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authorBonfaceKilz2021-03-10 19:22:32 +0300
committerBonfaceKilz2021-03-10 19:22:32 +0300
commit7f9a293929be021eb73aec35defe254351557dcb (patch)
treebb2b2013c3ba3239c1edff553d5d22e0d2a6fe43
parent3eae93bf7a6cdb014aaf4aded2087c6840155126 (diff)
downloadgenenetwork3-7f9a293929be021eb73aec35defe254351557dcb.tar.gz
Update docs with k-gwa endpoints demo
-rw-r--r--docs/gemma.ipynb85
1 files changed, 81 insertions, 4 deletions
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",
@@ -374,11 +374,88 @@
]
},
{
+ "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": {