Technology Matrix for the GOBii Stack

Owned by KevinPalis
Last updated: Apr 16, 2020 by Monica Franciscus (Unlicensed)
4 min read



Tech/Framework

Version

Programming Language

GOBii Module

Owner

Notes

Tech/Framework

Version

Programming Language

GOBii Module

Owner

Notes

Postgresql

9.5

SQL, Pl/pgsql

Data warehouse

Kevin Palis

plans of upgrading to 12 within the next few months

Liquibase

3.5.1

SQL with annotations

Data warehouse

Kevin Palis

used for database versioning and migration

HDF5

1.8.18

C/C++

Data warehouse

Dave Matthews

stores genotype data

Psycopg2

2.6.2 or above

Python

Data warehouse

Kevin Palis

used by the ETL, might get updated with Postgres12

Docker (with swarm)

18.06.1-ce

n/a

DevOps

Kevin Palis Roy Petrie

(almost) everything GOBii is now containerized

Ubuntu (Containers)

18.04 LTS

n/a

DevOps

Kevin Palis Roy Petrie

As of GDM 2.2, all our containers run this version of Ubuntu

Ubuntu (Hosts)

16.04.6 LTS

n/a

DevOps

@Roy Petrie , Kevin Palis

version of OS used for hosts

Bash

4.3.48(1)

bash

DevOps

@Roy Petrie

Version of bash for scripts/deployment

git

2.7.4

n/a

DevOps

@Roy Petrie

git version

Tomcat

9.0.27

n/a

DevOps

Kevin Palis

As of GDM 2.2, all our containers run this version of Tomcat

Atlassian Bamboo

6.6.0

Shell scripting (bash)

DevOps

Kevin Palis

main CI/CD pipeline

Selenium

3.0.2

Python

DevOps

Kevin Palis

used for testing the extractorUI

ZK CE

8.6.0.1

Java

Timescope

Angel Raquel

UI development for TImescope

Angular

4.2.4

Typescript

ExtractorUI, Web LoaderUI, PortalUI, Job StatusUI

Vishnu Govindaraj, PFR

UI development for the ExtractorUI

Vue

2.6.10

Javascript

PedVer,

Angel Raquel

UI development for Pedver

Leiningen

2.9.1

Clojure / Bash

Bert & Ernie

Luke Cook

Bash script for building Clojure Projects

JOOQ

3.10.4

Java

Timescope

Angel Raquel

used for fetching data from the database

Java SE

OpenJDK 13

Java

Middleware (Digesters, Extractors)

Josh Lamos-Sweeney



Linux Cron

Ubuntu 18.04's cron

Bash

Middleware (job queue)

Josh Lamos-Sweeney

currently just simple configurable cronjobs, but we plan on migrating to a job scheduler in the future

SMTP

any email provider that supports SMTP

Java

Notification system

Josh Lamos-Sweeney

GDM needs an email account to send out notifications on job status. We typically use GMail but it can be any email provider.

We plan on moving to a purely web-based notification system in the future (will come with the Job StatusUI)

Spring MVC

4.3.0

Java

GDM Web services

Vishnu Govindaraj

GDM Web services and Brapi Web Services

Hibernate

5.4.10

Java

GDM Web Services

Vishnu Govindaraj

Object Relational Mapping for Web service Data Access Layer

Celery

4.4.0

Python3

F1 Pedver

Vishnu Govindaraj

Framework to run analytics pipeline jobs like Filtering, Consensus calling and Pedigree Verification

Flask

1.1.0

Python3

F1 Pedver

Vishnu Govindaraj

F1 Pedver tool API to submit jobs with required data

Redis

5.0

Redis

F1 Pedver

Vishnu Govindaraj

Acts as a Message broker between Analytics pipeline and backend web services

Junit

4

Java

F1 Pedver

Vishnu Govindaraj

Testing Framework for GDM Webservices. Along with that we use Mockito and Spring Test which accessory Frameworks

GUnicorn

 

Python

F1 PedVer

@Vishnu Govindaraj

Python WSGI HTTP Server for UNIX

amqp==2.5.2
appnope==0.1.0
backcall==0.1.0
billiard==3.6.1.0
celery==4.3.0
certifi==2019.9.11
chardet==3.0.4
Click==7.0
config==0.4.2
decorator==4.4.0
Flask==1.1.1
idna==2.8
importlib-metadata==0.23
ipython-genutils==0.2.0
itsdangerous==1.1.0
jedi==0.15.1
Jinja2==2.10.3
kombu==4.6.6
MarkupSafe==1.1.1
more-itertools==7.2.0
numpy==1.17.3
pandas==0.24.2
parso==0.5.1
pexpect==4.7.0
pickleshare==0.7.5
prompt-toolkit==2.0.10
ptyprocess==0.6.0
Pygments==2.4.2
python-dateutil==2.8.0
python-dotenv==0.10.3
pytz==2019.3
redis==3.3.11
requests==2.22.0
six==1.12.0
traitlets==4.3.3
urllib3==1.25.6
vine==1.3.0
wcwidth==0.1.7
Werkzeug==0.16.0
zipp==0.6.0

see first column

Python

F1 PedVer

@Vishnu Govindaraj

This list is pulled from PedVer’s requirements.txt directly, please review and separate to individual rows, @Vishnu Govindaraj , @Angel Manica Raquel .

Framework

Version

Notes

Framework

Version

Notes

Angular:

@angular/animations @angular/common @angular/compiler @angular/core @angular/forms @angular/http @angular/language-service @angular/platform-browser @angular/platform-browser-dynamic @angular/router primeng

6+

 

NGRX

@ngrx/effects @ngrx/router-store @ngrx/store @ngrx/store-devtools

6+

 

Types

@types/core-js @types/jasmine @types/node

2.5.2+

3.4.5+

12.12.5+

 

3.3.7

 

2.4.1+

 

0.0.1+

 

3.0.2+

0.35.0+

 

4.7.0

 

1.6.3

1.2.1

 

6+

6.5.4

 

0.19.8+

 

0.8.4+

 

3.0.1+

 

0.1.8+

 



Main Project Pom:

Framework

Version

Notes

Framework

Version

Notes

junit

4.11

 

mokito

1.10.19

 

hamcrest

1.3

 

powermock

1.6.4

 

logback

1.1.3

 

SLF4J

1.7.5

 

janino

3.0.6

 

commons-lang

2.6

 

commons-io

2.4

 

commons-cli

1.3.1

 

commons-fileupload

1.3.1

 

javax.mail

1.4.3

Used in email generation by Digester and Extractor

spring-context

spring-orm

spring-web

spring-webmvc

spring-test

4.3.0.RELEASE

Both same version

spring-security-core
spring-security-config
spring-security-taglibs

spring-security-ldap

spring-security-web
spring-security-crypto

4.2.2.RELEASE

 

spring-ldap-core

2.3.1.RELEASE

 

gson

2.6.2

 

simple-xml

2.7.1

Used creating and reading gobii-web.xml and other xml config files

jackson-databind

2.9.8

 

jackson-mapper-asl

1.9.13

 

postgresql.

42.1.4

 

guava

19.0

Note in pom confused about why this had to be added

liquibase-core

3.3.2

 

hibernate-core

5.4.10.FINAL

 

hibernate-jpa-2.1-api

1.0.0.FINAL

 

javax.ws.rs-api

2.1-m05

 

jetty-server
jetty-servlet

9.4.5.v20170502

 

jersey-server
jersey-container-servlet-core
jersey-media-json-jackson

2.26-b03

 

tomcat-servlet-api

7.0.30

 

commons-dbcp

1.4

 

net.sf.opencsv

2.3

 

org.jboss.logging

3.3.0.FINAL

 

org.apache.httpcomponents
httpclient
httpclientcache
httpmime
fluent-hc

4.4

 

httpcore

4.4

 

docx4j

3.3.6

 

hibernate-c3p0

5.3.6.FINAL

 

maven-compiler-plugin

3.5.1

 

Gobii Process pom

Framework

Version

Notes

Framework

Version

Notes

spring-context
spring-tx
spring-security-core
spring-security-config
spring-security-taglibs

<inherited>

 

junit

<inherited>

 

commons-cli

<inherited>

 

mockito-all
hamcrest-library
powermock-api-mockito
powermock-module-junit4

<inherited>

 

guava

<inherited>

 

lombok

1.18.8

 

maven-assembly-plugin

2.4.1

 

Gobii Web pom

Framework

Version

Notes

Framework

Version

Notes

swagger-maven-plugin

3.1.7

 

spring-web
spring-webvmc
spring-context
spring-orm
spring-ldap-core
spring-security-core
spring-security-taglibs
spring-security-ldap
spring-security-web
spring-security-crypto
spring-tx

<inherited>

 

spring-aspects

explicitly declared to be parent’s spring.version

 

jboss-logging

<inherited>

 

hibernate-jpa-2.1-api

<inherited>

 

hibernate-core

5.4.10.Final

 

spring-test

3.2.3.RELEASE

 

junit

<inherited>

 

jttpclient
httpcore
httpclient-cache
httpmine
fluent-hc

<inherited>

 

liquibase-core

<inherited>

 

commons-dbcp

<inherited>

 

tomcat-servlet-api

<inherited>

 

jackson-databind
jackson-mapper-asl

<inherited>

 

opencsv

<inherited>

 

postgresql

<inherited>

 

commons-fileupload
commons-ui
commons-lang

<inherited>

 

swagger-jaxrs2
swagger-jaxrs2-servlet-initializer

2.0.0

 

mockito

<inherited>

 

json-path-assert

0.8.1

 

tika-core

1.2.2

 

jakarta.xml.bind-api

2.3.2

 

jaxb-runtime

2.3.2

 

hibernate-c3p0

5.3.6.FINAL

 

jetty-maven-plugin

9.1.3.v20140225

 

maven-compiler-plugin

3.2

 

grunt-maven-plugin

$grunt-version

 

frontend-maven-plugin

1.8.0

 

maven-resources-plugin

2.6

 

swagger-maven-plugin

3.1.8

 

jaxb.api

2.3.1

 

REMAINING POM FILES TODO - Similar content

 

A general overview of the architecture:



Disregard MonetDB as we've dropped support for that.