[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Thu Dec 11 18:22:02 UTC 2003
mwilkinson
Thu Dec 11 13:22:02 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv4393/Services
Modified Files:
LocalServices.pm
Log Message:
fixed the CRIB XML tag - it is CrossReference not CrossReferences. This also pointed me to an error in the API documentation which is also now fixed and consistent throughout
moby-live/Perl/scripts/Services LocalServices.pm,1.46,1.47
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.46
retrieving revision 1.47
diff -u -r1.46 -r1.47
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 18:08:14 1.46
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2003/12/11 18:22:02 1.47
@@ -284,9 +284,9 @@
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("<genbank-flatfile namespace='NCBI_gi' id='$gi'>
- <CrossReferences>
+ <CrossReference>
<Object namespace='$ns' id='$identifier'/>
- </CrossReferences>
+ </CrossReference>
<![CDATA[$gb]]></genbank-flatfile>",
"", $qID);
} else {
@@ -295,9 +295,9 @@
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("<genbank-flatfile namespace='NCBI_gi' id='$gi'>
- <CrossReferences>
+ <CrossReference>
<Object namespace='$ns' id='$identifier'/>
- </CrossReferences>
+ </CrossReference>
<![CDATA[$gb]]></genbank-flatfile>",
"", $qID);
}
@@ -359,12 +359,12 @@
my ($SEQ, $length, $seq) = _makeSeqObj($identifier);
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
- my $tempresponse = "<VirtualSequence namespace='NCBI_gi' id='$identifier'><CrossReferences>\n";
+ my $tempresponse = "<VirtualSequence namespace='NCBI_gi' id='$identifier'><CrossReference>\n";
if ($taxon){ $tempresponse .="<Object namespace='taxon' id='$taxon'/>\n"}
if ($kw){$tempresponse .="<Object namespace='Global_Keyword' id='$kw'/>\n"}
if ($acc){$tempresponse .="<Object namespace='NCBI_Acc' id='$acc'/>\n"}
$tempresponse .="<Object namespace='NCBI_gi' id='$identifier'/>\n";
- $tempresponse .="</CrossReferences>\n<Integer namespace='' id='' articleName='Length'>".($SEQ->length)."</Integer>
+ $tempresponse .="</CrossReference>\n<Integer namespace='' id='' articleName='Length'>".($SEQ->length)."</Integer>
</VirtualSequence>";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
} elsif ($ns eq $validNS{'NCBI_Acc'}){ # THIS ONE DOESN'T WORK YET????
@@ -373,13 +373,13 @@
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
- my $tempresponse = "<VirtualSequence namespace='NCBI_gi' id='$gi'>\n<CrossReferences>\n";
+ my $tempresponse = "<VirtualSequence namespace='NCBI_gi' id='$gi'>\n<CrossReference>\n";
if ($taxon){ $tempresponse .="<Object namespace='taxon' id='$taxon'/>\n"}
if ($kw){$tempresponse .="<Object namespace='Global_Keyword' id='$kw'/>\n"}
if ($acc){$tempresponse .="<Object namespace='NCBI_Acc' id='$acc'/>\n"}
$tempresponse .="<Object namespace='NCBI_gi' id='$gi'/>\n";
$tempresponse .="<Object namespace='$ns' id='$identifier'/>
- </CrossReferences>
+ </CrossReference>
<Integer namespace='' id='' articleName='Length'>".($SEQ->length)."</Integer>
</VirtualSequence>";
$MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
@@ -389,13 +389,13 @@
my ($SEQ, $length, $seq) = _makeSeqObj($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
- my $tempresponse = "<VirtualSequence namespace='NCBI_gi' id='$gi'>\n<CrossReferences>\n";
+ my $tempresponse = "<VirtualSequence namespace='NCBI_gi' id='$gi'>\n<CrossReference>\n";
if ($taxon){ $tempresponse .="<Object namespace='taxon' id='$taxon'/>\n"}
if ($kw){$tempresponse .="<Object namespace='Global_Keyword' id='$kw'/>\n"}
if ($acc){$tempresponse .="<Object namespace='NCBI_Acc' id='$acc'/>\n"}
$tempresponse .="<Object namespace='NCBI_gi' id='$gi'/>\n";
$tempresponse .="<Object namespace='$ns' id='$identifier'/>
- </CrossReferences>
+ </CrossReference>
<Integer namespace='' id='' articleName='Length'>".($SEQ->length)."</Integer>
</VirtualSequence>";
$MOBY_RESPONSE .= simpleResponse($tempresponse,"", $qID);
@@ -441,12 +441,12 @@
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'><CrossReferences>\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$identifier'><CrossReference>\n";
if ($taxon){ $tempresponse .="<Object namespace='taxon' id='$taxon'/>\n"}
if ($kw){$tempresponse .="<Object namespace='Global_Keyword' id='$kw'/>\n"}
if ($acc){$tempresponse .="<Object namespace='NCBI_Acc' id='$acc'/>\n"}
$tempresponse .="<Object namespace='NCBI_gi' id='$identifier'/>\n";
- $tempresponse .="</CrossReferences>\n<Integer namespace='' id='' articleName='Length'>".($SEQ->length)."</Integer>
+ $tempresponse .="</CrossReference>\n<Integer namespace='' id='' articleName='Length'>".($SEQ->length)."</Integer>
<String namespace='' id='' articleName='SequenceString'>".($SEQ->seq)."</String>
</$objType>";
$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
@@ -457,13 +457,13 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n<CrossReferences>\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n<CrossReference>\n";
if ($taxon){ $tempresponse .="<Object namespace='taxon' id='$taxon'/>\n"}
if ($kw){$tempresponse .="<Object namespace='Global_Keyword' id='$kw'/>\n"}
if ($acc){$tempresponse .="<Object namespace='NCBI_Acc' id='$acc'/>\n"}
$tempresponse .="<Object namespace='NCBI_gi' id='$gi'/>\n";
$tempresponse .="<Object namespace='$ns' id='$identifier'/>
- </CrossReferences>
+ </CrossReference>
<Integer namespace='' id='' articleName='Length'>".($SEQ->length)."</Integer>
<String namespace='' id='' articleName='SequenceString'>".($SEQ->seq)."</String>
</$objType>";
@@ -475,13 +475,13 @@
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $SEQ;
my ($acc, $kw, $taxon) = _getXrefs($SEQ);
my $objType = $objtype{$SEQ->alphabet};
- my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n<CrossReferences>\n";
+ my $tempresponse = "<$objType namespace='NCBI_gi' id='$gi'>\n<CrossReference>\n";
if ($taxon){ $tempresponse .="<Object namespace='taxon' id='$taxon'/>\n"}
if ($kw){$tempresponse .="<Object namespace='Global_Keyword' id='$kw'/>\n"}
if ($acc){$tempresponse .="<Object namespace='NCBI_Acc' id='$acc'/>\n"}
$tempresponse .="<Object namespace='NCBI_gi' id='$gi'/>\n";
$tempresponse .="<Object namespace='$ns' id='$identifier'/>
- </CrossReferences>
+ </CrossReference>
<Integer namespace='' id='' articleName='Length'>".($SEQ->length)."</Integer>
<String namespace='' id='' articleName='SequenceString'>".($SEQ->seq)."</String>
</$objType>";
@@ -532,9 +532,9 @@
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("<FASTA namespace='NCBI_gi' id='$gi'>
- <CrossReferences>
+ <CrossReference>
<Object namespace='$ns' id='$identifier'/>
- </CrossReferences>
+ </CrossReference>
<![CDATA[$gb]]></FASTA>",
"", $qID);
} else {
@@ -543,9 +543,9 @@
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
$MOBY_RESPONSE .= simpleResponse("<FASTA namespace='NCBI_gi' id='$gi'>
- <CrossReferences>
+ <CrossReference>
<Object namespace='$ns' id='$identifier'/>
- </CrossReferences>
+ </CrossReference>
<![CDATA[$gb]]></FASTA>",
"", $qID);
}
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