Author: echatellier Date: 2013-02-19 18:45:15 +0100 (Tue, 19 Feb 2013) New Revision: 134 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/134 Log: Fix dependencies (again:() and website generation Added: trunk/cantharella.data/src/site/ trunk/cantharella.data/src/site/rst/ trunk/cantharella.data/src/site/rst/index.rst trunk/cantharella.data/src/site/site.xml trunk/cantharella.service/src/site/ trunk/cantharella.service/src/site/rst/ trunk/cantharella.service/src/site/rst/index.rst trunk/cantharella.service/src/site/site.xml trunk/cantharella.utils/src/site/ trunk/cantharella.utils/src/site/rst/ trunk/cantharella.utils/src/site/rst/index.rst trunk/cantharella.utils/src/site/site.xml trunk/cantharella.web/src/site/rst/index.rst trunk/cantharella.web/src/site/site.xml Modified: trunk/cantharella.data/pom.xml trunk/cantharella.service/pom.xml trunk/cantharella.utils/src/main/java/nc/ird/cantharella/utils/CantharellaConfig.java trunk/cantharella.web/pom.xml trunk/cantharella.web/src/main/resources/log4j.xml trunk/cantharella.web/src/site/rst/devel/integration-chemdoodle.rst trunk/pom.xml trunk/src/code-formatter-conf/code-format.xml trunk/src/site/rst/configuration.rst trunk/src/site/rst/index.rst trunk/src/site/site.xml Modified: trunk/cantharella.data/pom.xml =================================================================== --- trunk/cantharella.data/pom.xml 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/cantharella.data/pom.xml 2013-02-19 17:45:15 UTC (rev 134) @@ -65,6 +65,11 @@ <scope>test</scope> </dependency> <dependency> + <groupId>log4j</groupId> + <artifactId>log4j</artifactId> + <scope>test</scope> + </dependency> + <dependency> <groupId>org.apache.commons</groupId> <artifactId>commons-lang3</artifactId> </dependency> @@ -77,6 +82,10 @@ <artifactId>commons-collections</artifactId> </dependency> <dependency> + <groupId>org.nuiton</groupId> + <artifactId>nuiton-utils</artifactId> + </dependency> + <dependency> <groupId>postgresql</groupId> <artifactId>postgresql</artifactId> </dependency> Added: trunk/cantharella.data/src/site/rst/index.rst =================================================================== --- trunk/cantharella.data/src/site/rst/index.rst (rev 0) +++ trunk/cantharella.data/src/site/rst/index.rst 2013-02-19 17:45:15 UTC (rev 134) @@ -0,0 +1,25 @@ +.. - +.. * #%L +.. * Cantharella :: Data +.. * $Id:$ +.. * $HeadURL:$ +.. * %% +.. * Copyright (C) 2009 - 2013 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% +.. - + +Cantharella data module +======================= Added: trunk/cantharella.data/src/site/site.xml =================================================================== (Binary files differ) Property changes on: trunk/cantharella.data/src/site/site.xml ___________________________________________________________________ Added: svn:mime-type + application/xml Modified: trunk/cantharella.service/pom.xml =================================================================== --- trunk/cantharella.service/pom.xml 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/cantharella.service/pom.xml 2013-02-19 17:45:15 UTC (rev 134) @@ -53,6 +53,10 @@ <scope>test</scope> </dependency> <dependency> + <groupId>org.nuiton</groupId> + <artifactId>nuiton-utils</artifactId> + </dependency> + <dependency> <groupId>com.h2database</groupId> <artifactId>h2</artifactId> <scope>test</scope> Added: trunk/cantharella.service/src/site/rst/index.rst =================================================================== --- trunk/cantharella.service/src/site/rst/index.rst (rev 0) +++ trunk/cantharella.service/src/site/rst/index.rst 2013-02-19 17:45:15 UTC (rev 134) @@ -0,0 +1,25 @@ +.. - +.. * #%L +.. * Cantharella :: Service +.. * $Id:$ +.. * $HeadURL:$ +.. * %% +.. * Copyright (C) 2009 - 2013 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% +.. - + +Cantharella service module +========================== Added: trunk/cantharella.service/src/site/site.xml =================================================================== (Binary files differ) Property changes on: trunk/cantharella.service/src/site/site.xml ___________________________________________________________________ Added: svn:mime-type + application/xml Modified: trunk/cantharella.utils/src/main/java/nc/ird/cantharella/utils/CantharellaConfig.java =================================================================== --- trunk/cantharella.utils/src/main/java/nc/ird/cantharella/utils/CantharellaConfig.java 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/cantharella.utils/src/main/java/nc/ird/cantharella/utils/CantharellaConfig.java 2013-02-19 17:45:15 UTC (rev 134) @@ -41,7 +41,7 @@ /** * force filename to cantharella.config - * @return + * @return cantharella configuration as properties * @throws ArgumentsParserException */ static public Properties getProperties() throws ArgumentsParserException { @@ -52,8 +52,8 @@ * This method take file name in argument, this permit to force filename for * example for unit tests * - * @param filename filename to used - * @return + * @param filename filename to use + * @return cantharella configuration as properties * @throws ArgumentsParserException */ static public Properties getProperties(String filename) throws ArgumentsParserException { Added: trunk/cantharella.utils/src/site/rst/index.rst =================================================================== --- trunk/cantharella.utils/src/site/rst/index.rst (rev 0) +++ trunk/cantharella.utils/src/site/rst/index.rst 2013-02-19 17:45:15 UTC (rev 134) @@ -0,0 +1,25 @@ +.. - +.. * #%L +.. * Cantharella :: Utils +.. * $Id:$ +.. * $HeadURL:$ +.. * %% +.. * Copyright (C) 2009 - 2013 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% +.. - + +Cantharella utils module +======================== Added: trunk/cantharella.utils/src/site/site.xml =================================================================== (Binary files differ) Property changes on: trunk/cantharella.utils/src/site/site.xml ___________________________________________________________________ Added: svn:mime-type + application/xml Modified: trunk/cantharella.web/pom.xml =================================================================== --- trunk/cantharella.web/pom.xml 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/cantharella.web/pom.xml 2013-02-19 17:45:15 UTC (rev 134) @@ -91,6 +91,10 @@ <artifactId>commons-collections</artifactId> </dependency> <dependency> + <groupId>org.nuiton</groupId> + <artifactId>nuiton-utils</artifactId> + </dependency> + <dependency> <groupId>com.h2database</groupId> <artifactId>h2</artifactId> <scope>test</scope> @@ -110,6 +114,10 @@ </dependency> <dependency> <groupId>org.springframework</groupId> + <artifactId>spring-core</artifactId> + </dependency> + <dependency> + <groupId>org.springframework</groupId> <artifactId>spring-context</artifactId> </dependency> <dependency> Modified: trunk/cantharella.web/src/main/resources/log4j.xml =================================================================== --- trunk/cantharella.web/src/main/resources/log4j.xml 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/cantharella.web/src/main/resources/log4j.xml 2013-02-19 17:45:15 UTC (rev 134) @@ -5,7 +5,7 @@ $Id$ $HeadURL$ %% - Copyright (C) 2009 - 2012 IRD (Institut de Recherche pour le Developpement) and by respective authors (see below) + Copyright (C) 2009 - 2013 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 @@ -17,9 +17,9 @@ 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% + 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% --> <!DOCTYPE log4j:configuration SYSTEM "http://logging.apache.org/log4j/1.2/apidocs/org/apache/log4j/xml/doc-files/log4j.dtd"> @@ -62,4 +62,4 @@ <level value="warn" /> <appender-ref ref="consoleRoot" /> </root> -</log4j:configuration> \ No newline at end of file +</log4j:configuration> Modified: trunk/cantharella.web/src/site/rst/devel/integration-chemdoodle.rst =================================================================== --- trunk/cantharella.web/src/site/rst/devel/integration-chemdoodle.rst 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/cantharella.web/src/site/rst/devel/integration-chemdoodle.rst 2013-02-19 17:45:15 UTC (rev 134) @@ -20,8 +20,12 @@ .. * along with this program. If not, see <http://www.gnu.org/licenses/>. .. * #L% .. - + +Intégration de ChemDoodle +========================= + Principe -======== +-------- Création de deux scripts qui ajout le rendu ou l'editeur de molecule via les methodes: addViewerMolecule et addEditorMolecule. @@ -38,13 +42,13 @@ avec l'id de l'element. Visulisation -============ +------------ Le canvas de rendu prend la place de l'element precedent en gardant le meme id Edition -======= +------- Le canvas d'edition ce position apres l'element de la formule. Cet element peut-etre un input de type hidden. @@ -54,14 +58,14 @@ edite sous le format Mol. Dans Wicket -=========== +----------- Très peu de modification, seulement l'ajout du behavior sur les champs qui represente la formule brut. Et utilisation d'un champs Hidden dans la page web d'edition. ChemDoodle -========== +---------- Tous les fichiers specifiques a ChemDoodle ont ete mis dans un seul repertoire pour facilement faire un changement de librairie si le besoin Added: trunk/cantharella.web/src/site/rst/index.rst =================================================================== --- trunk/cantharella.web/src/site/rst/index.rst (rev 0) +++ trunk/cantharella.web/src/site/rst/index.rst 2013-02-19 17:45:15 UTC (rev 134) @@ -0,0 +1,3 @@ + +Cantharella web module +====================== Added: trunk/cantharella.web/src/site/site.xml =================================================================== (Binary files differ) Property changes on: trunk/cantharella.web/src/site/site.xml ___________________________________________________________________ Added: svn:mime-type + application/xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/pom.xml 2013-02-19 17:45:15 UTC (rev 134) @@ -137,7 +137,7 @@ <version.cglib>2.2.2</version.cglib> <version.opencsv>2.3</version.opencsv> <version.poi>3.9</version.poi> - <version.nuiton-utils>2.6.6</version.nuiton-utils> + <version.nuiton-utils>2.6.8</version.nuiton-utils> <version.servlet-api>2.5</version.servlet-api> <version.wicket>6.5.0</version.wicket> @@ -293,6 +293,12 @@ <scope>runtime</scope> </dependency> <dependency> + <groupId>log4j</groupId> + <artifactId>log4j</artifactId> + <version>1.2.17</version> + <scope>runtime</scope> + </dependency> + <dependency> <groupId>org.apache.commons</groupId> <artifactId>commons-lang3</artifactId> <version>${version.commons-lang3}</version> @@ -541,7 +547,7 @@ </dependency> </dependencies> </dependencyManagement> - + <dependencies> <!-- shared dependencies --> <dependency> Modified: trunk/src/code-formatter-conf/code-format.xml =================================================================== --- trunk/src/code-formatter-conf/code-format.xml 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/src/code-formatter-conf/code-format.xml 2013-02-19 17:45:15 UTC (rev 134) @@ -1,4 +1,27 @@ <?xml version="1.0" encoding="UTF-8" standalone="no"?> +<!-- + #%L + Cantharella + $Id$ + $HeadURL$ + %% + Copyright (C) 2009 - 2013 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% + --> + <profiles version="11"> <profile kind="CodeFormatterProfile" name="code_formatter" version="11"> <setting id="org.eclipse.jdt.core.formatter.alignment_for_selector_in_method_invocation" value="16"/> Modified: trunk/src/site/rst/configuration.rst =================================================================== --- trunk/src/site/rst/configuration.rst 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/src/site/rst/configuration.rst 2013-02-19 17:45:15 UTC (rev 134) @@ -24,6 +24,9 @@ Configuration ============= +Configuration file +~~~~~~~~~~~~~~~~~~ + All configuration variables can be put in file **cantharella.conf**. This file can be in: - classpath @@ -69,7 +72,7 @@ java -Ddb.user=$USER -Dmail.host=localhost ... Configuration variables -======================= +~~~~~~~~~~~~~~~~~~~~~~~ You can put some variable in cantharella.conf file to change default value. Modified: trunk/src/site/rst/index.rst =================================================================== --- trunk/src/site/rst/index.rst 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/src/site/rst/index.rst 2013-02-19 17:45:15 UTC (rev 134) @@ -21,9 +21,12 @@ .. * #L% .. - -Description +Cantharella =========== +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 @@ -34,7 +37,7 @@ .. image:: images/Extraction.png Features -======== +-------- - Collaborative work between spatially disparate people - Secure access and "compartmentalized” according to data access rights Modified: trunk/src/site/site.xml =================================================================== --- trunk/src/site/site.xml 2013-02-19 11:02:25 UTC (rev 133) +++ trunk/src/site/site.xml 2013-02-19 17:45:15 UTC (rev 134) @@ -5,7 +5,7 @@ $Id$ $HeadURL$ %% - Copyright (C) 2009 - 2012 IRD (Institut de Recherche pour le Developpement) and by respective authors (see below) + Copyright (C) 2009 - 2013 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 @@ -21,9 +21,16 @@ along with this program. If not, see <http://www.gnu.org/licenses/>. #L% --> +<project name="Cantharella"> + <skin> + <groupId>org.apache.maven.skins</groupId> + <artifactId>maven-fluido-skin</artifactId> + <version>1.3.0</version> + </skin> -<project name="Cantharella"> + <publishDate position="right"/> + <version position="right" /> <bannerLeft> <name>${project.name}</name> @@ -44,7 +51,7 @@ </breadcrumbs> <links> - <item name="IRD" href="http://www.ird.fr/"/> + <item name="IRD" href="http://www.ird.fr"/> <item name="Code Lutin" href="http://www.codelutin.com"/> </links> @@ -52,6 +59,8 @@ <item name="About" href="index.html"/> <item name="Configuration" href="configuration.html"/> </menu> + + <menu ref="modules"/> <menu ref="reports"/> </body>