Migration tool specification

  1. Requirements
  2. QuickStart
  3. Files
  4. Images
  5. Plates
  6. Protocols
  7. Quota
  8. Reporters
  9. Roles
  10. Sample Origins
  11. BASE 1 tables description

Contributions by: Gregory
Last updated: $Date: 2009-04-06 14:52:39 +0200 (må, 06 apr 2009) $


Requirements

  1. Clean and working installation of BASE 2
  2. BASE 1 schemeVersion 1.2.20
  3. Local or NFS access to BASE 1 file repository

QuickStart

First verify that your BASE 2 installation is up and running before attempting migration. Best way to do this is to try to login using the root user through the web interface.
BASE_HOME - is the root directory of BASE 2 installation package e.g. /home/johndoe/base2-alpha5/

  1. Compile migration utility with
    > cd BASE_HOME
    > ant migrate
  2. Change migration properties in dist/www/WEB-INF/classes/migrate.properties
  3. Run migration utility with
    > cd BASE_HOME/dist/bin
    > ./migrate_from_1.2.sh
THERE IS CURRENTLY NO WAY TO CONTINUE A PREVIOUSLY INTERUPTED MIGRATION. YOU HAVE TO RECREATE THE DATABASE AND RERUN THE MIGRATION UTILITY.

Files

Images

Plates

Protocols

Quota

Reporters

Roles

Default BASE Roles

Role assignment is done according to the following protocol:

  1. If Admin privileges » Superuser is checked that user shall only be assigned to the BASE 2 role Administrator.
  2. If Admin privileges » Complete read access is checked that user shall be assigned to the BASE 2 role Supervisor.
  3. A user shall be assigned to at most one of the BASE 2 roles Guest, User and Power user:

If the user after this assignment has more permissions that couldn't be matched to a predefined role, the user is assigned to one or more of the migration roles. The migration roles are created by the migration program and have the same name as the BASE 1 permission with the prefix "BASE 1:" added to it.

C = Create, R = Read, U = Use, W = Write, D = Delete

BASE 1 permission BASE 2 Permissions
Administer users USER (CRUWD), GROUP (CRUWD), ROLE (CRUWD),
QUOTA (CRUWD), QUOTATYPE (RU), DIRECTORY (C)
Speak in left frame Not used by BASE 2.
Add plug-ins PLUGINDEFINITION (C), PLUGINCONFIGURATION (C), PLUGINTYPE (RU)
Add news NEWS (CRUWD)
Add protocols PROTOCOL (CRUWD), PROTOCOLTYPE (RU)
Add arrays/plates PLATEGEOMETRY (RU), PLATETYPE (C), PLATE (C), PLATEMAPPING (RU),
ARRAYDESIGN (C), ARRAYBATCH (C), ARRAYSLIDE (C), PROTOCOLTYPE (RU)
Add annotation types ANNOTATIONTYPE (C), ANNOTATIONTYPECATEGORY (C)
Add hardware/software HARDWARE (C), HARDWARETYPE (RU), SOFTWARE (C), SOFTWARETYPE (RU)
Add reporters REPORTER (CRUWD), REPORERTYPE (CRUWD), REPORTERLIST (C)
Add file formats PLUGINCONFIGURATION (C)
Read more user info -
Read plugins (if missing) PLUGINDEFINITION (DENIED), PLUGINCONFIGURATION (DENIED)
Create MAGE-ML file -
Share with world SHARE_TO_EVERYONE
Add biomaterials BIOSOURCE (C), SAMPLE (C), EXTRACT (C), LABELEDEXTRACT (C), LABEL (C)
Add hybridization HYBRIDIZATION (C), SCAN (C), RAWBIOASSAY (C)
Create experiments EXPERIMENT (C)
Edit experiments -
Upload files FILE (C), DIRECTORY (C)
Read arrays/plates (if missing) PLATEGEOMETRY (DENIED), PLATETYPE (DENIED), PLATE (DENIED),
PLATEMAPPING (DENIED), ARRAYDESIGN (DENIED),
ARRAYBATCH (DENIED), ARRAYSLIDE (DENIED)
Read user info (if missing) USER (DENIED)
Read biomaterials (if missing) BIOSOURCE (DENIED), SAMPLE (DENIED), EXTRACT (DENIED),
LABELEDEXTRACT (DENIED), LABEL (DENIED)
Read hybridizations (if missing) HYBRIDIZATION (DENIED), SCAN (DENIED), RAWBIOASSAY (DENIED)
Read experiments (if missing) EXPERIMENT (DENIED)
Read reporters REPORTER (RU), REPORTERTYPE (RU)

Sample Origins

  1. Sample origins are not available in BASE 2, though they are added to the description of each sample as
    eg. Human -> Cell Line -> ...