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imported>LutzKrause at 12:28, 25 April 2005

2005-04-25T12:28:44Z

← Older revision		Revision as of 14:28, 25 April 2005
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	stored in the database we provide a number of scripts for		stored in the database we provide a number of scripts for
	maintaining the system. A web frontend for managing users and members was also		maintaining the system. A web frontend for managing users and members was also
	implemented. For documentation how to maintain projects at the CeBiTec at the		implemented. For documentation on how to maintain projects at the CeBiTec at the
	Bielefeld University go the [http://www.cebitec.uni-bielefeld.de/groups/brf/internal/GPMSWiki/AdministratorDocumentation/AdminGPMSinBielefeld InternalWiki].		Bielefeld University go to the [http://www.cebitec.uni-bielefeld.de/groups/brf/internal/GPMSWiki/AdministratorDocumentation/AdminGPMSinBielefeld InternalWiki].

	=== GPMS scripts ===		=== GPMS scripts ===

imported>LutzKrause at 12:28, 25 April 2005

2005-04-25T12:28:16Z

← Older revision		Revision as of 14:28, 25 April 2005
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	stored in the database we provide a number of scripts for		stored in the database we provide a number of scripts for
	maintaining the system. A web frontend for managing users and members was also		maintaining the system. A web frontend for managing users and members was also
	implemented.		implemented. For documentation how to maintain projects at the CeBiTec at the
			Bielefeld University go the [http://www.cebitec.uni-bielefeld.de/groups/brf/internal/GPMSWiki/AdministratorDocumentation/AdminGPMSinBielefeld InternalWiki].

	=== GPMS scripts ===		=== GPMS scripts ===

imported>LutzKrause at 12:08, 25 April 2005

2005-04-25T12:08:16Z

← Older revision		Revision as of 14:08, 25 April 2005
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	In addition to the API that allows programmers to directly manipulate all objects		In addition to the API that allows programmers to directly manipulate all objects
	stored in the database we provide a number of scripts for		stored in the database we provide a number of scripts for
	maintaining the system ~~and a Gtk graphical user interface~~ for ~~the~~		maintaining the system. A web frontend for managing users and members was also
	~~management of~~ users and ~~project~~ members~~. A simplified web frontend~~ was also		implemented.
	implemented ~~that supports a restricted user management for "external"~~
	~~maintainers of projects~~.

	=== GPMS scripts ===		=== GPMS scripts ===

imported>LutzKrause at 11:51, 25 April 2005

2005-04-25T11:51:28Z

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Unknown user at 00:00, 1 January 1970

1970-01-01T00:00:00Z

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__NOTOC__
== 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.

{| border="1" cellpadding="2" cellspacing="0"
| 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
|}

{| border="1" cellpadding="2" cellspacing="0"
| 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
|}

{| border="1" cellpadding="2" cellspacing="0"
| 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: [http://www.cebitec.uni-bielefeld.de/~lkrause Lutz Krause]

GPMSWiki/AdministratorDocumentation/MaintainingGPMS - Revision history

Admin: 5 revisions

imported>LutzKrause at 12:28, 25 April 2005

imported>LutzKrause at 12:28, 25 April 2005

imported>LutzKrause at 12:08, 25 April 2005

imported>LutzKrause at 11:51, 25 April 2005

Unknown user at 00:00, 1 January 1970