GPMSWiki/AdministratorDocumentation/MaintainingGPMS
Interfaces
In this section we describe several ways for accessing and using the GPMS. In addition to the !API that allows programmers to directly manipulate all objects stored in the database we provide a number of scripts for maintaining the system and a Gtk graphical user interface for the management of users and project members. A simplified web frontend was also implemented that supports a restricted user management for "external" maintainers of projects.
GPMS scripts
The scripts listed in table 1 can be used to initially set up the system and for maintaining projects, users, and their memberships.
| name | description |
| add_host | add a new Host to the GPMS |
| add_datasource_!type | register a new DataSource |
| add_db_api_!type | register a new !API_!Type |
| add_dbms_!type | create a !DBMS_!Type |
| add_db | create a new !Database |
| add_project_class | create a new ProjectClass |
| add_project | create a new !Project |
| add_datasource2project | add a DataSource to a !Project |
| add_project_config | add configurations to a !Project |
| add_role | read and store the !Role definitions for a ProjectClass |
| add_rights | parse a !Right definition-file and store it in the GPMS |
| add_user | register a new !User |
| add_member | add an existing !User as a new Member to a !Project |
| add_meta_project | create a new Meta!Project |
| add_project2meta_project | add a !Project to a Meta!Project |
| del_host | remove a Host |
| del_datasource_!type | delete a DataSource_!Type |
| del_datasource | remove a DataSource from the GPMS |
| del_db_api_!type | delete a !DB_!API_!Type |
| del_dbms_!type | remove a !DBMS_!Type from the GPMS |
| del_project_class | delete a ProjectClass from the GPMS |
| del_project | delete a !Project |
| del_project_config | remove configurations from a !Project |
| del_role | remove roles from a ProjectClass |
| del_rights | delete rights from a ProjectClass |
| del_user | remove a !User from the GPMS |
| del_member | remove a !User from a !Project |
| change_member_role | change the !Role of an existing Member |
| export_members | print a list of all Members of a !Project or |
| all Members of all !Projects of a ProjectClass to a file | |
| rem_datasource_from_project | remove a DataSource from a !Project |
| rem_project_from_meta_project | remove a !Project from a Meta!Project |
| list_project_members | print a list of all Members of a !Project |
| list_projects | print a list of all !Projects and !Roles available for the !Project |
| list_user_projects | display a list of all !Projects that can be accessed by a !User |
| list_extern_user | print list of all extern !Users |
Available scripts for manipulating the GPMS. All currently implemented scripts for manipulating the GPMS are listed above. Executing a script without parameters will print a detailed description and a complete list of available options.
All scripts listed above are executed using the wrapper script GPMS which sets several installation specific environment variables. Executing this script without parameters will list all available scripts and print a usage message. The following paragraphs describe the use of each script and introduce their options.
add_datasource2project
add a !Datasource to a !Project in the GPMS
usage: add_datasource2project -D <datasource name> -p <project name> [-v]
where: -D <datasource name> name of the !Datasource
-p <project name> the Proejcts name
-v verbose
-h print this help message
example: add_datasource2project -D gendb_test -p gendbtest
add_datasource_!type
add a !Datasource_!Type to project management database
usage: add_datasource_!type -y <name> [-s <SQL_dump_file> -v]
where: -y <name> the !Datasource_!Types name
-s <SQL_dump_file> SQL dump file, with SQL statements creating
a !Database of this !Type
-v verbose
-h print this help message
example: add_datasource_!type -y !GENDB -s /vol/gendb/src/dbschema/!GenDB.sql
add_db
add a !Database (!Datasource::DB) to project management database
usage: add_db -H <hostname> -t <dbms_!type> -y <datasource_!type>
-A <db_api_!type> ( -D db_name | -p <project> )
[-d <description> -e -v]
where: -H <hostname> name of the !Databases Host
-t <dbms_!type> name of the !Databases !DBMS_!Type
-y <datasource_!type> name of the !Databases !Datasource_!Type
-A <db_api_!type name> name of the !Datasourced !DB_!API_!Type
-D the !Databases name
if -D is omitted !Database gets same name as !Project
-p <project> name of !Project the !Database shall be added to
Note that either -D or -p or both must be specified
-d <description> text describing the !Database
-e register existing !Database to gpms and therefore
without creating MySQL !Database
-v verbose
-h print this help message
example: add_db -D gendb_test -H dbhost -t MySQL-3.23.27 -y !GENDB -A O2DBI2
add_dbms_!type
add a !DBMS_!Type to project management database
usage: add_dbms_!type -t <name> -V <version number>
where: -t <name> the !DBMS_!Types name
-V <version number> the !DBMS_!Types version
-h print this help message
example: add_dbms_!type -t MySQL -V '3.23.27'
add_project2meta_project
add a !Project to a META !Project in the GPMS
usage: add_project2meta_project -p <project_name> -m <meta_project_name> [-v]
where: -p <project_name> the !Projects name
-m <meta_project_name> name of the META !Project
-v verbose
-h print this help message
example: add_project2meta_project -p gendb_test -m meta_test
del_project
removes a !Project and the project members from the GPMS
usage: del_project -p <project name> [-z -v]
where: -p <project name> name of the !Project
-z drop and remove the !Projects !Databases and !Datasources not used by
any other !Project from the gpms databases
-v verbose
-h print this help massage
example: del_project -p gendb_test
add_host
add a !Database Host to project management database
usage: add_host -H <hostname> [-P <port number>] [-d <description>]
where: -H <hostname> the Hosts name
-P <port number> the Hosts port number
-d <description> text decribing the Host
-h print this help message
example: add_host -H dbhost
add_member
add a new Member to a !Project in project management database
usage: add_member -l <user login> -p <project name> -r <role> [-v]
where: -l <user login> !User login of new Member
-p <project name> name of !Project the !User shall be added to as Member
-r <role> the new Members !Role
-v verbose
-h print this help message
example: add_member -l juser -p gendb_test -r Annotator
add_meta_project
use add_project with -m option!
add_project
add a new !Project to project management database
usage: add_project -p <name> -c <project_class> -d <description>
[-v -s <project sub class>]
where : -p <name> the !Projects name
-c <project_class> the !Projects !Project_!Class
-d <description> !Project description
-s <project sub class> subclass of ProjectManagement::!Project
available subclasses: EMMA, !GenDB, ProDB, Biomake, GPMS, META, WHOIS
-v verbose
-h print this help message
example: add_project -p gendb_test -c !GENDB -d "The !GenDB !DB" -s GenDG
del_rights
removes single !Right or all !Rights of a !Project_!Class from the GPMS
Note: before script can be used all !Roles using the !Rights of the !Project_!Class
must be removed!
usage: del_rights -c project_class (-r <right_name> | -a) [-v]
where: -r <right_name> name of a single !Right to be removed
-a remove all rights of the !Project_!Class
-v verbose
-h print this help message
example: del_rights -r use_gpmsdb -c !GENDB
add_project_class
add a !Project_!Class to project management database
usage: add_project_class -c <project class name> [-d description]
[-i <max instance number> -u <config file>]
where : -c <project class name> name of new !Project_!Class
-d <description> description of new !Project_!Class
-i <max instance number> maximal number of !Projects a
Meta !Project of this !Project_!Class may contain
-u <config file> default config file for new !Projects of this Class
-h print this help message
example: add_project_class -c !GENDB -d !GENDB !Projects
add_project_config
add !Project Configs to project management system
usage: add_project_config -p <project> -k <config_key> -V <config_value>
where: -p <project> the !Projects name
-k <config_key> the key of the Config to be added,
since !Project Configs are a hash
-V <config_value> the Configuration values
-h print this help message
example: add_project_config -p gendb_test -k genetik_code -V 11
add_rights
adds new !Rights to !Project_!Class to project management database
usage: add_rights -f <file name> [-v]
where: -f <file name> name of file defining the !Rights
-v verbose
-h print the help message
example: add_rights.pl -f "/vol/gendb/src/rights"
add_role
add new !Roles to a !Project_!Class in project management database
usage: add_role -f <file_name> [-v]
where: -f <file name> name of file defining the !Roles to be added
-v verbose
-h print this help message
example: add_role -f roles.txt
add_user
add a !User to project management database
usage: add_user -l <login> -f <full name> [-e <email address> -x]
where: -l <login> the !Users login
-f <full name> the !Users surname and first name
-e <email address> the !Users email adress
-x !User is extern
-h print this help message
example: add_user -l juser -f 'Joe !User' -e juser@Genetik.Uni-Bielefeld.DE
change_member_role
change the !Role from a !Project Member
usage: change_member_role.pl -l <user login> -p <project> -r <role> [-v]
where: -l <user login> the Members login
-p <project> name of the !Project
-r <role> the new !Role the Member shall get
-v verbose
-h print this help message
example: change_member_role.pl -l juser -p gendbtest -r Annotator
del_datasource
removes a !Datasource from project management database
usage: del_datasource.pl -D <datasource name> [-z -v]
where: -D <datasource name> the !Datasouces name
-z drop database from the MySQL !DB
-v verbose
-h print this help message
example: del_datasource.pl -D gendb_test -z
del_datasource_!type
removes a !Datasource_!Type from project management database
usage: del_datasource_!type.pl -y <datasource_!type name>
where: -y <datasource_!type name> name of the !Datasource_!Type to be removed
-h print this help message
example: del_datasource_!type.pl -y !GENDB
del_dbms_!type
removes a !DBMS_!Type from project management database
usage: del_dbms_!type -n <dbms_!type_name> -V <version> [-v]
where: -n <dbms_!type_name> name of the !DBMS_!Type
-V <version> the !DBMS_!Types version
-v verbose
-h print this help message
example: del_dbms_!type -n MySQL -V 3.23.48
del_host
removes a Host from project management database
usage: del_host -H <host_name> name
where: -H <host_name> name of Host to be removed
-h print this help message
example: del_host -H dbhost
del_member
removes single or all Members from a !Project
usage: del_member ( -a | -l <user login> [-q] ) -p <project name> [-f -v]
where: -p <project name> name of the !Project
-a remove all Members from !Project
-l user login from single Member to be removed
-q do not revoke MySQL privileges when removing single Member
-f force: Member is deleted even if the db privileges
can not be revoked
-v verbose
-h print this help message
example: del_member -l jouser -p gendbtest
del_role
removes one or all !Roles of a !Project_!Class from the GPMS
usage: del_role -c <project_class> (-a | -r <role name> ) [-f -v]
where: -c <project_class> name of the !Project_!Class
-a remove all !Roles of the !Project_!Class
-f force, Members of all !Projects of !Project_!Class first
-v verbose
-h print this help message
example: del_role -r !User -c !GENDB
del_project_class
removes a !Project_!Class from project management database
usage: del_project_class -c <project_class name>
where: -c <project_class name> name of the !Project_!Class
-h print this help message
example: del_project_class -c !GENDB
del_project_config
delete !Project Configs from project management system
usage: del_project_config -p <project_name> -k <config key>
where: -p <project_name> name of the !Project
-k <config key> the key value of configuration entry to be removed
-h print this help message
example: del_project_config -p gendb_test -k genetik_code
export_members
print a list of all Members of a !Project or all Members of all
!Projects of a !Project_!Class to a file
usage: export_members (-p <project name> | -c <project_class> | -a)
-f <file_name>
where: -p <project name> Print all Members of this !Project to a file
-c <project_class name> Print all Members of !Projects of this
!Project_!Class to a file
-a Print all Members of every !Project to a file
-h print this help message
example: export_members -p gendbtest -f gendbtest_members
del_user
removes a !User of project management database
usage: del_user -l <login> [-v]
where: -l <login> the !Users login
-v verbose
-h print this help message
example: del_user -l jouser
rem_datasource_from_project
removes a !Datasource from a !Project
usage: rem_datasource_from_project -D <datasource_name> -p <project_name>
[-f -v]
where: -D <datasource_name> name of the !Datasource to be removed from !Project
-p <project_name> name of the !Project
-f force: also remove datasource even if not all member privileges
could be revoked
-v verbose
-h print this help message
example: rem_datasource_from_project -D gendb_test -p gendb_test_project
list_projects
list !Projects with available !Roles from
project management database
usage: list_projects
where: -h print this help message
add_db_api_!type
add a !DB_!API_!Type to project management database
usage: add_db_api_!type -A <db_api_!type name> -d <description> [-v]
where: -A <db_api_!type name> the !DB_!API_!Types name
-d <description> text describing the !DB_!API_!Type
-v verbose
-h print this help message
example: add_db_api_!type -A O2DBI -d "The O2DBI I database api"
list_user_projects
get !Projects of a !User from project management database
usage: list_user_projects -l <user login>
where: -l <user login> the !Users login
-h print this help message
example: list_user_projects -l juser
del_db_api_!type
removes a !DB_!API_!Type from project management database
usage: del_db_api_!type -A <db_api_!type_name>
where: -A <db_api_!type_name> name of the !DB_!API_!Type
-h print this help message
example: del_db_api_!type -A O2DBI
list_project_members
list !Project Members with their !Role
usage: list_project_members -p <!Project name> [-r]
where: -p <!Project name> the !Projects name
-r sort Members by !Role
-h print this help message
example: list_project_members -p gendb_test
list_extern_users
list_extern_user - list all extern !Users and genereates MySQL statements to obtiain
consistent MySQL privileges for extern users
usage: list_user_projects [-g]
where: -g generate MySQL statements
-h print this help message
example: list_user_projects -l juser
rem_project_from_meta_project
removes a !Project from a META !Project
usage: rem_project_from_meta_project -p <project_name> -m <meta_project_name>
where: -p <project_name> name of !Project to be removed from META !Project
-m <meta_project_name> name of META !Project
-h print this help message
example: rem_project_from_meta_project -p gendb_test -m gendb_meta
Author: Lutz Krause