symbiota2 technical updatesymbiota2.org/wp-content/uploads/2019/03/s2... · installation •...

Symbiota2 Technical UpdateMary Barkworth – Utah State University

Ben Brandt – Northern Arizona UniversityNeil Cobb – Northern Arizona University

Curtis Dyreson – Utah State University Will Pearse – Utah State University

Outline• Installation

• Architecture

Installation• Symbiota site/portal manager installs and maintains

– Web server (typically apache)– DBMS (MySQL)– PHP– Search Engine (SOLR)– Symbiota code (from github)– Other goodies, e.g., phpmyadmin– Edits to various config files to configure

• Goal: make Symbiota2 easy to install, update, configure

Docker• Virtual machine, basic Linux environment• Runs on Mac, Windows, Linux, Android (but not Windows

CE, iOS)• Containers for various software

My Computer

Apache

MySQL

PHP …

DockerImageBuild

Your Computer

Docker Virtual MachineDockerImage

DockerImage

Symbiota2 Installation and Updates• Install Docker once

– Download Docker image from Symbiota2 github– Edit .env file to choose DBMS and configure– Run Docker at a terminal

docker-compose –up –d

– All necessary software provided in the image– Code example

• For developers– IDEs like PHPStorm update the Docker image– Canned starter database

Outline• Installation

• Architecture

Architecture of a Web Site - 1995

client server

GET http://symbiota2.org/api/index.htm

/api

foo.htm

index.htm

/junk

…

Architecture of a Web Site - 2005

client server

GET http://symbiota2.org/api/index.php

/api

foo.php

index.php

/junk

…

PHPInterpreter

MySQL DBMS

JavascriptInterpreter

Architecture of a Web Site - Current

client server

GET http://symbiota2.org/api/index

/api

foo.php

index.php

/junk

…

WebServices

MySQL DBMS

Router

…

…

…

ORM

Object-Relational Mapping (ORM)• Symbiota2 Tables and Relationships

– Next Slide

• Doctrine2 provides– Database abstraction

Drivers for MySQL, Postgres, SQLite– Map tables to objects

• Specify using annotations– Code Example

Benefits of Doctrine2 ORM• DBMS abstraction

Drivers for MySQL, Postgres, SQLite

• Schema is (completely) defined by ORM– Can generate DBMS schema from ORM– Define new ORM mappings, creates new tables in database– Change the ORM, changes pushed to the schema– Can migrate from MySQL to Postgres

JavascriptInterpreter

Architecture of a Web Site - Current

client server

GET http://symbiota2.org/api/index

/api

foo.php

index.php

/junk

…

WebServices

DBMS

Router

…

…

…

ORM

Doctrine2

API-Platform• Built on top of Symfony• Generates

– Router– Web services– Documentation

• Uses ORM and @API annotations– Code Example

JavascriptInterpreter

Architecture of a Web Site - Current

client server

GET http://symbiota2.org/api/index

/api

foo.php

index.php

/junk

…

WebServices

DBMS

Router

…

…

…

ORM

Doctrine2 API Platform

For Developers• Read-only developers

– Got you covered– Use an existing GET web service

• Data modification developers– Use an existing PUT web service– Use event model to attach data cleaners/transformers

• New kinds of data developers– Create ORM– Grow API Platform service end points from the ORM

Future - Controllers• Extra layer of abstraction

• ORM level may be too low-level• Can change ORM level

WebServicesORM

DBMS

Controllers

Future - Event-Based Model

• Cleaning plugin hooks into events between ORM and Web Services

• Translation plugin hooks into post Web Services events

JavascriptInterpreter

client server

GET http://smbiota2.org/api/index

/api

foo.php

index.php

/junk

…

WebServices

DBMS

Router

…

…

…

ORM

JavascriptInterpreter

client server

GET http://smbiota2.org/api/index

/api

foo.php

index.php

/junk

…

WebServices

DBMS

Router

…

…

…

ORM