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. A web frontend for managing users and members was also implemented. For documentation on how to maintain projects at the CeBiTec at the Bielefeld University go to the InternalWiki.
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 MetaProject |
| add_project2meta_project | add a Project to a MetaProject |
| 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 MetaProject |
| 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