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Ricardo Avila ravila4

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ravila4 / id_mapping_mygene.ipynb
Created November 16, 2020 16:04 — forked from newgene/id_mapping_mygene.ipynb
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ravila4 / gist:9aacae443c50a168b4267fca7448d88b
Created December 15, 2020 15:35
BASH_script_template.sh
#!/usr/bin/env bash
set -Eeuo pipefail
cd "$(dirname "${BASH_SOURCE[0]}")" >/dev/null 2>&1
trap cleanup SIGINT SIGTERM ERR EXIT
usage() {
cat <<EOF
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ravila4 / count_taxids.sh
Last active February 23, 2021 23:40
A demo of converting API responses to CSV format with JQ.
#!/bin/bash
# Genesets aggregated by taxid
aggs=`curl -s "https://mygeneset.info/v1/query?q=*&facets=taxid&facet_size=100"`
taxids=`echo $aggs | jq -r '.facets.taxid.terms | map(.term) | @csv'`
counts=`echo $aggs | jq -r '.facets.taxid.terms | map(.count) | @csv'`
# Query scientific name for each taxid
resp=`curl -s -X POST -d "q=${taxids}" "http://t.biothings.io/v1/query"`
species=`echo $resp | jq -r 'map(.scientific_name) | @csv'`
@ravila4
ravila4 / config.py
Last active November 13, 2022 01:42
MyGeneset test config
"""Web config to run MyGeneset API on GitHub Actions"""
import os
ES_INDEX = 'user_genesets'
COOKIE_SECRET = "JKA#9%Wc4ofuqM@C!&yLFsYE"
# ORCID keys
ORCID_CLIENT_ID = os.environ['ORCID_CLIENT_ID']
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ravila4 / gpt_completions.sh
Last active May 3, 2023 03:15
A simple curl wrapper around the OpenAI completions API.
#!/bin/bash
set -euo pipefail
# This script sends a request to the OpenAI completions endpoint and parses the output using jq.
# It is recommended that the API key is stored in an environment variable.
usage() {
echo "Usage: $0 [-k OPENAI_API_KEY] [-m MODEL] [-t MAX_TOKENS] PROMPT"
echo "Example: $0 -m text-davinci-002 -t 500 \"What is the capital of France?\""