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Table of Contents
Introduction
MOLGENIS application overview
- Browsing and editing
- CSV file loading
- Connecting to R
- Connecting to SOAP web services
- Connecting to REST web services using CURL
- Molgenis as a datasource for Galaxy
Toolkit Installation
- Preperation on Windows
- Preperation on Ubuntu/Linux
- Installation of Eclipse/Galileo
- Installation of Eclipse/Helios
- Installation of Eclipse/Indigo
- Download MOLGENIS
Generating your own applications
- MOLGENIS workspace basics
- Running the generator
- Modeling a new MOLGENIS
- Modeling an existing database
- molgenis.properties file
Adding plug-ins
Building on the MOLGENIS framework
MOLGENIS Data Modeling Language Reference
MOLGENIS User Interface Modeling Language Reference
MOLGENIS framework API
Frequently asked questions
- How to change molgenis url from /molgenis_distro to xyz
- How to change the MolgenisServlet, e.g. to add more services
- How to extend an existing database model
- Case sensitivity and issues between windows, linux and mac
- How to create a hyperlink from plugin to another form
- How to create a hyperlink from plugin to another form
- How to create a hyperlink from plugin to another form
<entity>
The <entity> element defines the structure of one data entity and will result in a table in the database, and several Java classes. Example usage of the <entity> element:
<entity name="my_class"> <description>This is my first entity.</description> <field name="name" type="string"/> <field name="investigation" type="string"/> <unique fields="name,investigation"/> </entity> <entity name="my_subclass" extends="my_class"> <description>This class extends my_class and will have fields name,investigation and otherField</description> <field name="otherField"/> </entity>
Required attributes
- name="name": globally unique name for this entity (within this blueprint).
Optional attributes
- label="Nice screen name": an user-friendly alias to show as form header (default: copied from name).
- extends="other_entity": you can use inheritance to make your entity inherit the fields of its 'superclass' using extends.
- abstract="true": you define what programmers call 'interfaces'. This are abstract objects that you can use as 'contract' for other entities to 'implement'..
- implements="abstract_entity": you can use inheritance to make your entity inherit the fields of its 'interface' using implements and refering to 'abstract' entities. The implemented fields are copied to this entity.
- decorator="package.class": you can add custom code to change the way entities are added, updated and removed. See the section on how to write a MappingDecorator plugin.
Child elements
The <entity> element can contain
- Zero or one <description> to describe this entity; a description can contain xhtml.
- zero or more <field> that detail entity structure.
- Zero or more <unique> indicating unique constraints on field(s).
Notes
- Cascading deletes can be configured via FieldElement where you can set xref_cascade