TService

Make research tool as a service.

Many tools are used in the research, but located in each computer. e.g. xps to pdf, convert rnaseq results to a report etc.

Why can't we do all these things in one place? TService is the answer.

For user

Configuration

Configuration File Mode

{:port 8089
 ;; when :nrepl-port is set the application starts the nREPL server on load
 :nrepl-port 7000
 ;; :database-url "postgresql://localhost:5432/tservice_dev?user=postgres&password=password"
 :database-url "jdbc:sqlite:./tservice/tservice_dev.db"
 :external-bin "/Users/choppy/Documents/Code/ClinicoOmics/ReportEngine/tservice-plugins/external:/Users/choppy/miniconda3/envs/multiqc/bin"
 :tservice-workdir "./tservice"
 :tservice-plugin-path "./tservice/"
 :tservice-run-mode "dev"
 :fs-services [{:fs-service             "minio"
                :fs-endpoint            "http://localhost:9000"
                :fs-access-key          "XXXXXXXXXXXX"
                :fs-secret-key          "XXXXXXXXXXXX"
                :fs-rootdir             "/data/minio"}
               {:fs-service             "oss"
                :fs-endpoint            "http://oss-cn-shanghai.aliyuncs.com"
                :fs-access-key          "XXXXXXXXXXXX"
                :fs-secret-key          "XXXXXXXXXXXX"
                :fs-rootdir             ""}]
 :default-fs-service "minio"
 :tasks {:sync-reports {:cron "0 */1 * * * ?"}}}

Environment Mode

# Port
export PORT=3000
# NREPL Port
export NREPL_PORT=7000

# Database(Support PostgreSQL, H2, SQLite)
## PostgreSQL
export DATABASE_URL="postgresql://localhost:5432/tservice_dev?user=postgres&password=password"

## H2
export DATABASE_URL="jdbc:h2:./tservice_dev.db"

## SQLite
export DATABASE_URL="jdbc:sqlite:./tservice_dev.db"

# TService Working Directory
export TSERVICE_WORKDIR=./

# TService Plugin Path
export TSERVICE_PLUGIN_PATH=./

Using docker image

1. Go to the Packages page in the https://github.com/clinico-omics/tservice
2. Choose a version
3. Pull your expected package with the following command

docker pull ghcr.io/clinico-omics/tservice:v0.3.2-9e3daa48

Download jar package

# TODO

For Developer

Prerequisites

1. You will need Leiningen 2.0 or above installed.

2. Clone the tservice repo

   git clone https://github.com/clinico-omics/tservice.git
   cd tservice
   

3. Prepare a configuration file and save as dev-config.edn into the tservice directory

   ;; WARNING
   ;; The dev-config.edn file is used for local environment variables, such as database credentials.
   ;; This file is listed in .gitignore and will be excluded from version control by Git.
   
   {:port 3000
    ;; when :nrepl-port is set the application starts the nREPL server on load
    :nrepl-port 7000
    :database-url "postgresql://localhost:5432/tservice_dev?user=postgres&password=password"
    :external-bin "~/miniconda3/envs/multiqc/bin"
    :tservice-workdir "~/Downloads/tservice"
    :tservice-plugin-path "~/Downloads/tservice/"
    :tservice-run-mode "dev"
    :fs-services [{:fs-service             "minio"
                    :fs-endpoint            "http://10.157.72.56:9000"
                    :fs-access-key          "test"
                    :fs-secret-key          "4gmPNjG5JKRXXXXXuxTqO"
                    :fs-rootdir             "/data/minio"}
                  {:fs-service             "oss"
                    :fs-endpoint            "http://oss-cn-shanghai.aliyuncs.com"
                    :fs-access-key          "LTAI4Fi5MEXXXXXzhjEEF43a"
                    :fs-secret-key          "hQhPB8tRFloXXXXXXhKv1GOLdwFVLgt"
                    :fs-rootdir             ""}]
    :default-fs-service "minio"
    :tasks {:sync-reports {:cron "0 */1 * * * ?"}}}
   

4. Install PostgreSQL and create the tservice_dev database for development

Install Dependencies

lein deps

Running

To start a web server for the application, run:

lein run 

How to reload application without the need to restart the REPL itself

(require '[user :as u])
(u/restart)

How to get a tservice plugin?

# TODO

How to develop a tservice plugin?

TService Plugin Manifest

info:
  name: Quartet DNA-Seq Report
  version: v1.0.1
  description: Parse the results of the quartet-dna-qc app and generate the report.
  category: Tool
  home: https://github.com/clinico-omics/tservice-plugins
  source: PGx
  short_name: quartet-dnaseq-report
  icons:
    - src: ""
      type: image/png
      sizes: 192x192
  author: Jingcheng Yang
plugin:
  name: quartet-dnaseq-report
  display-name: Quartet DNA-Seq Report
  lazy-load: false
init:
  # Unpack environment file to the directory, repository/envs/quartet-dnaseq-report
  - step: unpack-env
    envname: quartet-dnaseq-report
  - step: load-namespace
    namespace: tservice.plugins.quartet-dnaseq-report
  - step: register-plugin
    entrypoint: tservice.plugins.quartet-dnaseq-report/metadata
  - step: init-event
    entrypoint: tservice.plugins.quartet-dnaseq-report/events-init

How to auto-generate docs?

1. Commit all code modifications

2. Give a tag for the latest commit

3. Build your documentation with lein codox

4. To publish your docs to Github Pages, run the following commands

   cd docs
   git add .
   git commit -am "Update docs."
   git push -u origin gh-pages
   cd ..
   

How to build docker image?

make build-docker

How to create a database for development?

make dev-db

License

Copyright © 2015-2021 Eclipse Public License 2.0