diff options
| -rw-r--r-- | docs/gemma.ipynb | 147 |
1 files changed, 112 insertions, 35 deletions
diff --git a/docs/gemma.ipynb b/docs/gemma.ipynb index a66df47..956d1d3 100644 --- a/docs/gemma.ipynb +++ b/docs/gemma.ipynb @@ -21,7 +21,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 1, "metadata": {}, "outputs": [], "source": [ @@ -40,7 +40,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 2, "metadata": { "scrolled": true }, @@ -66,6 +66,27 @@ "\n", "Before you perform any computation, you need to ensure you have your data uploaded. For these examples, I'll use data provided [here](https://github.com/genetics-statistics/gemma-wrapper/tree/master/test/data/input)\n", "\n", + "An example of a metadata.json file:\n", + "\n", + "```\n", + "{\n", + " \"title\": \"This is my dataset for testing the REST API\",\n", + " \"description\": \"Longer description\",\n", + " \"date\": \"20210127\",\n", + " \"authors\": [\n", + " \"R. W. Williams\"\n", + " ],\n", + " \"cross\": \"BXD\",\n", + " \"geno\": \"/ipfs/QmakcPHuxKouUvuNZ5Gna1pyXSAPB5fFSkqFt5pDydd9A4/GN638/BXH.geno\",\n", + " \"pheno\": \"BXD_pheno.txt\",\n", + " \"snps\": \"BXD_snps.txt\",\n", + " \"covar\": \"BXD_covariates.txt\"\n", + "}\n", + "\n", + "```\n", + "\n", + "Note that you provide the genotype file with an ipfs valid address.\n", + "\n", "##### POST /api/metadata/upload/:token\n", "\n", "If token is provided, your user directory will be overridden with the new upload data!\n" @@ -73,14 +94,14 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 22, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "{'status': 0, 'token': 'VROD4N-XVW1L0'}\n" + "PEERO1-WE4BBX\n" ] } ], @@ -88,39 +109,49 @@ "# I intentionally upload the data file without having the metadata file so that I can upload it later.\n", "r = requests.post(\"http://gn3-test.genenetwork.org/api/metadata/upload/\",\n", " files=[('file', ('file.tar.gz',\n", - " open('/tmp/file.tar.gz',\n", + " open('/tmp/file-no-metadata.tar.gz',\n", " 'rb'), 'application/octet-stream'))])\n", "\n", - "print(r.json())" + "token_no_metadata = r.json()[\"token\"]\n", + "print(token_no_metadata)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "Now we overrlde the upload with the relevant metadatafile:" + "Now we can override the upload with the relevant metadatafile if we want. If the contents are the same, we get the same token!" ] }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 40, + "metadata": {}, + "outputs": [], + "source": [ + "r = requests.post(\"http://gn3-test.genenetwork.org/api/metadata/upload/VROD4N-XVW1L0\",\n", + " files=[('file', ('file.tar.gz',\n", + " open('/tmp/file.tar.gz',\n", + " 'rb'), 'application/octet-stream'))])\n", + "\n", + "token = r.json()[\"token\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 41, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "{'status': 0, 'token': 'VROD4N-XVW1L0'}\n" + "VROD4N-XVW1L0\n" ] } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/metadata/upload/VROD4N-XVW1L0\",\n", - " files=[('file', ('file-with-metadata.tar.gz',\n", - " open('/tmp/file-with-metadata.tar.gz',\n", - " 'rb'), 'application/octet-stream'))])\n", - "\n", - "print(r.json())" + "print(token)" ] }, { @@ -157,19 +188,20 @@ }, { "cell_type": "code", - "execution_count": 66, + "execution_count": 43, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "{'output_file': '8f4906862459e59dcb452fd8162d2cc1-output.json', 'status': 'queued', 'unique_id': 'cmd::2021-03-1005-1727-1727-7006dfef-8e60-4bb2-8390-0c174d15a17c'}\n" + "{'output_file': '5e9b1e32053f3d456418af2119a0a9e0-output.json', 'status': 'queued', 'unique_id': 'cmd::2021-03-2209-1901-1901-aef4973e-6d07-49f3-8216-ea883c6442b3'}\n" ] } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/k-compute/VROD4N-XVW1L0\")\n", + "r = requests.post(\"http://gn3-test.genenetwork.org/api/\"\n", + " f\"gemma/k-compute/{token}\")\n", "print(r.json())" ] }, @@ -180,7 +212,7 @@ "This generates the command:\n", "\n", "```\n", - "gemma-wrapper --json -- -g /tmp/VROD4N-XVW1L0/BXD_geno.txt.gz -p /tmp/VROD4N-XVW1L0/BXD_pheno.txt -a /tmp/VROD4N-XVW1L0/BXD_snps.txt -gk > /tmp/VROD4N-XVW1L0/8f4906862459e59dcb452fd8162d2cc1-output.json\n", + "gemma-wrapper --json -- -g /tmp/cache/QmRZpiWCPxn6d1sCaPLpFQBpDmaPaPygvZ165oK4B9myjy/GN602/BXD.geno -p /tmp/VROD4N-XVW1L0/BXD_pheno.txt -a /tmp/VROD4N-XVW1L0/BXD_snps.txt -gk > /tmp/VROD4N-XVW1L0/5e9b1e32053f3d456418af2119a0a9e0-output.json\n", "```" ] }, @@ -193,25 +225,52 @@ }, { "cell_type": "code", - "execution_count": 35, + "execution_count": 44, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "{'status': 'queued'}\n" + "{'status': 'error'}\n" ] } ], "source": [ - "r = requests.get(\"http://gn3-test.genenetwork.org/api/gemma/status/cmd%3A%3A2021-03-1005-1727-1727-7006dfef-8e60-4bb2-8390-0c174d15a17c\")\n", + "r = requests.get(\"http://gn3-test.genenetwork.org/api/gemma/\"\n", + " \"status/cmd%3A%3A2021-03-2209-1901-1901-aef4973e-6d07-\"\n", + " \"49f3-8216-ea883c6442b3\")\n", "print(r.json())" ] }, { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "Work as expected with the error log:\n", + "\n", + "```\n", + "Using GEMMA 0.98.4 (2020-12-15) by Xiang Zhou and team (C) 2012-2020\n", + "\n", + "Found 0.98.4, comparing against expected v0.98.0\n", + "\n", + "GEMMA 0.98.4 (2020-12-15) by Xiang Zhou and team (C) 2012-2020\n", + "Reading Files ...\n", + "**** FAILED: Parsing input file '/tmp/cache/QmRZpiWCPxn6d1sCaPLpFQBpDmaPaPygvZ165oK4B9myjy/GN602/BXD.geno' failed in function ReadFile_geno in src/gemma_io.cpp at line 744 \n", + "{\"warnings\":[],\"errno\":2,\"debug\":[],\"type\":\"K\",\"files\":[[null,\"/tmp/605220a4d963542392fb44c15060cf6a8cee659b.log.txt\",\"/tmp/605220a4d963542392fb44c15060cf6a8cee659b.cXX.txt\"]],\"gemma_command\":\"/gnu/store/yyrfmg0i18w190l4lb21cv86fqclalsk-gemma-gn2-git-0.98.3-47221d6/bin/gemma -g /tmp/cache/QmRZpiWCPxn6d1sCaPLpFQBpDmaPaPygvZ165oK4B9myjy/GN602/BXD.geno -p /tmp/VROD4N-XVW1L0/BXD_pheno.txt -a /tmp/VROD4N-XVW1L0/BXD_snps.txt -gk -outdir /tmp -o 605220a4d963542392fb44c15060cf6a8cee659b\"}Traceback (most recent call last): \n", + " 6: from /gnu/store/86df7mjr3y1mrz62k4zipm6bznj10faj-profile/bin/gemma-wrapper:4:in `<main>' \n", + " 5: from /gnu/store/86df7mjr3y1mrz62k4zipm6bznj10faj-profile/bin/gemma-wrapper:4:in `load' \n", + " 4: from /gnu/store/p1alkfcsw3m24vlgxfb6gk24zn67h8n2-gemma-wrapper-0.98.1/bin/.real/gemma-wrapper:23:in `<top (required)>' \n", + " 3: from /gnu/store/p1alkfcsw3m24vlgxfb6gk24zn67h8n2-gemma-wrapper-0.98.1/bin/.real/gemma-wrapper:23:in `load' \n", + " 2: from /gnu/store/p1alkfcsw3m24vlgxfb6gk24zn67h8n2-gemma-wrapper-0.98.1/lib/ruby/vendor_ruby/gems/bio-gemma-wrapper-0.98.1/bin/gemma-wrapper:345:in `<top (required)>' \n", + " 1: from /gnu/store/p1alkfcsw3m24vlgxfb6gk24zn67h8n2-gemma-wrapper-0.98.1/lib/ruby/vendor_ruby/gems/bio-gemma-wrapper-0.98.1/bin/gemma-wrapper:316:in `block in <top (required)>' \n", + "/gnu/store/p1alkfcsw3m24vlgxfb6gk24zn67h8n2-gemma-wrapper-0.98.1/lib/ruby/vendor_ruby/gems/bio-gemma-wrapper-0.98.1/bin/gemma-wrapper:278:in `block in <top (required)>': exit on GEMMA error 2 (RuntimeError) \n", + "```" + ] + }, + { "cell_type": "code", - "execution_count": 68, + "execution_count": 31, "metadata": { "scrolled": true }, @@ -220,13 +279,17 @@ "name": "stdout", "output_type": "stream", "text": [ - "{'status': 'success'}\n" + "{'status': 'error'}\n" ] } ], "source": [ "# After a short while:\n", - "r = requests.get(\"http://gn3-test.genenetwork.org/api/gemma/status/cmd%3A%3A2021-03-1005-1727-1727-7006dfef-8e60-4bb2-8390-0c174d15a17c\")\n", + "# Commands will throw error since I didn't know where the right\n", + "# genotype files for BXD are :(\n", + "r = requests.get(\"http://gn3-test.genenetwork.org/api/gemma/status/\"\n", + " \"cmd%3A%3A2021-03-2209-0015-\"\n", + " \"0015-bb5c765f-93a3-45d1-a50d-b817cd7192e7\")\n", "print(r.json())" ] }, @@ -259,7 +322,8 @@ } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/k-compute/loco/1%2C2%2C3%2C4/VROD4N-XVW1L0\")\n", + "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/\"\n", + " \"k-compute/loco/1%2C2%2C3%2C4/VROD4N-XVW1L0\")\n", "print(r.json())" ] }, @@ -288,7 +352,9 @@ } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/gwa-compute/8f4906862459e59dcb452fd8162d2cc1-output.json/VROD4N-XVW1L0\")\n", + "r = requests.post(\"http://gn3-test.genenetwork.org/api/\"\n", + " \"gemma/gwa-compute/8f4906862459e59dcb\"\n", + " \"452fd8162d2cc1-output.json/VROD4N-XVW1L0\")\n", "print(r.json())" ] }, @@ -315,7 +381,10 @@ } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/gwa-compute/covars/8f4906862459e59dcb452fd8162d2cc1-output.json/VROD4N-XVW1L0\")\n", + "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/\"\n", + " \"gwa-compute/covars/\"\n", + " \"8f4906862459e59dcb452fd8162d2cc1-output.json/\"\n", + " \"VROD4N-XVW1L0\")\n", "print(r.json())" ] }, @@ -342,7 +411,10 @@ } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/gwa-compute/8f4906862459e59dcb452fd8162d2cc1-output.json/loco/maf/9/VROD4N-XVW1L0\")\n", + "r = requests.post(\"http://gn3-test.genenetwork.org/api/\"\n", + " \"gemma/gwa-compute/\"\n", + " \"8f4906862459e59dcb452fd8162d2cc1-output.json/\"\n", + " \"loco/maf/9/VROD4N-XVW1L0\")\n", "print(r.json())" ] }, @@ -369,7 +441,9 @@ } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/gwa-compute/8f4906862459e59dcb452fd8162d2cc1-output.json/loco/covars/maf/9/VROD4N-XVW1L0\")\n", + "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/\"\n", + " \"gwa-compute/8f4906862459e59dcb452fd8162d2cc1\"\n", + " \"-output.json/loco/covars/maf/9/VROD4N-XVW1L0\")\n", "print(r.json())" ] }, @@ -403,7 +477,8 @@ } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/k-gwa-compute/covars/VROD4N-XVW1L0\")\n", + "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/\"\n", + " \"k-gwa-compute/covars/VROD4N-XVW1L0\")\n", "print(r.json())" ] }, @@ -428,7 +503,8 @@ } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/k-gwa-compute/loco/1%2C2%2C3/maf/9/VROD4N-XVW1L0\")\n", + "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/\"\n", + " \"k-gwa-compute/loco/1%2C2%2C3/maf/9/VROD4N-XVW1L0\")\n", "print(r.json())" ] }, @@ -453,7 +529,8 @@ } ], "source": [ - "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma//k-gwa-compute/covars/loco/1%2C2%2C3/maf/9/VROD4N-XVW1L0\")\n", + "r = requests.post(\"http://gn3-test.genenetwork.org/api/gemma/\"\n", + " \"k-gwa-compute/covars/loco/1%2C2%2C3/maf/9/VROD4N-XVW1L0\")\n", "print(r.json())" ] } @@ -461,7 +538,7 @@ "metadata": { "kernelspec": { "display_name": "Python 3", - "language": "/gnu/store/bvd09gb8ka642jzgxd2lpqlpdp160gn0-python-wrapper-3.8.2/bin/python", + "language": "python", "name": "python3" }, "language_info": { @@ -474,7 +551,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.8.2" + "version": "3.9.2" } }, "nbformat": 4, |