From 7f9a293929be021eb73aec35defe254351557dcb Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 10 Mar 2021 19:22:32 +0300
Subject: Update docs with k-gwa endpoints demo

---
 docs/gemma.ipynb | 85 +++++++++++++++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 81 insertions(+), 4 deletions(-)

(limited to 'docs/gemma.ipynb')

diff --git a/docs/gemma.ipynb b/docs/gemma.ipynb
index 4fbaab2..a66df47 100644
--- a/docs/gemma.ipynb
+++ b/docs/gemma.ipynb
@@ -8,7 +8,7 @@
     "\n",
     "This document outlines how to use gemma from Genenetwork3.\n",
     "\n",
-    "The current mechanism for how Gemma runs is that when you run one of the endpoints that runs the actual gemma, it constructs the command and queues it in to a REDIS queue; thereby bypassing any time-out issues with the endpoind for long running process. A worker(sheepdog) processes the endpoints.\n",
+    "The current mechanism for how Gemma runs is that when you run one of the endpoints that runs the actual gemma, it constructs the command and queues it in to a REDIS queue; thereby bypassing any time-out issues with the endpoint for a long running process. A worker(sheepdog) processes the endpoints.\n",
     "\n",
     "If you are running gn3 through a development environment, ensure that it is up and running by running the command:\n",
     "\n",
@@ -373,12 +373,89 @@
     "print(r.json())"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "## K-GWA computation\n",
+    "\n",
+    "Computing k and gwa in one full swoop. This is important since in GN2, gemma does this in one full swoop."
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##### POST /api/gemma/k-gwa-compute/covars/maf/:maf/:token\n"
+   ]
+  },
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 89,
    "metadata": {},
-   "outputs": [],
-   "source": []
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'output_file': 'c718773b04935405258315b9588d13e6-output.json', 'status': 'queued', 'unique_id': 'cmd::2021-03-1010-1138-1138-558d7849-793f-4625-aac9-73d6bbc6dfdb'}\n"
+     ]
+    }
+   ],
+   "source": [
+    "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/k-gwa-compute/covars/VROD4N-XVW1L0\")\n",
+    "print(r.json())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##### POST /api/gemma/k-gwa-compute/loco/:chromosomes/maf/:maf/:token"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 92,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'output_file': '8f4906862459e59dcb452fd8162d2cc1-output.json', 'status': 'queued', 'unique_id': 'cmd::2021-03-1010-1402-1402-1fe13423-e4f6-4f4f-9c1d-c855e3ab55b5'}\n"
+     ]
+    }
+   ],
+   "source": [
+    "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/k-gwa-compute/loco/1%2C2%2C3/maf/9/VROD4N-XVW1L0\")\n",
+    "print(r.json())"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "##### POST /api/k-gwa-compute/covars/loco/:chromosomes/maf/:maf/:token"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 93,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "{'output_file': 'c718773b04935405258315b9588d13e6-output.json', 'status': 'queued', 'unique_id': 'cmd::2021-03-1010-1947-1947-c07c85e7-1355-4fab-bf9c-6c5e68f91a36'}\n"
+     ]
+    }
+   ],
+   "source": [
+    "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma//k-gwa-compute/covars/loco/1%2C2%2C3/maf/9/VROD4N-XVW1L0\")\n",
+    "print(r.json())"
+   ]
   }
  ],
  "metadata": {
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