class(InvenioDepositSettings())
 
  def resolve_latest_id(
  self, record_id=None, doi=None, codemeta_identifier=None

src/hermes/commands/harvest/base.py

@@ -48,19 +48,19 @@ def __call__(self, args: argparse.Namespace) -> None:
  try:
  plugin_func = self.plugins[plugin_name]()
  harvested_data, tags = plugin_func(self)
- print(harvested_data)
- with HermesHarvestContext(
- ctx, plugin_name
- ) as harvest_ctx:
+
+ with HermesHarvestContext(ctx, plugin_name) as harvest_ctx:
  harvest_ctx.update_from(harvested_data,
  plugin=plugin_name,
  timestamp=datetime.now().isoformat(), **tags)
  for _key, ((_value, _tag), *_trace) in harvest_ctx._data.items():
  if any(v != _value and t == _tag for v, t in _trace):
  raise MergeError(_key, None, _value)
 
- except KeyError:
+ except KeyError as e:
  self.log.error("Plugin '%s' not found.", plugin_name)
+ self.errors.append(e)
 
  except HermesValidationError as e:
  self.log.error("Error while executing %s: %s", plugin_name, e)
+ self.errors.append(e)

src/hermes/commands/postprocess/invenio.py

@@ -24,7 +24,7 @@ def config_record_id(ctx):
  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
+ raise RuntimeError("No deposit.invenio configuration available to store record id in")
 
 
 def cff_doi(ctx):

src/hermes/commands/postprocess/invenio_rdm.py

@@ -23,4 +23,4 @@ def config_record_id(ctx):
  conf['deposit']['invenio_rdm']['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
+ raise RuntimeError("No deposit.invenio_rdm configuration available to store record id in")

src/hermes/commands/process/base.py

@@ -58,7 +58,8 @@ def __call__(self, args: argparse.Namespace) -> None:
  ctx.merge_contexts_from(harvest_context)
 
  if ctx._errors:
- self.log.error('!!! warning "Errors during merge"')
+ self.log.error('Errors during merge')
+ self.errors.extend(ctx._errors)
 
  for ep, error in ctx._errors:
  self.log.info(" - %s: %s", ep.name, error)

src/hermes/logger.py

@@ -31,7 +31,7 @@
  'class': "logging.FileHandler",
  'formatter': "logfile",
  'level': "DEBUG",
- 'filename': "./.hermes/hermes.log",
+ 'filename': "./hermes.log",
  },
 
  'auditfile': {
@@ -50,12 +50,6 @@
  },
 }
 
-# This dict caches all the different configuration sections already loaded
-_config = {
- # We need some basic logging configuration to get logging up and running at all
- 'logging': _logging_config,
-}
-
 _loggers = {}
 
 
@@ -64,14 +58,14 @@ def init_logging():
  return
 
  # Make sure the directories to hold the log files exists (or else create)
- pathlib.Path(_config['logging']['handlers']['logfile']['filename']).parent.mkdir(exist_ok=True, parents=True)
- pathlib.Path(_config['logging']['handlers']['auditfile']['filename']).parent.mkdir(exist_ok=True, parents=True)
+ pathlib.Path(_logging_config['handlers']['logfile']['filename']).parent.mkdir(exist_ok=True, parents=True)
+ pathlib.Path(_logging_config['handlers']['auditfile']['filename']).parent.mkdir(exist_ok=True, parents=True)
 
  # Inintialize logging system
  import logging.config
 
- logging.config.dictConfig(_config['logging'])
- for log_name in _config['logging']['loggers']:
+ logging.config.dictConfig(_logging_config)
+ for log_name in _logging_config['loggers']:
  _loggers[log_name] = logging.getLogger(log_name)
 
 

test/hermes_test/conftest.py

@@ -23,8 +23,10 @@ def __setitem__(self, path, data):
 
  def __enter__(self):
  self.test_path.mkdir(parents=True, exist_ok=True)
+
  for file_name, data in self.test_files.items():
  file_path = self.test_path / file_name
+ file_path.parent.mkdir(parents=True, exist_ok=True)
  file_path.write_text(data)
 
  os.chdir(self.test_path)

test/hermes_test/test_cli.py

@@ -9,23 +9,27 @@
 from hermes.commands import cli
 
 
-def test_hermes_full(capsys):
+def test_hermes_full():
  with pytest.raises(SystemExit) as se:
  cli.main()
  assert "choose from" in se
 
 
-@pytest.mark.skip(reason="Needs update")
 def test_hermes_harvest(hermes_env):
+ hermes_env['hermes.toml'] = ""
+
  with hermes_env:
  result = hermes_env.run("harvest")
 
  assert result.returncode == 0
 
 
-@pytest.mark.skip(reason="Needs update")
 def test_hermes_process(hermes_env):
+ hermes_env['hermes.toml'] = ""
+ hermes_env['.hermes/harvest/test.json'] = ""
+
  with hermes_env:
  result = hermes_env.run("process")
+ print(result.stdout.read())
 
  assert result.returncode == 0