major zenodo simplifaction. only one interface implementation needed

docs/userguide/repository/zenodo.ipynb

@@ -7,9 +7,13 @@
    "source": [
     "# Zenodo\n",
     "\n",
-    "There are two types of Zenodo interfaces. One interfaces to the public repositories (`ZenodoRecord`), the other is for testing and accessed the sandbox server (`ZenodoSandboxDeposit`).\n",
+    "The [Zenodo](https://zenodo.org/) repository is a concrete implementation of the `RepositoryInterface`. Other repositories such as `Figshare` (https://figshare.com/) could be possible future realizations of it.\n",
     "\n",
-    "The class diagram below shows how they are constructed. First, an abstract zenodo interface class (`AbstractZenodoInterface`) is derived. From this, the concrete interface classes are derived.\n",
+    "Zenodo provides a sandbox (testing environment) and a production environment. They work the same in principle. Therefore, only one implementation is needed, which is `ZenodoRecord` (the interface to a record in Zenodo). Pass `sandbox=True` to use the testing environment.\n",
+    "\n",
+    "The below diagram shows the abstract base class with its abstract methods (indicated by italics). Note, that `upload_file()` is *not* abstract. The subclasses must implement `__upload_file__`, which uploads a file to the repository record. `upload_file()` is basically a wrapper, which additionally allows generating metadata files of the uploaded files. We will explore this feature later in this section.\n",
+    "\n",
+    "The `RepositoryInterface` further defines the communication with files. A file object `RepositoryFile` is implemented, providing mandatory properties as well as a download method. A repository implementation (just like the one for Zenodo) must return a Dictionary of `RepositoryFile` objects for the `files` class property (see source code for in-depth explanation and the example at the end of this section).\n",
     "\n",
     "<img src=\"../../_static/repo_class_diagram.svg\"\n",
     "     alt=\"../../_static/repo_class_diagram.svg\"\n",
@@ -45,7 +49,7 @@
    "source": [
     "### 1. Init a Repo:\n",
     "\n",
-    "For testing purpose, let's use the sandbox environment of Zenodo (`ZenodoSandboxDeposit`)"
+    "As said, we use the testing interface, hence `sandbox=True`:"
    ]
   },
   {
@@ -55,7 +59,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "repo = zenodo.ZenodoSandboxDeposit(None)"
+    "repo = zenodo.ZenodoRecord(None, sandbox=True)"
    ]
   },
   {
@@ -176,18 +180,20 @@
    "metadata": {},
    "outputs": [
     {
-     "data": {
-      "text/plain": [
-       "['tmp0.hdf', 'tmp0.jsonld']"
-      ]
-     },
-     "execution_count": 7,
-     "metadata": {},
-     "output_type": "execute_result"
+     "ename": "AttributeError",
+     "evalue": "'str' object has no attribute 'name'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[1;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[1;31mAttributeError\u001b[0m                            Traceback (most recent call last)",
+      "Cell \u001b[1;32mIn[7], line 1\u001b[0m\n\u001b[1;32m----> 1\u001b[0m [f\u001b[38;5;241m.\u001b[39mname \u001b[38;5;28;01mfor\u001b[39;00m f \u001b[38;5;129;01min\u001b[39;00m repo\u001b[38;5;241m.\u001b[39mfiles]\n",
+      "Cell \u001b[1;32mIn[7], line 1\u001b[0m, in \u001b[0;36m<listcomp>\u001b[1;34m(.0)\u001b[0m\n\u001b[1;32m----> 1\u001b[0m [\u001b[43mf\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mname\u001b[49m \u001b[38;5;28;01mfor\u001b[39;00m f \u001b[38;5;129;01min\u001b[39;00m repo\u001b[38;5;241m.\u001b[39mfiles]\n",
+      "\u001b[1;31mAttributeError\u001b[0m: 'str' object has no attribute 'name'"
+     ]
     }
    ],
    "source": [
-    "repo.get_filenames()"
+    "[f.name for f in repo.files]"
    ]
   },
   {
@@ -202,7 +208,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 8,
+   "execution_count": null,
    "id": "fbf04793-b7eb-4377-a904-edb91542b056",
    "metadata": {},
    "outputs": [],
@@ -220,7 +226,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": null,
    "id": "02290359-b13b-413d-9b93-9706b3ab087d",
    "metadata": {},
    "outputs": [],
@@ -238,23 +244,13 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 12,
+   "execution_count": null,
    "id": "4e75f4fc-6311-470c-9204-93c1c5d768d0",
    "metadata": {},
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "tmp0.txt\n",
-      "tmp0.hdf\n",
-      "tmp0.jsonld\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "for file in repo.files:\n",
-    "    print(file.filename)"
+    "    print(file.name)"
    ]
   },
   {
@@ -282,7 +278,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.8.19"
   }
  },
  "nbformat": 4,

h5rdmtoolbox/convention/core.py

@@ -755,7 +755,7 @@ def from_zenodo(doi_or_recid: str,
     if not filename.exists() or force_download:
         record = zenodo.ZenodoRecord(rec_id)
 
-        filenames = record.get_filenames()
+        filenames = list(record.files.keys())
         if name is None:
             matches = [file for file in filenames if pathlib.Path(file).suffix == '.yaml']
         else:

h5rdmtoolbox/convention/standard_names/table.py

@@ -752,7 +752,7 @@ def from_zenodo(source: str = None, doi_or_recid=None) -> "StandardNameTable":
         z = zenodo.ZenodoRecord(rec_id)
         assert z.exists()
 
-        filenames = [file.download(target_folder=UserDir['standard_name_tables']) for file in z.files]
+        filenames = [file.download(target_folder=UserDir['standard_name_tables']) for file in z.files.values()]
         # filenames = z.download_files(target_folder=UserDir['standard_name_tables'])
         assert len(filenames) == 1
         filename = filenames[0]

h5rdmtoolbox/repository/interface.py

@@ -6,6 +6,8 @@
 
 import appdirs
 
+from h5rdmtoolbox.utils import deprecated
+
 logger = logging.getLogger('h5rdmtoolbox')
 
 
@@ -37,29 +39,34 @@ def _HDF2JSON(filename: Union[str, pathlib.Path], **kwargs) -> pathlib.Path:
     return hdf2jsonld(filename=filename, skipND=1)
 
 
-class RepositoryFile(abc.ABC):
+class RepositoryFile:
+    """The interface class to files in a repository"""
 
-    def __init__(self, identifier,
+    def __init__(self,
+                 identifier,
                  identifier_url,
                  download_url,
                  access_url,
                  checksum,
-                 filename,
+                 name,
                  size,
                  media_type,
                  access_token=None,
                  **kwargs):
         self.download_url = download_url
         self.access_url = access_url
         self.checksum = checksum
-        self.filename = filename
+        self.name = name
         self.media_type = media_type
         self.size = size
         self.identifier = identifier
         self.identifier_url = identifier_url
         self.access_token = access_token
         self.additional_data = kwargs
 
+    def __repr__(self):
+        return f"{self.__class__.__name__}({self.name})"
+
     def info(self) -> Dict:
         return dict(identifier=self.identifier,
                     identifier_url=self.identifier_url,
@@ -132,30 +139,31 @@ def set_metadata(self, metadata):
 
     @abc.abstractmethod
     def download_file(self, filename):
-        """Download a specific file from the repository."""
+        """Download a specific file from the repository.
+
+        ..note: This method is deprecated. Use method `.files.get(filename).download()` method instead.
+        """
 
     @abc.abstractmethod
     def download_files(self):
-        """Download all files from the repository."""
+        """Download all files from the repository.
 
+        ..note: This method is deprecated. Please iterate over `files` and call .download() on the items.
+        """
+
+    @deprecated(version='1.4.0rc1',
+                msg='Please use `list(self.files.keys())` instead')
     def get_filenames(self) -> List[str]:
         """Get a list of all filenames."""
-        return [file.filename for file in self.files]
+        return list(self.files.keys())
 
     @property
     @abc.abstractmethod
-    def files(self) -> List[RepositoryFile]:
+    def files(self) -> Dict[str, RepositoryFile]:
         """List of all files in the repository."""
 
-    def file(self, filename: str) -> RepositoryFile:
-        """Return the file matching the filename, e.g. file.pdf"""
-        for file in self.files:
-            if file.filename == filename:
-                return file
-        raise FileNotFoundError(f'The file "{filename}" does not exist in the repository.')
-
     @abc.abstractmethod
-    def _upload_file(self, filename: Union[str, pathlib.Path], overwrite: bool = False):
+    def __upload_file__(self, filename: Union[str, pathlib.Path], overwrite: bool = False):
         """Upload a file to the repository. This is a regular file uploader, hence the
         file can be of any type. This is a private method, which needs to be implemented
         by every repository interface. Will be called by `upload_file`"""
@@ -206,12 +214,16 @@ def upload_file(self,
         else:
             meta_data_file = None
 
-        self._upload_file(filename=filename, overwrite=overwrite)
+        self.__upload_file__(filename=filename, overwrite=overwrite)
 
         if meta_data_file is not None:
-            self._upload_file(filename=meta_data_file, overwrite=overwrite)
+            self.__upload_file__(filename=meta_data_file, overwrite=overwrite)
         self.refresh()
 
+    @deprecated(version='1.4.0rc1',
+                msg='This method is deprecated. '
+                    'Use `.upload_file(...)` instead and provide the '
+                    'metamapper parameter there')
     def upload_hdf_file(self,
                         filename,
                         metamapper: Callable[[Union[str, pathlib.Path]], pathlib.Path],