| ## | |
| ## Helps with managing dockers for coding and review. | |
| ## | |
| repoKey=$1 | |
| issueNum=$2 | |
| shortDescrip=$3 | |
| branch=$4 |
| ## | |
| ## Helps with managing dockers for coding and review. | |
| ## | |
| action=$1 | |
| repoKey=$2 | |
| suffix=$3 | |
| drupalVer=${4:-10.2.x-dev} | |
| phpVer=${5:-8.3} |
| #! /bin/bash | |
| ## This script will create a docker image and then run it. | |
| ## Use the args to set the image/container name. | |
| ## Expects to run from the directory you want | |
| ## the image build from and to be mounted in the container | |
| repoKey=$1 | |
| githubNum=$2 | |
| drupalVer=${3:-10.2.x-dev} | |
| phpVer=${4:-8.3} |
The chado data as mapped to content types currently included in the database dump are:
| // First get access to the chado database connection. | |
| $chado = \Drupal::service('tripal_chado.database'); | |
| // Create a function to make random strings. | |
| $randomString = function($len = 10) {$word = array_merge(range('a', 'z'), range('A', 'Z')); shuffle($word); return substr(implode($word), 0, $len);}; | |
| // Insert a set number of organisms | |
| $total = 5; | |
| $subspecies = 2868; // cvterm_id | |
| for ($i = 1; $i <= $total; $i++) { |
| <?php | |
| /** | |
| * These commands are expected to be used in the drush php:cli | |
| * but could likely be wrapped into a drush script or used elsewhere. | |
| */ | |
| // Load all Tripal Content Entities of type gene. | |
| $entities = \Drupal::entityTypeManager()->getStorage('tripal_entity')->loadByProperties(['type' => 'gene']); |
| git clone https://github.com/tripal/tripal tripal-testing4Stan | |
| cd tripal-testing4Stan | |
| docker build --tag=tripalproject/tripaldocker:drupal10.1.x-dev --build-arg drupalversion='10.1.x-dev' ./ | |
| docker run --publish=9001:80 --name=t4 -tid --volume=$(pwd):/var/www/drupal/web/modules/contrib/tripal tripalproject/tripaldocker:drupal10.1.x-dev | |
| docker exec t4 service postgresql start |
Save a copy of this script somewhere on your computer. I suggest creating a Dockers directory in your home directory to keep everything organized.
cd ~/
mkdir Dockers
cd Dockers
wget https://gist.githubusercontent.com/laceysanderson/9000a2ca2c68a3a9b9eb20f2f5630986/raw/0089f2b37523010d38d494cd5d901566bffa218e/build_testing_tripalDocker.sh
Save a copy of this script somewhere on your computer. I suggest creating a Dockers directory in your home directory to keep everything organized.
cd ~/
mkdir Dockers
cd Dockers
wget https://gist.githubusercontent.com/laceysanderson/24f987c942242c2570a1f17f210e24ab/raw/5a1e1cfc3826922476b87656996fc6b6f50b3b78/build_testing_tripalDocker.sh
We want to limit sequential scans which return lots of rows as they are very slow. When you see a high number of sequential scans on a table it lets you know that you are missing an important index.
To check this we are going to look at the pg_stat_all_tables PostgreSQL table which contains one row for each table in the current database and shows statistics about accesses to that specific table. I'm still looking into how to tell the time period over which these stats were collected.
SELECT
schemaname as schema,