GPMSWiki/CoreDocumentation/Implementation - Revision history

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2011-10-26T06:17:00Z

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imported>LutzKrause at 11:42, 25 April 2005

2005-04-25T11:42:32Z

← Older revision		Revision as of 13:42, 25 April 2005
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	extensively uses different roles for a sophisticated access control.		extensively uses different roles for a sophisticated access control.

	#
	# ROLES defined for GenDB-2.0		# ROLES defined for GenDB-2.0
	#		#
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	RIGHT basic_access		RIGHT basic_access

	~~####################################~~
	### RIGHTS defined for GenDB-2.0 ###		### RIGHTS defined for GenDB-2.0 ###
	~~####################################~~

	PROJECT_CLASS GENDB		PROJECT_CLASS GENDB
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	{\| border="1" cellpadding="2" cellspacing="0"		{\| border="1" cellpadding="2" cellspacing="0"
	\| name		\| name
	\| description		\| description
	\|
	\|-		\|-
	\| add_host		\| add_host
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	\| add_user		\| add_user
	\| register a new User		\| register a new User
	\|
	\|-		\|-
	\| add_member		\| add_member
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	\| del_user		\| del_user
	\| remove a User from the GPMS		\| remove a User from the GPMS
	\|
	\|-		\|-
	\| del_member		\| del_member
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	\|-		\|-
	\| all Members of all Projects of a ProjectClass to a file		\| all Members of all Projects of a ProjectClass to a file
	\|
	\|-		\|-
	\| rem_datasource_from_project		\| rem_datasource_from_project
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	\| list_extern_user		\| list_extern_user
	\| print list of all extern Users		\| print list of all extern Users
	\|
	\|}		\|}

imported>LutzKrause at 11:38, 25 April 2005

2005-04-25T11:38:20Z

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imported>LutzKrause at 11:35, 25 April 2005

2005-04-25T11:35:21Z

← Older revision		Revision as of 13:35, 25 April 2005
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	Genome Research, Bielefeld University).		Genome Research, Bielefeld University).

	=== ProjectClass ===		=== [[ProjectClass]] ===
	A projectclass arranges projects of the same type into		A projectclass arranges projects of the same type into
	groups. Additionally, a projectclass determines the available roles and		groups. Additionally, a projectclass determines the available roles and
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	below).		below).

	=== DataSource ===		=== [[DataSource]] ===
	Applications often need to access and store persistent external		Applications often need to access and store persistent external
	data. These are provided as a datasource which is attached to a		data. These are provided as a datasource which is attached to a
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	the correct datasource can be established automatically.		the correct datasource can be established automatically.

	=== DataSource::[[ApplicationServer]] ===		=== [[DataSource]]::[[ApplicationServer]] ===
	An [[ApplicationServer]] is a generic datasource that can provide data for an		An [[ApplicationServer]] is a generic datasource that can provide data for an
	application. The class inherits all attributes of the datasource		application. The class inherits all attributes of the datasource
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	of DataSource_Type).		of DataSource_Type).

	=== DataSource::DB ===		=== [[DataSource]]::DB ===
	This class represents all kinds of databases and extends the datasource		This class represents all kinds of databases and extends the datasource
	class. In addition to all inherited attributes of the		class. In addition to all inherited attributes of the
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	<!-- # user with read only permissions and almost completely restricted access -->		<!-- # user with read only permissions and almost completely restricted access -->
	<!-- # ~~toles~~ with the tag ext'' can be assigned to members via the external -->		<!-- # Roles with the tag ext can be assigned to members via the external -->
	<!-- # GPMS web frontend. Roles without this tag are not listed in the ext. -->		<!-- # GPMS web frontend. Roles without this tag are not listed in the ext. -->
	<!-- # web frontend. -->		<!-- # web frontend. -->

imported>LutzKrause at 11:31, 25 April 2005

2005-04-25T11:31:36Z

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imported>LutzKrause at 11:18, 25 April 2005

2005-04-25T11:18:02Z

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imported>LutzKrause at 10:32, 25 April 2005

2005-04-25T10:32:29Z

← Older revision		Revision as of 12:32, 25 April 2005
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	schema for the GPMS database (GPMSDB) as it has been generated by O2DBI-2.		schema for the GPMS database (GPMSDB) as it has been generated by O2DBI-2.

	~~beginfigure~~		[[Image:GPMSWiki$$CoreDocumentation$$Implementation$DBSchemaGPMS.png]]
	~~begincenter~~
	~~includegraphics~~[~~width=0~~.~~7columnwidth~~]~~../../../src/dbschema/GPMS~~
	~~endcenter~~
	~~caption[Database schema of the Project Management System.~~]~~The database~~
	~~schema of the GPMS. Black lines mark references between two classes and~~
	~~red lines show inherited class relationships.~~
	~~labelfig:data_model~~
	~~endfigure~~

	== Class descriptions ==		== Class descriptions ==
	The following sections briefly describe the relevant classes of the		The following sections briefly describe the relevant classes of the
	data schema (see figure 1). The five core classes		data schema (see figure 1). The five core classes Project, User, Member, Role and
	Project, User, Member, Role and		[[DataSource]] are complemented by several simple classes that store
	[[DataSource]] are complemented by several simple classes that store
	additional information.		additional information.

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	contain a reference to a file that defines the database schema so that a		contain a reference to a file that defines the database schema so that a
	newly created database can be filled with all tables automatically		newly created database can be filled with all tables automatically
	after creation.		after creation. A project may only have one DB and one
	A project may only have one DB and one		[[ApplicationServer]] of each datasourcetype so that the connection to
	[[ApplicationServer]] of each datasourcetype so that the connection to
	the correct datasource can be established automatically.		the correct datasource can be established automatically.

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	member-projects and inherits all the attributes of project.		member-projects and inherits all the attributes of project.

	=== Role and Right definitions ===		== Role and Right definitions ==
	The following paragraphs describe the roles and rights		The following paragraphs describe the roles and rights
	as defined for the genome annotation system GenDB-2.0 which		as defined for the genome annotation system GenDB-2.0 which
	extensively uses different roles for a sophisticated access control.		extensively uses different roles for a sophisticated access control.

	<!-- ~~#################################~~# -->		<!-- # -->
	<!-- ### ROLES defined for GenDB-2.0 ~~###~~ -->		<!-- # ROLES defined for GenDB-2.0 -->
	<!-- ~~##################################~~# -->		<!-- # -->

	PROJECT_CLASS GENDB		PROJECT_CLASS GENDB

imported>LutzKrause at 10:24, 25 April 2005

2005-04-25T10:24:17Z

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imported>LutzKrause at 16:53, 18 April 2005

2005-04-18T16:53:35Z

← Older revision	Revision as of 18:53, 18 April 2005
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Unknown user at 00:00, 1 January 1970

1970-01-01T00:00:00Z

New page

__NOTOC__
= Implementation =

\section{Implementation}
%% this section contains some details about the implementation of the GPMS:
%% database model, O2DBI, Perl, MySQL
This chapter contains details about the implementation of the \GPMS. We
describe the datamodel for the relational database and explain the attributes
of each class. Sample descriptions for the definition of \roles{} and
\rights{} complement this section by illustrating the implementation of
fine-grained access control.

\subsection{Database schema for the \GPMS}
The \PMS{} was developed as an object-oriented
application based on the data model described in the previous
section. Since the GPMS required a persistent storage backend we
decided to use the O2DBI-2 system \cite{otodbi2}
which automatically maps the XML class descriptions onto tables that can be stored in a relational
database (auto-generated object-relational mapping of Perl objects). At the same time,
O2DBI-2 provides a client-server architecture that allows remote
connections to the system via a Perl or C++ client. The automatically
generated Perl server modules for all described classes have been
extended with additional functionality and thus form the \gpms-API. MySQL is currently
used as the database backend but other relational database management
systems (RDBMS) can be used as they are supported by the O2DBI-2
software. Figure \ref{fig:data_model} displays the current database
schema for the GPMS database (\GPMSDB) as it has been generated by O2DBI-2.

\begin{figure}%[H]
\begin{center}
\includegraphics[width=0.7\columnwidth]{../../../src/dbschema/gpms}
\end{center}
\caption[Database schema of the Project Management System.]{The database
schema of the \GPMS{}. Black lines mark references between two classes and
red lines show inherited class relationships.}
\label{fig:data_model}
\end{figure}

\input{class_descriptions}

\input{[[RolesRights]]}

\newpage
\section{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.

\subsection{GPMS scripts}
The scripts listed in table \ref{tab:gpms_scripts} can be used to
initially set up the system and for maintaining \projects, \users, and their
memberships.

%\begin{tabular}{ll}\hline
\begin{table}[H]
\small
\begin{longtable}{|l|l|}
\multicolumn{2}{c}{\rule[-3mm]{0mm}{8mm} \textbf{\gpms \ scripts}}\\ \hline
%\multicolumn{2}{c}{\textbf{adding datasets}}\\ \hline
name & description \\ \hline
add\_host & add a new {\it Host} to the \gpms\\
add\_datasource\_type & register a new {\it [[DataSource]]}\\
add\_db\_api\_type & register a new {\it API\_Type}\\
add\_dbms\_type & create a {\it DBMS\_Type}\\
add\_db & create a new {\it Database}\\
add\_project\_class & create a new {\it [[ProjectClass]]}\\
add\_project & create a new {\it Project}\\
add\_datasource2project & add a {\it [[DataSource]]} to a {\it Project} \\
add\_project\_config & add configurations to a {\it Project}\\
add\_role & read and store the {\it Role} definitions for a {\it [[ProjectClass]]}\\
add\_rights & parse a {\it Right} definition-file and store it in the \gpms\\
add\_user & register a new {\it User}\\
add\_member & add an existing {\it User} as a new {\it Member} to a {\it Project}\\
add\_meta\_project & create a new {\it [[MetaProject]]}\\
add\_project2meta\_project & add a {\it Project} to a {\it [[MetaProject]]}\\
%add\_biomake\_project & adds a new biomake project to the \gpms\\
%add\_emma\_project & add a \emma {\it Project} to the \gpms\\
%add\_gendb\_project & add a \gendb {\it Project} to the \gpms\\\\
%add\_prodb\_project & create a \prodb {\it Project}\\
% & \\
\hline
%\multicolumn{2}{c}{\textbf{deleting data}}\\ \hline
%% name & description \\ \hline
del\_host & remove a {\it Host}\\
del\_datasource\_type & delete a {\it [[DataSource]]\_Type} \\
del\_datasource & remove a {\it [[DataSource]]} from the \gpms\\
del\_db\_api\_type & delete a {\it DB\_API\_Type}\\
del\_dbms\_type & remove a {\it DBMS\_Type} from the \gpms\\
del\_project\_class & delete a {\it [[ProjectClass]]} from the \gpms\\
del\_project & delete a {\it Project}\\
del\_project\_config & remove configurations from a {\it Project}\\
del\_role & remove roles from a {\it [[ProjectClass]]}\\
del\_rights & delete rights from a {\it [[ProjectClass]]}\\
del\_user & remove a {\it User} from the \gpms\\
del\_member & remove a {\it User} from a {\it Project}\\
%& \\
\hline
% \caption[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.}
% \label{tab:gpms_scripts}
\end{longtable}
\end{table}
\normalsize

\begin{table}[H]
\small
\begin{longtable}{|l|l|}
\multicolumn{2}{c}{\rule[-3mm]{0mm}{8mm} \textbf{\gpms \ scripts cont.}}\\ \hline
%\multicolumn{2}{c}{\textbf{other scripts}}\\ \hline
%% name & description \\ \hline
change\_member\_role & change the {\it Role} of an existing {\it Member}\\
export\_members & print a list of all {\it Member}s of a {\it Project} or\\
& all {\it Member}s of all {\it Project}s of a {\it [[ProjectClass]]} to a file\\
%%%%% !!! These should be named 'del_...' !!! %%%%%
rem\_datasource\_from\_project & remove a {\it [[DataSource]]} from a {\it Project}\\
rem\_project\_from\_meta\_project & remove a {\it Project} from a {\it [[MetaProject]]}\\
list\_project\_members & print a list of all {\it Members} of a {\it Project}\\
list\_projects & print a list of all {\it Project}s and {\it Roles} available for the {\it Project}\\
list\_user\_projects & display a list of all {\it Projects} that can be accessed by a {\it User}\\
list\_extern\_user & print list of all extern {\it Users} \\
gui & start the graphical user interface to maintain the \gpms\\ \hline

\caption[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.}
\label{tab:gpms_scripts}
\end{longtable}
\end{table}
%\end{tabular}
\normalsize

All scripts listed above are executed using the wrapper script {\bf
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.
%\input{script_descriptions}
\input{scripts}

\subsection{Using an Application Frame}
In addition to the standard classes of the \PMS{}
described in section \ref{classes}, we have implemented a general framework that
simplifies the necessary steps for accessing a project's data. Such an
\textit{Application Frame} uses the \gpms{} for accessing the
\datasources{} of a \project{} and it also provides a number of useful
methods that are often needed by the end applications. The following
description was directly included from the documentation of the Perl module.
\input{application_frame}

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