JTree

Database Access API for AMDL Results Database

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Getting started

This project requires Go to be installed. On OS X with Homebrew you can just run brew install go.

Installing this code: $ go get github.com/Bio-core/JTree

To get any missing dependencies run: $ bash go_get.sh

Running it then should be as simple as:

$ make database
$ make build
$ ./bin/jtree

To generate fake data, run $ ./bin/jtree -g=100, where 100 is the amount of dummy data requested To run on a spesific port run $ ./bin/jtree -p=8000, where 8000 is the desired port

Endpoints:

# QUERIES
# This will return all of the columns in the database
$ curl http://127.0.0.1:8000/Jtree/metadata/0.1.0/columns

# This will return all of the searchable fields in the database
$ curl http://127.0.0.1:8000/Jtree/metadata/0.1.0/searchable

# This will return all of the uneditable fields in the database
$ curl http://127.0.0.1:8000/Jtree/metadata/0.1.0/uneditable

# This is an example query that will return all data from every table in the database
$ curl http://127.0.0.1:8000/Jtree/metadata/0.1.0/query -X POST -H "content-type:application/json" /
-d '{"selected_fields":["*"],"selected_tables":["samples", "patients","experiments", "results", "resultdetails"],"selected_conditions":[[]]}'

# This is an example query that will return all data where the date of birth is greater than 1950
$ curl http://127.0.0.1:8000/Jtree/metadata/0.1.0/query -X POST -H "content-type:application/json" -d /
'{"selected_fields":["samples.sample_id", "patients.dob"],"selected_tables":["samples", "patients","experiments", "results", "resultdetails"],"selected_conditions":[["AND", "patients.dob", "Greater than", "1950"]]}'


# INSERTS and UPDATES
# Note that inserts and updates operate the same way, the only difference is that the public key is not passed with the object structure for in insert
# samples
$ curl -X POST -H "Content-Type: application/json" /
 -d '{`# See models.samples for object structure`}' 127.0.0.1:8000/Jtree/metadata/0.1.0/samples

# patients
$ curl -X POST -H "Content-Type: application/json" /
 -d '{`# See models.patients for object structure`}' 127.0.0.1:8000/Jtree/metadata/0.1.0/patients

# experiments
$ curl -X POST -H "Content-Type: application/json" /
 -d '{`# See models.experiments for object structure`}' 127.0.0.1:8000/Jtree/metadata/0.1.0/experiments

 # results
$ curl -X POST -H "Content-Type: application/json" /
 -d '{`# See models.results for object structure`}' 127.0.0.1:8000/Jtree/metadata/0.1.0/results

 # resultdetails
$ curl -X POST -H "Content-Type: application/json" /
 -d '{`# See models.resultdetails for object structure`}' 127.0.0.1:8000/Jtree/metadata/0.1.0/resultdetails

Docker

For golang code, may need to change the connection string with an updated IP address for the docker container

$ docker inspect <container name> | grep IPAddr

The base IP address for docker containers will need to be updated in the restapi/configure_jtree_metadata.go file then commit and push to master (because it does a goget) and run the docker commands below:

$ docker network create -d bridge mysql-network
$ docker run --name mysqldb -p 3306:3306 -e MYSQL_ROOT_PASSWORD=waterloo -d --network=mysql-network mysql/mysql-server
$ docker exec -i mysqldb mysql -u root -pwaterloo -e "CREATE DATABASE JTree"
$ docker exec -i mysqldb mysql -u root -pwaterloo JTree < ./sql/jtree_backup.sql
$ docker exec -i mysqldb mysql -u root -pwaterloo -e "CREATE USER 'select'@'%' identified by 'passwords';grant SELECT on JTree.* to 'select'@'%';flush privileges;CREATE USER 'update'@'%' identified by 'passwordu';grant SELECT,INSERT, UPDATE on JTree.* to 'update'@'%';flush privileges;"
$ docker build -t docker/jtree .
$ docker run --network=mysql-network --name jtree -p 8000:8000 -d docker/jtree