bradfordcondon’s gists

bradfordcondon / gist:ec7078b8514a422e65db5e8d6cd29858

Last active March 11, 2019 15:59

link organism to analysis via the Links field on node

	<?php
	$orgs = db_select('chado.organism', 'o')
	->fields('o')
	->execute();
	foreach ($orgs as $organism) {
	$organism_id = $organism->organism_id;
	$nid = chado_get_nid_from_id('organism', $organism_id);
	$node = node_load($nid);
	$links = $node->field_resource_links ?? NULL;
	if ($links) {

bradfordcondon / find_sequence.sh

Created January 2, 2019 21:32

one liner for extracting a particular fasta sequence from a file by name

perl -ne 'if(/^>(\S+)/){$c=grep{/^$1$/}qw(sequence_name)}print if $c' file.fasta > out.fasta

bradfordcondon / reset_website.sh

Created December 19, 2018 21:23

rebuild drupal database (developer)

	#!/usr/bin/env bash

	DB_NAME="drupal"
	DB_PASS="secret"
	DB_USER="drupal"

	ADMIN_PASS=secret

	echo "Dropping DB: $DB_NAME"
	sudo -u postgres dropdb $DB_NAME

bradfordcondon / Migrate_node_fields.php

Last active March 15, 2019 17:19

migrate tripal 2 node fields to chado properties for tripal 3 compatibility and best FAIR practices

	<?php
	//if we made this into a module, we would use the tripal jobs... but we dont so its commented out for now.
	//
	//global $user;
	//tripal_add_job(
	// "Convert fields to properties", 'no_module',
	// 'snippet_tripal_job_callback',
	// 'chado_update_existing_node_urls',
	// [],
	// $user->uid

bradfordcondon / gist:aa2c509975ed79ce4162e17955226fb3

Created July 31, 2018 17:53

delete all git branches except master

git branch | grep -v "master" | xargs git branch -D

bradfordcondon / helper.sql

Last active September 7, 2018 23:42

postgresql diagnostics cheathseet

	### What are my densest indexes?
	SELECT relname, relpages
	FROM pg_class
	ORDER BY relpages DESC;

	### What are my running queries
	ELECT pid, age(query_start, clock_timestamp()), usename, query
	FROM pg_stat_activity
	WHERE query != '<IDLE>' AND query NOT ILIKE '%pg_stat_activity%'
	ORDER BY query_start desc;

bradfordcondon / 1.3_indexes.sql

Last active June 13, 2018 16:45

chado 1.3 add missing indexes

	set search_path to chado;
	create index if not exists dbxref_idx1 on dbxref (db_id);
	create index if not exists dbxref_idx2 on dbxref (accession);
	create index if not exists dbxref_idx3 on dbxref (version);
	create index if not exists cvterm_idx1 on cvterm (cv_id);
	create index if not exists cvterm_idx2 on cvterm (name);
	create index if not exists cvterm_idx3 on cvterm (dbxref_id);
	COMMENT ON INDEX cvterm_c1 IS 'A name can mean different things in';
	COMMENT ON INDEX cvterm_c2 IS 'The OBO identifier is globally unique.';
	create index if not exists cvterm_relationship_idx1 on cvterm_relationship (type_id);

bradfordcondon / cmap.json

Last active May 11, 2018 17:00

cmap.js for HWG trial

	{
	"#": "cmap-js chinese chestnut configuration file",
	"header": ": Chinese Chestnut Genetic map",
	"attribution": "HWG",
	"initialView": [
	{
	"source": "Chinese Chestnut Genetic Map",
	"map": "A"
	},
	{

bradfordcondon / AOtrigger.sql

Last active May 9, 2018 14:31

sql for creating a trigger for organism_analysis table to update when feature's organisms change.

	CREATE TRIGGER check_ao_linker
	AFTER INSERT ON feature
	FOR ROW
	EXECUTE PROCEDURE update_ao_linker();

	CREATE TRIGGER check_ao_linker_update
	AFTER UPDATE ON feature ON organism_id
	FOR ROW
	EXECUTE PROCEDURE update_ao_linker();

bradfordcondon / gist:eef6a96544a921fda427565162c0a62f

Created May 3, 2018 13:27

squashing commits for clean PRs


	git rebase -i HEAD~4 # rebase branch back the number of commits

	git commit --amend # make sure the commit message is awesome

	git push origin branch-name --force # need to force the commits if you've already pushed

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