Migration tool specification

Requirements
QuickStart
Files
Images
Plates
Protocols
Quota
Reporters
Roles
Sample Origins
BASE 1 tables description

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

Requirements

Clean and working installation of BASE 2
BASE 1 schemeVersion 1.2.20
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/

Compile migration utility with
> cd BASE_HOME
> ant migrate
Change migration properties in dist/www/WEB-INF/classes/migrate.properties
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

File names may not have any of the characters "~\\/:;*?<>>|". These characters will automatically be replaced with and underscore '_' during migration.

Images

Image files from scans that are removed from the uploads shall only be visible to the owner.

Plates

In BASE 2 mapped plates can have parent plates in arbitrary positions.
Plates with parents using an external file for well mappings are currently not migrated correctly.

Protocols

Protocols that are linked to files with equal names as currently uploaded files but with different file content are stored in home/USER/protocols directory as ID_FILENAME. Also their creation date is stored in the description.

Quota

Each user is assigned one of default quotas.
Quota assignment depends on the fileQuota in base 1 and the total usage in BASE 2.

Reporters

Reporters do not get assigned any default ReporterType
Start and stop positions are not available in BASE 2
Last update date is updated during migration

Roles

Default BASE Roles

Role assignment is done according to the following protocol:

If Admin privileges » Superuser is checked that user shall only be assigned to the BASE 2 role Administrator.
- No read restrictions shall be set on users assigned to this role.
If Admin privileges » Complete read access is checked that user shall be assigned to the BASE 2 role Supervisor.
- No read restrictions shall be set on users assigned to this role.
- Additional roles may be assigned if the user has more permissions.
A user shall be assigned to at most one of the BASE 2 roles Guest, User and Power user:
- Guest: Upload files
- User: Guest + Add biomaterials, Add hybridizations, Create experiments
- Power user: User + Add file formats, Add reporters, Add hardware/software, Add annotation types, Add arrays/plates, Add protocols

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

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