diff --git a/src/MGRAST/tools/BulkLoader/BulkLoader.sh b/src/MGRAST/tools/BulkLoader/BulkLoader.sh index fc5f362d..5c01c4e2 100755 --- a/src/MGRAST/tools/BulkLoader/BulkLoader.sh +++ b/src/MGRAST/tools/BulkLoader/BulkLoader.sh @@ -6,7 +6,7 @@ TABLE='' INFILE='' OUTDIR='' JAVA=`which java` -JARS="/root/cassandra/lib /root/opencsv" +JARS="/root/cassandra/lib/*" while getopts hk:t:i:o: option; do case "${option}" @@ -46,10 +46,7 @@ if [ -z "$CASSANDRA_CONFIG" ]; then fi # set classpath -CLASSPATH=".:$CASSANDRA_CONFIG" -for path in $JARS; do - CLASSPATH="$CLASSPATH:$path/*" -done +CLASSPATH=".:$CASSANDRA_CONFIG:$JARS" # Compile echo "compile: javac -cp $CLASSPATH BulkLoader.java" diff --git a/src/MGRAST/tools/BulkLoader/opencsv-3.4.jar b/src/MGRAST/tools/BulkLoader/opencsv-3.4.jar new file mode 100644 index 00000000..2b1edc9e Binary files /dev/null and b/src/MGRAST/tools/BulkLoader/opencsv-3.4.jar differ diff --git a/src/MGRAST/tools/dump_annotation_for_cass.pl b/src/MGRAST/tools/dump_annotation_for_cass.pl index 81675dd4..26963867 100755 --- a/src/MGRAST/tools/dump_annotation_for_cass.pl +++ b/src/MGRAST/tools/dump_annotation_for_cass.pl @@ -126,7 +126,7 @@ print STDERR "Dumping protein data ...\n"; foreach my $md5 (@$pmd5s) { - my $data = $dbh->selectall_arrayref("SELECT DISTINCT m._id, s.source, a.id, f.name, o.name FROM md5_protein a INNER JOIN md5s m ON a.md5 = m.md5 LEFT OUTER JOIN functions f ON a.function = f._id LEFT OUTER JOIN organisms_ncbi o ON a.organism = o._id LEFT OUTER JOIN sources s ON a.source = s._id where a.md5='$md5'"); + my $data = $dbh->selectall_arrayref("SELECT DISTINCT m._id, s.name, a.id, f.name, o.name FROM md5_protein a INNER JOIN md5s m ON a.md5 = m.md5 LEFT OUTER JOIN functions f ON a.function = f._id LEFT OUTER JOIN organisms_ncbi o ON a.organism = o._id LEFT OUTER JOIN sources s ON a.source = s._id where a.md5='$md5'"); next unless ($data && @$data); my $mid = $data->[0][0]; my $srcs = {}; @@ -167,7 +167,7 @@ print STDERR "Dumping rna data ...\n"; foreach my $md5 (@$rmd5s) { - my $data = $dbh->selectall_arrayref("SELECT DISTINCT m._id, s.source, a.id, f.name, o.name FROM md5_rna a INNER JOIN md5s m ON a.md5 = m.md5 LEFT OUTER JOIN functions f ON a.function = f._id LEFT OUTER JOIN organisms_ncbi o ON a.organism = o._id LEFT OUTER JOIN sources s ON a.source = s._id where a.md5='$md5'"); + my $data = $dbh->selectall_arrayref("SELECT DISTINCT m._id, s.name, a.id, f.name, o.name FROM md5_rna a INNER JOIN md5s m ON a.md5 = m.md5 LEFT OUTER JOIN functions f ON a.function = f._id LEFT OUTER JOIN organisms_ncbi o ON a.organism = o._id LEFT OUTER JOIN sources s ON a.source = s._id where a.md5='$md5'"); next unless ($data && @$data); my $mid = $data->[0][0]; my $srcs = {}; @@ -208,7 +208,7 @@ print STDERR "Dumping ontology data ...\n"; foreach my $md5 (@$omd5s) { - my $data = $dbh->selectall_arrayref("SELECT DISTINCT m._id, s.source, a.id, f.name FROM md5_ontology a INNER JOIN md5s m ON a.md5 = m.md5 LEFT OUTER JOIN functions f ON a.function = f._id LEFT OUTER JOIN sources s ON a.source = s._id where a.md5='$md5'"); + my $data = $dbh->selectall_arrayref("SELECT DISTINCT m._id, s.name, a.id, f.name FROM md5_ontology a INNER JOIN md5s m ON a.md5 = m.md5 LEFT OUTER JOIN functions f ON a.function = f._id LEFT OUTER JOIN sources s ON a.source = s._id where a.md5='$md5'"); next unless ($data && @$data); my $mid = $data->[0][0]; my $srcs = {}; @@ -228,7 +228,7 @@ $acc =~ s/\"/\\"/g; $fun =~ s/\"/\\"/g; print IDUMP join(",", map { '"'.$_.'"' } ($mid, $src, $md5, "true", "", "[]", $acc, $fun, ""))."\n"; - print MDUMP join(",", map { '"'.$_.'"' } ($md5, $src, "true", "", "[]", $acc, $fun. ""))."\n"; + print MDUMP join(",", map { '"'.$_.'"' } ($md5, $src, "true", "", "[]", $acc, $fun, ""))."\n"; } }