From 957d295a859d6c5b9a65bc8dc77295e35fe94272 Mon Sep 17 00:00:00 2001
From: Matthias Probst <matth.probst@gmail.com>
Date: Mon, 24 Jun 2024 08:07:31 +0200
Subject: [PATCH] Update Examples.ipynb

---
 docs/userguide/layout/Examples.ipynb | 145 ++++++++++++++++++++++++++-
 1 file changed, 143 insertions(+), 2 deletions(-)

diff --git a/docs/userguide/layout/Examples.ipynb b/docs/userguide/layout/Examples.ipynb
index 594d400..d4dccfd 100644
--- a/docs/userguide/layout/Examples.ipynb
+++ b/docs/userguide/layout/Examples.ipynb
@@ -101,7 +101,7 @@
       "+--------------------------------------+--------+--------------------+---------------------------+---------------+---------------+-----------------------------------------+\n",
       "| id                                   |   flag | flag description   | description               | target_type   | target_name   | func                                    |\n",
       "|--------------------------------------+--------+--------------------+---------------------------+---------------+---------------+-----------------------------------------|\n",
-      "| 258da4da-f080-404a-bfdc-2faa6b32e60b |      1 | SUCCESSFUL         | String dataset must be 1D | Group         | tmp0.hdf      | h5rdmtoolbox.database.hdfdb.filedb.find |\n",
+      "| 39344777-7032-4f34-9f1f-ad14989430f5 |      1 | SUCCESSFUL         | String dataset must be 1D | Group         | tmp0.hdf      | h5rdmtoolbox.database.hdfdb.filedb.find |\n",
       "+--------------------------------------+--------+--------------------+---------------------------+---------------+---------------+-----------------------------------------+\n",
       "--> Layout is valid\n"
      ]
@@ -142,10 +142,151 @@
     "re.search('^(?!S).*', 'M123')"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "6d8709ac-3676-4a56-891a-832deca11db4",
+   "metadata": {},
+   "source": [
+    "## Defining RDF specifications\n",
+    "\n",
+    "All dataset must have the attribute units, which shall be semantically described by `http://w3id.org/nfdi4ing/metadata4ing#hasUnit`"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "b6bda83f-582e-48d0-a9dc-7b8fc0576520",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "rdf_lay = layout.Layout()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "a98ad451-b361-4f62-a24e-bc6840f9ae2f",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "is_dataset = rdf_lay.add(\n",
+    "    hdfdb.FileDB.find,\n",
+    "    flt={'units': {'$exists': True}},\n",
+    "    recursive=True,\n",
+    "    objfilter='dataset',\n",
+    "    description='String dataset must be 1D',\n",
+    "    n={'$gt': 0}\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "edbd9a8f-03a0-41e8-b954-a97b1b5d180c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from h5rdmtoolbox.database import rdf_find"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "515b96d8-9025-4696-a5d7-6a2d0bc996f4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "is_dataset = is_dataset.add(\n",
+    "    rdf_find,\n",
+    "    rdf_predicate=\"http://w3id.org/nfdi4ing/metadata4ing#hasUnit\",\n",
+    "    n=1\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "89fb9a00-eb31-42cf-9de1-e6e9785499b8",
+   "metadata": {},
+   "source": [
+    "Test the layout specification"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 16,
+   "id": "4605bae5-fca9-4e0f-9249-cb77c05aab2a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with h5tbx.File() as h5:\n",
+    "    ds =h5.create_dataset('velocity', data=4.5, attrs={'units': 'm/s'})"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 17,
+   "id": "83cd6254-f597-4dad-b281-7a594a0aec83",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "2024-06-23_15:25:31,621 ERROR    [core.py:330] Applying spec. \"LayoutSpecification(kwargs={'rdf_predicate': 'http://w3id.org/nfdi4ing/metadata4ing#hasUnit'})\" failed due to not matching the number of results: 1 != 0\n"
+     ]
+    },
+    {
+     "data": {
+      "text/plain": [
+       "False"
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rdf_lay.validate(h5.hdf_filename).is_valid()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 18,
+   "id": "bb359f6d-929e-46fa-a9c6-6c33e38658a3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "with h5tbx.File() as h5:\n",
+    "    ds =h5.create_dataset('velocity', data=4.5, attrs={'units': 'm/s'})\n",
+    "    ds.rdf['units'].predicate = \"http://w3id.org/nfdi4ing/metadata4ing#hasUnit\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 19,
+   "id": "264024ed-44a5-40ad-b2da-1075c7a58c69",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "True"
+      ]
+     },
+     "execution_count": 19,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "rdf_lay.validate(h5.hdf_filename).is_valid()"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "95ff9f7c-2f9d-4552-bdad-7139e4ea445d",
+   "id": "6d93fd9a-8df5-413a-ad92-23021ae8fc19",
    "metadata": {},
    "outputs": [],
    "source": []