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r781 - trunk
by tchemit＠users.forge.codelutin.com 25 Nov '12

25 Nov '12

Author: tchemit Date: 2012-11-25 12:16:13 +0100 (Sun, 25 Nov 2012) New Revision: 781 Url: http://forge.codelutin.com/repositories/revision/echobase/781 Log: fixes #1744: Updates to eugene 2.5.6.1 fixes #1745: Updates to topia 2.7.1 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-11-23 12:09:17 UTC (rev 780) +++ trunk/pom.xml 2012-11-25 11:16:13 UTC (rev 781) @@ -132,8 +132,8 @@  - <eugenePluginVersion>2.5</eugenePluginVersion> - <topiaVersion>2.7</topiaVersion> + <eugenePluginVersion>2.5.6.1</eugenePluginVersion> + <topiaVersion>2.7.1</topiaVersion> <nuitonUtilsVersion>2.6.4</nuitonUtilsVersion> <nuitonI18nVersion>2.5</nuitonI18nVersion> <nuitonWebVersion>1.12-beta-1</nuitonWebVersion>

1 0

r780 - in trunk: . echobase-domain echobase-services echobase-tools echobase-ui
by tchemit＠users.forge.codelutin.com 23 Nov '12

23 Nov '12

Author: tchemit Date: 2012-11-23 13:09:17 +0100 (Fri, 23 Nov 2012) New Revision: 780 Url: http://forge.codelutin.com/repositories/revision/echobase/780 Log: prepare next version Modified: trunk/echobase-domain/pom.xml trunk/echobase-services/pom.xml trunk/echobase-tools/pom.xml trunk/echobase-ui/pom.xml trunk/pom.xml Modified: trunk/echobase-domain/pom.xml =================================================================== --- trunk/echobase-domain/pom.xml 2012-11-23 12:08:18 UTC (rev 779) +++ trunk/echobase-domain/pom.xml 2012-11-23 12:09:17 UTC (rev 780) @@ -9,7 +9,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-services/pom.xml =================================================================== --- trunk/echobase-services/pom.xml 2012-11-23 12:08:18 UTC (rev 779) +++ trunk/echobase-services/pom.xml 2012-11-23 12:09:17 UTC (rev 780) @@ -6,7 +6,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-tools/pom.xml =================================================================== --- trunk/echobase-tools/pom.xml 2012-11-23 12:08:18 UTC (rev 779) +++ trunk/echobase-tools/pom.xml 2012-11-23 12:09:17 UTC (rev 780) @@ -11,7 +11,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-ui/pom.xml =================================================================== --- trunk/echobase-ui/pom.xml 2012-11-23 12:08:18 UTC (rev 779) +++ trunk/echobase-ui/pom.xml 2012-11-23 12:09:17 UTC (rev 780) @@ -7,7 +7,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-11-23 12:08:18 UTC (rev 779) +++ trunk/pom.xml 2012-11-23 12:09:17 UTC (rev 780) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2</version> <modules> <module>echobase-domain</module>

1 0

r779 - trunk
by tchemit＠users.forge.codelutin.com 23 Nov '12

23 Nov '12

Author: tchemit Date: 2012-11-23 13:08:18 +0100 (Fri, 23 Nov 2012) New Revision: 779 Url: http://forge.codelutin.com/repositories/revision/echobase/779 Log: fixes #1734: Updates to nuiton-utils 2.6.4 fixes #1735: Updates to mavenpom 3.4.4 fixes #1736: Updates to nuitonweb 1.12-beta-1 fixes #1737: Updates to struts 2.3.7 fixes #1738: Updates to jquery-struts2 3.4.0 fixes #1739: Updates to slf4j 1.7.2 Modified: trunk/pom.xml Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-11-23 12:03:48 UTC (rev 778) +++ trunk/pom.xml 2012-11-23 12:08:18 UTC (rev 779) @@ -6,7 +6,7 @@ <parent> <groupId>org.nuiton</groupId> <artifactId>mavenpom4redmine</artifactId> - <version>3.4.3</version> + <version>3.4.4</version> </parent> <groupId>fr.ifremer</groupId> @@ -134,15 +134,15 @@ <eugenePluginVersion>2.5</eugenePluginVersion> <topiaVersion>2.7</topiaVersion> - <nuitonUtilsVersion>2.6.3</nuitonUtilsVersion> + <nuitonUtilsVersion>2.6.4</nuitonUtilsVersion> <nuitonI18nVersion>2.5</nuitonI18nVersion> - <nuitonWebVersion>1.11</nuitonWebVersion> + <nuitonWebVersion>1.12-beta-1</nuitonWebVersion> <msaccessImporterVersion>1.4.1</msaccessImporterVersion> - <struts2Version>2.3.4.1</struts2Version> - <jqueryPluginVersion>3.3.3</jqueryPluginVersion> + <struts2Version>2.3.7</struts2Version> + <jqueryPluginVersion>3.4.0</jqueryPluginVersion> <h2Version>1.3.168</h2Version> <postgresqlVersion>9.1-901-1.jdbc4</postgresqlVersion> - <slf4jVersion>1.7.1</slf4jVersion> + <slf4jVersion>1.7.2</slf4jVersion> <jackcessVersion>1.2.7</jackcessVersion> <hibernateVersion>3.6.10.Final</hibernateVersion>

1 0

r778 - in trunk/echobase-tools: . src/test/echobase-2012-04-12 src/test/java/fr/ifremer/echobase/tools
by tchemit＠users.forge.codelutin.com 23 Nov '12

23 Nov '12

Author: tchemit Date: 2012-11-23 13:03:48 +0100 (Fri, 23 Nov 2012) New Revision: 778 Url: http://forge.codelutin.com/repositories/revision/echobase/778 Log: fixes #1733: Ne plus d?\195?\169ployer les fichiers de donn?\195?\169es lors d'une nouvelle version Removed: trunk/echobase-tools/src/test/echobase-2012-04-12/legacy-extraCells-1998_2004.echobase trunk/echobase-tools/src/test/echobase-2012-04-12/legacy-extraCells-2005_2010.echobase Modified: trunk/echobase-tools/pom.xml trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/EchoBaseDbZipCreatorIT.java Modified: trunk/echobase-tools/pom.xml =================================================================== --- trunk/echobase-tools/pom.xml 2012-11-23 12:01:27 UTC (rev 777) +++ trunk/echobase-tools/pom.xml 2012-11-23 12:03:48 UTC (rev 778) @@ -24,10 +24,7 @@ <csvVersion>2012-04-12</csvVersion> <redmine.releaseFiles> - ${basedir}/target/echobase-referentiel-${project.version}.echobase, - ${basedir}/target/echobase-legacyData-${project.version}.echobase, - ${basedir}/target/echobase-legacyData-extraCells-1998_2004-${project.version}.echobase, - ${basedir}/target/echobase-legacyData-extraCells-2005_2010-${project.version}.echobase + ${basedir}/target/echobase-referentiel-${project.version}.echobase </redmine.releaseFiles> </properties> @@ -229,8 +226,7 @@ </configuration> </plugin> - <plugin> -  +  </plugins> </build> </profile> Deleted: trunk/echobase-tools/src/test/echobase-2012-04-12/legacy-extraCells-1998_2004.echobase =================================================================== (Binary files differ) Deleted: trunk/echobase-tools/src/test/echobase-2012-04-12/legacy-extraCells-2005_2010.echobase =================================================================== (Binary files differ) Modified: trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/EchoBaseDbZipCreatorIT.java =================================================================== --- trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/EchoBaseDbZipCreatorIT.java 2012-11-23 12:01:27 UTC (rev 777) +++ trunk/echobase-tools/src/test/java/fr/ifremer/echobase/tools/EchoBaseDbZipCreatorIT.java 2012-11-23 12:03:48 UTC (rev 778) @@ -27,6 +27,7 @@ import org.apache.commons.io.FileUtils; import org.junit.Assert; import org.junit.BeforeClass; +import org.junit.Ignore; import org.junit.Test; import org.nuiton.util.FileUtil; @@ -67,6 +68,7 @@ FileUtil.createDirectoryIfNecessary(dbDesFile); } + @Ignore @Test public void createEchoBaseLegacyDataDb() throws Exception {

1 0

r777 - trunk/src/doc/reunions
by tchemit＠users.forge.codelutin.com 23 Nov '12

23 Nov '12

Author: tchemit Date: 2012-11-23 13:01:27 +0100 (Fri, 23 Nov 2012) New Revision: 777 Url: http://forge.codelutin.com/repositories/revision/echobase/777 Log: last CR Added: trunk/src/doc/reunions/reunion-2012-10-31.txt Added: trunk/src/doc/reunions/reunion-2012-10-31.txt =================================================================== --- trunk/src/doc/reunions/reunion-2012-10-31.txt (rev 0) +++ trunk/src/doc/reunions/reunion-2012-10-31.txt 2012-11-23 12:01:27 UTC (rev 777) @@ -0,0 +1,33 @@ +======== +Echobase +======== + +Mardi 31 octobre 2012 (Ifremer) + +Présents : Mathieu et Tony + +But +=== + +- Validation version 2.0 + +Fait +==== + +- installation dernière version (2.0-rc-1) sur acoustica +- import de toutes les données historiques +- création répertoire pour les scripts R-EchoBase + +Reste à faire +============= + +- Finir la doc d'import (acoustic) +- Vérifier qu'on importe bien des données unsorted même si pas de data. + + +Et la suite ? +============= + +Rien de prévu pour le moment,.. Il y aura peut-être un ou deux jours de +maintenance récupérés sur raptri. + Property changes on: trunk/src/doc/reunions/reunion-2012-10-31.txt ___________________________________________________________________ Added: svn:keywords + Author Date Id Revision HeadURL Added: svn:eol-style + native

1 0

r776 - trunk/echobase-services/src/main/resources/embedded
by tchemit＠users.forge.codelutin.com 23 Nov '12

23 Nov '12

Author: tchemit Date: 2012-11-23 12:15:21 +0100 (Fri, 23 Nov 2012) New Revision: 776 Url: http://forge.codelutin.com/repositories/revision/echobase/776 Log: fixes #1732: Can not start embedded application on Linux OS Modified: trunk/echobase-services/src/main/resources/embedded/startEchobase.sh Modified: trunk/echobase-services/src/main/resources/embedded/startEchobase.sh =================================================================== --- trunk/echobase-services/src/main/resources/embedded/startEchobase.sh 2012-11-11 13:48:26 UTC (rev 775) +++ trunk/echobase-services/src/main/resources/embedded/startEchobase.sh 2012-11-23 11:15:21 UTC (rev 776) @@ -11,7 +11,7 @@ OLDPWD=`pwd` cd `dirname $0` CURRENTPWD=`pwd` -ECHOBASE_OPTS="$JAVA_OPTS -Xms512m -Xmx10242m -Dechobase.log.dir=$CURRENTPWD/logs" +ECHOBASE_OPTS="$JAVA_OPTS -Xms512m -Xmx1024m -Dechobase.log.dir=$CURRENTPWD/logs" java $ECHOBASE_OPTS -jar echobase-ui-${project.version}-embedded.war $* cd "$OLDPWD"

1 0

r775 - in trunk: . echobase-domain echobase-services echobase-tools echobase-ui
by tchemit＠users.forge.codelutin.com 11 Nov '12

11 Nov '12

Author: tchemit Date: 2012-11-11 14:48:26 +0100 (Sun, 11 Nov 2012) New Revision: 775 Url: http://forge.codelutin.com/repositories/revision/echobase/775 Log: pass to rc2 Modified: trunk/echobase-domain/pom.xml trunk/echobase-services/pom.xml trunk/echobase-tools/pom.xml trunk/echobase-ui/pom.xml trunk/pom.xml Modified: trunk/echobase-domain/pom.xml =================================================================== --- trunk/echobase-domain/pom.xml 2012-11-11 13:16:54 UTC (rev 774) +++ trunk/echobase-domain/pom.xml 2012-11-11 13:48:26 UTC (rev 775) @@ -9,7 +9,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-services/pom.xml =================================================================== --- trunk/echobase-services/pom.xml 2012-11-11 13:16:54 UTC (rev 774) +++ trunk/echobase-services/pom.xml 2012-11-11 13:48:26 UTC (rev 775) @@ -6,7 +6,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-tools/pom.xml =================================================================== --- trunk/echobase-tools/pom.xml 2012-11-11 13:16:54 UTC (rev 774) +++ trunk/echobase-tools/pom.xml 2012-11-11 13:48:26 UTC (rev 775) @@ -11,7 +11,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-ui/pom.xml =================================================================== --- trunk/echobase-ui/pom.xml 2012-11-11 13:16:54 UTC (rev 774) +++ trunk/echobase-ui/pom.xml 2012-11-11 13:48:26 UTC (rev 775) @@ -7,7 +7,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-11-11 13:16:54 UTC (rev 774) +++ trunk/pom.xml 2012-11-11 13:48:26 UTC (rev 775) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> <modules> <module>echobase-domain</module>

1 0

r774 - in trunk: . echobase-domain echobase-services echobase-tools echobase-ui
by tchemit＠users.forge.codelutin.com 11 Nov '12

11 Nov '12

Author: tchemit Date: 2012-11-11 14:16:54 +0100 (Sun, 11 Nov 2012) New Revision: 774 Url: http://forge.codelutin.com/repositories/revision/echobase/774 Log: back to to rc-2 Modified: trunk/echobase-domain/pom.xml trunk/echobase-services/pom.xml trunk/echobase-tools/pom.xml trunk/echobase-ui/pom.xml trunk/pom.xml Modified: trunk/echobase-domain/pom.xml =================================================================== --- trunk/echobase-domain/pom.xml 2012-11-10 09:44:44 UTC (rev 773) +++ trunk/echobase-domain/pom.xml 2012-11-11 13:16:54 UTC (rev 774) @@ -9,7 +9,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-services/pom.xml =================================================================== --- trunk/echobase-services/pom.xml 2012-11-10 09:44:44 UTC (rev 773) +++ trunk/echobase-services/pom.xml 2012-11-11 13:16:54 UTC (rev 774) @@ -6,7 +6,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-tools/pom.xml =================================================================== --- trunk/echobase-tools/pom.xml 2012-11-10 09:44:44 UTC (rev 773) +++ trunk/echobase-tools/pom.xml 2012-11-11 13:16:54 UTC (rev 774) @@ -11,7 +11,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-ui/pom.xml =================================================================== --- trunk/echobase-ui/pom.xml 2012-11-10 09:44:44 UTC (rev 773) +++ trunk/echobase-ui/pom.xml 2012-11-11 13:16:54 UTC (rev 774) @@ -7,7 +7,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-11-10 09:44:44 UTC (rev 773) +++ trunk/pom.xml 2012-11-11 13:16:54 UTC (rev 774) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc2-SNAPSHOT</version> + <version>2.0-rc-2-SNAPSHOT</version> <modules> <module>echobase-domain</module>

1 0

r773 - in trunk: . echobase-domain echobase-services echobase-tools echobase-ui
by tchemit＠users.forge.codelutin.com 10 Nov '12

10 Nov '12

Author: tchemit Date: 2012-11-10 10:44:44 +0100 (Sat, 10 Nov 2012) New Revision: 773 Url: http://forge.codelutin.com/repositories/revision/echobase/773 Log: pass to rc-2 Modified: trunk/echobase-domain/pom.xml trunk/echobase-services/pom.xml trunk/echobase-tools/pom.xml trunk/echobase-ui/pom.xml trunk/pom.xml Modified: trunk/echobase-domain/pom.xml =================================================================== --- trunk/echobase-domain/pom.xml 2012-11-05 14:39:51 UTC (rev 772) +++ trunk/echobase-domain/pom.xml 2012-11-10 09:44:44 UTC (rev 773) @@ -9,7 +9,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-services/pom.xml =================================================================== --- trunk/echobase-services/pom.xml 2012-11-05 14:39:51 UTC (rev 772) +++ trunk/echobase-services/pom.xml 2012-11-10 09:44:44 UTC (rev 773) @@ -6,7 +6,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-tools/pom.xml =================================================================== --- trunk/echobase-tools/pom.xml 2012-11-05 14:39:51 UTC (rev 772) +++ trunk/echobase-tools/pom.xml 2012-11-10 09:44:44 UTC (rev 773) @@ -11,7 +11,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/echobase-ui/pom.xml =================================================================== --- trunk/echobase-ui/pom.xml 2012-11-05 14:39:51 UTC (rev 772) +++ trunk/echobase-ui/pom.xml 2012-11-10 09:44:44 UTC (rev 773) @@ -7,7 +7,7 @@ <parent> <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> </parent> <groupId>fr.ifremer.echobase</groupId> Modified: trunk/pom.xml =================================================================== --- trunk/pom.xml 2012-11-05 14:39:51 UTC (rev 772) +++ trunk/pom.xml 2012-11-10 09:44:44 UTC (rev 773) @@ -11,7 +11,7 @@ <groupId>fr.ifremer</groupId> <artifactId>echobase</artifactId> - <version>2.0-rc-2-SNAPSHOT</version> + <version>2.0-rc2-SNAPSHOT</version> <modules> <module>echobase-domain</module>

1 0

r772 - R-EchoBase
by mdoray＠users.forge.codelutin.com 05 Nov '12

05 Nov '12

Author: mdoray Date: 2012-11-05 15:39:51 +0100 (Mon, 05 Nov 2012) New Revision: 772 Url: http://forge.codelutin.com/repositories/revision/echobase/772 Log: Modified: R-EchoBase/R-echobaseLegacyCheck.r R-EchoBase/R-echobase_functions.r Modified: R-EchoBase/R-echobaseLegacyCheck.r =================================================================== --- R-EchoBase/R-echobaseLegacyCheck.r 2012-10-30 14:43:55 UTC (rev 771) +++ R-EchoBase/R-echobaseLegacyCheck.r 2012-11-05 14:39:51 UTC (rev 772) @@ -119,27 +119,13 @@ Voyages <- dbGetQuery(con,sqlVoyages) head(Voyages) -#Import all esdu cells +#Import all transits #-------------------------- -sqlCellsIndirect="SELECT voyage.name AS voyage_name, vessel.name AS vessel_name, -acousticinstrument.transceivermodel, acousticinstrument.frequency, -dataprocessing.processingtemplate, dataprocessing.processingdescription, -dataprocessing.sounderconstant, dataprocessing.eithresholdlow, -dataprocessing.acousticdensityunit, cell.name AS cell_name, -celltype.name AS celltype, celltype.id AS cell_id, cell.topiaid, -cell.cell FROM public.voyage AS voyage, public.mission AS mission, -public.transit AS transit, public.transect AS transect, -public.dataacquisition AS dataacquisition, -public.dataprocessing AS dataprocessing, public.cell AS cell, -public.vessel AS vessel, public.acousticinstrument AS acousticinstrument, -public.celltype AS celltype WHERE voyage.mission = mission.topiaid AND transit.voyage = voyage.topiaid AND transect.transit = transit.topiaid AND dataacquisition.transect = transect.topiaid AND dataprocessing.dataacquisition = dataacquisition.topiaid AND cell.dataprocessing = dataprocessing.topiaid AND transect.vessel = vessel.topiaid AND dataacquisition.acousticinstrument = acousticinstrument.topiaid AND cell.celltype = celltype.topiaid AND celltype.id = 'Esdu'" +sqlTransits="SELECT transit.startTime,transit.endTime,voyage.name, voyage.startdate, voyage.enddate FROM +public.voyage AS voyage, public.mission AS mission, public.transit AS transit +WHERE voyage.mission = mission.topiaid AND transit.voyage = voyage.topiaid" +Transits <- dbGetQuery(con,sqlTransits) -EsduCellsIndirect <- dbGetQuery(con,sqlCellsIndirect) -head(EsduCellsIndirect) -(NesduCells=dim(EsduCellsIndirect)[1]) -table(EsduCellsIndirect$voyage_name) -#EsduCellsIndirect[EsduCellsIndirect$voyage_name=='PELGAS2010','cell_name'] - #Import all data acquisition/processing #-------------------------- sqlDataAcqProc="SELECT voyage.name, dataprocessing.processingtemplate, dataprocessing.digitthreshold, dataprocessing.eithresholdlow, dataprocessing.eithresholdhigh, dataprocessing.transceiverprocessinggain, dataprocessing.processingsoftwareversion, dataprocessing.transceiverprocessingsacorrection, dataprocessing.transceiverprocessingabsorption, dataprocessing.transceiverprocessingabsorptiondescription, dataprocessing.transducerprocessingbeamangleathwartship, dataprocessing.transducerprocessingpsi, dataprocessing.transducerprocessingbeamanglealongship FROM public.voyage AS voyage, public.mission AS mission, public.transit AS transit, public.transect AS transect, public.dataacquisition AS dataacquisition, public.dataprocessing AS dataprocessing WHERE voyage.mission = mission.topiaid AND transit.voyage = voyage.topiaid AND transect.transit = transit.topiaid AND dataacquisition.transect = transect.topiaid AND dataprocessing.dataacquisition = dataacquisition.topiaid" @@ -169,7 +155,14 @@ EsduCells <- dbGetQuery(con,sqlEsduCells) head(EsduCells) dim(EsduCells) +# 33942 esdus vs. 34524 esdus in original baracouda, minus 577 bad esdus = 34847 valid esdus +#duplicated Esdu names? length(unique(EsduCells$cell_name)) +desdus=EsduCells$cell_name[duplicated(EsduCells$cell_name)] +desdus.year=substr(desdus,1,4) +table(desdus.year) +length(desdus) +# 630 duplicated esdus #Import all esdu cells data #-------------------------- @@ -183,32 +176,36 @@ public.mission AS mission, public.transit AS transit, public.transect AS transect, public.dataacquisition AS dataacquisition, public.dataprocessing AS dataprocessing, public.cell AS cell, public.vessel AS vessel, public.acousticinstrument AS acousticinstrument, public.celltype AS celltype, public.data AS data, public.datametadata AS datametadata WHERE voyage.mission = mission.topiaid AND transit.voyage = voyage.topiaid AND transect.transit = transit.topiaid AND dataacquisition.transect = transect.topiaid AND dataprocessing.dataacquisition = dataacquisition.topiaid AND cell.dataprocessing = dataprocessing.topiaid AND transect.vessel = vessel.topiaid AND dataacquisition.acousticinstrument = acousticinstrument.topiaid AND cell.celltype = celltype.topiaid AND data.cell = cell.topiaid AND data.datametadata = datametadata.topiaid AND celltype.id = 'Esdu'" EsduCellsData <- dbGetQuery(con,sqlEsduCellsData) head(EsduCellsData) +dim(EsduCellsData) length(unique(EsduCellsData$cell_name)) - -#same as esdu no. +# 33312 esdus with data +length(unique(EsduCellsData$cell_name)) +# 33312 unique esdus with data unique(EsduCellsData$cell_type) +#date time conversion stesdus=EsduCellsData[EsduCellsData$data_type=='TimeStart','data_value'] head(stesdus) -#date time conversion -#turn off locale-specific days of week for date import -Sys.setlocale("LC_TIME", "C") -tesdus <- strptime(paste(substr(stesdus,1,10),substr(stesdus,26,29), - substr(stesdus,12,19)),format="%a %b %d %Y %H:%M:%S") -tesdus <- strptime(paste(substr(stesdus,1,19)),format="%Y-%m-%d %H:%M:%S") -class(tesdus) -plot(tesdus,EsduCellsData[EsduCellsData$data_type=='TimeStart','data_value']) +#turn off locale-specific days of week for date import: deprecated +#Sys.setlocale("LC_TIME", "C") +# tesdus <- strptime(paste(substr(stesdus,1,10),substr(stesdus,26,29), +# substr(stesdus,12,19)),format="%a %b %d %Y %H:%M:%S") +tesdus <- strptime(stesdus,format="%Y-%m-%d %H:%M:%OS") + +#esdus in wide format esdus=cells4humans(df=EsduCellsData,idvar='cell_name') head(esdus) dim(esdus) esdus$esdu.id=paste(esdus$voyage_name,esdus$LongitudeStart,esdus$LatitudeStart) +esdus$t <- strptime(esdus$TimeStart,format="%Y-%m-%d %H:%M:%OS") +# No. of esdus per survey +esdus.survey=table(esdus$voyage_name) (NesduCellsData=dim(EsduCellsData)[1]) -#duplicated cell names? yes, for same PM/AM hour... +# No duplicated cell names with data unique(table(EsduCellsData$cell_name)) duplicated.EsduCellData=names(table(EsduCellsData$cell_name))[table(EsduCellsData$cell_name)==10] decd=EsduCellsData[EsduCellsData$cell_name%in%duplicated.EsduCellData,] -decd[decd$cell_name=='1983-04-24 07:03:00Z',] #import baracouda EI data path='~/.gvfs/q sur nantes/Projects/Acoustic biomass assessment/Methods/Database/Echobase/Baracouda2Echobase/RequetesAcoustics/resultats/VoyageEchotype.txt' @@ -222,24 +219,73 @@ df=EI.bara$LGDMC,xname="LGDMC",asNewColumn=FALSE) EI.bara$LATDMC=correct.positions( df=EI.bara$LATDMC,yname="LATDMC",asNewColumn=FALSE) - + +#import baracouda esdus data +#-------------------------------- +path.esdubara='~/.gvfs/donnees2 sur nantes/Campagnes/bd/Echobase/EchobaseLegacyCheck/BaracoudaExports/EI_ESU.txt' +esdus.bara2=read.table(path.esdubara,sep=';',header=TRUE) +head(esdus.bara2) +dim(esdus.bara2) +esdus.bara2$tesdus <- strptime(esdus.bara2$DHTU_ESDU,format="%d/%m/%Y %H:%M:%S") +# 35524 esdus in baracouda +esdus.bara2$DHTU_ESDU[duplicated(esdus.bara2$DHTU_ESDU)] +#no duplicated esdus + esdus.bara=EI.bara[EI.bara$LIBELLE_TRANCHE=='TOTAL',] esdus.bara$esdu.id=paste(esdus.bara$CAMPAGNE,esdus.bara$LGDMC,esdus.bara$LATDMC) -head(esdus.bara) -#date time conversion -baratime=esdus.bara$DHTU_ESDU +dim(esdus.bara) +# 26448 esdus with EI data in baracouda -bara.tesdus <- strptime(baratime,format="%d/%m/%Y %H:%M:%S") +dfs=esdus.bara[esdus.bara$CAMPAGNE=='PELGAS2004',] + +# Summary no. of esdus per cruise +#--------------------------------- +names(esdus.bara2) +tbaraEsdus=table(substr(esdus.bara2$DHTU_ESDU,7,10)) +tbaraEI=table(esdus.bara$CAMPAGNE) +esdus.survey=table(esdus$voyage_name) +tesdus2=esdus.survey[names(esdus.survey)%in%names(tbara)] +esdus.survey.comp=cbind(tesdus2,tbaraEI) +#duplicated esdus +esdus.bara$DHTU_ESDU[duplicated(esdus.bara$DHTU_ESDU)] + +esdus.bara$tesdus <- strptime(esdus.bara$DHTU_ESDU,format="%d/%m/%Y %H:%M:%S") table(is.element(bara.tesdus,tesdus)) -missing.esdus=esdus.bara[!is.element(bara.tesdus,tesdus),] + +#Missing esdus in Echobase +#---------------------------- +plot(esdus.bara2$tesdus,esdus.bara2$TOTAL) +points(esdus$t,esdus$NASC,pch=16,col=2) +missing.esdusEI1=esdus.bara[!is.element(esdus.bara$tesdus,tesdus),] + +dim(missing.esdusEI1) +names(esdus.bara) +esdus.bara$year=substr(esdus.bara[,"DHTU_ESDU"],7,10) +esdus.bara[,"DHTU_ESDU"][duplicated(esdus.bara[,"DHTU_ESDU"])] +missing.esdusEI2=esdus.bara[!is.element(esdus.bara$tesdus,substr(esdus$cell_name,1,19)),] +dim(missing.esdusEI2) +missing.esdus2=esdus.bara2[!is.element(esdus.bara2$tesdus,substr(esdus$cell_name,1,19)),] +dim(missing.esdus2) dim(esdus.bara) dim(missing.esdus) head(missing.esdus) path.missing='/home/mathieubuntu/Documents/Echobase/EchobaseLegacyCheck/BaracoudaExports/missingEsdus.txt' write.table(missing.esdus,path.missing,sep=';',row.names=FALSE) +dfs=esdus[esdus$voyage_name=='PELGAS2004',] +names(dfs) +dim(dfs) +dfs2=esdus.bara[esdus.bara$CAMPAGNE=='PELGAS2004',] +dim(dfs2) +names(dfs2) +dfs3=dfs2[!dfs2$tesdus%in%substr(dfs$cell_name,1,19),] +dim(dfs3) +plot(dfs2$LGDMC,dfs2$LATDMC) +points(dfs3$LGDMC,dfs3$LATDMC,pch=16) +names(esdus.bara$DHTU_ESDU) + x11() plot(esdus.bara$LGDMC,esdus.bara$LATDMC,pch=16) points(missing.esdus$LGDMC,missing.esdus$LATDMC,pch=16,col=2) @@ -279,7 +325,7 @@ dfs=missing.esdus[substr(missing.esdus$DHTU_ESDU,4,5)%in%'07',] dim(dfs) dfs=esdus.bara[substr(esdus.bara$DHTU_ESDU,4,5)%in%'07',] -#***EI data from July in Pelgas2008 and 2009... removed*** +#***577 EI data from July in Pelgas2008 and 2009... removed*** missing.esdus2=missing.esdus[!substr(missing.esdus$DHTU_ESDU,4,5)%in%'07',] plot(dfs$LGDMC,dfs$LATDMC) coast() @@ -383,6 +429,20 @@ Mcsv.base=Mcsv.base[,names(Mcsv.base)!='echo'] names(Mcsv.base) +#Check for missing esdus +table(substr(Mcsv.base[,"MOVIES_EILayer\\cellset\\datestart"],7,10)) +dft=Mcsv.base +dft$year=substr(dft[,"MOVIES_EILayer\\cellset\\datestart"],7,10) +dftu=unique(dft[,c("MOVIES_EILayer\\cellset\\datestart","year")]) +correct1=table(dftu$year)[-1] +esdus.survey.comps=data.frame(esdus.survey.comp[-seq(8),]) +esdus.survey.comps=cbind(esdus.survey.comps,correct1) +esdus.survey.comps$missing=esdus.survey.comps[,2]-esdus.survey.comps[,1] +sum(esdus.survey.comps$missing) + +es=Mcsv.base[substr(Mcsv.base[,"MOVIES_EILayer\\cellset\\datestart"],7,10)=='2004',] +length(unique(es[,"MOVIES_EILayer\\cellset\\datestart"])) + #check export file #----------------------- #All esdus cells Modified: R-EchoBase/R-echobase_functions.r =================================================================== --- R-EchoBase/R-echobase_functions.r 2012-10-30 14:43:55 UTC (rev 771) +++ R-EchoBase/R-echobase_functions.r 2012-11-05 14:39:51 UTC (rev 772) @@ -3,7 +3,8 @@ cells4humans=function(df,v.names="data_value",idvar="EIcell_id",correcXY=FALSE, timevar="data_type",snames=c("voyage_name","esdu_name", - "cell_type","cell_name","esdu_data_type",idvar)){ + "cell_type","cell_name","esdu_data_type",idvar, + "TimeStart","TimeEnd")){ #Cells in wide format #----------------------------------------- df.wide=reshape(df,v.names =v.names , idvar = idvar,

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