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fix bug in db dump #740

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Merged
teharrison merged 2 commits into from
Jun 30, 2015
Merged

fix bug in db dump #740

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51dbb98
fix bug in db dump
teharrison Jun 30, 2015
8d7dbc9
add bulkload dependency
teharrison Jun 30, 2015
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7 changes: 2 additions & 5 deletions 7 src/MGRAST/tools/BulkLoader/BulkLoader.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -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 "${option}"
Expand Down Expand Up @@ -46,10 +46,7 @@ if [ -z "$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"
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Binary file added BIN +33.1 KB src/MGRAST/tools/BulkLoader/opencsv-3.4.jar
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8 changes: 4 additions & 4 deletions 8 src/MGRAST/tools/dump_annotation_for_cass.pl
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Original file line number Diff line number Diff line change
Expand Up @@ -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 = {};
Expand Down Expand Up @@ -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 = {};
Expand Down Expand Up @@ -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 = {};
Expand All @@ -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";
}
}

Expand Down
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