EMMAWiki/AdministratorDocumentation/ProjectSetup: Difference between revisions

From BRF-Software
Jump to navigation Jump to search
imported>MichaelDondrup
No edit summary
imported>MichaelDondrup
No edit summary
Line 3: Line 3:
An EMMA 2.0 Project consists of a database and a corresponding user and group management, which is supplied by the GPMS-Project Management. The database uses the MAGE-OM object description scheme. After setting up a new project as it is described in the GPMS-Documentation, this database has to be "build up", attending the following steps:
An EMMA 2.0 Project consists of a database and a corresponding user and group management, which is supplied by the GPMS-Project Management. The database uses the MAGE-OM object description scheme. After setting up a new project as it is described in the GPMS-Documentation, this database has to be "build up", attending the following steps:


# If the project is created via GPMS the database will already be set up.  
Locate the xml-files needed for the setup:
# In the GPMS add the use ''emma - Emma Daemon'' to your project with role ''Daemon''
The XML-files are currently  in the CVS repository (Directory: '''CVSDIR/bioinfo/emma2/src/dbshema''').
# Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml)
 
1. If the project is created via GPMS the database will already be set up.  
 
2. In the GPMS add the use ''emma - Emma Daemon'' to your project with role ''Daemon''
 
3. Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml)
Command:  
Command:  
  <code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code>
  <code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code>


# Import the Ontology information (Ontology-COMPLETE.xml)
4. Import the Ontology information (Ontology-COMPLETE.xml)
Command:  
Command:  
  <code><nowiki>test_import -p "Project" XMLFILE </nowiki></code>
  <code><nowiki>test_import -p "Project" XMLFILE </nowiki></code>


# Import all necessary functions (AllTools.xml)
5. Import all necessary functions (AllTools.xml)
Command:  
Command:  
  <code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code>
  <code><nowiki> test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE </nowiki></code>


# Add the "ALL" group, if this has not already been done during the GPMS-Setup
6. Add the "ALL" group, if this has not already been done during the GPMS-Setup
Command:  
Command:  
  <code><nowiki> emma_start add_group -g ALL </nowiki></code> or use the EMMA 2.0 web interface
  <code><nowiki> emma_start add_group -g ALL </nowiki></code> or use the EMMA 2.0 web interface


# Create pipelines using the EMMA 2.0 web interface (Important: Don't forget the Import-Pipeline ArrayLayoutImport consisting of the ArrayLayout import function)
7. Create pipelines from the functions imported in step 6 using the EMMA 2.0 web interface  
# Now you are able to import arraylayouts (e.g. A-MEXP-85 from www.ebi.ac.uk) (Don't forget to assign the imported arraylayout to the group "ALL", if you wish that all users will afterwards be able to use it!)
/!\ Always create a pipline with the exact name  ''ArrayLayoutImport'' consisting solely of the function ''ArrayLayout Import''
 
8. Now you are able to import arraylayouts (e.g. A-MEXP-85 from www.ebi.ac.uk)  
 
9. Set up the permissions for the newly imported ArrayLayouts: Add the following group-permission


The XML-files are currently only available in the CVS repository (Directory: CVSROOT/bioinfo/emma2/src/dbshema).
{| border="1" cellpadding="2" cellspacing="0"
|  '''Group'''
|  '''Read'''
|  '''Edit'''
|  '''Reference'''
|  '''Delete'''
|  '''View permissions'''
|  '''Change permissions'''
|-
|  ALL
|  yes
|  undefined
|  yes
|  undefined
|  yes
|  undefined

Revision as of 16:01, 10 October 2005

An EMMA 2.0 Project consists of a database and a corresponding user and group management, which is supplied by the GPMS-Project Management. The database uses the MAGE-OM object description scheme. After setting up a new project as it is described in the GPMS-Documentation, this database has to be "build up", attending the following steps:

Locate the xml-files needed for the setup: The XML-files are currently in the CVS repository (Directory: CVSDIR/bioinfo/emma2/src/dbshema).

1. If the project is created via GPMS the database will already be set up.

2. In the GPMS add the use emma - Emma Daemon to your project with role Daemon

3. Import the Quantitationstypes and QuantitationtypeDimensions (QuantitationTypes-COMPLETE.xml) Command: 

 test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE

4. Import the Ontology information (Ontology-COMPLETE.xml) Command: 

test_import -p "Project" XMLFILE

5. Import all necessary functions (AllTools.xml) Command: 

 test_import -p "Project" -i "[[IdentifierRefAction]]=Reference" XMLFILE

6. Add the "ALL" group, if this has not already been done during the GPMS-Setup Command: 

 emma_start add_group -g ALL  or use the EMMA 2.0 web interface

7. Create pipelines from the functions imported in step 6 using the EMMA 2.0 web interface 

/!\ Always create a pipline with the exact name  ArrayLayoutImport consisting solely of the function ArrayLayout Import

8. Now you are able to import arraylayouts (e.g. A-MEXP-85 from www.ebi.ac.uk)

9. Set up the permissions for the newly imported ArrayLayouts: Add the following group-permission

Group Read Edit Reference Delete View permissions Change permissions
ALL yes undefined yes undefined yes undefined
Retrieved from "https://wiki.cebitec.uni-bielefeld.de/brf-software/index.php?title=EMMAWiki/AdministratorDocumentation/ProjectSetup&oldid=1928"