bugfix test zenodo tokens

README.md

@@ -7,7 +7,7 @@
 
 *Note, that the project is still under development!*
 
-The "HDF5 Research Data Management Toolbox" (h5RDMtoolbox) is a python package supporting everybody who is working with
+The "HDF5 Research Data Management Toolbox" (h5RDMtoolbox) is a Python package supporting everybody who is working with
 HDF5 to achieve a sustainable data lifecycle which follows
 the [FAIR (Findable, Accessible, Interoperable, Reusable)](https://www.nature.com/articles/sdata201618)
 principles. It specifically supports the five main steps of *planning*, *collecting*, *analyzing*, *sharing* and
@@ -18,7 +18,7 @@ information of try the [quickstart using colab](#quickstart).
 
 - Combining HDF5 and [xarray](https://docs.xarray.dev/en/stable/) to allow easy access to metadata and data during
   analysis and processing (
-  see [here](https://h5rdmtoolbox.readthedocs.io/en/latest/gettingstarted/quickoverview.html#datasets-xarray-interface).
+  see [here](https://h5rdmtoolbox.readthedocs.io/en/latest/gettingstarted/quickoverview.html#datasets-xarray-interface)).
 - Assigning [metadata with "globally unique and persistent identifiers"]() as required
   by [F1 of the FAIR principles](https://www.go-fair.org/fair-principles/f1-meta-data-assigned-globally-unique-persistent-identifiers/)
   . This "remove[s] ambiguity in the meaning of your published data...".

h5rdmtoolbox/_user.py

@@ -35,10 +35,18 @@ def __init__(self):
                           'tmp': tmp_dir,
                           'convention': _user_root_dir / 'convention',
                           'layouts': _user_root_dir / 'layouts',
+                          'repository': _user_root_dir / 'repository',
                           'standard_name_tables': _user_root_dir / 'standard_name_tables',
                           'cache': _user_root_dir / 'cache'}
         self.clear_cache(6)
 
+    def __str__(self):
+        dirs = ', '.join(f'{k}' for k in self.user_dirs.keys())
+        return f'{self.__class__.__name__}({dirs})'
+
+    def __repr__(self):
+        return self.__str__()
+
     def __getitem__(self, item):
         return self._get_dir(item)
 

h5rdmtoolbox/repository/zenodo/README.md

@@ -0,0 +1,21 @@
+# Zenodo repository interface
+
+
+## Provide Token(s)
+In order to connect to Zenodo and interact with it, tokens for either the productive or
+sandbox version must be provided. Either by providing a `zenodo.ini` file in the local
+user directory (find it here: `h5rdmtoolbox.get_user_dir()`)
+
+The file content should look like the following (displayed tokens are not real, replace them
+with yours):
+
+    [zenodo:sandbox]
+    access_token = 123kwadhulahw7d8o141lhualwedhuao810g208
+    [zenodo]
+    access_token = jdalwd814o8h3aulih7o3r01h12ulieh218e7081
+
+You may alo set them as environment variables. Please use `ZENODO_API_TOKEN` and `ZENODO_SANDBOX_API_TOKEN`,
+respectively.
+
+**Note**, that environment variables are checked first! If set the ini-file is not 
+checked!

h5rdmtoolbox/repository/zenodo/tokens.py

@@ -1,4 +1,3 @@
-import appdirs
 import configparser
 import logging
 import os
@@ -11,7 +10,8 @@
 
 def _parse_ini_file(zenodo_ini_filename: Union[str, pathlib.Path]):
     if zenodo_ini_filename is None:
-        zenodo_ini_filename = pathlib.Path(appdirs.user_data_dir('h5rdmtoolbox')) / 'zenodo.ini'
+        from h5rdmtoolbox import UserDir
+        zenodo_ini_filename = UserDir['repository'] / 'zenodo.ini'
     else:
         zenodo_ini_filename = pathlib.Path(zenodo_ini_filename)
     if not zenodo_ini_filename.exists():
@@ -21,7 +21,8 @@ def _parse_ini_file(zenodo_ini_filename: Union[str, pathlib.Path]):
 
 def get_api_token(sandbox: bool,
                   zenodo_ini_filename: Union[str, pathlib.Path] = None):
-    """Read the Zenodo API token from the config file."""
+    """Read the Zenodo API token from the environment variable or config file.
+    If an environment variable is found, a possibly existing ini file is ignored!"""
     if sandbox:
         env_token = os.environ.get('ZENODO_SANDBOX_API_TOKEN', None)
         # logger.debug('Took token from environment variable ZENODO_SANDBOX_API_TOKEN: %s', env_token)
@@ -32,29 +33,38 @@ def get_api_token(sandbox: bool,
     if env_token is not None:
         # logger.debug('Took zenodo token from environment variable:: %s', env_token)
         env_token = env_token.strip()
-        logger.debug('  Took token from environment variable ZENODO_SANDBOX_API_TOKEN.')
+        logger.debug(' Took token from environment variable ZENODO_SANDBOX_API_TOKEN.')
         return env_token
 
     logger.debug('No environment variable found for the zenodo token. Trying to read it from the config file '
                  '%s .' % zenodo_ini_filename)
 
     zenodo_ini_filename = _parse_ini_file(zenodo_ini_filename)
+    if zenodo_ini_filename.exists():
+        logger.debug(f'Zenodo ini file found: {zenodo_ini_filename}')
+
     config = configparser.ConfigParser()
     config.read(zenodo_ini_filename)
     if sandbox:
         try:
             access_token = config['zenodo:sandbox']['access_token']
+            logger.debug('Token read successfully.')
         except KeyError:
             access_token = None
+            logger.debug('Error reading sandbox token from section "zenodo:sandbox"')
     else:
         try:
             access_token = config['zenodo']['access_token']
+            logger.debug('Token read successfully.')
         except KeyError:
             access_token = None
+            logger.debug('Error reading sandbox token from section "zenodo"')
+
     if not access_token:
         warnings.warn(f'No API token found in {zenodo_ini_filename}. Please verify the correctness of the file '
                       f'{zenodo_ini_filename}. The access_token entry must be in the section [zenodo] or '
                       f'[zenodo:sandbox].')
+        logger.error('No token read. Neither file nor env variable found.')
     return access_token
 
 

requirements.txt

@@ -23,5 +23,4 @@ python-gitlab
 pypandoc>=1.11
 pydantic >= 2.3.0
 # other:
-tqdm>=4.64.0
 ontolutils

tests/repository/test_zenodo.py

@@ -2,11 +2,13 @@
 import logging
 import os
 import pathlib
-import pydantic
 import unittest
 from datetime import datetime
 
+import pydantic
+
 import h5rdmtoolbox as h5tbx
+from h5rdmtoolbox import UserDir
 from h5rdmtoolbox.repository import zenodo, upload_file
 from h5rdmtoolbox.repository.zenodo.metadata import Metadata, Creator, Contributor
 from h5rdmtoolbox.repository.zenodo.tokens import get_api_token, set_api_token
@@ -145,15 +147,18 @@ def test_get_api(self):
         else:
             bak_fname = None
 
+        zenodo_ini_filename = UserDir['repository'] / 'zenodo.ini'
+        if zenodo_ini_filename.exists():
+            tmp_zenodo_ini_filename = zenodo_ini_filename.rename(zenodo_ini_filename.with_suffix('.ini_bak'))
+        else:
+            tmp_zenodo_ini_filename = None
+
         with self.assertRaises(FileNotFoundError):
             _parse_ini_file(None)
 
         with self.assertRaises(FileNotFoundError):
             _parse_ini_file('invalid.ini')
 
-        with self.assertRaises(FileNotFoundError):
-            _parse_ini_file(None)
-
         if bak_fname:
             bak_fname.rename(fname)
 
@@ -163,6 +168,9 @@ def test_get_api(self):
         self.assertTrue(ini_filename.exists())
         ini_filename.unlink()
 
+        if tmp_zenodo_ini_filename:
+            tmp_zenodo_ini_filename.rename(tmp_zenodo_ini_filename.with_suffix('.ini'))
+
     def test_get_api_token(self):
         env_token_sb = os.environ.pop('ZENODO_SANDBOX_API_TOKEN', None)
         env_token = os.environ.pop('ZENODO_API_TOKEN', None)
@@ -181,9 +189,14 @@ def test_get_api_token(self):
         # reset environment variable
         if env_token_sb is not None:
             os.environ['ZENODO_SANDBOX_API_TOKEN'] = env_token_sb
-        self.assertEqual(env_token_sb, os.environ.get('ZENODO_SANDBOX_API_TOKEN', None))
+            self.assertEqual(env_token_sb, os.environ.get('ZENODO_SANDBOX_API_TOKEN', None))
+        else:
+            os.environ.pop('ZENODO_SANDBOX_API_TOKEN')
+
         if env_token is not None:
             os.environ['ZENODO_API_TOKEN'] = env_token
+        else:
+            os.environ.pop('ZENODO_API_TOKEN', None)
         self.assertEqual(env_token, os.environ.get('ZENODO_API_TOKEN', None))
 
     def test_set_api_token(self):

tests/test_user.py

@@ -37,7 +37,8 @@ def tearDownClass(cls) -> None:
 
     def test_user_dir(self):
         self.assertListEqual(sorted(h5tbx.UserDir.names),
-                             sorted(('root', 'tmp', 'layouts', 'standard_name_tables', 'cache', 'convention')))
+                             sorted(('root', 'tmp', 'layouts', 'repository',
+                                     'standard_name_tables', 'cache', 'convention')))
         self.assertTrue('root' in h5tbx.UserDir)
 
         cache_dir = h5tbx.UserDir['cache']