Backport notebook changes from main branch (#4846)

* Bumped forge config file to commit hash 638047f in mooc notebooks (#4818) * Update docs nnotebooks to point to d9f6cb8 forge config (#4823) --------- Co-authored-by: Mohameth François SY <[email protected]>
BlueBrain · Apr 5, 2024 · 897baad · 897baad
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Showing 4 changed files with 37 additions and 13 deletions.
diff --git a/...ting-started/notebooks/MOOC_Content_based_Recommender_System_using_Blue_Brain_Nexus.ipynb b/...ting-started/notebooks/MOOC_Content_based_Recommender_System_using_Blue_Brain_Nexus.ipynb
@@ -144,7 +144,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "r = requests.get('https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/rdfmodel/jsonldcontext.json')\n",
+    "r = requests.get('https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/rdfmodel/jsonldcontext.json')\n",
     "dirpath = './rdfmodel'\n",
     "Path(dirpath).mkdir(parents=True, exist_ok=True)\n",
     "with open(f'{dirpath}/jsonldcontext.json', 'w') as outfile:\n",
@@ -168,7 +168,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "forge = KnowledgeGraphForge(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/forge.yml\",\n",
+    "forge = KnowledgeGraphForge(\"https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/forge.yml\",\n",
     "                            bucket=f\"{ORG}/{PROJECT}\",\n",
     "                            endpoint=ENDPOINT,\n",
     "                            token=TOKEN)"

diff --git a/docs/src/main/paradox/docs/getting-started/notebooks/dataset_from_different_sources.ipynb b/docs/src/main/paradox/docs/getting-started/notebooks/dataset_from_different_sources.ipynb
@@ -136,7 +136,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "r = requests.get('https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/rdfmodel/jsonldcontext.json')\n",
+    "r = requests.get('https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/rdfmodel/jsonldcontext.json')\n",
     "dirpath = './rdfmodel'\n",
     "Path(dirpath).mkdir(parents=True, exist_ok=True)\n",
     "with open(f'{dirpath}/jsonldcontext.json', 'w') as outfile:\n",
@@ -159,7 +159,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "forge = KnowledgeGraphForge(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/forge.yml\",\n",
+    "forge = KnowledgeGraphForge(\"https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/forge.yml\",\n",
     "                            bucket=f\"{ORG}/{PROJECT}\",\n",
     "                            endpoint=\"https://sandbox.bluebrainnexus.io/v1\",\n",
     "                            token=TOKEN)"
@@ -483,7 +483,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "allen_nm_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_morphology_dataset.hjson\") # TODO\n",
+    "allen_nm_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_morphology_dataset.hjson\") # TODO\n",
     "nm_allen_resources = forge.map(nm_allen_metadata, allen_nm_mapping)"
    ]
   },
@@ -501,7 +501,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "allen_ephys_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_ephys_dataset.hjson\") # TODO\n",
+    "allen_ephys_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_ephys_dataset.hjson\") # TODO\n",
     "nephys_allen_resources = forge.map(nm_allen_metadata, allen_ephys_mapping)"
    ]
   },
@@ -519,7 +519,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "mouselight_nm_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/mouselight_dataset.hjson\") # TODO\n",
+    "mouselight_nm_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/mappings/mouselight_dataset.hjson\") # TODO\n",
     "nm_mouselight_resources = forge.map(nm_mouselight_metadata, mouselight_nm_mapping)"
    ]
   },

diff --git a/docs/src/main/paradox/docs/getting-started/notebooks/file-to-resource-mapping.hjson b/docs/src/main/paradox/docs/getting-started/notebooks/file-to-resource-mapping.hjson
@@ -0,0 +1,25 @@
+{
+    type: DataDownload
+    contentSize:
+    {
+        unitCode: f"bytes"
+        value: x._bytes
+    }
+    digest:
+    {
+        algorithm: x._digest._algorithm
+        value: x._digest._value
+    }
+    encodingFormat: x._mediaType
+    name: x._filename
+    contentUrl: x._self
+    atLocation:
+    {
+        type: Location
+        store: 
+        {
+            id: x._storage["@id"]
+        }
+        location: x._location if '_location' in x else None
+    }
+}
diff --git a/docs/src/main/paradox/docs/getting-started/notebooks/one_cell_minds.ipynb b/docs/src/main/paradox/docs/getting-started/notebooks/one_cell_minds.ipynb
@@ -139,7 +139,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "r = requests.get('https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/rdfmodel/jsonldcontext.json')\n",
+    "r = requests.get('https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/rdfmodel/jsonldcontext.json')\n",
     "dirpath = './rdfmodel'\n",
     "Path(dirpath).mkdir(parents=True, exist_ok=True)\n",
     "with open(f'{dirpath}/jsonldcontext.json', 'w') as outfile:\n",
@@ -162,11 +162,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "forge = KnowledgeGraphForge(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/forge.yml\",\n",
+    "forge = KnowledgeGraphForge(\"https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/forge.yml\",\n",
     "                            bucket=f\"{ORG}/{PROJECT}\",\n",
     "                            endpoint=\"https://sandbox.bluebrainnexus.io/v1\",\n",
-    "                            token=TOKEN,\n",
-    "                            file_resource_mapping='https://raw.githubusercontent.com/BlueBrain/nexus-forge/5580e906eb1df9e3b3970a735b82f609207df717/examples/configurations/nexus-store/file-to-resource-mapping.hjson'))"
+    "                            token=TOKEN)"
    ]
   },
   {
@@ -334,7 +333,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "allen_nm_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_morphology_dataset.hjson\")\n",
+    "allen_nm_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_morphology_dataset.hjson\")\n",
     "nm_allen_resources = forge.map(nm_allen_metadata, allen_nm_mapping, na='')"
    ]
   },
@@ -351,7 +350,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "allen_ephys_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/ef830192d4e7bb95f9351c4bdab7b0114c27e2f0/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_ephys_dataset.hjson\")\n",
+    "allen_ephys_mapping = DictionaryMapping.load(\"https://raw.githubusercontent.com/BlueBrain/nexus/d9f6cb83a27149c29bc604f3c34ea00c9ad64e67/docs/src/main/paradox/docs/getting-started/notebooks/mappings/allen_ephys_dataset.hjson\")\n",
     "nephys_allen_resources = forge.map(nm_allen_metadata, allen_ephys_mapping, na='')"
    ]
   },