Author: acheype Date: 2013-04-30 12:52:22 +0200 (Tue, 30 Apr 2013) New Revision: 213 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/213 Log: - Add the Installation page in the web site - Update the index and configuration page in the web site Added: trunk/src/site/resources/images/cantharella_with_title.jpg trunk/src/site/rst/installation.rst Modified: trunk/ trunk/src/site/rst/configuration.rst trunk/src/site/rst/index.rst trunk/src/site/site.xml Property changes on: trunk ___________________________________________________________________ Modified: svn:ignore - target *.ipr *.iws *.iml .idea .classpath .project .settings + *.ipr .classpath *.iws .project .idea *.iml target nbactions.xml .settings Added: trunk/src/site/resources/images/cantharella_with_title.jpg =================================================================== (Binary files differ) Property changes on: trunk/src/site/resources/images/cantharella_with_title.jpg ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Modified: trunk/src/site/rst/configuration.rst =================================================================== --- trunk/src/site/rst/configuration.rst 2013-04-30 09:24:32 UTC (rev 212) +++ trunk/src/site/rst/configuration.rst 2013-04-30 10:52:22 UTC (rev 213) @@ -41,65 +41,79 @@ Classpath --------- -This file contains default value and is found in cantharella jar file +This file contains default value and is found in cantharella WAR archive. System configuration directory ------------------------------ -- Unix : /etc/cantharella.conf -- Windows : C:\\Windows\\System32\\cantharella.conf -- Mac OS : /etc/cantharella.conf +- Linux : */etc/cantharella.conf* +- Windows : *C:\\Windows\\System32\\cantharella.conf* +- Mac OS X : */etc/cantharella.conf* User configuration directory ---------------------------- -- Unix : ${user.home}/.config/cantharella.conf -- Windows : ${user.home}\\Application Data\\cantharella.conf -- Mac OS x : ${user.home}/Library/Application Support/cantharella.conf +- Linux : *${user.home}/.config/cantharella.conf* +- Windows : *${user.home}\\Application Data\\cantharella.conf* +- Mac OS X : *${user.home}/Library/Application Support/cantharella.conf* Current directory ----------------- -Directory used to launch application +The directory used to launch application. JVM variables ------------- You can add parameter to JVM command line to set variable. -example:: +Example:: java -Ddb.user=$USER -Dmail.host=localhost ... -Configuration variables +Adapt the variables ~~~~~~~~~~~~~~~~~~~~~~~ -You can put some variable in cantharella.conf file to change default value. +The default *cantharella.conf* file is listed below. You have to tune the variables available in +order to adapt it to your need. +To launch the application in your environment, the first need is to set **db.url**, **db.user**, +**db.password**, **mail.from** and **mail.host**. :: -List of all variables with default values:: - + # + # DATABASE CONFIGURATION # - # DATA - # db.url=jdbc:postgresql:cantharella db.user=cantharella db.password=cantharella - db.debug=true + db.debug=false db.hbm2ddl=validate - + + # Hibernate search lucene index location on filesystem. + hibernate.search.indexBase=/tmp/cantharella + # Hibernate search analyzer + hibernate.search.analyzer=org.apache.lucene.analysis.fr.FrenchAnalyzer + + # + # SERVICE CONFIGURATION # - # SERVICE - # - mail.debug=true + mail.debug=false mail.from=no-reply@ird.fr mail.host=smtp - + + # default administration login/password admin.courriel=ISlog@ird.fr admin.password=password + # Document's allowed extensions + document.extension.allowed=jpeg,jpg,gif,png,xls,doc,pdf,cdx,mol + # - # WEB + # WEB CONFIGURATION # - app.debug=true - app.optimize=false - wicket.configuration=development + app.debug=false + app.optimize=true + wicket.configuration=deployment + log4j.config=classpath:log4j_prod.xml + + #document file max upload size (Mb) + document.maxUploadSize=1 \ No newline at end of file Modified: trunk/src/site/rst/index.rst =================================================================== --- trunk/src/site/rst/index.rst 2013-04-30 09:24:32 UTC (rev 212) +++ trunk/src/site/rst/index.rst 2013-04-30 10:52:22 UTC (rev 213) @@ -21,26 +21,44 @@ .. * #L% .. - -Cantharella -=========== +.. image:: images/cantharella_with_title.jpg + Description ----------- -The information system (IS) “Cantharella: Pharmacochemical database of natural -substances” share and sustain pharmacochemical data of all organisms collected -for the study of their natural substances, with a controlled access via -internet. +The information system (IS) **Cantharella: Pharmacochemical database of natural substances**, +designed and developed by IRD, share and sustain pharmacochemical data of all organisms collected +for the study of their natural substances, with a controlled access via the Internet. -.. image:: images/Home.png -.. image:: images/Station.png -.. image:: images/Extraction.png +The IS provides access to **harvest and taxonomic data**, monitor various chemical processes of +extraction and purification, and finally centralize all **biological activities**. +The database is progressive according to the extraction and purification methods needed and the +biological tests performed. Features -------- -- Collaborative work between spatially disparate people -- Secure access and "compartmentalized” according to data access rights -- Traceability of the chemical process leading to the active compounds -- Capitalization of data and related documents (to be developed) -- Interoperability with other IS (to be developed) +- **Collaborative** work between spatially disparate people +- **Secure access** and 'compartmentalized' according to data access rights +- **Traceability** of the chemical process leading to the active compounds +- **Capitalization** of data and related documents + +Screenshots +----------- + +.. figure:: images/Home.png + +Home + +.. figure:: images/Station.png + +Location form + +.. figure:: images/Extraction.png + +Extraction form + + + + Copied: trunk/src/site/rst/installation.rst (from rev 210, trunk/src/site/rst/configuration.rst) =================================================================== --- trunk/src/site/rst/installation.rst (rev 0) +++ trunk/src/site/rst/installation.rst 2013-04-30 10:52:22 UTC (rev 213) @@ -0,0 +1,87 @@ +.. - +.. * #%L +.. * Cantharella +.. * $Id: +.. * $HeadURL: +.. * %% +.. * Copyright (C) 2009 - 2012 IRD (Institut de Recherche pour le Developpement) and by respective authors (see below) +.. * %% +.. * This program is free software: you can redistribute it and/or modify +.. * it under the terms of the GNU Affero General Public License as published by +.. * the Free Software Foundation, either version 3 of the License, or +.. * (at your option) any later version. +.. * +.. * This program is distributed in the hope that it will be useful, +.. * but WITHOUT ANY WARRANTY; without even the implied warranty of +.. * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +.. * GNU General Public License for more details. +.. * +.. * You should have received a copy of the GNU Affero General Public License +.. * along with this program. If not, see <http://www.gnu.org/licenses/>. +.. * #L% +.. - + +Installation +============ + +This section describes how to install on the Tomcat application server in a linux system. + +Software requirements +--------------------- + +You will first need to install the following prerequisites: + +- Java Development Kit 1.7 or higher +- Tomcat 7.0 or higher +- PostgreSQL 9.0 or higher + +Get the war and the database script +----------------------------------- + +You can download the last release version files from here_, that is the WAR archive and the SQL +script to create the database schema. :: + + cd /tmp + wget http://forge.codelutin.com/attachments/download/686/cantharella.web-1.1-rc-1... + wget http://forge.codelutin.com/attachments/download/700/cantharella_schema_1.1.s... + +.. _here: http://forge.codelutin.com/projects/cantharella/files + +Install the database +-------------------- + +To begin, start the SQL command with the postgres user. :: + + su postgres + psql + +Then, in the SQL command, add the user (don't forget to change the password!), the database and +its rights. :: + + CREATE ROLE cantharella LOGIN PASSWORD 'cantharella'; + CREATE DATABASE cantharella WITH ENCODING='UTF8' OWNER=cantharella; + GRANT ALL ON DATABASE cantharella TO cantharella; + \connect cantharella + ALTER SCHEMA public OWNER TO cantharella; + GRANT ALL ON SCHEMA public TO cantharella; + \q + +And still with the postgres user, import the database creation script. :: + + psql -d cantharella -f /tmp/cantharella_schema_1.1.sql + exit + +Deploy the WAR in Tomcat +------------------------ + +By default, Tomcat deploy automatically the WAR file in its webapps directory. Assuming that Tomcat +path is */opt/tomcat*, then do:: + + cp /tmp/cantharella.web-1.1-rc-1.war /opt/tomcat/webapps + +Then, you have to configure your Cantharella instance as described in this section_. + +.. _section: configuration.html + +After the configuration step, you can restart your tomcat server, read the logs in the */opt/tomcat/logs* directory and verify that they +don't contain any errors. By default, the application logs will be in the *cantharella.log* file. \ No newline at end of file Modified: trunk/src/site/site.xml =================================================================== --- trunk/src/site/site.xml 2013-04-30 09:24:32 UTC (rev 212) +++ trunk/src/site/site.xml 2013-04-30 10:52:22 UTC (rev 213) @@ -57,6 +57,7 @@ <menu name="User"> <item name="About" href="index.html"/> + <item name="Installation" href="installation.html"/> <item name="Configuration" href="configuration.html"/> </menu>