diff --git a/build.xml b/build.xml index 1b251187a504eae42c9d66430ce77ae5f044e0f6..0888a108e5aaeb910b2b525b43be202c3a78818d 100644 --- a/build.xml +++ b/build.xml @@ -109,8 +109,8 @@ <!-- tested --> <target name="lint" depends="bind" description="Check sources for warnings"> <echo message="Setting property..."/> - <!-- values: cast,deprecation,divzero,empty,unchecked[3],fallthrough,path[5],serial,finally,overrides,all,none --> - <!--property name="javacargs" value="-Xlint:unchecked" /--> + <!-- values: all,cast,classfile,deprecation,dep-ann,divzero,empty,fallthrough,finally,options,overrides,path,processing,rawtypes,serial,static,try,unchecked,varargs,-cast,-classfile,-deprecation,-dep-ann,-divzero,-empty,-fallthrough,-finally,-options,-overrides,-path,-processing,-rawtypes,-serial,-static,-try,-unchecked,-varargs,none --> + <!--property name="javacargs" value="-Xlint:" /--> <property name="javacargs" value="-Xlint:all" /> <antcall target="compileall"/> </target> diff --git a/html/relnotes.html b/html/relnotes.html index 69c425507ad7b8e8122ef2d64cffc68952332352..23fe4907893662740d2e8622c7eef8d840b957b9 100644 --- a/html/relnotes.html +++ b/html/relnotes.html @@ -81,6 +81,7 @@ with a warning: <li>Fixed a few mistakes in <tt>SilkRendererVisitor</tt> (impl)</li> <li>Fixed several bugs in <tt>GraphPatternRendererVisitor</tt> (impl)</li> <li>Fixed a bug in server updating (impl)</li> +<li>Fixed the compareTo implementation in <tt>BasicCell</tt> (impl)</li> <li>Implemented linkkeys in EDOAL (edoal)</li> <li>Implemented (fully) extension parsing in RDFParser (parser)</li> <li>Reorganised AlignmentServices into transport (HTTP) and service (HTML/Web service) (serv)</li> diff --git a/test/clitest.sh b/test/clitest.sh index 414d7b20ee06b6c7a3e7fd950b56a056951c4b81..5bceeef81330f9a75bd13d78364c85453cdf49f4 100644 --- a/test/clitest.sh +++ b/test/clitest.sh @@ -405,11 +405,9 @@ if [ -s $RESDIR/smalltest/gentestempty1/edna2.rdf ]; then diff $RESDIR/smalltest if [ -s $RESDIR/smalltest/diffedna.txt ]; then echo error with GRAL-IMPL4; fi #------------------- -# This test in fact does not work because there are too many 1. values. -# I have checked that it works independently (add a bad distance name!) echo "\t-Dn=v" -java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -w $RESDIR/smalltest -o lev1.rdf +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAlign -i fr.inrialpes.exmo.align.impl.method.StringDistAlignment -DstringFunction=levenshteinDistance -w $RESDIR/smalltest -Dtype=\*\* -o lev1.rdf sed -i '' "s;<alext\:time>[^<]*</alext\:time>;;g" $RESDIR/smalltest/gentestempty1/lev1.rdf if [ -s $RESDIR/smalltest/gentestempty1/lev1.rdf ]; then diff $RESDIR/smalltest/gentestempty1/edna1.rdf $RESDIR/smalltest/gentestempty1/lev1.rdf > $RESDIR/smalltest/diffstredna.txt ; else echo error with GRAL-DV1; fi if [ ! -s $RESDIR/smalltest/diffstredna.txt ]; then echo error with GRAL-DV2; fi @@ -470,6 +468,108 @@ if [ -s $RESDIR/smalltest/gentestempty1/strpr3.rdf ]; then echo error with GRAL- echo "\t-P,--params <FILE>" echo "\t(same as Procalign)" +######################################################################## +# GroupAggreg +######################################################################## + +echo "\t\t *** Testing GroupAggreg ***" + +#------------------- +echo "\tEMPTY" +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg &> $RESDIR/groupagg-empty.txt +if [ ! -s $RESDIR/groupagg-empty.txt ]; then echo error with GRAG-EMPTY1; fi + +#------------------- +echo "\t-z, -zzz" + +java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg -z &> $RESDIR/zerr.txt +grep "Unrecognized option: -z" $RESDIR/zerr.txt > $RESDIR/err.txt +if [ ! -s $RESDIR/err.txt ]; then echo error with GRAG-ERR1; fi +java -Dlog.level=INFO -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg --zzz &> $RESDIR/zzzerr.txt +grep "Unrecognized option: --zzz" $RESDIR/zzzerr.txt > $RESDIR/err.txt +if [ ! -s $RESDIR/err.txt ]; then echo error with GRAG-ERR2; fi + +#------------------- +echo "\t-h, --help" + +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg -h &> $RESDIR/groupagg-h.txt +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg --help &> $RESDIR/groupagg-help.txt +if [ -s $RESDIR/groupagg-h.txt ]; then diff $RESDIR/groupagg-h.txt $RESDIR/groupagg-help.txt; else echo error with GRAGAL-HELP; fi + +#------------------- +echo "\t-l,--list <FILE>" + +#refalign,lev1,streq1 + +cd $RESDIR/smalltest/ +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg -l "lev1,streq1" +if [ ! -s gentestempty1.rdf ]; then echo error with GRAG-LIST1; fi +mv gentestempty1.rdf oldgentestempty1.rdf +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg --list "lev1,streq1" +if [ -s gentestempty1.rdf ]; then diff gentestempty1.rdf oldgentestempty1.rdf ; else echo error with GRAG-LIST2; fi + +#------------------- +echo "\t-o <D>, --outputDir <D>" + +mkdir $RESDIR/aggreg1a $RESDIR/aggreg1b +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg -l "lev1,streq1" -o $RESDIR/aggreg1a +if [ -s $RESDIR/aggreg1a/gentestempty1.rdf ]; then diff $RESDIR/aggreg1a/gentestempty1.rdf $RESDIR/smalltest/gentestempty1.rdf ; else echo error with GRAG-OUT1; fi +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg --list "lev1,streq1" --output $RESDIR/aggreg1b +if [ -s $RESDIR/aggreg1b/gentestempty1.rdf ]; then diff $RESDIR/aggreg1a/gentestempty1.rdf $RESDIR/aggreg1b/gentestempty1.rdf ; else echo error with GRAG-OUT3; fi + +cd $CWD + +#------------------- +echo "\t-w,--directory <DIR>" + +mkdir $RESDIR/aggreg2a $RESDIR/aggreg2b +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg -l "lev1,streq1" -w $RESDIR/smalltest -o $RESDIR/aggreg2a +if [ -s $RESDIR/aggreg2a/gentestempty1.rdf ]; then diff $RESDIR/aggreg1a/gentestempty1.rdf $RESDIR/aggreg2a/gentestempty1.rdf > $RESDIR/smalltest/diffgrag-w1.txt ; else echo error with GRAG-DIR1; fi +if [ -s $RESDIR/smalltest/diffgrag-w1.txt ]; then echo error with GRAG-DIR2; fi +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg --list "lev1,streq1" --directory $RESDIR/smalltest --output $RESDIR/aggreg2b +if [ -s $RESDIR/aggreg2b/gentestempty1.rdf ]; then diff $RESDIR/aggreg2a/gentestempty1.rdf $RESDIR/aggreg2b/gentestempty1.rdf ; else echo error with GRAG-DIR3; fi + +#------------------- +echo "\t-m,--aggmethod <METHOD>" +# -m min/max + +mkdir $RESDIR/aggreg3a $RESDIR/aggreg3b +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg -l "lev1,streq1" -w $RESDIR/smalltest -o $RESDIR/aggreg3a -m max +if [ -s $RESDIR/aggreg3a/gentestempty1.rdf ]; then diff $RESDIR/aggreg1a/gentestempty1.rdf $RESDIR/aggreg3a/gentestempty1.rdf > $RESDIR/smalltest/diffgrag-m1.txt ; else echo error with GRAG-METH1; fi +if [ ! -s $RESDIR/smalltest/diffgrag-m1.txt ]; then echo error with GRAG-METH2; fi +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg --list "lev1,streq1" --directory $RESDIR/smalltest --output $RESDIR/aggreg3b --aggmethod max +if [ -s $RESDIR/aggreg3b/gentestempty1.rdf ]; then diff $RESDIR/aggreg3a/gentestempty1.rdf $RESDIR/aggreg3b/gentestempty1.rdf ; else echo error with GRAG-METH3; fi + +#------------------- +echo "\t-t,--threshold <DOUBLE>" + +mkdir $RESDIR/aggreg4a $RESDIR/aggreg4b +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg -l "lev1,streq1" -w $RESDIR/smalltest -o $RESDIR/aggreg4a -m max -t 0.6 +if [ -s $RESDIR/aggreg4a/gentestempty1.rdf ]; then diff $RESDIR/aggreg1a/gentestempty1.rdf $RESDIR/aggreg4a/gentestempty1.rdf > $RESDIR/smalltest/diffgrag-t1.txt ; else echo error with GRAG-THRES1; fi +if [ ! -s $RESDIR/smalltest/diffgrag-t1.txt ]; then echo error with GRAG-THRES2; fi +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg --list "lev1,streq1" --directory $RESDIR/smalltest --output $RESDIR/aggreg4b --aggmethod max --threshold 0.6 +if [ -s $RESDIR/aggreg4b/gentestempty1.rdf ]; then diff $RESDIR/aggreg4a/gentestempty1.rdf $RESDIR/aggreg4b/gentestempty1.rdf ; else echo error with GRAG-THRES3; fi + +#------------------- +echo "\t-T,--cutmethod <METHOD>" +# -c hard (with default 0.) + +mkdir $RESDIR/aggreg5a $RESDIR/aggreg5b +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg -l "lev1,streq1" -w $RESDIR/smalltest -o $RESDIR/aggreg5a -m max -t 0.6 -T perc +if [ -s $RESDIR/aggreg5a/gentestempty1.rdf ]; then diff $RESDIR/aggreg4a/gentestempty1.rdf $RESDIR/aggreg5a/gentestempty1.rdf > $RESDIR/smalltest/diffgrag-tt1.txt ; else echo error with GRAG-CUT1; fi +if [ ! -s $RESDIR/smalltest/diffgrag-tt1.txt ]; then echo error with GRAG-CUT2; fi +java -cp $CP fr.inrialpes.exmo.align.cli.GroupAggreg --list "lev1,streq1" --directory $RESDIR/smalltest --output $RESDIR/aggreg5b --aggmethod max --threshold 0.6 --cutmethod perc +if [ -s $RESDIR/aggreg5b/gentestempty1.rdf ]; then diff $RESDIR/aggreg5a/gentestempty1.rdf $RESDIR/aggreg5b/gentestempty1.rdf ; else echo error with GRAG-CUT3; fi + +#------------------- +echo "\t-Dn=v" +echo "\t(same as Procalign; useless: no parameters involved so far)" + +#------------------- +echo "\t-P,--params <FILE>" +echo "\t(same as Procalign; useless: no parameters involved so far)" + + ######################################################################## # GroupEval ######################################################################## @@ -547,7 +647,7 @@ java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval --reference lev1.rdf -l "refa if [ -s $RESDIR/groupeval-r2.html ]; then diff $RESDIR/groupeval-r1.html $RESDIR/groupeval-r2.html ; else echo error with GREV-REF3; fi #------------------- -echo "\t-t,--type <TYPE> Output TYPE (html|xml|tex|ascii|triangle" +echo "\t-t,--type <TYPE> Output TYPE (html|xml|tex|ascii|triangle)" java -cp $CP fr.inrialpes.exmo.align.cli.GroupEval -t triangle -l "refalign,edna1,streq1,streq1n,streq1x,streq2,streq2n,streq2x,lev1" -w $RESDIR/smalltest -o $RESDIR/groupeval-ttr1.tex if [ -s $RESDIR/groupeval-ttr1.tex ]; then diff $RESDIR/groupeval-w1.html $RESDIR/groupeval-ttr1.tex > $RESDIR/smalltest/diffgrev-t1.txt ; else echo error with GREV-TYP1; fi if [ ! -s $RESDIR/smalltest/diffgrev-t1.txt ]; then echo error with GREV-TYP2; fi @@ -1061,7 +1161,6 @@ java -cp $CP fr.inrialpes.exmo.align.cli.TransformQuery -P $RESDIR/params.xml -a if [ -s $RESDIR/queryt-P1.rdf ]; then diff $RESDIR/queryt-P1.rdf $RESDIR/queryt-d1.rdf > $RESDIR/diff-prefix2.txt; else echo error with TRANSQ-PREFIX3; fi if [ -s $RESDIR/diff-prefix2.txt ]; then echo error with TRANSQ-PREFIX4; fi -exit ######################################################################## # AlignmentService ######################################################################## @@ -1102,12 +1201,12 @@ kill -TERM $! #------------------- echo "\t-i,--impl <CLASS>" -java -Dlog.level=WARN -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -i fr.inrialpes.exmo.align.cli.GenPlot &> $Resdir/err.txt & +java -Dlog.level=WARN -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -i fr.inrialpes.exmo.align.cli.GenPlot &> $RESDIR/err.txt & sleep 5; if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-IMPL1; else grep "Cannot create service for fr.inrialpes.exmo.align.cli.GenPlot" $RESDIR/err.txt > $RESDIR/ierr.txt; fi if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-IMPL2; fi kill -TERM $! -java -Dlog.level=WARN -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --impl fr.inrialpes.exmo.align.cli.GenPlot2 &> $Resdir/err.txt & +java -Dlog.level=WARN -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --impl fr.inrialpes.exmo.align.cli.GenPlot2 &> $RESDIR/err.txt & sleep 5; if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-IMPL3; else grep "Cannot create service for fr.inrialpes.exmo.align.cli.GenPlot2" $RESDIR/err.txt > $RESDIR/ierr.txt; fi if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-IMPL4; fi @@ -1145,7 +1244,7 @@ java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService - sleep 5; kill -TERM $! if [ -s $RESDIR/err.txt ]; then echo error with ASERV-HTTP1; fi -java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --http 5555 &> $Resdir/err.txt & +java -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --http 5555 &> $RESDIR/err.txt & sleep 5; kill -TERM $! if [ -s $RESDIR/err.txt ]; then echo error with ASERV-HTTP2; fi @@ -1198,10 +1297,10 @@ if [ -s $RESDIR/err.txt ]; then echo error with ASERV-URIP2; fi #------------------- echo "\t-B,--dbms <DBMS>" java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService -B postgres &> $RESDIR/err.txt -if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBMS1; else grep "Connection refused." $RESDIR/err.txt > $RESDIR/dberr.txt; fi +if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBMS1; else grep "Cannot connect to database" $RESDIR/err.txt > $RESDIR/dberr.txt; fi if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBMS2; fi java -Dlog.level=ERROR -cp $CP:lib/alignsvc.jar fr.inrialpes.exmo.align.service.AlignmentService --dbms postgres &> $RESDIR/err.txt -if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBMS3; else grep "Connection refused." $RESDIR/err.txt > $RESDIR/dberr.txt; fi +if [ ! -s $RESDIR/err.txt ]; then echo error with ASERV-DBMS3; else grep "Cannot connect to database" $RESDIR/err.txt > $RESDIR/dberr.txt; fi if [ ! -s $RESDIR/dberr.txt ]; then echo error with ASERV-DBMS4; fi #------------------- @@ -1258,7 +1357,7 @@ echo "\t-P,--params <FILE>" echo "\t(same as Procalign)" ######################################################################## -echo Evrything is fine +echo Here I reach the end