Merge branch 'master' of git+ssh://git.renater.fr:2222/osug-doi

566a9dee · Véronique Chaffard · 0b983e6d · a0fa610a · 566a9dee · 566a9dee
Commit 566a9dee authored 8 years ago by Véronique Chaffard
--- a/assembly-release.xml
+++ b/assembly-release.xml
@@ -32,7 +32,7 @@
            <directory>${project.basedir}/target/</directory>
            <outputDirectory>bin/</outputDirectory>
            <includes>
-                <include>doi-csv-trunk.jar</include>
+                <include>${project.artifactId}-${project.version}.jar</include>
            </includes>
        </fileSet>
    </fileSets>

--- a/bin/ammacatch-process.sh
+++ b/bin/ammacatch-process.sh
@@ -2,7 +2,7 @@
 PROJECT=AMMA-CATCH
-DO_GET=1
+DO_GET=0
 CONF=../conf/$PROJECT
 INPUT=$CONF/inputs/

--- a/bin/env.sh
+++ b/bin/env.sh
@@ -17,5 +17,5 @@ export JAVA_OPTS="$JAVA_OPTS -Dfile.encoding=UTF-8"
 export APP_CMD="java $JAVA_OPTS -jar doimgr-trunk.jar --v=3"
-echo "JAVA_OPTS: $JAVA_OPTS"
+#echo "JAVA_OPTS: $JAVA_OPTS"
--- a/bin/ohmcv-process.sh
+++ b/bin/ohmcv-process.sh
@@ -18,19 +18,38 @@ mkdir -p $TMP
 # 0. GetRecords from sedoo:
 if [ $DO_GET -eq 1 ]
 then
-    for url in $(cat $INPUT/urls.txt)
+    # Prepare data access url mapping:
+    echo "# DOI_suffix;data_access_url" > $CONF/doi_url_data_access.csv
+    for row in $(cat $INPUT/doi_id.txt)
    do
+        doi=${row%;*}
+        id=${row#*;}
+        echo "doi: $doi"
+#        echo "id:  $id"
+        url="http://mistrals.sedoo.fr/xml/bdToIso.php?datsId=$id"
        if [ ${url:0:4} = "http" ]; then
-            echo $url
+#            echo $url
+#            wget -O $TMP/${doi}.xml $url
+#           cp $TMP/${doi}.xml $INPUT/mistrals/
+            # fix bad <xml> header (manual)
-            filename=$(basename $url)
+            xsltproc -o $INPUT/${doi}.csv --stringparam DOI_SUFFIX_START "$PROJECT" --stringparam USE_END_DATE "true" $XSL/csw2txt_ohmcv.xsl $INPUT/mistrals/${doi}.xml
-            id=${filename##*id=}
-            echo $id
+            # replace Hymex ID by DOI
+            EXPR="s/identifier:DOI;.*/identifier:DOI;10.5072\/${doi}/"
-            wget -O $TMP/$id.xml $url
+            sed -i "$EXPR" $INPUT/${doi}.csv
-            xsltproc -o $INPUT/$id.csv --stringparam DOI_SUFFIX_START "$PROJECT" --stringparam USE_END_DATE "true" $XSL/csw2txt_ohmcv.xsl $TMP/$id.xml
+            # add url data access:
+            url="http://www.ohmcv.fr/P000_download.php?fic=$id"
+            echo "${doi};$url" >> $CONF/doi_url_data_access.csv
            if [ $? -ne 0 ]; then
                 echo "xsltproc failed"

--- a/conf/AMMA-CATCH/names_override.csv
+++ b/conf/AMMA-CATCH/names_override.csv
 #Name;affiliation;nameIdentifier:ORCID
 Christophe Peugeot;IRD/HSM;0000-0003-2161-125X
+Emmanuel Lawin;UAC/INE;0000-0003-4751-3439
 Eric Mougin;CNRS/GET;0000-0002-7569-5906
 Gérémy Panthou;UGA/IGE;
 Ibrahim Bouzou Moussa;UAM/Dept Géographie;0000-0002-3140-8987
 Jean-Martial Cohard;UGA/IGE;
 Jérôme Demarty;IRD/HSM;0000-0001-5173-9030
 Marielle Gosset;IRD/GET;0000-0003-1064-7003
+Monique Oï;IRD/HSM;
 Pierre Hiernaux;CNRS/GET;0000-0002-1764-9178
 Sylvie Galle;IRD/IGE;0000-0002-3100-8510
 Thierry Lebel;IRD/IGE;0000-0002-1297-6751

--- a/conf/OHMCV/access_instruction.html
+++ b/conf/OHMCV/access_instruction.html
 <?xml version="1.0" encoding="utf-8"?>
 <html xmlns="http://www.w3.org/1999/xhtml">
    <body>
-        Data is available online through the web portal http://www.ohmcv.fr/P400_bdd.html.
+        The data can be accessed from the link on this page. You will then be directed to the OHMCV website and you will be asked for your e-mail address. A download link will then be sent to this e-mail address.
-        <br/>
-        To dowload a specific dataset:
-        <ol>
-            <li>TODO: describe how to ...</li>
-        </ol>
    </body>
 </html>
--- a/conf/OHMCV/doi_url_data_access.csv
+++ b/conf/OHMCV/doi_url_data_access.csv
+# DOI_suffix;data_access_url
+OHMCV.DSD.PVI.11-14.1;http://www.ohmcv.fr/P000_download.php?fic=436
+OHMCV.DSD.MRE.11-14.1;http://www.ohmcv.fr/P000_download.php?fic=679
+OHMCV.DSD.SEF.12-14.1;http://www.ohmcv.fr/P000_download.php?fic=744
+OHMCV.DSD.VB1.11-14.1;http://www.ohmcv.fr/P000_download.php?fic=680
+OHMCV.DSD.VB2.11-14.1;http://www.ohmcv.fr/P000_download.php?fic=681
+OHMCV.DSD.VB3.11-14.1;http://www.ohmcv.fr/P000_download.php?fic=682
+OHMCV.RTS.AUZ.11-14.1;http://www.ohmcv.fr/P000_download.php?fic=656
+OHMCV.REA.CEV.07-14.1;http://www.ohmcv.fr/P000_download.php?fic=1183
+OHMCV.HSS.CLA.11-14.1;http://www.ohmcv.fr/P000_download.php?fic=993
+OHMCV.ADV.CLA.13-14.1;http://www.ohmcv.fr/P000_download.php?fic=1349
+OHMCV.ERO.PRA.11-13.1;http://www.ohmcv.fr/P000_download.php?fic=1347
+OHMCV.LIM.CLA.12-14.1;http://www.ohmcv.fr/P000_download.php?fic=994
+OHMCV.SMO.CLA.13-14.1;http://www.ohmcv.fr/P000_download.php?fic=1350
--- a/conf/OHMCV/inputs/28027.csv
+++ b/conf/OHMCV/inputs/28027.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-1349-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.1349
+identifier:DOI;10.5072/OHMCV.ADV.CLA.13-14.1
 title;Acoustic Doppler Velocimeter IQ Plus, Claduègne
 publicationYear;2013
-subject:main;Velocity profile
+subject:main;Surface Water
-subject:main;Terrestrial Hydrosphere > Surface Water
 subject:main;ADCP > Acoustic Doppler Current Profiler
 subject:main;Fixed Observation Stations
 contributorName:WorkPackageLeader;Nord Guillaume;affiliation;LTHE

--- a/conf/OHMCV/inputs/28021.csv
+++ b/conf/OHMCV/inputs/28021.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-0679-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.679
+identifier:DOI;10.5072/OHMCV.DSD.MRE.11-14.1
 title;DSD network, Mont-Redon
 publicationYear;2011
 subject:main;Atmospheric conditions
-subject:main;Fall Velocity
+subject:main;Precipitation
-subject:main;Droplet size distribution
+subject:main;Precipitation Rate
-subject:main;Atmosphere > Precipitation
+subject:main;Droplet Size
-subject:main;Atmosphere > Precipitation > Droplet Size
-subject:main;Atmosphere > Precipitation > Precipitation Rate
 subject:main;DISDROMETERS
+subject:main;Ground networks
+subject:main;Hydrometeorological sites
 subject:main;Fixed Observation Stations
 contributorName:WorkPackageLeader;Boudevillain Brice;affiliation;LTHE
 date:Collected;2011-09-10/

--- a/conf/OHMCV/inputs/28025.csv
+++ b/conf/OHMCV/inputs/28025.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-0436-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.436
+identifier:DOI;10.5072/OHMCV.DSD.PVI.11-14.1
 title;DSD network, Pradel-Vignes
 publicationYear;2009
 subject:main;Atmospheric conditions
-subject:main;Droplet size distribution
+subject:main;Precipitation Rate
-subject:main;Atmosphere > Precipitation > Droplet Size
+subject:main;Droplet Size
-subject:main;Atmosphere > Precipitation > Precipitation Rate
 subject:main;DISDROMETERS
+subject:main;Ground networks
+subject:main;Hydrometeorological sites
 subject:main;Fixed Observation Stations
 contributorName:WorkPackageLeader;Boudevillain Brice;affiliation;LTHE
 date:Collected;2009-03-12/

--- a/conf/OHMCV/inputs/28028.csv
+++ b/conf/OHMCV/inputs/28028.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-0744-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.744
+identifier:DOI;10.5072/OHMCV.DSD.SEF.12-14.1
 title;DSD network, Saint-Etienne-de-Fontbellon
 publicationYear;2012
 subject:main;Atmospheric conditions
-subject:main;Droplet size distribution
+subject:main;Precipitation Rate
-subject:main;Atmosphere > Precipitation > Droplet Size
+subject:main;Droplet Size
-subject:main;Atmosphere > Precipitation > Precipitation Rate
 subject:main;DISDROMETERS
+subject:main;Ground networks
+subject:main;Hydrometeorological sites
 subject:main;Fixed Observation Stations
 contributorName:WorkPackageLeader;Boudevillain Brice;affiliation;LTHE
 date:Collected;2012-09-05/2015-12-31

--- a/conf/OHMCV/inputs/28024.csv
+++ b/conf/OHMCV/inputs/28024.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-0680-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.680
+identifier:DOI;10.5072/OHMCV.DSD.VB1.11-14.1
 title;DSD network, Villeneuve-de-Berg-1
 publicationYear;2011
 subject:main;Atmospheric conditions
-subject:main;Droplet size distribution
+subject:main;Precipitation Rate
-subject:main;Atmosphere > Precipitation > Droplet Size
+subject:main;Droplet Size
-subject:main;Atmosphere > Precipitation > Precipitation Rate
 subject:main;DISDROMETERS
+subject:main;Ground networks
+subject:main;Hydrometeorological sites
 subject:main;Fixed Observation Stations
 contributorName:WorkPackageLeader;Boudevillain Brice;affiliation;LTHE
 date:Collected;2011-11-24/

--- a/conf/OHMCV/inputs/28026.csv
+++ b/conf/OHMCV/inputs/28026.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-0681-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.681
+identifier:DOI;10.5072/OHMCV.DSD.VB2.11-14.1
 title;DSD network, Villeneuve-de-Berg-2
 publicationYear;2011
 subject:main;Atmospheric conditions
-subject:main;Droplet size distribution
+subject:main;Precipitation Amount
-subject:main;Atmosphere > Precipitation > Droplet Size
+subject:main;Precipitation Rate
-subject:main;Atmosphere > Precipitation > Precipitation Rate
+subject:main;Droplet Size
-subject:main;Atmosphere > Precipitation > Precipitation Amount
 subject:main;DISDROMETERS
+subject:main;Ground networks
+subject:main;Hydrometeorological sites
 subject:main;Fixed Observation Stations
 contributorName:WorkPackageLeader;Boudevillain Brice;affiliation;LTHE
 date:Collected;2011-11-24/

--- a/conf/OHMCV/inputs/28022.csv
+++ b/conf/OHMCV/inputs/28022.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-0682-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.682
+identifier:DOI;10.5072/OHMCV.DSD.VB3.11-14.1
 title;DSD network, Villeneuve-de-Berg-3
 publicationYear;2011
 subject:main;Atmospheric conditions
-subject:main;Fall Velocity
+subject:main;Precipitation
-subject:main;Droplet size distribution
+subject:main;Precipitation Rate
-subject:main;Atmosphere > Precipitation
+subject:main;Droplet Size
-subject:main;Atmosphere > Precipitation > Droplet Size
-subject:main;Atmosphere > Precipitation > Precipitation Rate
 subject:main;DISDROMETERS
+subject:main;Ground networks
+subject:main;Hydrometeorological sites
 subject:main;Fixed Observation Stations
 contributorName:WorkPackageLeader;Boudevillain Brice;affiliation;LTHE
 date:Collected;2011-11-24/

--- a/conf/OHMCV/inputs/28020.csv
+++ b/conf/OHMCV/inputs/28020.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-1347-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.1347
+identifier:DOI;10.5072/OHMCV.ERO.PRA.11-13.1
 title;Runoff and erosion plots, Pradel
 publicationYear;2009
-subject:main;Terrestrial Hydrosphere > Water Quality/Water Chemistry > Suspended Solids
+subject:main;Discharge/Flow
-subject:main;Terrestrial Hydrosphere > Surface Water > Stage Height
+subject:main;Stage Height
-subject:main;Terrestrial Hydrosphere > Surface Water > Discharge/Flow
+subject:main;Suspended Solids
 subject:main;SEDIMENT METERS
 subject:main;WATER LEVEL GAUGES
 subject:main;Fixed Observation Stations

--- a/conf/OHMCV/inputs/28029.csv
+++ b/conf/OHMCV/inputs/28029.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-0993-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.993
+identifier:DOI;10.5072/OHMCV.HSS.CLA.11-14.1
 title;Gazel and Claduègne hydro-sedimentary stations
 publicationYear;2011
-subject:main;Surface velocity
+subject:main;Discharge/Flow
-subject:main;Terrestrial Hydrosphere > Surface Water > Stage Height
+subject:main;Surface Water
-subject:main;Terrestrial Hydrosphere > Water Quality/Water Chemistry > Water Temperature
+subject:main;Turbidity
-subject:main;Terrestrial Hydrosphere > Surface Water > Discharge/Flow
+subject:main;Conductivity
-subject:main;Terrestrial Hydrosphere > Water Quality/Water Chemistry > Conductivity
+subject:main;Stage Height
-subject:main;Terrestrial Hydrosphere > Surface Water
+subject:main;Water Temperature
-subject:main;Terrestrial Hydrosphere > Water Quality/Water Chemistry > Turbidity
+subject:main;Suspended Solids
-subject:main;Terrestrial Hydrosphere > Water Quality/Water Chemistry > Suspended Solids
-subject:main;WATER LEVEL GAUGES
-subject:main;CONDUCTIVITY METERS
-subject:main;RADAR > Radio Detection and Ranging
-subject:main;SEDIMENT METERS
-subject:main;SEDIMENT METERS
 subject:main;WATER LEVEL GAUGES
 subject:main;Ground networks
 contributorName:WorkPackageLeader;Nord Guillaume;affiliation;LTHE

--- a/conf/OHMCV/inputs/27999.csv
+++ b/conf/OHMCV/inputs/27999.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-0994-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.994
+identifier:DOI;10.5072/OHMCV.LIM.CLA.12-14.1
 title;limnimeter network, Gazel and Claduègne catchments
 publicationYear;2012
 subject:main;Atmospheric conditions
-subject:main;Terrestrial Hydrosphere > Surface Water > Water Pressure
+subject:main;Atmospheric Pressure Measurements
-subject:main;Terrestrial Hydrosphere > Surface Water > Water Depth
+subject:main;Water Depth
-subject:main;Terrestrial Hydrosphere > Water Quality/Water Chemistry > Water Temperature
+subject:main;Conductivity
-subject:main;Terrestrial Hydrosphere > Surface Water > Stage Height
+subject:main;Stage Height
-subject:main;Terrestrial Hydrosphere > Water Quality/Water Chemistry > Conductivity
+subject:main;Water Pressure
-subject:main;Atmosphere > Atmospheric Pressure > Atmospheric Pressure Measurements
+subject:main;Water Temperature
-subject:main;Atmosphere > Atmospheric Temperature > Air Temperature
+subject:main;Air Temperature
 subject:main;WATER LEVEL GAUGES
 subject:main;CTD > Conductivity, Temperature, Depth
 subject:main;PRESSURE SENSORS

--- a/conf/OHMCV/inputs/28019.csv
+++ b/conf/OHMCV/inputs/28019.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-1183-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.1183
+identifier:DOI;10.5072/OHMCV.REA.CEV.07-14.1
 title;Pluviometric reanalysis Cévennes-Vivarais
 publicationYear;2007
 subject:main;Atmospheric conditions
-subject:main;Atmosphere > Precipitation > Rain
+subject:main;Rain
 subject:main;Geographic Regions
 subject:main;Value-added dataset
 date:Collected;2007-01-22/2012-12-15

--- a/conf/OHMCV/inputs/28000.csv
+++ b/conf/OHMCV/inputs/28000.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-0656-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.656
+identifier:DOI;10.5072/OHMCV.RTS.AUZ.11-14.1
 title;Hpiconet rain gauge network
 publicationYear;2010
 subject:main;Atmospheric conditions
-subject:main;Atmosphere > Precipitation > Precipitation Amount
+subject:main;Precipitation Amount
 subject:main;RAIN GAUGES
 contributorName:WorkPackageLeader;Molinié Gilles;affiliation;LTHE
 date:Collected;2010-10-09/2014-11-04
+description:Abstract;"A report of the raingauge survey is available in the file tournee_etat_stations.xlsx
+A interactive software based on R allows to interactively plot and extract the data to the EXCEL format. 
+(http://www.ohmcv.fr/plot_hpiconet_series.zip)"
 description:SeriesInformation;The data provided are 5-min rainfall amounts at 19 raingauges situated in an area of about 7x5km^2. Rainfall data are provided only for rainfall events which are defined as a succession of rainy days during which at least 2 raingauges have recorded 10mm or more.
-geoLocationPlace;Hpiconet
 geoLocationBox;4.44838 44.54993 4.5148 44.6141
 # END;
--- a/conf/OHMCV/inputs/27998.csv
+++ b/conf/OHMCV/inputs/27998.csv
 # Generated by csw2txt.xsl;
 # BEGIN;
 # ID;74bbe692-584b-11e3-1350-ce3f5508acd9
-identifier:DOI;10.5072/OHMCV.1350
+identifier:DOI;10.5072/OHMCV.SMO.CLA.13-14.1
 title;Soil moisture sensor network, Gazel and Claduègne catchments
 publicationYear;2013
-subject:main;Land Surface > Soils > Soil Moisture/Water Content
+subject:main;Soil Moisture/Water Content
 subject:main;SOIL MOISTURE PROBE
 subject:main;Ground networks
 contributorName:WorkPackageLeader;Vandervaere Jean-pierre;affiliation;LTHE