cco_poc

Proof of concept files for an implementation of an information model for complex natural science collections objects.
Example to illustrate a manuscript by Morris, Macklin, Kelly, and Tocci and for discussion by the DINA consortium.

Schemas

DDL for a minimal example (entirely proof of concept) schema is in:
src/main/resources/edu/harvard/huh/specify/datamodel/cco_poc/db/tables.sql and
src/main/resources/edu/harvard/huh/specify/datamodel/cco_poc/db/changes.sql

DDL for a much more complete schema suitable for implementation is in:
src/main/resources/edu/harvard/huh/specify/datamodel/cco_full/db/tables.sql

Example data illustrating intended use of the schema for various sorts of simple and complex collections data is in:
src/main/resources/edu/harvard/huh/specify/datamodel/cco_full/db/exampledata.sql

The outline of a human readable information model is at:
src/main/resources/edu/harvard/huh/specify/datamodel/cco_full/model/model.md

Building CCO_FULL directly

mysql> drop database cco_full;
mysql> create database cco_full;

$ cd src/main/resources/edu_harvard/huh/specify/datamodel/cco_full/db/
$ mysql -p cco_full < tables.sql
$ mysql -p cco_full < functions.sql
$ mysql -p cco_full < baselinedata.sql
$ mysql -p cco_full < exampledata.sql

Building CCO_FULL with liquibase

This draft incorporates liquibase markup, but it should not yet be considered stable - you must drop and create a new database from scratch with each update.

Prerequisites

Software

1. java ( tested with OpenJDK ver. 1.7.0_95 and Java 1.8.0_73 )
2. maven
3. either MariaDB/MySQL or postgreSQL

Default database

The default database should be MySQL in this repo, defined in the file liquibase.properties
You MUST create the database 'cco_full' before running the project.

mysql> drop database cco_full;
mysql> create database cco_full;

Liquibase database properties

At this time there is support for 2 DBMSes (MariaDB/MySQL and postgresql).

The basic configuration is in the following 2 template files in the config directory, you must copy one of these to config/liquibase_cco_full.properties, and then provide your user credentials.

1. for MariaDB/MySQL see the liquibase_cco_full.properties.mysqltemplate file
2. for postgreSQL see the liquibase_cco_full.properties.postgrestemplate file

config/liquibase_cco_full.properties is in .gitignore and should not be put under version control (as it contains your credentials).

For MariaDB/MySQL

You must copy the config/liquibase_cco_full.properties.mysqltemplate to config/liquibase_cco_full.properties, and then add your credentials to the file.

$ cp config/liquibase_cco_full.properties.mysqltemplate config/liquibase_cco_full.properties
$ vim config/liquibase_cco_full.properties

For Postgresql

1. be sure that you have postgreSQL installed

2. create the schema 'cco_full', check the credentials in the liquibase.postgresql.properties-file

3. replace liquibase_cco_full.properties with the liquibase_cco_full.properties.postgrestemplate.

   $ cp config/liquibase_cco_full.properties.postgresqltemplate config/liquibase_cco_full.properties $ vim config/liquibase_cco_full.properties

To build the database with Liquibase

To run the project type 'mvn clean install' in the same directory that the pom.xml-file resides. You must have first met the prerequisites listed above, including creating the database schema and having copied a template to config/liquibase_cco_full.properties and added your database credentials to that file.

mvn clean install

If you wish to include the examples, use the cco_full_examples profile instead:

mvn clean install -P cco_full_examples

Configuration Files

For maven.

• pom.xml
  • db: mysql-connector-java (version '5.1.37')
  • db: mysql ( version 5.5.49)
  • db: postgresql (version '9.1-901-1.jdbc4')
  • liquibase (version '3.4.2')
  • liquibase-maven-plugin (version '3.0.5')

For the liquibase-project.

• config/liquibase.properties (you must create from one of the templates and set your credentials)
  • contains : driver and url to the database
  • contains : credentials
  • contains : path to the master.xml-file
  • contains : additional such as ; 'verbose = true', 'dropFirst = false'
• master.xml
  • contains : path to 'db.changelog-x.y.xml' , x.y are version-nr.