updatedocs

docs/userguide/misc/UserDirectories.ipynb

@@ -0,0 +1,180 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "e93ec3be-9e45-4540-88fc-370310b3273b",
+   "metadata": {},
+   "source": [
+    "# User directories\n",
+    "\n",
+    "The `h5rdmtoolbox` uses a couple of local directories to store temporary files or manage cache files."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "2190644a-d72a-4aa4-b6b3-e61fe9f496e1",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "Failed to import module h5tbx\n"
+     ]
+    }
+   ],
+   "source": [
+    "import h5rdmtoolbox as h5tbx"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c6a80526-de72-4c29-b484-82ba6ae4ad15",
+   "metadata": {},
+   "source": [
+    "The `UserDir` variable manages the paths. The `__repr__` indicates the different paths:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "f9b2d695-b91e-486a-89d9-02d3b6a16c59",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "DirManger(root, tmp, convention, layouts, repository, standard_name_tables, cache)"
+      ]
+     },
+     "execution_count": 2,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "h5tbx.UserDir"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6efea3fa-b401-49d9-92b1-7c54456413f8",
+   "metadata": {},
+   "source": [
+    "## Examples\n",
+    "Temporary files, e.g. created when empty `h5tbx.File` objects are created, will be put here:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "8eb9f616-2efc-463a-9915-b668f64958e0",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "WindowsPath('C:/Users/Matthias/AppData/Local/h5rdmtoolbox/h5rdmtoolbox/tmp/tmp_0')"
+      ]
+     },
+     "execution_count": 6,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "h5tbx.UserDir['tmp']"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "3c6b0e27-5236-4102-9fbe-ea0873bba947",
+   "metadata": {},
+   "source": [
+    "Let's check it: "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "a59dc11f-85b3-4db1-9642-5daa7a05307e",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "WindowsPath('C:/Users/Matthias/AppData/Local/h5rdmtoolbox/h5rdmtoolbox/tmp/tmp_0/tmp2.hdf')"
+      ]
+     },
+     "execution_count": 10,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "with h5tbx.File() as h5:\n",
+    "    filename = h5.hdf_filename\n",
+    "filename"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "c50b5275-ce80-403b-91ce-88c904497b4d",
+   "metadata": {},
+   "source": [
+    "Tokens for repositories, e.g. Zenodo, should be put here:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "ca53b6db-6f20-4500-91a7-1f738fd6bb5d",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "WindowsPath('C:/Users/Matthias/AppData/Local/h5rdmtoolbox/h5rdmtoolbox/repository')"
+      ]
+     },
+     "execution_count": 7,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "h5tbx.UserDir['repository']"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "3f703cb7-7f4d-49b0-a12f-18b3a9fa9cd6",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.8.19"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

docs/userguide/misc/index.rst

@@ -16,4 +16,5 @@ of the sub-package implementations. This section outlines them.
     identifiers.ipynb
     Extensions.ipynb
     Visualization.ipynb
-    Time.ipynb
+    Time.ipynb
+    UserDirectories.ipynb

h5rdmtoolbox/layout/core.py

@@ -1,13 +1,14 @@
 """Layout validation module"""
 import enum
-import h5py
 import logging
 import pathlib
 import types
 import uuid
 import warnings
 from typing import Dict, Union, List, Protocol, Optional, Callable, Tuple
 
+import h5py
+
 import h5rdmtoolbox as h5tbx
 
 logger = logging.getLogger('h5rdmtoolbox')
@@ -106,7 +107,7 @@ class LayoutSpecification:
 
     def __init__(self,
                  func: QueryCallable,
-                 kwargs,
+                 kwargs: Dict,
                  n: Union[int, None, Dict],
                  description: Optional[str] = None,
                  parent: Optional["LayoutSpecification"] = None):
@@ -327,7 +328,7 @@ def __call__(self, target: Union[h5py.Group, h5py.Dataset]):
     def add(self,
             func: QueryCallable,
             *,
-            n: Union[int, None, Dict],
+            n: Optional[Union[int, None, Dict]] = None,
             description: Optional[str] = None,
             **kwargs):
         """
@@ -566,6 +567,9 @@ class Layout(LayoutSpecification):
     def __init__(self):
         self.specifications: List[LayoutSpecification] = []
 
+    def __repr__(self):
+        return f'{self.__class__.__name__}'
+
     def __eq__(self, other):
         if not isinstance(other, Layout):
             return False

h5rdmtoolbox/wrapper/jsonld.py

@@ -1,16 +1,17 @@
-import h5py
 import json
 import logging
+import pathlib
+import warnings
+from typing import Dict, List
+from typing import Optional, Union, Iterable, Tuple, Any
+
+import h5py
 import numpy as np
 import ontolutils
-import pathlib
 import rdflib
-import warnings
 from ontolutils.classes.utils import split_URIRef
 from rdflib import Graph, URIRef, Literal, BNode, XSD, RDF
 from rdflib.plugins.shared.jsonld.context import Context
-from typing import Dict, List
-from typing import Optional, Union, Iterable, Tuple, Any
 
 from h5rdmtoolbox.convention import hdf_ontology
 from .core import Dataset, File
@@ -661,6 +662,8 @@ def _add_hdf_node(name, obj, ctx):
                     list_node = build_node_list(g, av.tolist())
                 else:
                     list_node = build_node_list(g, av)
+            elif isinstance(av, (h5py.Dataset, h5py.Group)):
+                attr_literal = rdflib.Literal(av.name)
             else:
                 try:
                     attr_literal = rdflib.Literal(json.dumps(av))

requirements-doc.txt

@@ -6,4 +6,5 @@ sphinx_book_theme
 sphinx-copybutton
 sphinx-design
 myst-nb
-sphinxcontrib-bibtex
+sphinxcontrib-bibtex
+pivmetalib @ git+https://github.com/matthiasprobst/pivmetalib@main

requirements.txt

@@ -23,4 +23,4 @@ python-gitlab
 pypandoc>=1.11
 pydantic >= 2.3.0
 # other:
-ontolutils
+ontolutils >= 0.2.20

setup.cfg

@@ -35,7 +35,7 @@ install_requires =
     pint_xarray # >= 0.2.1
     regex # >= 2023
     packaging
-    ontolutils
+    ontolutils>=0.2.20
     python-forge # == 18.6.0
     requests
     pydantic >= 2.3.0
@@ -80,6 +80,7 @@ docs =
     simplejson
     myst-nb
     sphinxcontrib-bibtex
+    pivmetalib @ git+https://github.com/matthiasprobst/pivmetalib@main
 complete =
     %(gui)s
     %(test)s

tests/layouts/test_core.py

@@ -110,19 +110,27 @@ def test_alternative_specification(self):
     def test_is_single_result(self):
         self.assertEqual(is_single_result(None), False)
 
-        lay = layout.Layout()
-        spec = lay.add(hdfdb.ObjDB.find_one, flt={'$name': '/u'}, n=None)
+        lay1 = layout.Layout()
+        lay2 = layout.Layout()
+        spec = lay1.add(hdfdb.ObjDB.find_one, flt={'$name': '/u'}, n=None)
         sub_spec = spec.add(hdfdb.ObjDB.find, flt={'$shape': (3, 4)}, n=None)
 
+        # note, in the following find_one is used also for the sub_spec:
+        spec2 = lay2.add(hdfdb.FileDB.find, flt={'$name': '/u'}, n=1)
+        sub_spec2 = spec2.add(hdfdb.ObjDB.find_one, flt={'$shape': (3, 4)}, n=1)
+
         self.assertFalse(spec.is_valid())
         self.assertFalse(sub_spec.is_valid())
         self.assertEqual([], spec.get_valid())
 
         with h5tbx.File() as h5:
             h5.create_dataset('u', shape=(3, 4), dtype='float32')
 
-            res = lay.validate(h5)
+            res = lay1.validate(h5)
             self.assertTrue(res.is_valid())
+            res2 = lay2.validate(h5)
+            self.assertTrue(res2.is_valid())
+
             self.assertTrue(spec.is_valid())
             self.assertTrue(sub_spec.is_valid())
             self.assertEqual([spec, sub_spec], spec.get_valid())