Introduce allow disconnected option to the CytoscapeViewer (#111)

jupyrdf · Apr 26, 2021 · 684edff · 684edff
1 parent cad19ce
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diff --git a/examples/Cytoscape_Viewer.ipynb b/examples/Cytoscape_Viewer.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "preliminary-enzyme",
+   "id": "ad8c22f5",
    "metadata": {},
    "source": [
     "# CytoscapeViewer Example\n",
@@ -13,7 +13,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "ambient-black",
+   "id": "16b0a0c7",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -25,15 +25,15 @@
   },
   {
    "cell_type": "markdown",
-   "id": "varied-estimate",
+   "id": "021f0068",
    "metadata": {},
    "source": [
     "Let's start by getting our graph loaded in."
    ]
   },
   {
    "cell_type": "markdown",
-   "id": "aquatic-richardson",
+   "id": "c4a173f9",
    "metadata": {},
    "source": [
     "Explain why we need a subgraph (too many nodes causes issues with cytoscape)."
@@ -42,7 +42,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "about-berlin",
+   "id": "2de0b9b6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -70,6 +70,7 @@
     "            (film:4)\n",
     "            (planet:1)\n",
     "            (planet:2)\n",
+    "            (planet:5)\n",
     "        }\n",
     "    }\n",
     "    \"\"\"\n",
@@ -80,7 +81,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "neural-there",
+   "id": "9e7a7dc0",
    "metadata": {},
    "source": [
     "## Now we can initiate the `CytoscapeViewer` object, which allows us to get a nice representation of an RDF or networkx graph"
@@ -89,7 +90,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "solid-shakespeare",
+   "id": "5f8f01cb",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -101,7 +102,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "legitimate-interest",
+   "id": "d3cbac63",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -110,7 +111,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "annoying-michigan",
+   "id": "7f286413",
    "metadata": {},
    "source": [
     "> The literal data from the RDF graph is collapsed onto the node based on the `RDF2NX`\n",

diff --git a/examples/InteractiveViewer.ipynb b/examples/InteractiveViewer.ipynb
@@ -2,7 +2,7 @@
  "cells": [
   {
    "cell_type": "markdown",
-   "id": "micro-contract",
+   "id": "e86027be",
    "metadata": {},
    "source": [
     "## `InteractiveViewer` Example\n",
@@ -20,7 +20,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "fluid-native",
+   "id": "28312451",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -33,7 +33,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "independent-hydrogen",
+   "id": "445b989a",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -96,15 +96,25 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "guided-cigarette",
+   "id": "ccf71ad7",
    "metadata": {},
    "outputs": [],
    "source": [
     "# Run the widget and assign the graph\n",
     "iv = InteractiveViewer()\n",
-    "iv.graph = simple_graph\n",
+    "iv.rdf_graph = simple_graph\n",
     "iv"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0e34fcee",
+   "metadata": {},
+   "source": [
+    "> Note: the `allow disconnected` option is disabled due to issues with async behavior of\n",
+    "> the underlying cytoscape widget. Track this issue within the `ipyradiant` library\n",
+    "> [here](https://github.com/jupyrdf/ipyradiant/issues/110)."
+   ]
   }
  ],
  "metadata": {

diff --git a/examples/RDF_to_NX_Custom.ipynb b/examples/RDF_to_NX_Custom.ipynb
@@ -268,37 +268,10 @@
     "\n",
     "The purpose of creating these projections is often to generate a view that is easier for\n",
     "humans to interpret (or to leverage graph algorithms for LPGs). The following cells\n",
-    "demonstrate how the `ipyradiant` visualization widget `CytoscapeViewer` can be used\n",
-    "together with a simple class for checking JSON data in order to visualize and inspect an\n",
-    "LPG graph."
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "import ipywidgets as ipyw\n",
-    "from IPython.display import JSON, display\n",
-    "\n",
-    "\n",
-    "# a simple class for visualizing JSON output for cytoscape graphs\n",
-    "class CombinedExample(ipyw.VBox):\n",
-    "    def __init__(self, *args, **kwargs):\n",
-    "        super().__init__(*args, **kwargs)\n",
-    "        self.json_output = ipyw.Output()\n",
-    "        self.graph_widget = kwargs[\"graph_widget\"]\n",
-    "        self.children = [self.graph_widget, self.json_output]\n",
-    "        self.graph_widget.cytoscape_widget.on(\"node\", \"click\", self.load_json)\n",
-    "\n",
-    "    def load_json(self, node):\n",
-    "        data = node[\"data\"]\n",
-    "        data.pop(\"_label\", None)\n",
-    "        data.pop(\"_attrs\", None)\n",
-    "        with self.json_output:\n",
-    "            self.json_output.clear_output()\n",
-    "            display(JSON(data))"
+    "demonstrate how the `ipyradiant` visualization widget `InteractiveViewer` can be used\n",
+    "to visualize and inspect an LPG graph.\n",
+    "\n",
+    "> Note: the option to remove disconnected nodes will be enabled on ticket [#110](https://github.com/jupyrdf/ipyradiant/issues/110)"
    ]
   },
   {
@@ -307,15 +280,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from ipyradiant.visualization import CytoscapeViewer\n",
-    "\n",
-    "cv = CytoscapeViewer()\n",
-    "# specify the label key for the nx graph (default=\"label\")\n",
-    "cv._nx_label = \"rdfs:label\"\n",
-    "cv.graph = nx_graph\n",
+    "from ipyradiant.visualization import InteractiveViewer\n",
     "\n",
-    "ce = CombinedExample(graph_widget=cv)\n",
-    "ce"
+    "iv = InteractiveViewer()\n",
+    "iv._rdf_converter = RDF2NX\n",
+    "iv.rdf_graph = lw.graph\n",
+    "iv"
    ]
   },
   {

diff --git a/examples/Test_CytoscapeViewer.ipynb b/examples/Test_CytoscapeViewer.ipynb
@@ -4,7 +4,11 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# A Basic Test for the Cytoscape Viewer"
+    "# A Basic Test for the Cytoscape Viewer\n",
+    "\n",
+    "TODO:\n",
+    "\n",
+    "- Test the `allow_disconnected` flag"
    ]
   },
   {
@@ -121,7 +125,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.9"
+   "version": "3.7.10"
   }
  },
  "nbformat": 4,