- Cantharella-commits - mailman.cloud.codelutin.com

r281 - in trunk: . cantharella.web/src/main/resources src/site/rst
by acheype＠users.forge.codelutin.com Aug. 21, 2017

Aug. 21, 2017

Author: acheype Date: 2017-08-21 07:57:25 +0200 (Mon, 21 Aug 2017) New Revision: 281 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/281 Log: Add month&day in each log (dev and prod) Added: trunk/cantharella.web/src/main/resources/old_log4j.xml Removed: trunk/cantharella.web/src/main/resources/log4j_prod.xml Modified: trunk/README.md trunk/cantharella.web/src/main/resources/log4j.xml trunk/src/site/rst/configuration.rst Modified: trunk/README.md =================================================================== --- trunk/README.md 2017-08-10 08:05:10 UTC (rev 280) +++ trunk/README.md 2017-08-21 05:57:25 UTC (rev 281) @@ -153,9 +153,9 @@ [Service] User=root -ExecStartPre=-/usr/local/bin/docker-compose -f /data/cantharella.git/docker/docker-compose-prod.yml down -ExecStart=/usr/local/bin/docker-compose -f /data/cantharella.git/docker/docker-compose-prod.yml up -ExecStop=/usr/local/bin/docker-compose -f /data/cantharella.git/docker/docker-compose-prod.yml stop +ExecStartPre=-/usr/local/bin/docker-compose -f /data/cantharella.git/docker/prod/docker-compose.yml down +ExecStart=/usr/local/bin/docker-compose -f /data/cantharella.git/docker/prod/docker-compose.yml up +ExecStop=/usr/local/bin/docker-compose -f /data/cantharella.git/docker/prod/docker-compose.yml stop [Install] WantedBy=multi-user.target Modified: trunk/cantharella.web/src/main/resources/log4j.xml =================================================================== --- trunk/cantharella.web/src/main/resources/log4j.xml 2017-08-10 08:05:10 UTC (rev 280) +++ trunk/cantharella.web/src/main/resources/log4j.xml 2017-08-21 05:57:25 UTC (rev 281) @@ -29,7 +29,7 @@ <appender name="consoleIRD" class="org.apache.log4j.ConsoleAppender"> <param name="threshold" value="debug" /> <layout class="org.apache.log4j.PatternLayout"> - <param name="ConversionPattern" value="%d{HH:mm:ss} %5p (%F:%M:%L) %m%n" /> + <param name="ConversionPattern" value="%d{MM-dd/HH:mm:ss} %5p (%F:%M:%L) %m%n" /> </layout> </appender> @@ -37,7 +37,7 @@ <appender name="consoleRoot" class="org.apache.log4j.ConsoleAppender"> <param name="threshold" value="debug" /> <layout class="org.apache.log4j.PatternLayout"> - <param name="ConversionPattern" value="%d{HH:mm:ss} %5p (%c) %m%n" /> + <param name="ConversionPattern" value="%d{MM-dd/HH:mm:ss} %5p (%c) %m%n" /> </layout> </appender> Deleted: trunk/cantharella.web/src/main/resources/log4j_prod.xml =================================================================== --- trunk/cantharella.web/src/main/resources/log4j_prod.xml 2017-08-10 08:05:10 UTC (rev 280) +++ trunk/cantharella.web/src/main/resources/log4j_prod.xml 2017-08-21 05:57:25 UTC (rev 281) @@ -1,93 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> - - <!DOCTYPE log4j:configuration SYSTEM - "http://logging.apache.org/log4j/1.2/apidocs/org/apache/log4j/xml/doc-files/…"> -<log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/"> - -  -  - -  -  - -  - <appender name="consoleIRD" class="org.apache.log4j.ConsoleAppender"> - <param name="threshold" value="debug" /> - <layout class="org.apache.log4j.PatternLayout"> - <param name="ConversionPattern" value="%d{MM-dd/HH:mm:ss} %5p (%F:%M:%L) %m%n" /> - </layout> - </appender> - -  - <appender name="consoleRoot" class="org.apache.log4j.ConsoleAppender"> - <param name="threshold" value="debug" /> - <layout class="org.apache.log4j.PatternLayout"> - <param name="ConversionPattern" value="%d{MM-dd/HH:mm:ss} %5p (%c) %m%n" /> - </layout> - </appender> - -  - <logger name="nc.ird" additivity="false"> - <level value="info" /> - <appender-ref ref="consoleIRD" /> - </logger> - -  - <logger name="org.hibernate.SQL" additivity="false"> - <level value="OFF" /> - <appender-ref ref="consoleRoot" /> - </logger> - <logger name="org.hibernate.pretty" additivity="false"> - <level value="OFF" /> - <appender-ref ref="consoleRoot" /> - </logger> - -  - <root> - <level value="WARN" /> - <appender-ref ref="consoleRoot" /> - </root> - -</log4j:configuration> \ No newline at end of file Copied: trunk/cantharella.web/src/main/resources/old_log4j.xml (from rev 277, trunk/cantharella.web/src/main/resources/log4j_prod.xml) =================================================================== --- trunk/cantharella.web/src/main/resources/old_log4j.xml (rev 0) +++ trunk/cantharella.web/src/main/resources/old_log4j.xml 2017-08-21 05:57:25 UTC (rev 281) @@ -0,0 +1,93 @@ +<?xml version="1.0" encoding="UTF-8"?> + + <!DOCTYPE log4j:configuration SYSTEM + "http://logging.apache.org/log4j/1.2/apidocs/org/apache/log4j/xml/doc-files/…"> +<log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/"> + +  +  + +  +  + +  + <appender name="consoleIRD" class="org.apache.log4j.ConsoleAppender"> + <param name="threshold" value="debug" /> + <layout class="org.apache.log4j.PatternLayout"> + <param name="ConversionPattern" value="%d{HH:mm:ss} %5p (%F:%M:%L) %m%n" /> + </layout> + </appender> + +  + <appender name="consoleRoot" class="org.apache.log4j.ConsoleAppender"> + <param name="threshold" value="debug" /> + <layout class="org.apache.log4j.PatternLayout"> + <param name="ConversionPattern" value="%d{HH:mm:ss} %5p (%c) %m%n" /> + </layout> + </appender> + +  + <logger name="nc.ird" additivity="false"> + <level value="info" /> + <appender-ref ref="consoleIRD" /> + </logger> + +  + <logger name="org.hibernate.SQL" additivity="false"> + <level value="OFF" /> + <appender-ref ref="consoleRoot" /> + </logger> + <logger name="org.hibernate.pretty" additivity="false"> + <level value="OFF" /> + <appender-ref ref="consoleRoot" /> + </logger> + +  + <root> + <level value="WARN" /> + <appender-ref ref="consoleRoot" /> + </root> + +</log4j:configuration> \ No newline at end of file Modified: trunk/src/site/rst/configuration.rst =================================================================== --- trunk/src/site/rst/configuration.rst 2017-08-10 08:05:10 UTC (rev 280) +++ trunk/src/site/rst/configuration.rst 2017-08-21 05:57:25 UTC (rev 281) @@ -113,7 +113,7 @@ app.debug=false app.optimize=true wicket.configuration=deployment - log4j.config=classpath:log4j_prod.xml + log4j.config=classpath:log4j.xml #document file max upload size (Mb) document.maxUploadSize=1 \ No newline at end of file

1 0

r280 - in trunk: . docker docker/dev docker/prod
by acheype＠users.forge.codelutin.com Aug. 10, 2017

Aug. 10, 2017

Author: acheype Date: 2017-08-10 10:05:10 +0200 (Thu, 10 Aug 2017) New Revision: 280 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/280 Log: Divide the docker directory in two : dev and prod + adapt the README.md Added: trunk/docker/dev/ trunk/docker/dev/cantharella-web/ trunk/docker/prod/ trunk/docker/prod/docker-compose.yml Removed: trunk/docker/cantharella-web/ trunk/docker/docker-compose-prod.yml trunk/docker/docker-compose.yml Modified: trunk/README.md Modified: trunk/README.md =================================================================== --- trunk/README.md 2017-08-09 07:34:34 UTC (rev 279) +++ trunk/README.md 2017-08-10 08:05:10 UTC (rev 280) @@ -11,7 +11,7 @@ Cantharella is an open source information system based on Java components and a PostgreSQL database. -***News from 2017-08:***The application have been dockerized. See [Deployment with Docker](#deployment-with-docker) +**News from 2017-08:**The application have been dockerized. See [Deployment with Docker](#deployment-with-docker) section. More info on the project, [here](src/site/rst/index.rst). @@ -69,27 +69,27 @@ #### Building -First construct the war from the project sources with mvn (from the project root) +First, from the project root, construct the war from the project sources with mvn : mvn clean package -Then copy this war and the sql scripts (if needed, replace the version number) +Then copy this war and the sql scripts (if needed, replace the version number) : - cp cantharella.web/target/cantharella-1.2.2.war docker/cantharella-web/cantharella.war - cp -R sql docker/cantharella-db/docker-entrypoint-initdb.d + cp cantharella.web/target/cantharella-1.2.2.war docker/dev/cantharella-web/cantharella.war + cp -R sql docker/dev/cantharella-db/docker-entrypoint-initdb.d -Then build the images (cantharella.db and cantharella.web) +Then build the project images (`cantharella-db` and `cantharella-web` at the same time) - cd docker + cd docker/dev docker-compose build #### Starting the application -Go into the docker directory and launch the application with the docker-compose command : +Go into the `docker/dev` directory and launch the application with the docker-compose command : docker-compose up -Then, you can verify the status of the two containers (cantharella.db and cantharella.web) : +Then, you can verify the status of the two containers (`cantharella-db` and `cantharella-web`) : docker ps @@ -99,14 +99,14 @@ ### In production environment -### Starting the application +#### Starting the application -In the production environment, the compose configuration file is the `docker-compose-prod.yml` in the docker directory. +In the production environment, the compose configuration file is in the `docker/prod` directory. -Only this file is needed to start the application, the two containers (cantharella.db and cantharella.web) are -created from version-tagged image downloaded from the Docker Hub. +Only this file is needed to start the application, the two containers, `cantharella.db` and `cantharella.web`, are +created from the version-tagged image downloaded from the Docker Hub. -First next to the `docker-compose-prod.yml`, create two config files necessary to define your passwords. The first one +First next to the `docker-compose-prod.yml`, create two config files needed to define your passwords. The first one `cantharella-db.env` must have this content : POSTGRES_PASSWORD=thePasswordForTheAdminCountOfTheDB @@ -117,14 +117,29 @@ DB.PASSWORD=thePasswordOfTheCantharellaUserUsedConnectingTheWebAppToTheDB In the latter, you can also define other variables of the web application configuration file (see the documentation -file /src/site/rst/configuration.rst for more details). +file `/src/site/rst/configuration.rst` for more details). When the configuration file are set, you can launch the application with the docker-compose command : - docker-compose -f docker-compose-prod.yml + docker-compose up -### Autostart using Systemd +As with the dev environment, you can verify the status of the containers with `docker ps` and stop properly the +application with `docker-compose down`. +The database data will be stored in the directory `/data/postgres`. If this location refer to an existing postgres +data directory, the application expects that a cantharella database already exists. However, the container will +create a new postgres directory and init an empty cantharella database. + +If needed, it's possible to modify the postgres data directory location by changing in the `docker-compose.yml` the +part before `:` in that section : + +``` +volumes: + - /data/postgresql:/var/lib/postgresql/data +``` + +#### Autostart using Systemd + For linux system which rely on systemd, the followed configuration will automatically execute a Cantharella service at system startup. @@ -145,7 +160,7 @@ [Install] WantedBy=multi-user.target ``` -(adapt the path for the docker-compose.yml according to your situation) +(adapt the path for the `docker-compose.yml` according to your situation) Then enable the start at startup : Deleted: trunk/docker/docker-compose-prod.yml =================================================================== --- trunk/docker/docker-compose-prod.yml 2017-08-09 07:34:34 UTC (rev 279) +++ trunk/docker/docker-compose-prod.yml 2017-08-10 08:05:10 UTC (rev 280) @@ -1,28 +0,0 @@ -version: '3' -services: - tomcat: - container_name: cantharella-web - image: acheype/cantharella-web:1.2.2 - ports: - - "80:8080" - links: - - "postgres" - env_file: ./cantharella-web.env - # please define the variable DB.PASSWORD in the cantharella-db.env file. You can also define other variables - # of the configuration file (see the documentation file /src/site/rst/configuration.rst for more details) - # example of the environment file content : - # DB.PASSWORD=ctrl4 - - postgres: - container_name: cantharella-db - image: acheype/cantharella-db:1.2 - volumes: - - /data/postgresql:/var/lib/postgresql/data - ports: - - "5432:5432" - env_file: ./cantharella-db.env - # please define the variables POSTGRES_PASSWORD and CANTHARELLA_PASSWORD (same value as DB.PASSWORD) in the - # cantharella-db .env file - # example of the environment file content : - # POSTGRES_PASSWORD=postgres - # CANTHARELLA_PASSWORD=ctrl4 \ No newline at end of file Deleted: trunk/docker/docker-compose.yml =================================================================== --- trunk/docker/docker-compose.yml 2017-08-09 07:34:34 UTC (rev 279) +++ trunk/docker/docker-compose.yml 2017-08-10 08:05:10 UTC (rev 280) @@ -1,23 +0,0 @@ -version: '3' -services: - tomcat: - container_name: cantharella-web - build: ./cantharella-web - image: acheype/cantharella-web - ports: - - "80:8080" - links: - - "postgres" - - postgres: - container_name: cantharella-db - build: ./cantharella-db - image: acheype/cantharella-db - volumes: - - /data/postgresql:/var/lib/postgresql/data - ports: - - "5432:5432" - environment: - - POSTGRES_PASSWORD=postgres - # password of the user cantharella, only useful for db creation (if no data in /data/postgresql) - - CANTHARELLA_PASSWORD=ctrl4 \ No newline at end of file Copied: trunk/docker/prod/docker-compose.yml (from rev 279, trunk/docker/docker-compose-prod.yml) =================================================================== --- trunk/docker/prod/docker-compose.yml (rev 0) +++ trunk/docker/prod/docker-compose.yml 2017-08-10 08:05:10 UTC (rev 280) @@ -0,0 +1,28 @@ +version: '3' +services: + tomcat: + container_name: cantharella-web + image: acheype/cantharella-web:1.2.2 + ports: + - "80:8080" + links: + - "postgres" + env_file: ./cantharella-web.env + # please define the variable DB.PASSWORD in the cantharella-db.env file. You can also define other variables + # of the configuration file (see the documentation file /src/site/rst/configuration.rst for more details) + # example of the environment file content : + # DB.PASSWORD=ctrl4 + + postgres: + container_name: cantharella-db + image: acheype/cantharella-db:1.2 + volumes: + - /data/postgresql:/var/lib/postgresql/data + ports: + - "5432:5432" + env_file: ./cantharella-db.env + # please define the variables POSTGRES_PASSWORD and CANTHARELLA_PASSWORD (same value as DB.PASSWORD) in the + # cantharella-db .env file + # example of the environment file content : + # POSTGRES_PASSWORD=postgres + # CANTHARELLA_PASSWORD=ctrl4 \ No newline at end of file

1 0

r279 - in trunk: . cantharella.data cantharella.service cantharella.utils cantharella.web docker docker/cantharella-db docker/cantharella-db/docker-entrypoint-initdb.d sql
by acheype＠users.forge.codelutin.com Aug. 9, 2017

Aug. 9, 2017

Author: acheype Date: 2017-08-09 09:34:34 +0200 (Wed, 09 Aug 2017) New Revision: 279 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/279 Log: Improve the docker deployment and update this section in the README.md Added: trunk/docker/docker-compose-prod.yml Removed: trunk/docker/cantharella-db/create_db.sql trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/ Modified: trunk/README.md trunk/README.txt trunk/cantharella.data/README.txt trunk/cantharella.service/README.txt trunk/cantharella.utils/README.txt trunk/cantharella.web/README.txt trunk/docker/cantharella-db/docker-entrypoint-initdb.d/init-cantharella-db.sh trunk/docker/docker-compose.yml trunk/sql/create_db.sql Modified: trunk/README.md =================================================================== --- trunk/README.md 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/README.md 2017-08-09 07:34:34 UTC (rev 279) @@ -1,11 +1,10 @@ # Cantharella -*The GitHub repository in only a mirror of [the one hosted by Code Lutin](https://forge.codelutin -.com/projects/cantharella).* +*The GitHub repository in only a mirror of [the one hosted by Code Lutin](https://forge.codelutin.com/projects/cantharella).* The information system (IS) Cantharella: Pharmacochemical database of natural substances, designed and developed by -IRD (www.ird.fr) share and sustain pharmacochemical data of all organisms collected for the study of their natural -substances, with a controlled access via internet. +[IRD](http://www.ird.fr), share and sustain pharmacochemical data of all organisms collected for the study of their +natural substances, with a controlled access via internet. 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. @@ -36,20 +35,20 @@ Cantharella is dependent to some librairies from another open source projects. This is the list of the dependencies and their licenses. - - Apache Commons (http://commons.apache.org) under the Apache License 2.0 - - JUnit (www.junit.org) under the Common Public License 1.0 - - ICU4J (http://www.icu-project.org) under the ICU License (compatible with GNU GPL) - - Log4j (http://logging.apache.org/log4j) under the Apache License 2.0 - - SFL4J (http://www.slf4j.org) under the MIT license - - AspectJ (http://www.eclipse.org/aspectj) under the Common Public License 1.0 - - Spring (http://www.springsource.org) under the Apache License 2.0 - - Javassist (http://www.jboss.org/javassist) under the GNU Lesser General Public License 2.1 - - Cglib (http://cglib.sourceforge.net) under the Apache License 1.1 - - Hibernate (http://www.hibernate.org) under the GNU Lesser General Public License 2.1 - - POI (http://poi.apache.org) under the Apache License 2.0 - - Wicket (http://wicket.apache.org) under the Apache License 2.0 - - PostgreSQL JDBC Driver (http://jdbc.postgresql.org) under the BSD License (same as the SGBD) - - ChemDoodle Web Components (http://web.chemdoodle.com) under GNU General Public License, version 3.0 + - [Apache Commons](http://commons.apache.org), under the Apache License 2.0 + - [JUnit](www.junit.org), under the Common Public License 1.0 + - [ICU4J](http://www.icu-project.org), under the ICU License (compatible with GNU GPL) + - [Log4j](http://logging.apache.org/log4j), under the Apache License 2.0 + - [SFL4J](http://www.slf4j.org), under the MIT license + - [AspectJ](http://www.eclipse.org/aspectj), under the Common Public License 1.0 + - [Spring](http://www.springsource.org), under the Apache License 2.0 + - [Javassist](http://www.jboss.org/javassist), under the GNU Lesser General Public License 2.1 + - [Cglib](http://cglib.sourceforge.net), under the Apache License 1.1 + - [Hibernate](http://www.hibernate.org), under the GNU Lesser General Public License 2.1 + - [POI](http://poi.apache.org), under the Apache License 2.0 + - [Wicket](http://wicket.apache.org), under the Apache License 2.0 + - [PostgreSQL JDBC Driver](http://jdbc.postgresql.org), under the BSD License (same as the SGBD) + - [ChemDoodle Web Components](http://web.chemdoodle.com), under GNU General Public License, version 3.0 You can refer to the licenses folder of the project to see each license conditions. The dependency libraries are managed by the the Maven build tool (http://maven.apache.org) The Maven's dependency @@ -66,8 +65,10 @@ - https://docs.docker.com/engine/installation/ - https://docs.docker.com/compose/install/ -### Building +### In dev environment +#### Building + First construct the war from the project sources with mvn (from the project root) mvn clean package @@ -82,9 +83,9 @@ cd docker docker-compose build -### Starting the application +#### Starting the application -Launch the application with the docker-compose command : +Go into the docker directory and launch the application with the docker-compose command : docker-compose up @@ -95,3 +96,57 @@ To stop properly the application (with the delete of the containers), execute this command : docker-compose down + +### In production environment + +### Starting the application + +In the production environment, the compose configuration file is the `docker-compose-prod.yml` in the docker directory. + +Only this file is needed to start the application, the two containers (cantharella.db and cantharella.web) are +created from version-tagged image downloaded from the Docker Hub. + +First next to the `docker-compose-prod.yml`, create two config files necessary to define your passwords. The first one +`cantharella-db.env` must have this content : + + POSTGRES_PASSWORD=thePasswordForTheAdminCountOfTheDB + CANTHARELLA_PASSWORD=thePasswordOfTheCantharellaUser + +And the second one `cantharella-web.env` has this one : + + DB.PASSWORD=thePasswordOfTheCantharellaUserUsedConnectingTheWebAppToTheDB + +In the latter, you can also define other variables of the web application configuration file (see the documentation +file /src/site/rst/configuration.rst for more details). + +When the configuration file are set, you can launch the application with the docker-compose command : + + docker-compose -f docker-compose-prod.yml + +### Autostart using Systemd + +For linux system which rely on systemd, the followed configuration will automatically execute a Cantharella service +at system startup. + +First create the service file and add the followed content with `vi /etc/systemd/system/cantharella.service` : + +``` +[Unit] +Description=cantharella +Requires=docker.service +After=docker.service + +[Service] +User=root +ExecStartPre=-/usr/local/bin/docker-compose -f /data/cantharella.git/docker/docker-compose-prod.yml down +ExecStart=/usr/local/bin/docker-compose -f /data/cantharella.git/docker/docker-compose-prod.yml up +ExecStop=/usr/local/bin/docker-compose -f /data/cantharella.git/docker/docker-compose-prod.yml stop + +[Install] +WantedBy=multi-user.target +``` +(adapt the path for the docker-compose.yml according to your situation) + +Then enable the start at startup : + + systemctl enable cantharella \ No newline at end of file Modified: trunk/README.txt =================================================================== --- trunk/README.txt 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/README.txt 2017-08-09 07:34:34 UTC (rev 279) @@ -1,49 +1 @@ -Cantharella -=========== - -This is the readme file for the Cantharella projet. - -The information system (IS) Cantharella: Pharmacochemical database of natural substances, designed and developed by -IRD (www.ird.fr) share and sustain pharmacochemical data of all organisms collected for the study of their natural -substances, with a controlled access via internet. -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. - -Cantharella is an open source information system based on Java components and a PostgreSQL database. - -License -------- - -Cantharella is distributed under the terms of the under the terms of the GNU General Public License, version 3.0. The -text is included in the file LICENSE iq in the root of the project. - -Java and database servers requirements -------------------------------------------------- - -Cantharella requires at least Java 1.6. The application server for running your web application should adhere to the -servlet specification version 2.5 or newer. Tomcat 6 or newer is recommended. -For the database, the IS requires a PostgreSQL database (version 8.0 or newer). - -Dependencies ------------- -Cantharella is dependent to some librairies from another open source projects. This is the list of the dependencies and -their licenses. - - Apache Commons (http://commons.apache.org) under the Apache License 2.0 - - JUnit (www.junit.org) under the Common Public License 1.0 - - ICU4J (http://www.icu-project.org) under the ICU License (compatible with GNU GPL) - - Log4j (http://logging.apache.org/log4j) under the Apache License 2.0 - - SFL4J (http://www.slf4j.org) under the MIT license - - AspectJ (http://www.eclipse.org/aspectj) under the Common Public License 1.0 - - Spring (http://www.springsource.org) under the Apache License 2.0 - - Javassist (http://www.jboss.org/javassist) under the GNU Lesser General Public License 2.1 - - Cglib (http://cglib.sourceforge.net) under the Apache License 1.1 - - Hibernate (http://www.hibernate.org) under the GNU Lesser General Public License 2.1 - - POI (http://poi.apache.org) under the Apache License 2.0 - - Wicket (http://wicket.apache.org) under the Apache License 2.0 - - PostgreSQL JDBC Driver (http://jdbc.postgresql.org) under the BSD License (same as the server) - -You can refer to the licenses folder of the project to see each license conditions. -The dependency libraries are managed by the the Maven build tool (http://maven.apache.org) The Maven's dependency -mechanism will download all the necessary libraries automatically. You can see the dependencies declared in the -pom.xml files to known each library version. \ No newline at end of file +please refer to the README.md in the project root directory \ No newline at end of file Modified: trunk/cantharella.data/README.txt =================================================================== --- trunk/cantharella.data/README.txt 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/cantharella.data/README.txt 2017-08-09 07:34:34 UTC (rev 279) @@ -1,49 +1 @@ -Cantharella -=========== - -This is the readme file for the Cantharella projet. - -The information system (IS) Cantharella: Pharmacochemical database of natural substances, designed and developed by -IRD (www.ird.fr) share and sustain pharmacochemical data of all organisms collected for the study of their natural -substances, with a controlled access via internet. -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. - -Cantharella is an open source information system based on Java components and a PostgreSQL database. - -License -------- - -Cantharella is distributed under the terms of the under the terms of the GNU General Public License, version 3.0. The -text is included in the file LICENSE iq in the root of the project. - -Java and database servers requirements -------------------------------------------------- - -Cantharella requires at least Java 1.6. The application server for running your web application should adhere to the -servlet specification version 2.5 or newer. Tomcat 6 or newer is recommended. -For the database, the IS requires a PostgreSQL database (version 8.0 or newer). - -Dependencies ------------- -Cantharella is dependent to some librairies from another open source projects. This is the list of the dependencies and -their licenses. - - Apache Commons (http://commons.apache.org) under the Apache License 2.0 - - JUnit (www.junit.org) under the Common Public License 1.0 - - ICU4J (http://www.icu-project.org) under the ICU License (compatible with GNU GPL) - - Log4j (http://logging.apache.org/log4j) under the Apache License 2.0 - - SFL4J (http://www.slf4j.org) under the MIT license - - AspectJ (http://www.eclipse.org/aspectj) under the Common Public License 1.0 - - Spring (http://www.springsource.org) under the Apache License 2.0 - - Javassist (http://www.jboss.org/javassist) under the GNU Lesser General Public License 2.1 - - Cglib (http://cglib.sourceforge.net) under the Apache License 1.1 - - Hibernate (http://www.hibernate.org) under the GNU Lesser General Public License 2.1 - - POI (http://poi.apache.org) under the Apache License 2.0 - - Wicket (http://wicket.apache.org) under the Apache License 2.0 - - PostgreSQL JDBC Driver (http://jdbc.postgresql.org) under the BSD License (same as the server) - -You can refer to the licenses folder of the project to see each license conditions. -The dependency libraries are managed by the the Maven build tool (http://maven.apache.org) The Maven's dependency -mechanism will download all the necessary libraries automatically. You can see the dependencies declared in the -pom.xml files to known each library version. \ No newline at end of file +please refer to the README.md in the project root directory \ No newline at end of file Modified: trunk/cantharella.service/README.txt =================================================================== --- trunk/cantharella.service/README.txt 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/cantharella.service/README.txt 2017-08-09 07:34:34 UTC (rev 279) @@ -1,49 +1 @@ -Cantharella -=========== - -This is the readme file for the Cantharella projet. - -The information system (IS) Cantharella: Pharmacochemical database of natural substances, designed and developed by -IRD (www.ird.fr) share and sustain pharmacochemical data of all organisms collected for the study of their natural -substances, with a controlled access via internet. -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. - -Cantharella is an open source information system based on Java components and a PostgreSQL database. - -License -------- - -Cantharella is distributed under the terms of the under the terms of the GNU General Public License, version 3.0. The -text is included in the file LICENSE iq in the root of the project. - -Java and database servers requirements -------------------------------------------------- - -Cantharella requires at least Java 1.6. The application server for running your web application should adhere to the -servlet specification version 2.5 or newer. Tomcat 6 or newer is recommended. -For the database, the IS requires a PostgreSQL database (version 8.0 or newer). - -Dependencies ------------- -Cantharella is dependent to some librairies from another open source projects. This is the list of the dependencies and -their licenses. - - Apache Commons (http://commons.apache.org) under the Apache License 2.0 - - JUnit (www.junit.org) under the Common Public License 1.0 - - ICU4J (http://www.icu-project.org) under the ICU License (compatible with GNU GPL) - - Log4j (http://logging.apache.org/log4j) under the Apache License 2.0 - - SFL4J (http://www.slf4j.org) under the MIT license - - AspectJ (http://www.eclipse.org/aspectj) under the Common Public License 1.0 - - Spring (http://www.springsource.org) under the Apache License 2.0 - - Javassist (http://www.jboss.org/javassist) under the GNU Lesser General Public License 2.1 - - Cglib (http://cglib.sourceforge.net) under the Apache License 1.1 - - Hibernate (http://www.hibernate.org) under the GNU Lesser General Public License 2.1 - - POI (http://poi.apache.org) under the Apache License 2.0 - - Wicket (http://wicket.apache.org) under the Apache License 2.0 - - PostgreSQL JDBC Driver (http://jdbc.postgresql.org) under the BSD License (same as the server) - -You can refer to the licenses folder of the project to see each license conditions. -The dependency libraries are managed by the the Maven build tool (http://maven.apache.org) The Maven's dependency -mechanism will download all the necessary libraries automatically. You can see the dependencies declared in the -pom.xml files to known each library version. \ No newline at end of file +please refer to the README.md in the project root directory \ No newline at end of file Modified: trunk/cantharella.utils/README.txt =================================================================== --- trunk/cantharella.utils/README.txt 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/cantharella.utils/README.txt 2017-08-09 07:34:34 UTC (rev 279) @@ -1,33 +1 @@ -Module.utils -============ - -This is the readme file for the utils module of the Cantharella projet. -This module gathers tools usable in common Java projects. - -The information system (IS) Cantharella: Pharmacochemical database of natural substances, designed and developed by -IRD (www.ird.fr) share and sustain pharmacochemical data of all organisms collected for the study of their natural -substances, with a controlled access via internet. -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. - -Cantharella is an open source information system based on Java components and a PostgreSQL database. - -License -------- - -Cantharella is distributed under the terms of the under the terms of the GNU General Public License, version 3.0. The -text is included in the file LICENSE is in the root of the project. - -Dependencies ------------- -Module.utils is dependent to some librairies from another open source projects. This is the list of the dependencies and -their licenses. - - Apache Commons (http://commons.apache.org) under the Apache License 2.0 - - JUnit (www.junit.org) under the Common Public License 1.0 - - ICU4J (http://www.icu-project.org) under the ICU License (compatible with GNU GPL) - -You can refer to the licenses folder of the project to see each license conditions. -The dependency libraries are managed by the the Maven build tool (http://maven.apache.org) The Maven's dependency -mechanism will download all the necessary libraries automatically. You can see the dependencies declared in the -pom.xml files to known each library version. \ No newline at end of file +please refer to the README.md in the project root directory \ No newline at end of file Modified: trunk/cantharella.web/README.txt =================================================================== --- trunk/cantharella.web/README.txt 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/cantharella.web/README.txt 2017-08-09 07:34:34 UTC (rev 279) @@ -1,49 +1 @@ -Cantharella -=========== - -This is the readme file for the Cantharella projet. - -The information system (IS) Cantharella: Pharmacochemical database of natural substances, designed and developed by -IRD (www.ird.fr) share and sustain pharmacochemical data of all organisms collected for the study of their natural -substances, with a controlled access via internet. -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. - -Cantharella is an open source information system based on Java components and a PostgreSQL database. - -License -------- - -Cantharella is distributed under the terms of the under the terms of the GNU General Public License, version 3.0. The -text is included in the file LICENSE iq in the root of the project. - -Java and database servers requirements -------------------------------------------------- - -Cantharella requires at least Java 1.6. The application server for running your web application should adhere to the -servlet specification version 2.5 or newer. Tomcat 6 or newer is recommended. -For the database, the IS requires a PostgreSQL database (version 8.0 or newer). - -Dependencies ------------- -Cantharella is dependent to some librairies from another open source projects. This is the list of the dependencies and -their licenses. - - Apache Commons (http://commons.apache.org) under the Apache License 2.0 - - JUnit (www.junit.org) under the Common Public License 1.0 - - ICU4J (http://www.icu-project.org) under the ICU License (compatible with GNU GPL) - - Log4j (http://logging.apache.org/log4j) under the Apache License 2.0 - - SFL4J (http://www.slf4j.org) under the MIT license - - AspectJ (http://www.eclipse.org/aspectj) under the Common Public License 1.0 - - Spring (http://www.springsource.org) under the Apache License 2.0 - - Javassist (http://www.jboss.org/javassist) under the GNU Lesser General Public License 2.1 - - Cglib (http://cglib.sourceforge.net) under the Apache License 1.1 - - Hibernate (http://www.hibernate.org) under the GNU Lesser General Public License 2.1 - - POI (http://poi.apache.org) under the Apache License 2.0 - - Wicket (http://wicket.apache.org) under the Apache License 2.0 - - PostgreSQL JDBC Driver (http://jdbc.postgresql.org) under the BSD License (same as the server) - -You can refer to the licenses folder of the project to see each license conditions. -The dependency libraries are managed by the the Maven build tool (http://maven.apache.org) The Maven's dependency -mechanism will download all the necessary libraries automatically. You can see the dependencies declared in the -pom.xml files to known each library version. \ No newline at end of file +please refer to the README.md in the project root directory \ No newline at end of file Deleted: trunk/docker/cantharella-db/create_db.sql =================================================================== --- trunk/docker/cantharella-db/create_db.sql 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/docker/cantharella-db/create_db.sql 2017-08-09 07:34:34 UTC (rev 279) @@ -1,29 +0,0 @@ ---- --- #%L --- Cantharella :: Data --- $Id: create_db.sql 133 2013-02-19 11:02:25Z acheype $ --- $HeadURL: https://svn.codelutin.com/cantharella/trunk/cantharella.data/src/main/sql/c… $ --- %% --- 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% ---- -CREATE ROLE cantharella LOGIN PASSWORD 'ctrl4'; -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 Modified: trunk/docker/cantharella-db/docker-entrypoint-initdb.d/init-cantharella-db.sh =================================================================== --- trunk/docker/cantharella-db/docker-entrypoint-initdb.d/init-cantharella-db.sh 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/docker/cantharella-db/docker-entrypoint-initdb.d/init-cantharella-db.sh 2017-08-09 07:34:34 UTC (rev 279) @@ -10,9 +10,8 @@ trap onexit EXIT echo "--- Init Cantharella DB ---" -echo "$SCRIPT_DIR" echo "No 'cantharella' database found. The database is going to be created." -psql --username "$POSTGRES_USER" -f "$SCRIPT_DIR/sql/create_db.sql" +psql --username "$POSTGRES_USER" --set=cantharella_password=$CANTHARELLA_PASSWORD -f "$SCRIPT_DIR/sql/create_db.sql" echo "* create_db.sql imported *" psql --username cantharella -d cantharella -f $SCRIPT_DIR/sql/cantharella_schema_1.2.sql echo "* cantharella_schema_1.2.sql imported *" Copied: trunk/docker/docker-compose-prod.yml (from rev 277, trunk/docker/docker-compose.yml) =================================================================== --- trunk/docker/docker-compose-prod.yml (rev 0) +++ trunk/docker/docker-compose-prod.yml 2017-08-09 07:34:34 UTC (rev 279) @@ -0,0 +1,28 @@ +version: '3' +services: + tomcat: + container_name: cantharella-web + image: acheype/cantharella-web:1.2.2 + ports: + - "80:8080" + links: + - "postgres" + env_file: ./cantharella-web.env + # please define the variable DB.PASSWORD in the cantharella-db.env file. You can also define other variables + # of the configuration file (see the documentation file /src/site/rst/configuration.rst for more details) + # example of the environment file content : + # DB.PASSWORD=ctrl4 + + postgres: + container_name: cantharella-db + image: acheype/cantharella-db:1.2 + volumes: + - /data/postgresql:/var/lib/postgresql/data + ports: + - "5432:5432" + env_file: ./cantharella-db.env + # please define the variables POSTGRES_PASSWORD and CANTHARELLA_PASSWORD (same value as DB.PASSWORD) in the + # cantharella-db .env file + # example of the environment file content : + # POSTGRES_PASSWORD=postgres + # CANTHARELLA_PASSWORD=ctrl4 \ No newline at end of file Modified: trunk/docker/docker-compose.yml =================================================================== --- trunk/docker/docker-compose.yml 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/docker/docker-compose.yml 2017-08-09 07:34:34 UTC (rev 279) @@ -18,4 +18,6 @@ ports: - "5432:5432" environment: - - POSTGRES_PASSWORD=CHANGE_PASSWORD \ No newline at end of file + - POSTGRES_PASSWORD=postgres + # password of the user cantharella, only useful for db creation (if no data in /data/postgresql) + - CANTHARELLA_PASSWORD=ctrl4 \ No newline at end of file Modified: trunk/sql/create_db.sql =================================================================== --- trunk/sql/create_db.sql 2017-08-03 03:12:39 UTC (rev 278) +++ trunk/sql/create_db.sql 2017-08-09 07:34:34 UTC (rev 279) @@ -20,10 +20,10 @@ -- along with this program. If not, see <http://www.gnu.org/licenses/>. -- #L% --- -CREATE ROLE cantharella LOGIN PASSWORD 'ctrl4'; +CREATE ROLE cantharella LOGIN PASSWORD :'cantharella_password'; 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 +\q \ No newline at end of file

1 0

r278 - in trunk: . src/site/resources/images src/site/rst
by acheype＠users.forge.codelutin.com Aug. 3, 2017

Aug. 3, 2017

Author: acheype Date: 2017-08-03 05:12:39 +0200 (Thu, 03 Aug 2017) New Revision: 278 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/278 Log: Update of the documentation Added: trunk/src/site/resources/images/Molecule.jpg Modified: trunk/README.md trunk/src/site/rst/index.rst trunk/src/site/rst/installation.rst Modified: trunk/README.md =================================================================== --- trunk/README.md 2017-08-03 01:32:51 UTC (rev 277) +++ trunk/README.md 2017-08-03 03:12:39 UTC (rev 278) @@ -1,8 +1,8 @@ # Cantharella -*The GitHub repository in only a mirror of the one hosted by Code Lutin [here]()* +*The GitHub repository in only a mirror of [the one hosted by Code Lutin](https://forge.codelutin +.com/projects/cantharella).* - The information system (IS) Cantharella: Pharmacochemical database of natural substances, designed and developed by IRD (www.ird.fr) share and sustain pharmacochemical data of all organisms collected for the study of their natural substances, with a controlled access via internet. @@ -15,9 +15,11 @@ ***News from 2017-08:***The application have been dockerized. See [Deployment with Docker](#deployment-with-docker) section. +More info on the project, [here](src/site/rst/index.rst). + ![](src/site/resources/images/Home.jpg) -More info on the project, [here](src/site/rst/index.rst). +![](src/site/resources/images/Molecule.jpg) ### License @@ -92,4 +94,4 @@ To stop properly the application (with the delete of the containers), execute this command : - docker-compose down \ No newline at end of file + docker-compose down Added: trunk/src/site/resources/images/Molecule.jpg =================================================================== (Binary files differ) Index: trunk/src/site/resources/images/Molecule.jpg =================================================================== --- trunk/src/site/resources/images/Molecule.jpg 2017-08-03 01:32:51 UTC (rev 277) +++ trunk/src/site/resources/images/Molecule.jpg 2017-08-03 03:12:39 UTC (rev 278) Property changes on: trunk/src/site/resources/images/Molecule.jpg ___________________________________________________________________ Added: svn:mime-type ## -0,0 +1 ## +application/octet-stream \ No newline at end of property Modified: trunk/src/site/rst/index.rst =================================================================== --- trunk/src/site/rst/index.rst 2017-08-03 01:32:51 UTC (rev 277) +++ trunk/src/site/rst/index.rst 2017-08-03 03:12:39 UTC (rev 278) @@ -22,7 +22,7 @@ .. - -.. image:: images/cantharella_with_title.jpg +.. image:: ../resources/images/cantharella_with_title.jpg Description ----------- @@ -47,18 +47,22 @@ Screenshots ----------- -.. figure:: images/Home.jpg +.. figure:: ../resources/images/Home.jpg Home -.. figure:: images/Station.jpg +.. figure:: ../resources/images/Station.jpg Location form -.. figure:: images/Extraction.jpg +.. figure:: ../resources/images/Extraction.jpg Extraction form +.. figure:: ../resources/images/Molecule.jpg + +Molecule form + Modified: trunk/src/site/rst/installation.rst =================================================================== --- trunk/src/site/rst/installation.rst 2017-08-03 01:32:51 UTC (rev 277) +++ trunk/src/site/rst/installation.rst 2017-08-03 03:12:39 UTC (rev 278) @@ -81,7 +81,7 @@ Then, you have to configure your Cantharella instance as described in this section_. -.. _section: configuration.html +.. _section: configuration.rst 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

1 0

r277 - in trunk: . cantharella.data cantharella.data/src/main cantharella.data/src/main/resources cantharella.service cantharella.utils cantharella.web cantharella.web/src/main/java/nc/ird/cantharella/web/pages cantharella.web/src/main/resources cantharella.web/src/main/webapp/images docker docker/cantharella-db docker/cantharella-db/docker-entrypoint-initdb.d docker/cantharella-db/docker-entrypoint-initdb.d/sql docker/cantharella-web sql src/site/rst
by acheype＠users.forge.codelutin.com Aug. 3, 2017

Aug. 3, 2017

Author: acheype Date: 2017-08-03 03:32:51 +0200 (Thu, 03 Aug 2017) New Revision: 277 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/277 Log: - IRD Logo changed - Chairman of IRD changed for the imprint - Dockerization of the app Added: trunk/README.md trunk/docker/ trunk/docker/cantharella-db/ trunk/docker/cantharella-db/Dockerfile trunk/docker/cantharella-db/create_db.sql trunk/docker/cantharella-db/docker-entrypoint-initdb.d/ trunk/docker/cantharella-db/docker-entrypoint-initdb.d/init-cantharella-db.sh trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/ trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.0.sql trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.1.sql trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.2.sql trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/create_db.sql trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/dev_update_1.0_to_1.1.sql trunk/docker/cantharella-web/ trunk/docker/cantharella-web/Dockerfile trunk/docker/docker-compose.yml trunk/sql/ Removed: trunk/cantharella.data/src/main/sql/ trunk/sql/init.sql Modified: trunk/cantharella.data/pom.xml trunk/cantharella.data/src/main/resources/cantharella.conf trunk/cantharella.service/pom.xml trunk/cantharella.utils/pom.xml trunk/cantharella.web/ trunk/cantharella.web/pom.xml trunk/cantharella.web/src/main/java/nc/ird/cantharella/web/pages/ImprintPage.html trunk/cantharella.web/src/main/java/nc/ird/cantharella/web/pages/TemplatePage.html trunk/cantharella.web/src/main/resources/cantharella.conf trunk/cantharella.web/src/main/resources/log4j.xml trunk/cantharella.web/src/main/resources/log4j_prod.xml trunk/cantharella.web/src/main/resources/web_en.properties trunk/cantharella.web/src/main/resources/web_fr.properties trunk/cantharella.web/src/main/webapp/images/ird.png trunk/pom.xml trunk/sql/cantharella_schema_1.2.sql trunk/src/site/rst/index.rst Copied: trunk/README.md (from rev 276, trunk/README.txt) =================================================================== --- trunk/README.md (rev 0) +++ trunk/README.md 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,95 @@ +# Cantharella + +*The GitHub repository in only a mirror of the one hosted by Code Lutin [here]()* + + +The information system (IS) Cantharella: Pharmacochemical database of natural substances, designed and developed by +IRD (www.ird.fr) share and sustain pharmacochemical data of all organisms collected for the study of their natural +substances, with a controlled access via internet. +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. + +Cantharella is an open source information system based on Java components and a PostgreSQL database. + +***News from 2017-08:***The application have been dockerized. See [Deployment with Docker](#deployment-with-docker) +section. + +![](src/site/resources/images/Home.jpg) + +More info on the project, [here](src/site/rst/index.rst). + +### License + +Cantharella is distributed under the terms of the under the terms of the GNU General Public License, version 3.0. The +text is included in the file LICENSE in the root of the project. + +### Java and database servers requirements + +Cantharella requires at least Java 1.6. The application server for running your web application should adhere to the +servlet specification version 2.5 or newer. Tomcat 6 or newer is recommended. +For the database, the IS requires a PostgreSQL database (version 8.0 or newer). + +### Dependencies + +Cantharella is dependent to some librairies from another open source projects. This is the list of the dependencies and +their licenses. + - Apache Commons (http://commons.apache.org) under the Apache License 2.0 + - JUnit (www.junit.org) under the Common Public License 1.0 + - ICU4J (http://www.icu-project.org) under the ICU License (compatible with GNU GPL) + - Log4j (http://logging.apache.org/log4j) under the Apache License 2.0 + - SFL4J (http://www.slf4j.org) under the MIT license + - AspectJ (http://www.eclipse.org/aspectj) under the Common Public License 1.0 + - Spring (http://www.springsource.org) under the Apache License 2.0 + - Javassist (http://www.jboss.org/javassist) under the GNU Lesser General Public License 2.1 + - Cglib (http://cglib.sourceforge.net) under the Apache License 1.1 + - Hibernate (http://www.hibernate.org) under the GNU Lesser General Public License 2.1 + - POI (http://poi.apache.org) under the Apache License 2.0 + - Wicket (http://wicket.apache.org) under the Apache License 2.0 + - PostgreSQL JDBC Driver (http://jdbc.postgresql.org) under the BSD License (same as the SGBD) + - ChemDoodle Web Components (http://web.chemdoodle.com) under GNU General Public License, version 3.0 + +You can refer to the licenses folder of the project to see each license conditions. +The dependency libraries are managed by the the Maven build tool (http://maven.apache.org) The Maven's dependency +mechanism will download all the necessary libraries automatically. You can see the dependencies declared in the +pom.xml files to known each library version. + +## Deployment with Docker + +*You can find the detailled instruction for a classic installation [here](src/site/rst/installation.rst).* + +### Requirement + +Please first install Docker CE (Community Edition) and Docker Compose by following the official instructions : + - https://docs.docker.com/engine/installation/ + - https://docs.docker.com/compose/install/ + +### Building + +First construct the war from the project sources with mvn (from the project root) + + mvn clean package + +Then copy this war and the sql scripts (if needed, replace the version number) + + cp cantharella.web/target/cantharella-1.2.2.war docker/cantharella-web/cantharella.war + cp -R sql docker/cantharella-db/docker-entrypoint-initdb.d + +Then build the images (cantharella.db and cantharella.web) + + cd docker + docker-compose build + +### Starting the application + +Launch the application with the docker-compose command : + + docker-compose up + +Then, you can verify the status of the two containers (cantharella.db and cantharella.web) : + + docker ps + +To stop properly the application (with the delete of the containers), execute this command : + + docker-compose down \ No newline at end of file Modified: trunk/cantharella.data/pom.xml =================================================================== --- trunk/cantharella.data/pom.xml 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.data/pom.xml 2017-08-03 01:32:51 UTC (rev 277) @@ -5,7 +5,7 @@ <parent> <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2.1-SNAPSHOT</version> + <version>1.2.2</version> </parent> <artifactId>cantharella.data</artifactId> Modified: trunk/cantharella.data/src/main/resources/cantharella.conf =================================================================== --- trunk/cantharella.data/src/main/resources/cantharella.conf 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.data/src/main/resources/cantharella.conf 2017-08-03 01:32:51 UTC (rev 277) @@ -24,9 +24,9 @@ # # DATABASE CONFIGURATION # -db.url=jdbc:postgresql:cantharella +db.url=jdbc:postgresql://postgres:5432/cantharella db.user=cantharella -db.password=cantharella +db.password=ctrl4 db.debug=true # value for production #db.debug=false Modified: trunk/cantharella.service/pom.xml =================================================================== --- trunk/cantharella.service/pom.xml 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.service/pom.xml 2017-08-03 01:32:51 UTC (rev 277) @@ -5,7 +5,7 @@ <parent> <artifactId>cantharella</artifactId> <groupId>nc.ird</groupId> - <version>1.2.1-SNAPSHOT</version> + <version>1.2.2</version> </parent> <artifactId>cantharella.service</artifactId> Modified: trunk/cantharella.utils/pom.xml =================================================================== --- trunk/cantharella.utils/pom.xml 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.utils/pom.xml 2017-08-03 01:32:51 UTC (rev 277) @@ -5,7 +5,7 @@ <parent> <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2.1-SNAPSHOT</version> + <version>1.2.2</version> </parent> <artifactId>cantharella.utils</artifactId> Index: trunk/cantharella.web =================================================================== --- trunk/cantharella.web 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.web 2017-08-03 01:32:51 UTC (rev 277) Property changes on: trunk/cantharella.web ___________________________________________________________________ Modified: svn:ignore ## -2,7 +2,6 ## nb-configuration.xml *.iws .classpath -*.iml .idea .project target Modified: trunk/cantharella.web/pom.xml =================================================================== --- trunk/cantharella.web/pom.xml 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.web/pom.xml 2017-08-03 01:32:51 UTC (rev 277) @@ -5,7 +5,7 @@ <parent> <artifactId>cantharella</artifactId> <groupId>nc.ird</groupId> - <version>1.2.1-SNAPSHOT</version> + <version>1.2.2</version> </parent> <artifactId>cantharella.web</artifactId> Modified: trunk/cantharella.web/src/main/java/nc/ird/cantharella/web/pages/ImprintPage.html =================================================================== --- trunk/cantharella.web/src/main/java/nc/ird/cantharella/web/pages/ImprintPage.html 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.web/src/main/java/nc/ird/cantharella/web/pages/ImprintPage.html 2017-08-03 01:32:51 UTC (rev 277) @@ -30,7 +30,10 @@ <p><wicket:message key="ImprintPage.AccessRights.Address"/></p> <h3><wicket:message key="ImprintPage.Editor"/></h3> - <p><wicket:message key="ImprintPage.Editor.Director"/></p> + <p><wicket:message key="ImprintPage.Editor.Director.1"/>  + <a href="https://www.ird.fr/l-ird/l-organigramme/presidence/president-directeur-gene…"> + <wicket:message key="ImprintPage.Editor.Director.2"/></a> + </p> <p><wicket:message key="ImprintPage.Editor.Administrator"/></p> <h3><wicket:message key="ImprintPage.Hosting"/></h3> Modified: trunk/cantharella.web/src/main/java/nc/ird/cantharella/web/pages/TemplatePage.html =================================================================== --- trunk/cantharella.web/src/main/java/nc/ird/cantharella/web/pages/TemplatePage.html 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.web/src/main/java/nc/ird/cantharella/web/pages/TemplatePage.html 2017-08-03 01:32:51 UTC (rev 277) @@ -171,12 +171,16 @@ </div></div> <div id="footer"> - <div class="f_base"> - <p class="titre">Cantharella - <wicket:message key="TemplatePage.Subtitle"/></p> - <p><a wicket:id="ContactPage"><wicket:message key="ContactPage" /></a> - - <a wicket:id="ImprintPage"><wicket:message key="ImprintPage" /></a> - - <wicket:message key="TemplatePage.Copyright" /> - <span wicket:id="Year" /> <a href="http://www.ird.fr/"><img src="images/ird.png" alt="IRD" height="41" width="75"/></a></p> - </div> + <div class="f_base" style="height: 160px;"> + <p class="titre">Cantharella - <wicket:message key="TemplatePage.Subtitle"/></p> + <p> + <a href="http://www.ird.fr/"><img style="float: right; margin-left:1.5rem;" src="images/ird.png" alt="IRD"></a> + <p style="margin-top:45px"> + <a wicket:id="ContactPage"><wicket:message key="ContactPage" /></a> - <a wicket:id="ImprintPage"><wicket:message key="ImprintPage" /></a><br> + <wicket:message key="TemplatePage.Copyright" /> - <span wicket:id="Year" /> + </p> + </p> + </div> </div> <div id="AjaxIndicator" style="display: none;"></div> Modified: trunk/cantharella.web/src/main/resources/cantharella.conf =================================================================== --- trunk/cantharella.web/src/main/resources/cantharella.conf 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.web/src/main/resources/cantharella.conf 2017-08-03 01:32:51 UTC (rev 277) @@ -36,8 +36,6 @@ wicket.configuration=deployment log4j.config=classpath:log4j.xml -# value for production -#log4j.config=/home/tomcat/.config/log4j_prod.xml #document file max upload size (Mb) document.maxUploadSize=1 Modified: trunk/cantharella.web/src/main/resources/log4j.xml =================================================================== --- trunk/cantharella.web/src/main/resources/log4j.xml 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.web/src/main/resources/log4j.xml 2017-08-03 01:32:51 UTC (rev 277) @@ -25,41 +25,54 @@ "http://logging.apache.org/log4j/1.2/apidocs/org/apache/log4j/xml/doc-files/…"> <log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/"> -  +  <appender name="consoleIRD" class="org.apache.log4j.ConsoleAppender"> <param name="threshold" value="debug" /> <layout class="org.apache.log4j.PatternLayout"> - <param name="ConversionPattern" value="%d{HH:mm:ss.SSS} %5p (%F:%M:%L) %m%n" /> + <param name="ConversionPattern" value="%d{HH:mm:ss} %5p (%F:%M:%L) %m%n" /> </layout> </appender> -  +  <appender name="consoleRoot" class="org.apache.log4j.ConsoleAppender"> <param name="threshold" value="debug" /> <layout class="org.apache.log4j.PatternLayout"> - <param name="ConversionPattern" value="%d{HH:mm:ss.SSS} %5p (%c) %m%n" /> + <param name="ConversionPattern" value="%d{HH:mm:ss} %5p (%c) %m%n" /> </layout> </appender> +  +  +  +  +  +  +  <logger name="nc.ird" additivity="false"> - <level value="debug" /> + <level value="info" /> <appender-ref ref="consoleIRD" /> </logger> -  +  <logger name="org.hibernate.SQL" additivity="false"> - <level value="info" /> - <appender-ref ref="consoleRoot" /> - </logger> + <level value="OFF" /> + <appender-ref ref="consoleRoot" /> + </logger> <logger name="org.hibernate.pretty" additivity="false"> - <level value="info" /> + <level value="OFF" /> <appender-ref ref="consoleRoot" /> </logger> - + +  +  +  +  +  <root> - <level value="warn" /> + <level value="WARN" /> <appender-ref ref="consoleRoot" /> </root> + </log4j:configuration> Modified: trunk/cantharella.web/src/main/resources/log4j_prod.xml =================================================================== --- trunk/cantharella.web/src/main/resources/log4j_prod.xml 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.web/src/main/resources/log4j_prod.xml 2017-08-03 01:32:51 UTC (rev 277) @@ -26,7 +26,7 @@ <log4j:configuration xmlns:log4j="http://jakarta.apache.org/log4j/">  - <appender name="file" class="org.apache.log4j.DailyRollingFileAppender"> +   - <appender name="mail" class="org.apache.log4j.net.SMTPAppender"> +  + +  + <appender name="consoleIRD" class="org.apache.log4j.ConsoleAppender"> + <param name="threshold" value="debug" /> + <layout class="org.apache.log4j.PatternLayout"> + <param name="ConversionPattern" value="%d{MM-dd/HH:mm:ss} %5p (%F:%M:%L) %m%n" /> + </layout> </appender> +  + <appender name="consoleRoot" class="org.apache.log4j.ConsoleAppender"> + <param name="threshold" value="debug" /> + <layout class="org.apache.log4j.PatternLayout"> + <param name="ConversionPattern" value="%d{MM-dd/HH:mm:ss} %5p (%c) %m%n" /> + </layout> + </appender> +  <logger name="nc.ird" additivity="false"> <level value="info" /> - <appender-ref ref="async" /> + <appender-ref ref="consoleIRD" /> </logger> -  - <logger name="org.hibernate" additivity="false"> -  - <level value="off"/> +  + <logger name="org.hibernate.SQL" additivity="false"> + <level value="OFF" /> + <appender-ref ref="consoleRoot" /> </logger> - - <logger name="org.hibernate.validator" additivity="false"> - <level value="error" /> - <appender-ref ref="async" /> + <logger name="org.hibernate.pretty" additivity="false"> + <level value="OFF" /> + <appender-ref ref="consoleRoot" /> </logger> -  +  <root> - <level value="warn" /> - <appender-ref ref="async" /> + <level value="WARN" /> + <appender-ref ref="consoleRoot" /> </root> </log4j:configuration> \ No newline at end of file Modified: trunk/cantharella.web/src/main/resources/web_en.properties =================================================================== --- trunk/cantharella.web/src/main/resources/web_en.properties 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.web/src/main/resources/web_en.properties 2017-08-03 01:32:51 UTC (rev 277) @@ -85,7 +85,8 @@ ImprintPage.AccessRights.Info=According to the law n° 78-17 of 6 January 1978 on Data Processing, Data Files and Individual Liberties, you have a right of opposition (art. 26) of access (art. 34 - 38), of rectification (art. 36) and of deletion of any data which concerns you. You can practice this right by e-mail at <a href="mailto:dsi@ird.fr">dsi(a)ird.fr</a> or mail: ImprintPage.AccessRights.Address=Institut de recherche pour le développement<br />DSI<br />44, boulevard de Dunkerque, CS 90009<br />13752 Marseille cedex 02 ImprintPage.Editor=Publisher -ImprintPage.Editor.Director=Publisher : Michel Laurent, Président +ImprintPage.Editor.Director1=Publisher : +ImprintPage.Editor.Director2=Chairman - general director of the IRD ImprintPage.Editor.Administrator=IS Administrator : Sylvain PETEK and Adrien CHEYPE ImprintPage.Hosting=Hosting ImprintPage.Hosting.Info=The website <a href="http://cantharella.ird.nc/">http://cantharella.ird.nc</a> is hosted by the IRD. Modified: trunk/cantharella.web/src/main/resources/web_fr.properties =================================================================== --- trunk/cantharella.web/src/main/resources/web_fr.properties 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/cantharella.web/src/main/resources/web_fr.properties 2017-08-03 01:32:51 UTC (rev 277) @@ -84,7 +84,8 @@ ImprintPage.AccessRights.Info=Conformément à la loi n° 78-17 du 6 janvier 1978 relative à l'informatique, aux fichiers et aux libertés, vous disposez d'un droit d'opposition (art. 26) d'accès (art. 34 à 38), de rectification (art. 36) et de suppression des données qui vous concernent. Vous pouvez exercer ce droit par courrier électronique à <a href="mailto:dsi@ird.fr">dsi(a)ird.fr</a> ou postal : ImprintPage.AccessRights.Address=Institut de recherche pour le développement<br />DSI<br />44, boulevard de Dunkerque, CS 90009<br />13752 Marseille cedex 02 ImprintPage.Editor=Editeur -ImprintPage.Editor.Director=Directeur de la publication : Michel Laurent, Président +ImprintPage.Editor.Director.1=Directeur de la publication : +ImprintPage.Editor.Director.2=Président-directeur général de l'IRD ImprintPage.Editor.Administrator=Administrateurs du SI : Sylvain PETEK et Adrien CHEYPE ImprintPage.Hosting=Hébergement ImprintPage.Hosting.Info=Le site <a href="http://cantharella.ird.nc/">http://cantharella.ird.nc</a> est hébergé par l'IRD. Modified: trunk/cantharella.web/src/main/webapp/images/ird.png =================================================================== (Binary files differ) Added: trunk/docker/cantharella-db/Dockerfile =================================================================== --- trunk/docker/cantharella-db/Dockerfile (rev 0) +++ trunk/docker/cantharella-db/Dockerfile 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,5 @@ +FROM postgres:9.6.3 +MAINTAINER Adrien Cheype <adrien.cheype(a)ird.fr> + +COPY ./docker-entrypoint-initdb.d/ /docker-entrypoint-initdb.d/ +RUN chmod 0755 /docker-entrypoint-initdb.d/init-cantharella-db.sh \ No newline at end of file Added: trunk/docker/cantharella-db/create_db.sql =================================================================== --- trunk/docker/cantharella-db/create_db.sql (rev 0) +++ trunk/docker/cantharella-db/create_db.sql 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,29 @@ +--- +-- #%L +-- Cantharella :: Data +-- $Id: create_db.sql 133 2013-02-19 11:02:25Z acheype $ +-- $HeadURL: https://svn.codelutin.com/cantharella/trunk/cantharella.data/src/main/sql/c… $ +-- %% +-- 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% +--- +CREATE ROLE cantharella LOGIN PASSWORD 'ctrl4'; +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 Added: trunk/docker/cantharella-db/docker-entrypoint-initdb.d/init-cantharella-db.sh =================================================================== --- trunk/docker/cantharella-db/docker-entrypoint-initdb.d/init-cantharella-db.sh (rev 0) +++ trunk/docker/cantharella-db/docker-entrypoint-initdb.d/init-cantharella-db.sh 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,26 @@ +#!/bin/bash + +function onexit(){ + echo "An error occured - init_cantharella_db script exiting !" +} + +SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )" + +set -e +trap onexit EXIT + +echo "--- Init Cantharella DB ---" +echo "$SCRIPT_DIR" +echo "No 'cantharella' database found. The database is going to be created." +psql --username "$POSTGRES_USER" -f "$SCRIPT_DIR/sql/create_db.sql" +echo "* create_db.sql imported *" +psql --username cantharella -d cantharella -f $SCRIPT_DIR/sql/cantharella_schema_1.2.sql +echo "* cantharella_schema_1.2.sql imported *" +echo "--- End of Init Cantharella DB ---" +echo -e "\n" +echo "**** You can login with an admin account with : ****" +echo "**** - email : islog(a)ird.fr ****" +echo "**** - password : password ****" +echo -e "\n" + + Added: trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.0.sql =================================================================== --- trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.0.sql (rev 0) +++ trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.0.sql 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,593 @@ +--- +-- #%L +-- Cantharella :: Data +-- $Id: cantharella_schema_1.0.sql 211 2013-04-30 07:31:44Z acheype $ +-- $HeadURL: https://svn.codelutin.com/cantharella/trunk/cantharella.data/src/main/sql/c… $ +-- %% +-- 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% +--- + +-- insert once connected to cantharella database with the user cantharella +BEGIN; + + create table Campagne ( + idCampagne int4 not null, + codePays varchar(255) not null, + complement text, + dateDeb date not null, + dateFin date not null, + mentionLegale text, + nom varchar(255) unique not null, + programme varchar(255), + createur_idPersonne int4 not null, + primary key (idCampagne) + ); + + create table CampagneGroupeDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idCampagne int4 not null, + pk2_idGroupe int4 not null, + primary key (pk1_idCampagne, pk2_idGroupe) + ); + + create table CampagnePersonneDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idCampagne int4 not null, + pk2_idPersonne int4 not null, + primary key (pk1_idCampagne, pk2_idPersonne) + ); + + create table CampagnePersonneParticipant ( + complement text, + pk1_idCampagne int4 not null, + pk2_idPersonne int4 not null, + primary key (pk1_idCampagne, pk2_idPersonne) + ); + + create table Campagne_Station ( + campagnes_idCampagne int4 not null, + stations_idStation int4 not null + ); + + create table ErreurTestBio ( + idErreurTest int4 not null, + description text not null, + nom varchar(255) not null, + primary key (idErreurTest), + unique (nom) + ); + + create table Extraction ( + idExtraction int4 not null, + complement text, + date date not null, + masseDepart numeric(9, 4), + ref varchar(255) unique not null, + createur_idPersonne int4 not null, + lot_idLot int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodeExtraction int4 not null, + primary key (idExtraction) + ); + + create table Extrait ( + id int4 not null, + extraction_idExtraction int4 not null, + typeExtrait_idTypeExtrait int4 not null, + primary key (id) + ); + + create table Fraction ( + indice varchar(255) not null, + id int4 not null, + purification_idPurification int4 not null, + primary key (id) + ); + + create table Groupe ( + idGroupe int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idGroupe) + ); + + create table Lot ( + idLot int4 not null, + complement text, + dateRecolte date not null, + echantillonColl bool not null, + echantillonIdent bool not null, + echantillonPhylo bool not null, + masseFraiche numeric(9, 4), + masseSeche numeric(9, 4), + ref varchar(255) unique not null, + campagne_idCampagne int4 not null, + createur_idPersonne int4 not null, + partie_idPartie int4, + specimenRef_idSpecimen int4 not null, + station_idStation int4 not null, + primary key (idLot) + ); + + create table LotGroupeDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idLot int4 not null, + pk2_idGroupe int4 not null, + primary key (pk1_idLot, pk2_idGroupe) + ); + + create table LotPersonneDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk2_idPersonne int4 not null, + pk1_idLot int4 not null, + primary key (pk1_idLot, pk2_idPersonne) + ); + + create table MethodeExtraction ( + idMethodeExtraction int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idMethodeExtraction) + ); + + create table MethodePurification ( + idMethodePurification int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idMethodePurification) + ); + + create table MethodeTestBio ( + idMethodeTest int4 not null, + cible varchar(255) unique not null, + critereActivite varchar(255) not null, + description text not null, + domaine varchar(255) not null, + nom varchar(255) unique not null, + uniteResultat varchar(255) not null, + valeurMesuree varchar(255) not null, + primary key (idMethodeTest) + ); + + create table ParamMethoPuri ( + idParamMethoPuri int4 not null, + description text not null, + index int4 not null, + nom varchar(255) not null, + methodePurification_idMethodePurification int4 not null, + primary key (idParamMethoPuri) + ); + + create table ParamMethoPuriEffectif ( + idParamMethoPuriEffectif int4 not null, + valeur varchar(255), + param_idParamMethoPuri int4 not null, + purification_idPurification int4 not null, + primary key (idParamMethoPuriEffectif) + ); + + create table Partie ( + idPartie int4 not null, + nom varchar(255) unique not null, + primary key (idPartie) + ); + + create table Personne ( + idPersonne int4 not null, + adressePostale text not null, + codePays varchar(255) not null, + codePostal varchar(255) not null, + courriel varchar(255) unique not null, + fax varchar(255), + fonction varchar(255), + nom varchar(255) not null, + organisme varchar(255) not null, + prenom varchar(255) not null, + tel varchar(255), + ville varchar(255) not null, + primary key (idPersonne), + unique (nom, prenom) + ); + + create table Produit ( + id int4 not null, + masseObtenue numeric(9, 4), + ref varchar(255) unique not null, + primary key (id) + ); + + create table Purification ( + idPurification int4 not null, + complement text, + confidentiel bool not null, + date date not null, + dateConfidentialite date, + masseDepart numeric(9, 4), + ref varchar(255) unique not null, + createur_idPersonne int4 not null, + lotSource_idLot int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodePurification int4 not null, + produit_id int4 not null, + primary key (idPurification) + ); + + create table ResultatTestBio ( + id int4 not null, + concMasse numeric(9, 4), + estActif bool, + produitTemoin varchar(255), + repere varchar(255) not null, + stade int4, + typeResultat int4 not null, + uniteConcMasse int4, + valeur numeric(9, 4), + erreur_idErreurTest int4, + produit_id int4, + testBio_idTestBio int4 not null, + typeExtraitSource_idTypeExtrait int4, + primary key (id) + ); + + create table Specimen ( + idSpecimen int4 not null, + complement text, + dateDepot date, + embranchement varchar(255) not null, + espece varchar(255), + famille varchar(255), + genre varchar(255), + lieuDepot varchar(255), + numDepot varchar(255), + ref varchar(255) unique not null, + sousEspece varchar(255), + typeOrganisme int4, + variete varchar(255), + createur_idPersonne int4 not null, + identificateur_idPersonne int4, + station_idStation int4, + primary key (idSpecimen) + ); + + create table Station ( + idStation int4 not null, + codePays varchar(255) not null, + complement text, + latitude varchar(255), + localite varchar(255), + longitude varchar(255), + nom varchar(255) unique not null, + referentiel int4, + createur_idPersonne int4 not null, + primary key (idStation) + ); + + create table TestBio ( + idTestBio int4 not null, + complement text, + concMasseDefaut numeric(9, 4), + confidentiel bool not null, + date date not null, + dateConfidentialite date, + organismeTesteur varchar(255) not null, + ref varchar(255) unique not null, + stadeDefaut int4, + uniteConcMasseDefaut int4, + createur_idPersonne int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodeTest int4 not null, + primary key (idTestBio) + ); + + create table TypeDocument ( + idTypeDocument int4 not null, + description text not null, + domaine varchar(255), + estImage bool, + nom varchar(255) unique, + primary key (idTypeDocument), + unique (nom) + ); + + create table TypeExtrait ( + idTypeExtrait int4 not null, + description text not null, + initiales varchar(255) unique not null, + methodeExtraction_idMethodeExtraction int4 not null, + primary key (idTypeExtrait) + ); + + create table Utilisateur ( + dateValiditeCompte date, + estValide bool not null, + passwordHash varchar(255) not null, + typeDroit int4 not null, + idPersonne int4 not null, + groupe_idGroupe int4, + primary key (idPersonne) + ); + + alter table Campagne + add constraint FKFB835E7E822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table CampagneGroupeDroits + add constraint FK3AFBE26B905CBAAF + foreign key (pk2_idGroupe) + references Groupe; + + alter table CampagneGroupeDroits + add constraint FK3AFBE26B975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneDroits + add constraint FK81782471975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneDroits + add constraint FK81782471E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table CampagnePersonneParticipant + add constraint FK72EE0469975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneParticipant + add constraint FK72EE0469E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table Campagne_Station + add constraint FK61A84053557B2C21 + foreign key (campagnes_idCampagne) + references Campagne; + + alter table Campagne_Station + add constraint FK61A840531AE541CD + foreign key (stations_idStation) + references Station; + + alter table Extraction + add constraint FKA39DBC077106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table Extraction + add constraint FKA39DBC07822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Extraction + add constraint FKA39DBC07F7C7FFC0 + foreign key (methode_idMethodeExtraction) + references MethodeExtraction; + + alter table Extraction + add constraint FKA39DBC07AE638899 + foreign key (lot_idLot) + references Lot; + + alter table Extrait + add constraint FK156B751B9547CE24 + foreign key (id) + references Produit; + + alter table Extrait + add constraint FK156B751B252FD5C9 + foreign key (typeExtrait_idTypeExtrait) + references TypeExtrait; + + alter table Extrait + add constraint FK156B751BE48A1121 + foreign key (extraction_idExtraction) + references Extraction; + + alter table Fraction + add constraint FKA14826229547CE24 + foreign key (id) + references Produit; + + alter table Fraction + add constraint FKA1482622859CB52B + foreign key (purification_idPurification) + references Purification; + + alter table Lot + add constraint FK12B311AA103F8 + foreign key (campagne_idCampagne) + references Campagne; + + alter table Lot + add constraint FK12B3168370809 + foreign key (partie_idPartie) + references Partie; + + alter table Lot + add constraint FK12B31822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Lot + add constraint FK12B31DDF1E8FF + foreign key (specimenRef_idSpecimen) + references Specimen; + + alter table Lot + add constraint FK12B31CBED0F02 + foreign key (station_idStation) + references Station; + + alter table LotGroupeDroits + add constraint FK9AC53A9E905CBAAF + foreign key (pk2_idGroupe) + references Groupe; + + alter table LotGroupeDroits + add constraint FK9AC53A9E87AF0F1E + foreign key (pk1_idLot) + references Lot; + + alter table LotPersonneDroits + add constraint FK144C3BE4E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table LotPersonneDroits + add constraint FK144C3BE487AF0F1E + foreign key (pk1_idLot) + references Lot; + + alter table ParamMethoPuri + add constraint FK1476479225A42085 + foreign key (methodePurification_idMethodePurification) + references MethodePurification; + + alter table ParamMethoPuriEffectif + add constraint FK8F7FA020B4F23AD1 + foreign key (param_idParamMethoPuri) + references ParamMethoPuri; + + alter table ParamMethoPuriEffectif + add constraint FK8F7FA020859CB52B + foreign key (purification_idPurification) + references Purification; + + create index courriel on Personne (courriel); + + alter table Purification + add constraint FKD1727611FE19187A + foreign key (produit_id) + references Produit; + + alter table Purification + add constraint FKD17276117106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table Purification + add constraint FKD1727611822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Purification + add constraint FKD1727611626E4F54 + foreign key (methode_idMethodePurification) + references MethodePurification; + + alter table Purification + add constraint FKD1727611C4943FB4 + foreign key (lotSource_idLot) + references Lot; + + create index typeResultat on ResultatTestBio (typeResultat); + + alter table ResultatTestBio + add constraint FK5DFD5BC6FE19187A + foreign key (produit_id) + references Produit; + + alter table ResultatTestBio + add constraint FK5DFD5BC65033BE68 + foreign key (testBio_idTestBio) + references TestBio; + + alter table ResultatTestBio + add constraint FK5DFD5BC64B1883E5 + foreign key (erreur_idErreurTest) + references ErreurTestBio; + + alter table ResultatTestBio + add constraint FK5DFD5BC6ABE26DE4 + foreign key (typeExtraitSource_idTypeExtrait) + references TypeExtrait; + + alter table Specimen + add constraint FK84B96728822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Specimen + add constraint FK84B96728D2CE02CA + foreign key (identificateur_idPersonne) + references Personne; + + alter table Specimen + add constraint FK84B96728CBED0F02 + foreign key (station_idStation) + references Station; + + alter table Station + add constraint FKF2249914822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F67106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F6822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F67DBA1C52 + foreign key (methode_idMethodeTest) + references MethodeTestBio; + + alter table TypeExtrait + add constraint FK40F3D8811D52927 + foreign key (methodeExtraction_idMethodeExtraction) + references MethodeExtraction; + + create index estValide on Utilisateur (estValide); + + create index typeDroit on Utilisateur (typeDroit); + + alter table Utilisateur + add constraint FK407FDB6370C95760 + foreign key (groupe_idGroupe) + references Groupe; + + alter table Utilisateur + add constraint FK407FDB63A1338A53 + foreign key (idPersonne) + references Personne; + + create sequence hibernate_sequence; + + + +COMMIT; Added: trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.1.sql =================================================================== --- trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.1.sql (rev 0) +++ trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.1.sql 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,727 @@ +--- +-- #%L +-- Cantharella :: Data +-- $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% +--- + +-- insert once connected to cantharella database with the user cantharella +BEGIN; + + create table Campagne ( + idCampagne int4 not null, + codePays varchar(255) not null, + complement text, + dateDeb date not null, + dateFin date not null, + mentionLegale text, + nom varchar(255) unique not null, + programme varchar(255), + createur_idPersonne int4 not null, + primary key (idCampagne) + ); + + create table CampagneGroupeDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idCampagne int4 not null, + pk2_idGroupe int4 not null, + primary key (pk1_idCampagne, pk2_idGroupe) + ); + + create table CampagnePersonneDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idCampagne int4 not null, + pk2_idPersonne int4 not null, + primary key (pk1_idCampagne, pk2_idPersonne) + ); + + create table CampagnePersonneParticipant ( + complement text, + pk1_idCampagne int4 not null, + pk2_idPersonne int4 not null, + primary key (pk1_idCampagne, pk2_idPersonne) + ); + + create table Campagne_Station ( + campagnes_idCampagne int4 not null, + stations_idStation int4 not null + ); + + create table ErreurTestBio ( + idErreurTest int4 not null, + description text not null, + nom varchar(255) not null, + primary key (idErreurTest), + unique (nom) + ); + + create table Extraction ( + idExtraction int4 not null, + complement text, + date date not null, + masseDepart numeric(9, 4), + ref varchar(255) unique not null, + createur_idPersonne int4 not null, + lot_idLot int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodeExtraction int4 not null, + primary key (idExtraction) + ); + + create table Extrait ( + id int4 not null, + extraction_idExtraction int4 not null, + typeExtrait_idTypeExtrait int4 not null, + primary key (id) + ); + + create table Fraction ( + indice varchar(255) not null, + id int4 not null, + purification_idPurification int4 not null, + primary key (id) + ); + + create table Groupe ( + idGroupe int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idGroupe) + ); + + create table Lot ( + idLot int4 not null, + complement text, + dateRecolte date not null, + echantillonColl bool not null, + echantillonIdent bool not null, + echantillonPhylo bool not null, + masseFraiche numeric(9, 4), + masseSeche numeric(9, 4), + ref varchar(255) unique not null, + campagne_idCampagne int4 not null, + createur_idPersonne int4 not null, + partie_idPartie int4, + specimenRef_idSpecimen int4 not null, + station_idStation int4 not null, + primary key (idLot) + ); + + create table LotGroupeDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idLot int4 not null, + pk2_idGroupe int4 not null, + primary key (pk1_idLot, pk2_idGroupe) + ); + + create table LotPersonneDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk2_idPersonne int4 not null, + pk1_idLot int4 not null, + primary key (pk1_idLot, pk2_idPersonne) + ); + + create table MethodeExtraction ( + idMethodeExtraction int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idMethodeExtraction) + ); + + create table MethodePurification ( + idMethodePurification int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idMethodePurification) + ); + + create table MethodeTestBio ( + idMethodeTest int4 not null, + cible varchar(255) unique not null, + critereActivite varchar(255) not null, + description text not null, + domaine varchar(255) not null, + nom varchar(255) unique not null, + uniteResultat varchar(255) not null, + valeurMesuree varchar(255) not null, + primary key (idMethodeTest) + ); + + create table ParamMethoPuri ( + idParamMethoPuri int4 not null, + description text not null, + index int4 not null, + nom varchar(255) not null, + methodePurification_idMethodePurification int4 not null, + primary key (idParamMethoPuri) + ); + + create table ParamMethoPuriEffectif ( + idParamMethoPuriEffectif int4 not null, + valeur varchar(255), + param_idParamMethoPuri int4 not null, + purification_idPurification int4 not null, + primary key (idParamMethoPuriEffectif) + ); + + create table Partie ( + idPartie int4 not null, + nom varchar(255) unique not null, + primary key (idPartie) + ); + + create table Personne ( + idPersonne int4 not null, + adressePostale text not null, + codePays varchar(255) not null, + codePostal varchar(255) not null, + courriel varchar(255) unique not null, + fax varchar(255), + fonction varchar(255), + nom varchar(255) not null, + organisme varchar(255) not null, + prenom varchar(255) not null, + tel varchar(255), + ville varchar(255) not null, + primary key (idPersonne), + unique (nom, prenom) + ); + + create table Produit ( + id int4 not null, + masseObtenue numeric(9, 4), + ref varchar(255) unique not null, + primary key (id) + ); + + create table Purification ( + idPurification int4 not null, + complement text, + confidentiel bool not null, + date date not null, + dateConfidentialite date, + masseDepart numeric(9, 4), + ref varchar(255) unique not null, + createur_idPersonne int4 not null, + lotSource_idLot int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodePurification int4 not null, + produit_id int4 not null, + primary key (idPurification) + ); + + create table ResultatTestBio ( + id int4 not null, + concMasse numeric(9, 4), + estActif bool, + produitTemoin varchar(255), + repere varchar(255) not null, + stade int4, + typeResultat int4 not null, + uniteConcMasse int4, + valeur numeric(9, 4), + erreur_idErreurTest int4, + produit_id int4, + testBio_idTestBio int4 not null, + typeExtraitSource_idTypeExtrait int4, + primary key (id) + ); + + create table Specimen ( + idSpecimen int4 not null, + complement text, + dateDepot date, + embranchement varchar(255) not null, + espece varchar(255), + famille varchar(255), + genre varchar(255), + lieuDepot varchar(255), + numDepot varchar(255), + ref varchar(255) unique not null, + sousEspece varchar(255), + typeOrganisme int4, + variete varchar(255), + createur_idPersonne int4 not null, + identificateur_idPersonne int4, + station_idStation int4, + primary key (idSpecimen) + ); + + create table Station ( + idStation int4 not null, + codePays varchar(255) not null, + complement text, + latitude varchar(255), + localite varchar(255), + longitude varchar(255), + nom varchar(255) unique not null, + referentiel int4, + createur_idPersonne int4 not null, + primary key (idStation) + ); + + create table TestBio ( + idTestBio int4 not null, + complement text, + concMasseDefaut numeric(9, 4), + confidentiel bool not null, + date date not null, + dateConfidentialite date, + organismeTesteur varchar(255) not null, + ref varchar(255) unique not null, + stadeDefaut int4, + uniteConcMasseDefaut int4, + createur_idPersonne int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodeTest int4 not null, + primary key (idTestBio) + ); + + create table TypeExtrait ( + idTypeExtrait int4 not null, + description text not null, + initiales varchar(255) unique not null, + methodeExtraction_idMethodeExtraction int4 not null, + primary key (idTypeExtrait) + ); + + create table Utilisateur ( + dateValiditeCompte date, + estValide bool not null, + passwordHash varchar(255) not null, + typeDroit int4 not null, + idPersonne int4 not null, + groupe_idGroupe int4, + primary key (idPersonne) + ); + + alter table Campagne + add constraint FKFB835E7E822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table CampagneGroupeDroits + add constraint FK3AFBE26B905CBAAF + foreign key (pk2_idGroupe) + references Groupe; + + alter table CampagneGroupeDroits + add constraint FK3AFBE26B975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneDroits + add constraint FK81782471975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneDroits + add constraint FK81782471E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table CampagnePersonneParticipant + add constraint FK72EE0469975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneParticipant + add constraint FK72EE0469E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table Campagne_Station + add constraint FK61A84053557B2C21 + foreign key (campagnes_idCampagne) + references Campagne; + + alter table Campagne_Station + add constraint FK61A840531AE541CD + foreign key (stations_idStation) + references Station; + + alter table Extraction + add constraint FKA39DBC077106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table Extraction + add constraint FKA39DBC07822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Extraction + add constraint FKA39DBC07F7C7FFC0 + foreign key (methode_idMethodeExtraction) + references MethodeExtraction; + + alter table Extraction + add constraint FKA39DBC07AE638899 + foreign key (lot_idLot) + references Lot; + + alter table Extrait + add constraint FK156B751B9547CE24 + foreign key (id) + references Produit; + + alter table Extrait + add constraint FK156B751B252FD5C9 + foreign key (typeExtrait_idTypeExtrait) + references TypeExtrait; + + alter table Extrait + add constraint FK156B751BE48A1121 + foreign key (extraction_idExtraction) + references Extraction; + + alter table Fraction + add constraint FKA14826229547CE24 + foreign key (id) + references Produit; + + alter table Fraction + add constraint FKA1482622859CB52B + foreign key (purification_idPurification) + references Purification; + + alter table Lot + add constraint FK12B311AA103F8 + foreign key (campagne_idCampagne) + references Campagne; + + alter table Lot + add constraint FK12B3168370809 + foreign key (partie_idPartie) + references Partie; + + alter table Lot + add constraint FK12B31822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Lot + add constraint FK12B31DDF1E8FF + foreign key (specimenRef_idSpecimen) + references Specimen; + + alter table Lot + add constraint FK12B31CBED0F02 + foreign key (station_idStation) + references Station; + + alter table LotGroupeDroits + add constraint FK9AC53A9E905CBAAF + foreign key (pk2_idGroupe) + references Groupe; + + alter table LotGroupeDroits + add constraint FK9AC53A9E87AF0F1E + foreign key (pk1_idLot) + references Lot; + + alter table LotPersonneDroits + add constraint FK144C3BE4E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table LotPersonneDroits + add constraint FK144C3BE487AF0F1E + foreign key (pk1_idLot) + references Lot; + + alter table ParamMethoPuri + add constraint FK1476479225A42085 + foreign key (methodePurification_idMethodePurification) + references MethodePurification; + + alter table ParamMethoPuriEffectif + add constraint FK8F7FA020B4F23AD1 + foreign key (param_idParamMethoPuri) + references ParamMethoPuri; + + alter table ParamMethoPuriEffectif + add constraint FK8F7FA020859CB52B + foreign key (purification_idPurification) + references Purification; + + create index courriel on Personne (courriel); + + alter table Purification + add constraint FKD1727611FE19187A + foreign key (produit_id) + references Produit; + + alter table Purification + add constraint FKD17276117106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table Purification + add constraint FKD1727611822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Purification + add constraint FKD1727611626E4F54 + foreign key (methode_idMethodePurification) + references MethodePurification; + + alter table Purification + add constraint FKD1727611C4943FB4 + foreign key (lotSource_idLot) + references Lot; + + create index typeResultat on ResultatTestBio (typeResultat); + + alter table ResultatTestBio + add constraint FK5DFD5BC6FE19187A + foreign key (produit_id) + references Produit; + + alter table ResultatTestBio + add constraint FK5DFD5BC65033BE68 + foreign key (testBio_idTestBio) + references TestBio; + + alter table ResultatTestBio + add constraint FK5DFD5BC64B1883E5 + foreign key (erreur_idErreurTest) + references ErreurTestBio; + + alter table ResultatTestBio + add constraint FK5DFD5BC6ABE26DE4 + foreign key (typeExtraitSource_idTypeExtrait) + references TypeExtrait; + + alter table Specimen + add constraint FK84B96728822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Specimen + add constraint FK84B96728D2CE02CA + foreign key (identificateur_idPersonne) + references Personne; + + alter table Specimen + add constraint FK84B96728CBED0F02 + foreign key (station_idStation) + references Station; + + alter table Station + add constraint FKF2249914822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F67106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F6822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F67DBA1C52 + foreign key (methode_idMethodeTest) + references MethodeTestBio; + + alter table TypeExtrait + add constraint FK40F3D8811D52927 + foreign key (methodeExtraction_idMethodeExtraction) + references MethodeExtraction; + + create index estValide on Utilisateur (estValide); + + create index typeDroit on Utilisateur (typeDroit); + + alter table Utilisateur + add constraint FK407FDB6370C95760 + foreign key (groupe_idGroupe) + references Groupe; + + alter table Utilisateur + add constraint FK407FDB63A1338A53 + foreign key (idPersonne) + references Personne; + + create sequence hibernate_sequence; + + -- Documents (16/11/2012) - update (25/03/2013) + create table TypeDocument ( + idTypeDocument int4 not null, + description text not null, + domaine varchar(60) not null, + nom varchar(60) not null unique, + primary key (idTypeDocument), + unique (nom) + ); + + -- Molecules (07/01/2013) + create table Molecule ( + idMolecule int4 not null, + complement text, + familleChimique varchar(60), + formuleBrute varchar(60) not null, + formuleDevMol text, + identifieePar varchar(60), + masseMolaire numeric(9, 4) check (masseMolaire<=99999 AND masseMolaire>=0), + nomCommun varchar(100), + nomIupca varchar(255), + nouvMolecul boolean not null, + publiOrigine text, + campagne_idCampagne int4, + createur_idPersonne int4 not null, + primary key (idMolecule) + ); + + create table MoleculeProvenance ( + id int4 not null, + pourcentage numeric(9, 4) check (pourcentage>=0 AND pourcentage<=100), + molecule_idMolecule int4 not null, + produit_id int4 not null, + primary key (id) + ); + + alter table Molecule + add constraint FKEC979EA61AA103F8 + foreign key (campagne_idCampagne) + references Campagne; + + alter table Molecule + add constraint FKEC979EA6822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table MoleculeProvenance + add constraint FK8B39E567F44F1B20 + foreign key (molecule_idMolecule) + references Molecule; + + alter table MoleculeProvenance + add constraint FK8B39E567FE19187A + foreign key (produit_id) + references Produit; + + create sequence molecule_sequence; + + -- Document (12/02/2013) + create table Document ( + idDocument int4 not null, + contrainteLegale varchar(100), + dateCreation date not null, + description text, + editeur varchar(100) not null, + fileContent bytea, + fileContentThumb bytea, + fileMimetype varchar(60), + fileName varchar(60) not null, + langue varchar(2), + titre varchar(100) not null, + ajoutePar_idPersonne int4 not null, + createur_idPersonne int4 not null, + typeDocument_idTypeDocument int4 not null, + specimen int4, + campagne int4, + personne int4, + extraction int4, + station int4, + purification int4, + lot int4, + resultatTestBio int4, + molecule int4, + primary key (idDocument) + ); + + alter table Document + add constraint FK3737353B2F46DB31 + foreign key (ajoutePar_idPersonne) + references Personne; + + alter table Document + add constraint FK3737353B822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Document + add constraint FK3737353BBECBA92F + foreign key (typeDocument_idTypeDocument) + references TypeDocument; + + alter table Document + add constraint FK3737353B51427EB0 + foreign key (specimen) + references Specimen; + + alter table Document + add constraint FK3737353B3ED66D5C + foreign key (campagne) + references Campagne; + + alter table Document + add constraint FK3737353B8458C838 + foreign key (personne) + references Personne; + + alter table Document + add constraint FK3737353BD9E0906E + foreign key (extraction) + references Extraction; + + alter table Document + add constraint FK3737353BC591F5C8 + foreign key (station) + references Station; + + alter table Document + add constraint FK3737353B20A56C82 + foreign key (purification) + references Purification; + + alter table Document + add constraint FK3737353B767DEA02 + foreign key (lot) + references Lot; + + alter table Document + add constraint FK3737353B8923169C + foreign key (resultatTestBio) + references TestBio; + + alter table Document + add constraint FK3737353B20FEEDAC + foreign key (molecule) + references Molecule; + +COMMIT; Added: trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.2.sql =================================================================== --- trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.2.sql (rev 0) +++ trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/cantharella_schema_1.2.sql 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,780 @@ +--- +-- #%L +-- Cantharella :: Data +-- $Id: dev_update_1.1_to_1.2.sql 211 2013-04-30 07:31:44Z acheype $ +-- $HeadURL: http://svn.forge.codelutin.com/svn/cantharella/trunk/cantharella.data/src/m… $ +-- %% +-- Copyright (C) 2014 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% +--- + +-- insert once connected to cantharella database with the user cantharella +BEGIN; + + -- SCHEMA 1.1 + + create table Campagne ( + idCampagne int4 not null, + codePays varchar(255) not null, + complement text, + dateDeb date not null, + dateFin date not null, + mentionLegale text, + nom varchar(255) unique not null, + programme varchar(255), + createur_idPersonne int4 not null, + primary key (idCampagne) + ); + + create table CampagneGroupeDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idCampagne int4 not null, + pk2_idGroupe int4 not null, + primary key (pk1_idCampagne, pk2_idGroupe) + ); + + create table CampagnePersonneDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idCampagne int4 not null, + pk2_idPersonne int4 not null, + primary key (pk1_idCampagne, pk2_idPersonne) + ); + + create table CampagnePersonneParticipant ( + complement text, + pk1_idCampagne int4 not null, + pk2_idPersonne int4 not null, + primary key (pk1_idCampagne, pk2_idPersonne) + ); + + create table Campagne_Station ( + campagnes_idCampagne int4 not null, + stations_idStation int4 not null + ); + + create table ErreurTestBio ( + idErreurTest int4 not null, + description text not null, + nom varchar(255) not null, + primary key (idErreurTest), + unique (nom) + ); + + create table Extraction ( + idExtraction int4 not null, + complement text, + date date not null, + masseDepart numeric(9, 4), + ref varchar(255) unique not null, + createur_idPersonne int4 not null, + lot_idLot int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodeExtraction int4 not null, + primary key (idExtraction) + ); + + create table Extrait ( + id int4 not null, + extraction_idExtraction int4 not null, + typeExtrait_idTypeExtrait int4 not null, + primary key (id) + ); + + create table Fraction ( + indice varchar(255) not null, + id int4 not null, + purification_idPurification int4 not null, + primary key (id) + ); + + create table Groupe ( + idGroupe int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idGroupe) + ); + + create table Lot ( + idLot int4 not null, + complement text, + dateRecolte date not null, + echantillonColl bool not null, + echantillonIdent bool not null, + echantillonPhylo bool not null, + masseFraiche numeric(9, 4), + masseSeche numeric(9, 4), + ref varchar(255) unique not null, + campagne_idCampagne int4 not null, + createur_idPersonne int4 not null, + partie_idPartie int4, + specimenRef_idSpecimen int4 not null, + station_idStation int4 not null, + primary key (idLot) + ); + + create table LotGroupeDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idLot int4 not null, + pk2_idGroupe int4 not null, + primary key (pk1_idLot, pk2_idGroupe) + ); + + create table LotPersonneDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk2_idPersonne int4 not null, + pk1_idLot int4 not null, + primary key (pk1_idLot, pk2_idPersonne) + ); + + create table MethodeExtraction ( + idMethodeExtraction int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idMethodeExtraction) + ); + + create table MethodePurification ( + idMethodePurification int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idMethodePurification) + ); + + create table MethodeTestBio ( + idMethodeTest int4 not null, + cible varchar(255) unique not null, + critereActivite varchar(255) not null, + description text not null, + domaine varchar(255) not null, + nom varchar(255) unique not null, + uniteResultat varchar(255) not null, + valeurMesuree varchar(255) not null, + primary key (idMethodeTest) + ); + + create table ParamMethoPuri ( + idParamMethoPuri int4 not null, + description text not null, + index int4 not null, + nom varchar(255) not null, + methodePurification_idMethodePurification int4 not null, + primary key (idParamMethoPuri) + ); + + create table ParamMethoPuriEffectif ( + idParamMethoPuriEffectif int4 not null, + valeur varchar(255), + param_idParamMethoPuri int4 not null, + purification_idPurification int4 not null, + primary key (idParamMethoPuriEffectif) + ); + + create table Partie ( + idPartie int4 not null, + nom varchar(255) unique not null, + primary key (idPartie) + ); + + create table Personne ( + idPersonne int4 not null, + adressePostale text not null, + codePays varchar(255) not null, + codePostal varchar(255) not null, + courriel varchar(255) unique not null, + fax varchar(255), + fonction varchar(255), + nom varchar(255) not null, + organisme varchar(255) not null, + prenom varchar(255) not null, + tel varchar(255), + ville varchar(255) not null, + primary key (idPersonne), + unique (nom, prenom) + ); + + create table Produit ( + id int4 not null, + masseObtenue numeric(9, 4), + ref varchar(255) unique not null, + primary key (id) + ); + + create table Purification ( + idPurification int4 not null, + complement text, + confidentiel bool not null, + date date not null, + dateConfidentialite date, + masseDepart numeric(9, 4), + ref varchar(255) unique not null, + createur_idPersonne int4 not null, + lotSource_idLot int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodePurification int4 not null, + produit_id int4 not null, + primary key (idPurification) + ); + + create table ResultatTestBio ( + id int4 not null, + concMasse numeric(9, 4), + estActif bool, + produitTemoin varchar(255), + repere varchar(255) not null, + stade int4, + typeResultat int4 not null, + uniteConcMasse int4, + valeur numeric(9, 4), + erreur_idErreurTest int4, + produit_id int4, + testBio_idTestBio int4 not null, + typeExtraitSource_idTypeExtrait int4, + primary key (id) + ); + + create table Specimen ( + idSpecimen int4 not null, + complement text, + dateDepot date, + embranchement varchar(255) not null, + espece varchar(255), + famille varchar(255), + genre varchar(255), + lieuDepot varchar(255), + numDepot varchar(255), + ref varchar(255) unique not null, + sousEspece varchar(255), + typeOrganisme int4, + variete varchar(255), + createur_idPersonne int4 not null, + identificateur_idPersonne int4, + station_idStation int4, + primary key (idSpecimen) + ); + + create table Station ( + idStation int4 not null, + codePays varchar(255) not null, + complement text, + latitude varchar(255), + localite varchar(255), + longitude varchar(255), + nom varchar(255) unique not null, + referentiel int4, + createur_idPersonne int4 not null, + primary key (idStation) + ); + + create table TestBio ( + idTestBio int4 not null, + complement text, + concMasseDefaut numeric(9, 4), + confidentiel bool not null, + date date not null, + dateConfidentialite date, + organismeTesteur varchar(255) not null, + ref varchar(255) unique not null, + stadeDefaut int4, + uniteConcMasseDefaut int4, + createur_idPersonne int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodeTest int4 not null, + primary key (idTestBio) + ); + + create table TypeExtrait ( + idTypeExtrait int4 not null, + description text not null, + initiales varchar(255) unique not null, + methodeExtraction_idMethodeExtraction int4 not null, + primary key (idTypeExtrait) + ); + + create table Utilisateur ( + dateValiditeCompte date, + estValide bool not null, + passwordHash varchar(255) not null, + typeDroit int4 not null, + idPersonne int4 not null, + groupe_idGroupe int4, + primary key (idPersonne) + ); + + alter table Campagne + add constraint FKFB835E7E822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table CampagneGroupeDroits + add constraint FK3AFBE26B905CBAAF + foreign key (pk2_idGroupe) + references Groupe; + + alter table CampagneGroupeDroits + add constraint FK3AFBE26B975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneDroits + add constraint FK81782471975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneDroits + add constraint FK81782471E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table CampagnePersonneParticipant + add constraint FK72EE0469975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneParticipant + add constraint FK72EE0469E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table Campagne_Station + add constraint FK61A84053557B2C21 + foreign key (campagnes_idCampagne) + references Campagne; + + alter table Campagne_Station + add constraint FK61A840531AE541CD + foreign key (stations_idStation) + references Station; + + alter table Extraction + add constraint FKA39DBC077106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table Extraction + add constraint FKA39DBC07822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Extraction + add constraint FKA39DBC07F7C7FFC0 + foreign key (methode_idMethodeExtraction) + references MethodeExtraction; + + alter table Extraction + add constraint FKA39DBC07AE638899 + foreign key (lot_idLot) + references Lot; + + alter table Extrait + add constraint FK156B751B9547CE24 + foreign key (id) + references Produit; + + alter table Extrait + add constraint FK156B751B252FD5C9 + foreign key (typeExtrait_idTypeExtrait) + references TypeExtrait; + + alter table Extrait + add constraint FK156B751BE48A1121 + foreign key (extraction_idExtraction) + references Extraction; + + alter table Fraction + add constraint FKA14826229547CE24 + foreign key (id) + references Produit; + + alter table Fraction + add constraint FKA1482622859CB52B + foreign key (purification_idPurification) + references Purification; + + alter table Lot + add constraint FK12B311AA103F8 + foreign key (campagne_idCampagne) + references Campagne; + + alter table Lot + add constraint FK12B3168370809 + foreign key (partie_idPartie) + references Partie; + + alter table Lot + add constraint FK12B31822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Lot + add constraint FK12B31DDF1E8FF + foreign key (specimenRef_idSpecimen) + references Specimen; + + alter table Lot + add constraint FK12B31CBED0F02 + foreign key (station_idStation) + references Station; + + alter table LotGroupeDroits + add constraint FK9AC53A9E905CBAAF + foreign key (pk2_idGroupe) + references Groupe; + + alter table LotGroupeDroits + add constraint FK9AC53A9E87AF0F1E + foreign key (pk1_idLot) + references Lot; + + alter table LotPersonneDroits + add constraint FK144C3BE4E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table LotPersonneDroits + add constraint FK144C3BE487AF0F1E + foreign key (pk1_idLot) + references Lot; + + alter table ParamMethoPuri + add constraint FK1476479225A42085 + foreign key (methodePurification_idMethodePurification) + references MethodePurification; + + alter table ParamMethoPuriEffectif + add constraint FK8F7FA020B4F23AD1 + foreign key (param_idParamMethoPuri) + references ParamMethoPuri; + + alter table ParamMethoPuriEffectif + add constraint FK8F7FA020859CB52B + foreign key (purification_idPurification) + references Purification; + + create index courriel on Personne (courriel); + + alter table Purification + add constraint FKD1727611FE19187A + foreign key (produit_id) + references Produit; + + alter table Purification + add constraint FKD17276117106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table Purification + add constraint FKD1727611822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Purification + add constraint FKD1727611626E4F54 + foreign key (methode_idMethodePurification) + references MethodePurification; + + alter table Purification + add constraint FKD1727611C4943FB4 + foreign key (lotSource_idLot) + references Lot; + + create index typeResultat on ResultatTestBio (typeResultat); + + alter table ResultatTestBio + add constraint FK5DFD5BC6FE19187A + foreign key (produit_id) + references Produit; + + alter table ResultatTestBio + add constraint FK5DFD5BC65033BE68 + foreign key (testBio_idTestBio) + references TestBio; + + alter table ResultatTestBio + add constraint FK5DFD5BC64B1883E5 + foreign key (erreur_idErreurTest) + references ErreurTestBio; + + alter table ResultatTestBio + add constraint FK5DFD5BC6ABE26DE4 + foreign key (typeExtraitSource_idTypeExtrait) + references TypeExtrait; + + alter table Specimen + add constraint FK84B96728822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Specimen + add constraint FK84B96728D2CE02CA + foreign key (identificateur_idPersonne) + references Personne; + + alter table Specimen + add constraint FK84B96728CBED0F02 + foreign key (station_idStation) + references Station; + + alter table Station + add constraint FKF2249914822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F67106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F6822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F67DBA1C52 + foreign key (methode_idMethodeTest) + references MethodeTestBio; + + alter table TypeExtrait + add constraint FK40F3D8811D52927 + foreign key (methodeExtraction_idMethodeExtraction) + references MethodeExtraction; + + create index estValide on Utilisateur (estValide); + + create index typeDroit on Utilisateur (typeDroit); + + alter table Utilisateur + add constraint FK407FDB6370C95760 + foreign key (groupe_idGroupe) + references Groupe; + + alter table Utilisateur + add constraint FK407FDB63A1338A53 + foreign key (idPersonne) + references Personne; + + create sequence hibernate_sequence; + + -- Documents (16/11/2012) - update (25/03/2013) + create table TypeDocument ( + idTypeDocument int4 not null, + description text not null, + domaine varchar(60) not null, + nom varchar(60) not null unique, + primary key (idTypeDocument), + unique (nom) + ); + + -- Molecules (07/01/2013) + create table Molecule ( + idMolecule int4 not null, + complement text, + familleChimique varchar(60), + formuleBrute varchar(60) not null, + formuleDevMol text, + identifieePar varchar(60), + masseMolaire numeric(9, 4) check (masseMolaire<=99999 AND masseMolaire>=0), + nomCommun varchar(100), + nomIupca varchar(255), + nouvMolecul boolean not null, + publiOrigine text, + campagne_idCampagne int4, + createur_idPersonne int4 not null, + primary key (idMolecule) + ); + + create table MoleculeProvenance ( + id int4 not null, + pourcentage numeric(9, 4) check (pourcentage>=0 AND pourcentage<=100), + molecule_idMolecule int4 not null, + produit_id int4 not null, + primary key (id) + ); + + alter table Molecule + add constraint FKEC979EA61AA103F8 + foreign key (campagne_idCampagne) + references Campagne; + + alter table Molecule + add constraint FKEC979EA6822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table MoleculeProvenance + add constraint FK8B39E567F44F1B20 + foreign key (molecule_idMolecule) + references Molecule; + + alter table MoleculeProvenance + add constraint FK8B39E567FE19187A + foreign key (produit_id) + references Produit; + + create sequence molecule_sequence; + + -- Document (12/02/2013) + create table Document ( + idDocument int4 not null, + contrainteLegale varchar(100), + dateCreation date not null, + description text, + editeur varchar(100) not null, + fileContent bytea, + fileContentThumb bytea, + fileMimetype varchar(60), + fileName varchar(60) not null, + langue varchar(2), + titre varchar(100) not null, + ajoutePar_idPersonne int4 not null, + createur_idPersonne int4 not null, + typeDocument_idTypeDocument int4 not null, + specimen int4, + campagne int4, + personne int4, + extraction int4, + station int4, + purification int4, + lot int4, + resultatTestBio int4, + molecule int4, + primary key (idDocument) + ); + + alter table Document + add constraint FK3737353B2F46DB31 + foreign key (ajoutePar_idPersonne) + references Personne; + + alter table Document + add constraint FK3737353B822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Document + add constraint FK3737353BBECBA92F + foreign key (typeDocument_idTypeDocument) + references TypeDocument; + + alter table Document + add constraint FK3737353B51427EB0 + foreign key (specimen) + references Specimen; + + alter table Document + add constraint FK3737353B3ED66D5C + foreign key (campagne) + references Campagne; + + alter table Document + add constraint FK3737353B8458C838 + foreign key (personne) + references Personne; + + alter table Document + add constraint FK3737353BD9E0906E + foreign key (extraction) + references Extraction; + + alter table Document + add constraint FK3737353BC591F5C8 + foreign key (station) + references Station; + + alter table Document + add constraint FK3737353B20A56C82 + foreign key (purification) + references Purification; + + alter table Document + add constraint FK3737353B767DEA02 + foreign key (lot) + references Lot; + + alter table Document + add constraint FK3737353B8923169C + foreign key (resultatTestBio) + references TestBio; + + alter table Document + add constraint FK3737353B20FEEDAC + foreign key (molecule) + references Molecule; + + -- END OF SCHEMA 1.1 + + -- MIGRATION FROM SCHEMA 1.1 TO 1.2 + + -- DocumentContent (05/05/2014) + create table DocumentContent ( + idDocumentContent int4 not null, + fileContent bytea not null, + tmpDocument int4, + tmpDocumentThumb int4, + primary key (idDocumentContent) + ); + + -- move all file content to new table + insert into DocumentContent (idDocumentContent, fileContent, tmpDocument) + SELECT nextval('hibernate_sequence'), fileContent, idDocument from document; + -- move all thumbnail content to new table + insert into DocumentContent (idDocumentContent, fileContent, tmpDocumentThumb) + SELECT nextval('hibernate_sequence'), fileContentThumb, idDocument FROM document where fileContentThumb is not NULL; + + -- link documentcontent to document + alter table Document add column fileContent_idDocumentContent int4; + alter table Document add column fileContentThumb_idDocumentContent int4; + + update Document SET fileContent_idDocumentContent = subquery.idDocumentContent + FROM (SELECT idDocumentContent, tmpDocument FROM DocumentContent) AS subquery + WHERE subquery.tmpDocument = Document.idDocument; + update Document SET fileContentThumb_idDocumentContent = subquery.idDocumentContent + FROM (SELECT idDocumentContent, tmpDocumentThumb FROM DocumentContent) AS subquery + WHERE subquery.tmpDocumentThumb = Document.idDocument; + + alter table Document + alter column fileContent_idDocumentContent set not null; + + alter table Document + add constraint FK_3l4n85rsmw88bewfx57o7gg9g + foreign key (fileContent_idDocumentContent) + references DocumentContent; + + alter table Document + add constraint FK_mphot3xs24tg4u5na1bgo1h85 + foreign key (fileContentThumb_idDocumentContent) + references DocumentContent; + + -- clean + alter table Document drop column fileContent; + alter table Document drop column fileContentThumb; + alter table DocumentContent drop column tmpDocument; + alter table DocumentContent drop column tmpDocumentThumb; + + -- END OF MIGRATION FROM SCHEMA 1.1 TO 1.2 +COMMIT; \ No newline at end of file Added: trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/create_db.sql =================================================================== --- trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/create_db.sql (rev 0) +++ trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/create_db.sql 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,29 @@ +--- +-- #%L +-- Cantharella :: Data +-- $Id: create_db.sql 133 2013-02-19 11:02:25Z acheype $ +-- $HeadURL: https://svn.codelutin.com/cantharella/trunk/cantharella.data/src/main/sql/c… $ +-- %% +-- 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% +--- +CREATE ROLE cantharella LOGIN PASSWORD 'ctrl4'; +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 Added: trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/dev_update_1.0_to_1.1.sql =================================================================== --- trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/dev_update_1.0_to_1.1.sql (rev 0) +++ trunk/docker/cantharella-db/docker-entrypoint-initdb.d/sql/dev_update_1.0_to_1.1.sql 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,174 @@ +--- +-- #%L +-- Cantharella :: Data +-- $Id: dev_update_1.0_to_1.1.sql 211 2013-04-30 07:31:44Z acheype $ +-- $HeadURL: https://svn.codelutin.com/cantharella/trunk/cantharella.data/src/main/sql/d… $ +-- %% +-- Copyright (C) 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% +--- +-- Mise à jour à appliquer à la base de données +-- pour les modifications effectuées pendant le développement + + +BEGIN; +-- Documents (16/11/2012) - update (25/03/2013) + create table TypeDocument ( + idTypeDocument int4 not null, + description text not null, + domaine varchar(60) not null, + nom varchar(60) not null unique, + primary key (idTypeDocument), + unique (nom) + ); + +-- Molecules (07/01/2013) + create table Molecule ( + idMolecule int4 not null, + complement text, + familleChimique varchar(60), + formuleBrute varchar(60) not null, + formuleDevMol text, + identifieePar varchar(60), + masseMolaire numeric(9, 4) check (masseMolaire<=99999 AND masseMolaire>=0), + nomCommun varchar(100), + nomIupca varchar(255), + nouvMolecul boolean not null, + publiOrigine text, + campagne_idCampagne int4, + createur_idPersonne int4 not null, + primary key (idMolecule) + ); + + create table MoleculeProvenance ( + id int4 not null, + pourcentage numeric(9, 4) check (pourcentage>=0 AND pourcentage<=100), + molecule_idMolecule int4 not null, + produit_id int4 not null, + primary key (id) + ); + + alter table Molecule + add constraint FKEC979EA61AA103F8 + foreign key (campagne_idCampagne) + references Campagne; + + alter table Molecule + add constraint FKEC979EA6822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table MoleculeProvenance + add constraint FK8B39E567F44F1B20 + foreign key (molecule_idMolecule) + references Molecule; + + alter table MoleculeProvenance + add constraint FK8B39E567FE19187A + foreign key (produit_id) + references Produit; + + create sequence molecule_sequence; + +-- Document (12/02/2013) + create table Document ( + idDocument int4 not null, + contrainteLegale varchar(100), + dateCreation date not null, + description text, + editeur varchar(100) not null, + fileContent bytea, + fileContentThumb bytea, + fileMimetype varchar(60), + fileName varchar(60) not null, + langue varchar(2), + titre varchar(100) not null, + ajoutePar_idPersonne int4 not null, + createur_idPersonne int4 not null, + typeDocument_idTypeDocument int4 not null, + specimen int4, + campagne int4, + personne int4, + extraction int4, + station int4, + purification int4, + lot int4, + resultatTestBio int4, + molecule int4, + primary key (idDocument) + ); + + alter table Document + add constraint FK3737353B2F46DB31 + foreign key (ajoutePar_idPersonne) + references Personne; + + alter table Document + add constraint FK3737353B822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Document + add constraint FK3737353BBECBA92F + foreign key (typeDocument_idTypeDocument) + references TypeDocument; + + alter table Document + add constraint FK3737353B51427EB0 + foreign key (specimen) + references Specimen; + + alter table Document + add constraint FK3737353B3ED66D5C + foreign key (campagne) + references Campagne; + + alter table Document + add constraint FK3737353B8458C838 + foreign key (personne) + references Personne; + + alter table Document + add constraint FK3737353BD9E0906E + foreign key (extraction) + references Extraction; + + alter table Document + add constraint FK3737353BC591F5C8 + foreign key (station) + references Station; + + alter table Document + add constraint FK3737353B20A56C82 + foreign key (purification) + references Purification; + + alter table Document + add constraint FK3737353B767DEA02 + foreign key (lot) + references Lot; + + alter table Document + add constraint FK3737353B8923169C + foreign key (resultatTestBio) + references TestBio; + + alter table Document + add constraint FK3737353B20FEEDAC + foreign key (molecule) + references Molecule; + +COMMIT; \ No newline at end of file Added: trunk/docker/cantharella-web/Dockerfile =================================================================== --- trunk/docker/cantharella-web/Dockerfile (rev 0) +++ trunk/docker/cantharella-web/Dockerfile 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,5 @@ +FROM tomcat:6.0.53-jre7 +MAINTAINER Adrien Cheype <adrien.cheype(a)ird.fr> + +RUN rm -rf /usr/local/tomcat/webapps/* +COPY ./cantharella.war /usr/local/tomcat/webapps/ROOT.war \ No newline at end of file Added: trunk/docker/docker-compose.yml =================================================================== --- trunk/docker/docker-compose.yml (rev 0) +++ trunk/docker/docker-compose.yml 2017-08-03 01:32:51 UTC (rev 277) @@ -0,0 +1,21 @@ +version: '3' +services: + tomcat: + container_name: cantharella-web + build: ./cantharella-web + image: acheype/cantharella-web + ports: + - "80:8080" + links: + - "postgres" + + postgres: + container_name: cantharella-db + build: ./cantharella-db + image: acheype/cantharella-db + volumes: + - /data/postgresql:/var/lib/postgresql/data + ports: + - "5432:5432" + environment: + - POSTGRES_PASSWORD=CHANGE_PASSWORD \ No newline at end of file Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/pom.xml 2017-08-03 01:32:51 UTC (rev 277) @@ -10,7 +10,7 @@ <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2.1-SNAPSHOT</version> + <version>1.2.2</version> <packaging>pom</packaging> <name>Cantharella</name> <description>Pharmacochemical database of natural substances</description> Modified: trunk/sql/cantharella_schema_1.2.sql =================================================================== --- trunk/cantharella.data/src/main/sql/cantharella_schema_1.2.sql 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/sql/cantharella_schema_1.2.sql 2017-08-03 01:32:51 UTC (rev 277) @@ -23,6 +23,713 @@ -- insert once connected to cantharella database with the user cantharella BEGIN; + + -- SCHEMA 1.1 + + create table Campagne ( + idCampagne int4 not null, + codePays varchar(255) not null, + complement text, + dateDeb date not null, + dateFin date not null, + mentionLegale text, + nom varchar(255) unique not null, + programme varchar(255), + createur_idPersonne int4 not null, + primary key (idCampagne) + ); + + create table CampagneGroupeDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idCampagne int4 not null, + pk2_idGroupe int4 not null, + primary key (pk1_idCampagne, pk2_idGroupe) + ); + + create table CampagnePersonneDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idCampagne int4 not null, + pk2_idPersonne int4 not null, + primary key (pk1_idCampagne, pk2_idPersonne) + ); + + create table CampagnePersonneParticipant ( + complement text, + pk1_idCampagne int4 not null, + pk2_idPersonne int4 not null, + primary key (pk1_idCampagne, pk2_idPersonne) + ); + + create table Campagne_Station ( + campagnes_idCampagne int4 not null, + stations_idStation int4 not null + ); + + create table ErreurTestBio ( + idErreurTest int4 not null, + description text not null, + nom varchar(255) not null, + primary key (idErreurTest), + unique (nom) + ); + + create table Extraction ( + idExtraction int4 not null, + complement text, + date date not null, + masseDepart numeric(9, 4), + ref varchar(255) unique not null, + createur_idPersonne int4 not null, + lot_idLot int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodeExtraction int4 not null, + primary key (idExtraction) + ); + + create table Extrait ( + id int4 not null, + extraction_idExtraction int4 not null, + typeExtrait_idTypeExtrait int4 not null, + primary key (id) + ); + + create table Fraction ( + indice varchar(255) not null, + id int4 not null, + purification_idPurification int4 not null, + primary key (id) + ); + + create table Groupe ( + idGroupe int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idGroupe) + ); + + create table Lot ( + idLot int4 not null, + complement text, + dateRecolte date not null, + echantillonColl bool not null, + echantillonIdent bool not null, + echantillonPhylo bool not null, + masseFraiche numeric(9, 4), + masseSeche numeric(9, 4), + ref varchar(255) unique not null, + campagne_idCampagne int4 not null, + createur_idPersonne int4 not null, + partie_idPartie int4, + specimenRef_idSpecimen int4 not null, + station_idStation int4 not null, + primary key (idLot) + ); + + create table LotGroupeDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk1_idLot int4 not null, + pk2_idGroupe int4 not null, + primary key (pk1_idLot, pk2_idGroupe) + ); + + create table LotPersonneDroits ( + droitExtrait bool, + droitPuri bool, + droitRecolte bool, + droitTestBio bool, + pk2_idPersonne int4 not null, + pk1_idLot int4 not null, + primary key (pk1_idLot, pk2_idPersonne) + ); + + create table MethodeExtraction ( + idMethodeExtraction int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idMethodeExtraction) + ); + + create table MethodePurification ( + idMethodePurification int4 not null, + description text not null, + nom varchar(255) unique not null, + primary key (idMethodePurification) + ); + + create table MethodeTestBio ( + idMethodeTest int4 not null, + cible varchar(255) unique not null, + critereActivite varchar(255) not null, + description text not null, + domaine varchar(255) not null, + nom varchar(255) unique not null, + uniteResultat varchar(255) not null, + valeurMesuree varchar(255) not null, + primary key (idMethodeTest) + ); + + create table ParamMethoPuri ( + idParamMethoPuri int4 not null, + description text not null, + index int4 not null, + nom varchar(255) not null, + methodePurification_idMethodePurification int4 not null, + primary key (idParamMethoPuri) + ); + + create table ParamMethoPuriEffectif ( + idParamMethoPuriEffectif int4 not null, + valeur varchar(255), + param_idParamMethoPuri int4 not null, + purification_idPurification int4 not null, + primary key (idParamMethoPuriEffectif) + ); + + create table Partie ( + idPartie int4 not null, + nom varchar(255) unique not null, + primary key (idPartie) + ); + + create table Personne ( + idPersonne int4 not null, + adressePostale text not null, + codePays varchar(255) not null, + codePostal varchar(255) not null, + courriel varchar(255) unique not null, + fax varchar(255), + fonction varchar(255), + nom varchar(255) not null, + organisme varchar(255) not null, + prenom varchar(255) not null, + tel varchar(255), + ville varchar(255) not null, + primary key (idPersonne), + unique (nom, prenom) + ); + + create table Produit ( + id int4 not null, + masseObtenue numeric(9, 4), + ref varchar(255) unique not null, + primary key (id) + ); + + create table Purification ( + idPurification int4 not null, + complement text, + confidentiel bool not null, + date date not null, + dateConfidentialite date, + masseDepart numeric(9, 4), + ref varchar(255) unique not null, + createur_idPersonne int4 not null, + lotSource_idLot int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodePurification int4 not null, + produit_id int4 not null, + primary key (idPurification) + ); + + create table ResultatTestBio ( + id int4 not null, + concMasse numeric(9, 4), + estActif bool, + produitTemoin varchar(255), + repere varchar(255) not null, + stade int4, + typeResultat int4 not null, + uniteConcMasse int4, + valeur numeric(9, 4), + erreur_idErreurTest int4, + produit_id int4, + testBio_idTestBio int4 not null, + typeExtraitSource_idTypeExtrait int4, + primary key (id) + ); + + create table Specimen ( + idSpecimen int4 not null, + complement text, + dateDepot date, + embranchement varchar(255) not null, + espece varchar(255), + famille varchar(255), + genre varchar(255), + lieuDepot varchar(255), + numDepot varchar(255), + ref varchar(255) unique not null, + sousEspece varchar(255), + typeOrganisme int4, + variete varchar(255), + createur_idPersonne int4 not null, + identificateur_idPersonne int4, + station_idStation int4, + primary key (idSpecimen) + ); + + create table Station ( + idStation int4 not null, + codePays varchar(255) not null, + complement text, + latitude varchar(255), + localite varchar(255), + longitude varchar(255), + nom varchar(255) unique not null, + referentiel int4, + createur_idPersonne int4 not null, + primary key (idStation) + ); + + create table TestBio ( + idTestBio int4 not null, + complement text, + concMasseDefaut numeric(9, 4), + confidentiel bool not null, + date date not null, + dateConfidentialite date, + organismeTesteur varchar(255) not null, + ref varchar(255) unique not null, + stadeDefaut int4, + uniteConcMasseDefaut int4, + createur_idPersonne int4 not null, + manipulateur_idPersonne int4 not null, + methode_idMethodeTest int4 not null, + primary key (idTestBio) + ); + + create table TypeExtrait ( + idTypeExtrait int4 not null, + description text not null, + initiales varchar(255) unique not null, + methodeExtraction_idMethodeExtraction int4 not null, + primary key (idTypeExtrait) + ); + + create table Utilisateur ( + dateValiditeCompte date, + estValide bool not null, + passwordHash varchar(255) not null, + typeDroit int4 not null, + idPersonne int4 not null, + groupe_idGroupe int4, + primary key (idPersonne) + ); + + alter table Campagne + add constraint FKFB835E7E822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table CampagneGroupeDroits + add constraint FK3AFBE26B905CBAAF + foreign key (pk2_idGroupe) + references Groupe; + + alter table CampagneGroupeDroits + add constraint FK3AFBE26B975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneDroits + add constraint FK81782471975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneDroits + add constraint FK81782471E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table CampagnePersonneParticipant + add constraint FK72EE0469975C19C0 + foreign key (pk1_idCampagne) + references Campagne; + + alter table CampagnePersonneParticipant + add constraint FK72EE0469E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table Campagne_Station + add constraint FK61A84053557B2C21 + foreign key (campagnes_idCampagne) + references Campagne; + + alter table Campagne_Station + add constraint FK61A840531AE541CD + foreign key (stations_idStation) + references Station; + + alter table Extraction + add constraint FKA39DBC077106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table Extraction + add constraint FKA39DBC07822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Extraction + add constraint FKA39DBC07F7C7FFC0 + foreign key (methode_idMethodeExtraction) + references MethodeExtraction; + + alter table Extraction + add constraint FKA39DBC07AE638899 + foreign key (lot_idLot) + references Lot; + + alter table Extrait + add constraint FK156B751B9547CE24 + foreign key (id) + references Produit; + + alter table Extrait + add constraint FK156B751B252FD5C9 + foreign key (typeExtrait_idTypeExtrait) + references TypeExtrait; + + alter table Extrait + add constraint FK156B751BE48A1121 + foreign key (extraction_idExtraction) + references Extraction; + + alter table Fraction + add constraint FKA14826229547CE24 + foreign key (id) + references Produit; + + alter table Fraction + add constraint FKA1482622859CB52B + foreign key (purification_idPurification) + references Purification; + + alter table Lot + add constraint FK12B311AA103F8 + foreign key (campagne_idCampagne) + references Campagne; + + alter table Lot + add constraint FK12B3168370809 + foreign key (partie_idPartie) + references Partie; + + alter table Lot + add constraint FK12B31822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Lot + add constraint FK12B31DDF1E8FF + foreign key (specimenRef_idSpecimen) + references Specimen; + + alter table Lot + add constraint FK12B31CBED0F02 + foreign key (station_idStation) + references Station; + + alter table LotGroupeDroits + add constraint FK9AC53A9E905CBAAF + foreign key (pk2_idGroupe) + references Groupe; + + alter table LotGroupeDroits + add constraint FK9AC53A9E87AF0F1E + foreign key (pk1_idLot) + references Lot; + + alter table LotPersonneDroits + add constraint FK144C3BE4E49019FB + foreign key (pk2_idPersonne) + references Personne; + + alter table LotPersonneDroits + add constraint FK144C3BE487AF0F1E + foreign key (pk1_idLot) + references Lot; + + alter table ParamMethoPuri + add constraint FK1476479225A42085 + foreign key (methodePurification_idMethodePurification) + references MethodePurification; + + alter table ParamMethoPuriEffectif + add constraint FK8F7FA020B4F23AD1 + foreign key (param_idParamMethoPuri) + references ParamMethoPuri; + + alter table ParamMethoPuriEffectif + add constraint FK8F7FA020859CB52B + foreign key (purification_idPurification) + references Purification; + + create index courriel on Personne (courriel); + + alter table Purification + add constraint FKD1727611FE19187A + foreign key (produit_id) + references Produit; + + alter table Purification + add constraint FKD17276117106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table Purification + add constraint FKD1727611822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Purification + add constraint FKD1727611626E4F54 + foreign key (methode_idMethodePurification) + references MethodePurification; + + alter table Purification + add constraint FKD1727611C4943FB4 + foreign key (lotSource_idLot) + references Lot; + + create index typeResultat on ResultatTestBio (typeResultat); + + alter table ResultatTestBio + add constraint FK5DFD5BC6FE19187A + foreign key (produit_id) + references Produit; + + alter table ResultatTestBio + add constraint FK5DFD5BC65033BE68 + foreign key (testBio_idTestBio) + references TestBio; + + alter table ResultatTestBio + add constraint FK5DFD5BC64B1883E5 + foreign key (erreur_idErreurTest) + references ErreurTestBio; + + alter table ResultatTestBio + add constraint FK5DFD5BC6ABE26DE4 + foreign key (typeExtraitSource_idTypeExtrait) + references TypeExtrait; + + alter table Specimen + add constraint FK84B96728822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Specimen + add constraint FK84B96728D2CE02CA + foreign key (identificateur_idPersonne) + references Personne; + + alter table Specimen + add constraint FK84B96728CBED0F02 + foreign key (station_idStation) + references Station; + + alter table Station + add constraint FKF2249914822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F67106663B + foreign key (manipulateur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F6822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table TestBio + add constraint FKE6F36F67DBA1C52 + foreign key (methode_idMethodeTest) + references MethodeTestBio; + + alter table TypeExtrait + add constraint FK40F3D8811D52927 + foreign key (methodeExtraction_idMethodeExtraction) + references MethodeExtraction; + + create index estValide on Utilisateur (estValide); + + create index typeDroit on Utilisateur (typeDroit); + + alter table Utilisateur + add constraint FK407FDB6370C95760 + foreign key (groupe_idGroupe) + references Groupe; + + alter table Utilisateur + add constraint FK407FDB63A1338A53 + foreign key (idPersonne) + references Personne; + + create sequence hibernate_sequence; + + -- Documents (16/11/2012) - update (25/03/2013) + create table TypeDocument ( + idTypeDocument int4 not null, + description text not null, + domaine varchar(60) not null, + nom varchar(60) not null unique, + primary key (idTypeDocument), + unique (nom) + ); + + -- Molecules (07/01/2013) + create table Molecule ( + idMolecule int4 not null, + complement text, + familleChimique varchar(60), + formuleBrute varchar(60) not null, + formuleDevMol text, + identifieePar varchar(60), + masseMolaire numeric(9, 4) check (masseMolaire<=99999 AND masseMolaire>=0), + nomCommun varchar(100), + nomIupca varchar(255), + nouvMolecul boolean not null, + publiOrigine text, + campagne_idCampagne int4, + createur_idPersonne int4 not null, + primary key (idMolecule) + ); + + create table MoleculeProvenance ( + id int4 not null, + pourcentage numeric(9, 4) check (pourcentage>=0 AND pourcentage<=100), + molecule_idMolecule int4 not null, + produit_id int4 not null, + primary key (id) + ); + + alter table Molecule + add constraint FKEC979EA61AA103F8 + foreign key (campagne_idCampagne) + references Campagne; + + alter table Molecule + add constraint FKEC979EA6822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table MoleculeProvenance + add constraint FK8B39E567F44F1B20 + foreign key (molecule_idMolecule) + references Molecule; + + alter table MoleculeProvenance + add constraint FK8B39E567FE19187A + foreign key (produit_id) + references Produit; + + create sequence molecule_sequence; + + -- Document (12/02/2013) + create table Document ( + idDocument int4 not null, + contrainteLegale varchar(100), + dateCreation date not null, + description text, + editeur varchar(100) not null, + fileContent bytea, + fileContentThumb bytea, + fileMimetype varchar(60), + fileName varchar(60) not null, + langue varchar(2), + titre varchar(100) not null, + ajoutePar_idPersonne int4 not null, + createur_idPersonne int4 not null, + typeDocument_idTypeDocument int4 not null, + specimen int4, + campagne int4, + personne int4, + extraction int4, + station int4, + purification int4, + lot int4, + resultatTestBio int4, + molecule int4, + primary key (idDocument) + ); + + alter table Document + add constraint FK3737353B2F46DB31 + foreign key (ajoutePar_idPersonne) + references Personne; + + alter table Document + add constraint FK3737353B822055B9 + foreign key (createur_idPersonne) + references Personne; + + alter table Document + add constraint FK3737353BBECBA92F + foreign key (typeDocument_idTypeDocument) + references TypeDocument; + + alter table Document + add constraint FK3737353B51427EB0 + foreign key (specimen) + references Specimen; + + alter table Document + add constraint FK3737353B3ED66D5C + foreign key (campagne) + references Campagne; + + alter table Document + add constraint FK3737353B8458C838 + foreign key (personne) + references Personne; + + alter table Document + add constraint FK3737353BD9E0906E + foreign key (extraction) + references Extraction; + + alter table Document + add constraint FK3737353BC591F5C8 + foreign key (station) + references Station; + + alter table Document + add constraint FK3737353B20A56C82 + foreign key (purification) + references Purification; + + alter table Document + add constraint FK3737353B767DEA02 + foreign key (lot) + references Lot; + + alter table Document + add constraint FK3737353B8923169C + foreign key (resultatTestBio) + references TestBio; + + alter table Document + add constraint FK3737353B20FEEDAC + foreign key (molecule) + references Molecule; + + -- END OF SCHEMA 1.1 + + -- MIGRATION FROM SCHEMA 1.1 TO 1.2 + -- DocumentContent (05/05/2014) create table DocumentContent ( idDocumentContent int4 not null, @@ -68,4 +775,6 @@ alter table Document drop column fileContentThumb; alter table DocumentContent drop column tmpDocument; alter table DocumentContent drop column tmpDocumentThumb; + + -- END OF MIGRATION FROM SCHEMA 1.1 TO 1.2 COMMIT; \ No newline at end of file Deleted: trunk/sql/init.sql =================================================================== --- trunk/cantharella.data/src/main/sql/init.sql 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/sql/init.sql 2017-08-03 01:32:51 UTC (rev 277) @@ -1,29 +0,0 @@ ---- --- #%L --- Cantharella :: Data --- $Id$ --- $HeadURL$ --- %% --- 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% ---- -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 \ No newline at end of file Modified: trunk/src/site/rst/index.rst =================================================================== --- trunk/src/site/rst/index.rst 2014-05-07 08:30:33 UTC (rev 276) +++ trunk/src/site/rst/index.rst 2017-08-03 01:32:51 UTC (rev 277) @@ -47,15 +47,15 @@ Screenshots ----------- -.. figure:: images/Home.png +.. figure:: images/Home.jpg Home -.. figure:: images/Station.png +.. figure:: images/Station.jpg Location form -.. figure:: images/Extraction.png +.. figure:: images/Extraction.jpg Extraction form

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r276 - in trunk: . cantharella.data cantharella.service cantharella.utils cantharella.web
by maven-release＠users.forge.codelutin.com May 7, 2014

May 7, 2014

Author: maven-release Date: 2014-05-07 10:30:33 +0200 (Wed, 07 May 2014) New Revision: 276 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/276 Log: [maven-release-plugin] prepare for next development iteration Modified: trunk/cantharella.data/pom.xml trunk/cantharella.service/pom.xml trunk/cantharella.utils/pom.xml trunk/cantharella.web/pom.xml trunk/pom.xml Modified: trunk/cantharella.data/pom.xml =================================================================== --- trunk/cantharella.data/pom.xml 2014-05-07 08:30:25 UTC (rev 275) +++ trunk/cantharella.data/pom.xml 2014-05-07 08:30:33 UTC (rev 276) @@ -5,7 +5,7 @@ <parent> <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2</version> + <version>1.2.1-SNAPSHOT</version> </parent> <artifactId>cantharella.data</artifactId> Modified: trunk/cantharella.service/pom.xml =================================================================== --- trunk/cantharella.service/pom.xml 2014-05-07 08:30:25 UTC (rev 275) +++ trunk/cantharella.service/pom.xml 2014-05-07 08:30:33 UTC (rev 276) @@ -5,7 +5,7 @@ <parent> <artifactId>cantharella</artifactId> <groupId>nc.ird</groupId> - <version>1.2</version> + <version>1.2.1-SNAPSHOT</version> </parent> <artifactId>cantharella.service</artifactId> Modified: trunk/cantharella.utils/pom.xml =================================================================== --- trunk/cantharella.utils/pom.xml 2014-05-07 08:30:25 UTC (rev 275) +++ trunk/cantharella.utils/pom.xml 2014-05-07 08:30:33 UTC (rev 276) @@ -5,7 +5,7 @@ <parent> <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2</version> + <version>1.2.1-SNAPSHOT</version> </parent> <artifactId>cantharella.utils</artifactId> Modified: trunk/cantharella.web/pom.xml =================================================================== --- trunk/cantharella.web/pom.xml 2014-05-07 08:30:25 UTC (rev 275) +++ trunk/cantharella.web/pom.xml 2014-05-07 08:30:33 UTC (rev 276) @@ -5,7 +5,7 @@ <parent> <artifactId>cantharella</artifactId> <groupId>nc.ird</groupId> - <version>1.2</version> + <version>1.2.1-SNAPSHOT</version> </parent> <artifactId>cantharella.web</artifactId> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-05-07 08:30:25 UTC (rev 275) +++ trunk/pom.xml 2014-05-07 08:30:33 UTC (rev 276) @@ -10,7 +10,7 @@ <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2</version> + <version>1.2.1-SNAPSHOT</version> <packaging>pom</packaging> <name>Cantharella</name> <description>Pharmacochemical database of natural substances</description> @@ -67,9 +67,9 @@ </developers> <scm> - <url>https://svn.codelutin.com/cantharella/tags/cantharella-1.2</url> - <connection>scm:svn:https://svn.codelutin.com/cantharella/tags/cantharella-1.2</connection> - <developerConnection>scm:svn:https://svn.codelutin.com/cantharella/tags/cantharella-1.2</developerConnection> + <url>https://svn.codelutin.com/cantharella/trunk</url> + <connection>scm:svn:https://svn.codelutin.com/cantharella/trunk</connection> + <developerConnection>scm:svn:https://svn.codelutin.com/cantharella/trunk</developerConnection> </scm> <distributionManagement>

1 0

r275 - tags
by maven-release＠users.forge.codelutin.com May 7, 2014

May 7, 2014

Author: maven-release Date: 2014-05-07 10:30:25 +0200 (Wed, 07 May 2014) New Revision: 275 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/275 Log: [maven-release-plugin] copy for tag cantharella-1.2 Added: tags/cantharella-1.2/

1 0

r274 - in trunk: . cantharella.data cantharella.service cantharella.utils cantharella.web
by maven-release＠users.forge.codelutin.com May 7, 2014

May 7, 2014

Author: maven-release Date: 2014-05-07 10:30:08 +0200 (Wed, 07 May 2014) New Revision: 274 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/274 Log: [maven-release-plugin] prepare release cantharella-1.2 Modified: trunk/cantharella.data/pom.xml trunk/cantharella.service/pom.xml trunk/cantharella.utils/pom.xml trunk/cantharella.web/pom.xml trunk/pom.xml Modified: trunk/cantharella.data/pom.xml =================================================================== --- trunk/cantharella.data/pom.xml 2014-05-07 08:28:03 UTC (rev 273) +++ trunk/cantharella.data/pom.xml 2014-05-07 08:30:08 UTC (rev 274) @@ -5,7 +5,7 @@ <parent> <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2-SNAPSHOT</version> + <version>1.2</version> </parent> <artifactId>cantharella.data</artifactId> Modified: trunk/cantharella.service/pom.xml =================================================================== --- trunk/cantharella.service/pom.xml 2014-05-07 08:28:03 UTC (rev 273) +++ trunk/cantharella.service/pom.xml 2014-05-07 08:30:08 UTC (rev 274) @@ -5,7 +5,7 @@ <parent> <artifactId>cantharella</artifactId> <groupId>nc.ird</groupId> - <version>1.2-SNAPSHOT</version> + <version>1.2</version> </parent> <artifactId>cantharella.service</artifactId> Modified: trunk/cantharella.utils/pom.xml =================================================================== --- trunk/cantharella.utils/pom.xml 2014-05-07 08:28:03 UTC (rev 273) +++ trunk/cantharella.utils/pom.xml 2014-05-07 08:30:08 UTC (rev 274) @@ -5,7 +5,7 @@ <parent> <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2-SNAPSHOT</version> + <version>1.2</version> </parent> <artifactId>cantharella.utils</artifactId> Modified: trunk/cantharella.web/pom.xml =================================================================== --- trunk/cantharella.web/pom.xml 2014-05-07 08:28:03 UTC (rev 273) +++ trunk/cantharella.web/pom.xml 2014-05-07 08:30:08 UTC (rev 274) @@ -5,7 +5,7 @@ <parent> <artifactId>cantharella</artifactId> <groupId>nc.ird</groupId> - <version>1.2-SNAPSHOT</version> + <version>1.2</version> </parent> <artifactId>cantharella.web</artifactId> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-05-07 08:28:03 UTC (rev 273) +++ trunk/pom.xml 2014-05-07 08:30:08 UTC (rev 274) @@ -10,7 +10,7 @@ <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2-SNAPSHOT</version> + <version>1.2</version> <packaging>pom</packaging> <name>Cantharella</name> <description>Pharmacochemical database of natural substances</description> @@ -67,9 +67,9 @@ </developers> <scm> - <url>https://svn.codelutin.com/cantharella/trunk</url> - <connection>scm:svn:https://svn.codelutin.com/cantharella/trunk</connection> - <developerConnection>scm:svn:https://svn.codelutin.com/cantharella/trunk</developerConnection> + <url>https://svn.codelutin.com/cantharella/tags/cantharella-1.2</url> + <connection>scm:svn:https://svn.codelutin.com/cantharella/tags/cantharella-1.2</connection> + <developerConnection>scm:svn:https://svn.codelutin.com/cantharella/tags/cantharella-1.2</developerConnection> </scm> <distributionManagement>

1 0

r273 - trunk
by echatellier＠users.forge.codelutin.com May 7, 2014

May 7, 2014

Author: echatellier Date: 2014-05-07 10:28:03 +0200 (Wed, 07 May 2014) New Revision: 273 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/273 Log: Fix release Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-05-07 08:25:45 UTC (rev 272) +++ trunk/pom.xml 2014-05-07 08:28:03 UTC (rev 273) @@ -67,14 +67,14 @@ </developers> <scm> - <url>http://svn.codelutin.com/cantharella/trunk</url> - <connection>scm:svn:http://svn.codelutin.com/cantharella/trunk</connection> - <developerConnection>scm:svn:http://svn.codelutin.com/cantharella/trunk</developerConnection> + <url>https://svn.codelutin.com/cantharella/trunk</url> + <connection>scm:svn:https://svn.codelutin.com/cantharella/trunk</connection> + <developerConnection>scm:svn:https://svn.codelutin.com/cantharella/trunk</developerConnection> </scm> <distributionManagement> <site> - <id>${platform}</id> + <id>doc.${platform}</id> <url>${our.site.repository}/${projectId}</url> </site> </distributionManagement>

1 0

r272 - in trunk: . cantharella.data cantharella.service cantharella.utils cantharella.web
by maven-release＠users.forge.codelutin.com May 7, 2014

May 7, 2014

Author: maven-release Date: 2014-05-07 10:25:45 +0200 (Wed, 07 May 2014) New Revision: 272 Url: http://forge.codelutin.com/projects/cantharella/repository/revisions/272 Log: [maven-release-plugin] rollback the release of cantharella-1.2 Modified: trunk/cantharella.data/pom.xml trunk/cantharella.service/pom.xml trunk/cantharella.utils/pom.xml trunk/cantharella.web/pom.xml trunk/pom.xml Modified: trunk/cantharella.data/pom.xml =================================================================== --- trunk/cantharella.data/pom.xml 2014-05-07 08:25:10 UTC (rev 271) +++ trunk/cantharella.data/pom.xml 2014-05-07 08:25:45 UTC (rev 272) @@ -5,7 +5,7 @@ <parent> <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2</version> + <version>1.2-SNAPSHOT</version> </parent> <artifactId>cantharella.data</artifactId> Modified: trunk/cantharella.service/pom.xml =================================================================== --- trunk/cantharella.service/pom.xml 2014-05-07 08:25:10 UTC (rev 271) +++ trunk/cantharella.service/pom.xml 2014-05-07 08:25:45 UTC (rev 272) @@ -5,7 +5,7 @@ <parent> <artifactId>cantharella</artifactId> <groupId>nc.ird</groupId> - <version>1.2</version> + <version>1.2-SNAPSHOT</version> </parent> <artifactId>cantharella.service</artifactId> Modified: trunk/cantharella.utils/pom.xml =================================================================== --- trunk/cantharella.utils/pom.xml 2014-05-07 08:25:10 UTC (rev 271) +++ trunk/cantharella.utils/pom.xml 2014-05-07 08:25:45 UTC (rev 272) @@ -5,7 +5,7 @@ <parent> <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2</version> + <version>1.2-SNAPSHOT</version> </parent> <artifactId>cantharella.utils</artifactId> Modified: trunk/cantharella.web/pom.xml =================================================================== --- trunk/cantharella.web/pom.xml 2014-05-07 08:25:10 UTC (rev 271) +++ trunk/cantharella.web/pom.xml 2014-05-07 08:25:45 UTC (rev 272) @@ -5,7 +5,7 @@ <parent> <artifactId>cantharella</artifactId> <groupId>nc.ird</groupId> - <version>1.2</version> + <version>1.2-SNAPSHOT</version> </parent> <artifactId>cantharella.web</artifactId> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2014-05-07 08:25:10 UTC (rev 271) +++ trunk/pom.xml 2014-05-07 08:25:45 UTC (rev 272) @@ -10,7 +10,7 @@ <groupId>nc.ird</groupId> <artifactId>cantharella</artifactId> - <version>1.2</version> + <version>1.2-SNAPSHOT</version> <packaging>pom</packaging> <name>Cantharella</name> <description>Pharmacochemical database of natural substances</description> @@ -67,9 +67,9 @@ </developers> <scm> - <url>http://svn.codelutin.com/cantharella/tags/cantharella-1.2</url> - <connection>scm:svn:http://svn.codelutin.com/cantharella/tags/cantharella-1.2</connection> - <developerConnection>scm:svn:http://svn.codelutin.com/cantharella/tags/cantharella-1.2</developerConnection> + <url>http://svn.codelutin.com/cantharella/trunk</url> + <connection>scm:svn:http://svn.codelutin.com/cantharella/trunk</connection> + <developerConnection>scm:svn:http://svn.codelutin.com/cantharella/trunk</developerConnection> </scm> <distributionManagement>

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