View source for GPMSWiki/AdministratorDocumentation/MaintainingGPMS

__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. A web frontend for managing users and members was also
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 ===
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  [[MetaProject]]
|-
| add_project2meta_project 
|  add a  Project to a  [[MetaProject]]
|}

{| 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  [[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: [http://www.cebitec.uni-bielefeld.de/~lkrause Lutz Krause]