wiki:MolgenisIndex
Last modified 3 years ago

Table of Contents

  1. Generating MOLGENIS from scratch, the Address Book Example
    1. 1. Create the data model in addressbook_db.xml
      1. Create a “Contact” data type
      2. Add properties to “Contact”
      3. Create a “Address” data type
      4. Link Addresses to Contact.
    2. 2. Model the user interface in addressbook_ui.xml
    3. Generate the application
      1. Configure the molgenis.properties file.
      2. Create an addressbook mysql instance
      3. Generate and compile your database
    4. 3. Expected result
  2. Stories for the research portal release of 31 dec 2011
  3. MOLGENIS Apps
    1. For researchers
    2. For developers
    3. Getting started
    4. Description of all project elements
      1. build scripts
      2. /apps
      3. /modules
      4. /generated (svn:ignore)
      5. /WebContent
      6. /dist (svn:ignore)
    5. Creating a new app
  4. Architecture overview
  5. Using Molgenis as a datasource for Galaxy
  6. Batch loading of data
    1. Loading csv data using the UI
      1. Load data for Contact.
      2. Load data for Address, including 'xref by name'
  7. MOLGENIS bookshelf
  8. Running MOLGENIS from the commandline
    1. Create
    2. Import
    3. Update
    4. Generate
    5. Run
  9. MOLGENIS suite overview: modules and products
    1. = Graphical overview of modules =
  10. Adding Custom buttons to the generated code
    1. 1. Define the custom commands in your *ui.xml
    2. 2. Implement the button
  11. MOLGENIS data model mapping overview
  12. Accessing the database via Molgenis Database
    1. In a standalone program
  13. Database API
    1. Get a database
    2. Add objects in batch
    3. Queries made simple
    4. Shorthand for query by primary key (id)
  14. How to deploy a MOLGENIS project under a different name
    1. Project name
    2. Database name
    3. Deploy name
    4. Optional: add or remove security
    5. Final note
  15. Documentation
    1. Software
    2. SOPs
  16. Download latest version from Subversion
  17. Download Eclipse workspace from sourceforge
  18. Download as source code
  19. MOLGENIS language definition
  20. <molgenis>
    1. Required attributes
    2. Optional attributes
    3. Child elements
  21. Emaling from within your MOLGENIS application
    1. Set your email settings in 'molgenis.properties'
    2. Add the following code to your plugin
  22. Enhancements for MOLGENIS on various levels
    1. Core
    2. Generators
    3. Plugins
  23. MOLGENIS FAQ
    1. Customizing look & layout
    2. Statement.GeneratedKeysNotRequested?
    3. It doesn't work after checkout!
    4. I want to automatically select my plugin
    5. Create new MOLGENIS project
    6. Can/should I use Infobright / Brigthouse for big data
    7. How to remove *.svn directories
  24. MolgenisFile
    1. Overview
      1. Field is file
      2. Entity is file
    2. Merging
    3. Technical
      1. Decorating
      2. Setting storage location
      3. Java API
      4. Services: uploading and downloading
      5. Practical example
      6. Java API extension example
    4. Notes
  25. Layout of MOLGENIS projects
  26. Subversion
  27. Extract MOLGENIS model from existing database
    1. Generating a MOLGENIS for an existing database
    2. Example
  28. MOLGENIS generator basics
  29. Join the MOLGENIS Google group
  30. MOLGENIS development manual
  31. MOLGENIS related internships
  32. Introduction
    1. Why MOLGENIS?
    2. What will you achieve with this guide?
  33. MOLGENIS Java Doc
    1. JPA Manual
      1. JPA documentation
      2. Usage of JPA within Molgenis
      3. DatabaseFactory AND persistence.xml
      4. Logging
      5. Database Mappers and EntityManager
      6. Primary Key generation
      7. Cascade Rules
      8. Decorators and EntityListeners
      9. Helper
  35. Language reference
    1. Database language (*_db.xml)
    2. User interface language (*_ui.xml)
    3. DTD
  36. MOLGENIS language reference in one page (easy for searching and printing)
  37. The MOLGENIS database language knows the following elements
  38. The MOLGENIS user interface language knows the following elements
  39. Overview of MOLGENIS modules
    1. Manually curated list
    2. Automatic generated list
  40. Movies about MOLGENIS
    1. Demos
  41. Example movie
  42. Eclipse install
    1. Frequently asked questions
  43. How to develop MOLGENIS on Eclipse/Helios?
    1. 1. Install eclipse helios
    2. 2. install SVN plugin 'subclipse'
    3. 3. install freemarker plugin 'Freemarker IDE'
    4. 4. checkout molgenis projects
    5. 5. Develop
    6. FAQ
      1. Q1: how to add/manage J2EE dependencies
      2. Q2: I get 404 errors when starting the server
      3. Q3: I get a very long 'loading web service DOM'
  44. Eclipse install
    1. Frequently asked questions
  45. Getting MOLGENIS running on Ubuntu
    1. Installing Ubuntu inside Windows using VirtualBox
    2. Install MySQL, Tomcat, Java, Eclipse on Ubuntu
  46. Get from a clean Windows install up to the point where you can generate, …
    1. Install Java,Tomcat,MySQL and Eclipse
    2. Create a database in MySQL
    3. Open the MOLGENIS workspace using Eclipse
  47. Creating a user interface plug-in
    1. 1. Define the plugin in the 'addressbook_ui.xml'
    2. 2. Add reload logic to 'plugin.pubmed.PubmedPlugin.java'
      1. Edit the reload function to produce a pubmed query URL
    3. 3. Create a html layout in plugin.pubmed.PubmedPlugin.ftl to show Pubmed …
    4. 4. Add user input handling to enable users to choose year
  48. title
    1. List of Plugins
  50. Quick Molgenis polls
  51. MolgenisProcessing
    1. Use Cases
    2. PBS best practices
  52. MOLGENIS progress update Jan - Jun 2010
    1. highlights
    2. Progress
    3. Bottlenecks
    4. Scientific output
    5. Collaborations
  53. About MOLGENIS
    1. MOLGENIS Contributors
  54. MOLGENIS partners
    1. MOLGENIS Partners
  55. Overview of Projects
  56. molgenis.properties file
    1. molgenis.passwd file
  57. How to rename a MOLGENIS project in Eclipse
    1. Step 1: Checkout MOLGENIS distro
    2. Step 2: Disconnect from SVN
    3. Step 3: Rename the web address
    4. Step 4: Regenerate your MOLGENIS as usual
  58. Posting data to MOLGENIS using REST API
    1. Using simple GET commands
    2. Using CURL
  59. Using the R interface
  60. GCC SCRUM page
  61. Backlog
  62. Notes from End-of-sprint demo 11.27, July 4 2011
    1. Report of Team 2, Sprint 7, 11.27
      1. Story: directory structure.
      2. Story: LifeLines import into Oracle
      3. Story: OSGi pilot …
      4. Story: BBMRI catalogue user want simpler search and download
    2. Report of team 1
  63. Selected user stories for the LifeLines research portal demo
    1. Below complete backlog of LifeLines related stories
  64. MOLGENIS Research Platform - Sprint 1
    1. Lessons learned
    1. MOLGENIS Research Platform - Sprint 2
    2. User stories selected by Matrix team
    3. User stories selected by Protocol team
    4. User stories moved to the Sprint Backlog
    5. Lessons Learnt from evaluation session of Sprint 2 on Mar. 3rd
  66. MOLGENIS Research Platform - Sprint 11.12
    1. Lessons Learnt from evaluation session of Sprint 3 (11.12) on Mar. 25th
    2. User story suggestions from end-of-sprint demo's
  67. MOLGENIS Research Platform - Sprint 11.16
    1. Team 1: Research Platform
    2. Team 2: LIMS
  68. MOLGENIS Research Platform - Sprint 11.20
    1. Team 1: NGS
    2. Team 2: LifeLines
    3. Team 3: Pheno
  69. MOLGENIS Research Platform - Sprint 11.20
    1. Team 1: NGS
    2. Team 2: …
  70. List of MOLGENIS servers
  71. List of MOLGENIS test servers
  72. FAQ for servers and VMs
    1. General
    2. Access
    3. Operating system
    4. Storage and backups
    5. Configuration
    6. Hosting
  73. SOPs
    1. Install and run standalone
    2. Install on tomcat6 and mysql
    3. Copy a file from sftp to molgenis VM
    4. Installation of SUSE VM
    5. Upload metadata
  74. NOTE
    1. How to change firewall
  75. Discussion
  76. Using the SOAP interface in Taverna
  77. MOLGENIS source code
    1. What do I need?
    2. What is in the other packages?
  78. Rapid generation of biosoftware you want to have
  79. Using MOLGENIS
  80. Getting involved
  81. MOLGENIS Users
    1. MOLGENIS is being used in the following projects:
  83. MOLGENIS Testing Framework
    1. Unit tests for Modules
    2. Integration tests
    3. UI web tests
  84. How to make good tickets?
    1. What is a ticket?
    2. What makes a good ticket?
    3. Size of tickets?
    4. How to use Milestones?
    5. What ticket type to use?
  85. Molgenis UI components
  86. Manual for Molgenis UI components
    1. How to make your plugin Freemarker-less
    2. What components to choose from
      1. The most important components
      2. Components that seem to offer no added value at this moment
      3. Components that should not be used at the moment
      4. Desired components
    3. How to integrate the components into your plugin
    4. Fancy JavaScript actions
    5. Code example
  87. Using the user interface
  88. Open the MOLGENIS workspace in Eclipse