Merge pull request #27 from TheJacksonLaboratory/task/add-client-logi…

…n-tutorial Adding geneweaver client login tutorial
TheJacksonLaboratory · Nov 29, 2023 · 0398f19 · 0398f19
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diff --git a/docs/tutorial/geneweaver_client_login.ipynb b/docs/tutorial/geneweaver_client_login.ipynb
@@ -0,0 +1,272 @@
+{
+ "nbformat": 4,
+ "nbformat_minor": 0,
+ "metadata": {
+  "colab": {
+   "provenance": []
+  },
+  "kernelspec": {
+   "name": "python3",
+   "display_name": "Python 3"
+  },
+  "language_info": {
+   "name": "python"
+  }
+ },
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "source": [
+    "# Client Login\n",
+    "\n",
+    "The following tutorial will demonstrate how to use the Geneweaver Client package to log\n",
+    "in to the Geneweaver API. This will allow you to access the Geneweaver API from the\n",
+    "command line or from within a Python script.\n",
+    "\n",
+    "The Geneweaver Client (`geneweaver-client`) package is available on PyPI and can be\n",
+    "installed with pip or poetry. The package provides many useful functions for interacting\n",
+    "with Geneweaver from a client context, including utility functions to make\n",
+    "authentication simple.\n",
+    "\n",
+    "This tutorial will demonstrate these utility functions from a Jupyter Notebook, but they\n",
+    "can also be used from the command line or from within a Python script.\n",
+    "\n",
+    "\n",
+    "###Install the `geneweaver-client` package"
+   ],
+   "metadata": {
+    "id": "qXfFhL8myKJd"
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {
+    "id": "Hs7pLPIhx7fE"
+   },
+   "outputs": [],
+   "source": [
+    "!pip install geneweaver-client"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Using The Command Line Client\n",
+    "### Access Help Documentation"
+   ],
+   "metadata": {
+    "id": "HIBxnwBPyWwc"
+   }
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "!gweave beta auth --help"
+   ],
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "id": "5mrdO2jjx-LQ",
+    "outputId": "45579f02-5f98-4657-fd8b-16b6c45da569"
+   },
+   "execution_count": 2,
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stdout",
+     "text": [
+      "\u001B[1m                                                                                                    \u001B[0m\n",
+      "\u001B[1m \u001B[0m\u001B[1;33mUsage: \u001B[0m\u001B[1mgweave beta auth [OPTIONS] COMMAND [ARGS]...\u001B[0m\u001B[1m                                               \u001B[0m\u001B[1m \u001B[0m\n",
+      "\u001B[1m                                                                                                    \u001B[0m\n",
+      " The auth commands allow you to authenticate with the GeneWeaver API.                               \n",
+      "                                                                                                    \n",
+      "\u001B[2m╭─\u001B[0m\u001B[2m Options \u001B[0m\u001B[2m───────────────────────────────────────────────────────────────────────\u001B[0m\u001B[2m─╮\u001B[0m\n",
+      "\u001B[2m│\u001B[0m \u001B[1;36m-\u001B[0m\u001B[1;36m-help\u001B[0m          Show this message and exit.                                      \u001B[2m│\u001B[0m\n",
+      "\u001B[2m╰──────────────────────────────────────────────────────────────────────────────────╯\u001B[0m\n",
+      "\u001B[2m╭─\u001B[0m\u001B[2m Commands \u001B[0m\u001B[2m──────────────────────────────────────────────────────────────────────\u001B[0m\u001B[2m─╮\u001B[0m\n",
+      "\u001B[2m│\u001B[0m \u001B[1;36mlogin                           \u001B[0m\u001B[1;36m \u001B[0m Run the device authorization flow.             \u001B[2m│\u001B[0m\n",
+      "\u001B[2m│\u001B[0m \u001B[1;36mprint-access-token              \u001B[0m\u001B[1;36m \u001B[0m Print the current user's access token.         \u001B[2m│\u001B[0m\n",
+      "\u001B[2m│\u001B[0m \u001B[1;36mprint-identity-token            \u001B[0m\u001B[1;36m \u001B[0m Print the current user's identity token.       \u001B[2m│\u001B[0m\n",
+      "\u001B[2m╰──────────────────────────────────────────────────────────────────────────────────╯\u001B[0m\n",
+      "\n"
+     ]
+    }
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "### Login To Geneweaver"
+   ],
+   "metadata": {
+    "id": "U2Xelf5Xyk1x"
+   }
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "!gweave beta auth login"
+   ],
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "id": "IDPInF0WyhGf",
+    "outputId": "53bad9b8-e0c8-458d-ecd2-9d056859f400"
+   },
+   "execution_count": 4,
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stdout",
+     "text": [
+      "1. On your computer or mobile device navigate to:  https://geneweaver.auth0.com/activate?user_code=PNTH-VVCC\n",
+      "2. Enter the following code:  PNTH-VVCC\n",
+      "Authenticated!\n",
+      "- Id Token: eyJhbGciOi...\n"
+     ]
+    }
+   ]
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "!gweave beta auth print-access-token"
+   ],
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "id": "nuOAds5gyqqY",
+    "outputId": "32c37920-daff-4547-c62b-84a902191944"
+   },
+   "execution_count": 5,
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stdout",
+     "text": [
+      "eyJhbGciOiJSUzI1...\n"
+     ]
+    }
+   ]
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "!gweave beta auth print-identity-token"
+   ],
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "id": "x62YK2twzR8J",
+    "outputId": "51f064f2-811b-4743-f6b1-b42c636f5241"
+   },
+   "execution_count": 6,
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stdout",
+     "text": [
+      "eyJhbGciOiJSUzI1...\n"
+     ]
+    }
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## Using The Python Package\n",
+    "### Login To Geneweaver"
+   ],
+   "metadata": {
+    "id": "vZf6SfxrzZMX"
+   }
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "from geneweaver.client.auth import login"
+   ],
+   "metadata": {
+    "id": "wQWHglhJzha6"
+   },
+   "execution_count": 7,
+   "outputs": []
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "# Run the login function and follow the link in the output.\n",
+    "# Confirm that the code matches the output here,\n",
+    "# then sign-up or login.\n",
+    "login()\n",
+    "# Wait for the \"Authenticated!\" message, then continue."
+   ],
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/"
+    },
+    "id": "f_8mne96zt8d",
+    "outputId": "469ffac6-a789-41e7-b6f2-18547b31628e"
+   },
+   "execution_count": 8,
+   "outputs": [
+    {
+     "output_type": "stream",
+     "name": "stdout",
+     "text": [
+      "1. On your computer or mobile device navigate to:  https://geneweaver.auth0.com/activate?user_code=RNPC-MKQJ\n",
+      "2. Enter the following code:  RNPC-MKQJ\n",
+      "Authenticated!\n",
+      "- Id Token: eyJhbGciOi...\n"
+     ]
+    }
+   ]
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "from geneweaver.client.auth import get_access_token"
+   ],
+   "metadata": {
+    "id": "8knTLojQzxIs"
+   },
+   "execution_count": 12,
+   "outputs": []
+  },
+  {
+   "cell_type": "code",
+   "source": [
+    "get_access_token()"
+   ],
+   "metadata": {
+    "colab": {
+     "base_uri": "https://localhost:8080/",
+     "height": 105
+    },
+    "id": "2SSTSFVkz1EF",
+    "outputId": "756d5123-45fa-47c9-b471-1f3734df3ba9"
+   },
+   "execution_count": 13,
+   "outputs": [
+    {
+     "output_type": "execute_result",
+     "data": {
+      "text/plain": [
+       "'eyJhbGciOiJSUzI1N...'"
+      ],
+      "application/vnd.google.colaboratory.intrinsic+json": {
+       "type": "string"
+      }
+     },
+     "metadata": {},
+     "execution_count": 13
+    }
+   ]
+  }
+ ]
+}
diff --git a/mkdocs.yml b/mkdocs.yml
@@ -79,6 +79,7 @@ nav:
       - Package Based Architecture: concepts/package-based-architecture.md
   - Tutorial:
       - tutorial/index.md
+      - Client Login: tutorial/geneweaver_client_login.ipynb
       - NCI-60 Example Workflow: tutorial/nci_60_example_01.ipynb
       - Download Genesets: tutorial/download_genesets.ipynb
 #      - Accessing Geneweaver Data: tutorial/accessing-geneweaver-data.md