[MOBY-guts] biomoby commit
Mark Wilkinson
mwilkinson at pub.open-bio.org
Mon Feb 23 21:31:53 UTC 2004
mwilkinson
Mon Feb 23 16:31:53 EST 2004
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv7531/Services
Modified Files:
LocalServices.pm
Log Message:
updating my services to remove illegal whitespace from objects that inherit from a primitive. Will send a note about this to the mailing list with further comment
moby-live/Perl/scripts/Services LocalServices.pm,1.61,1.62
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.61
retrieving revision 1.62
diff -u -r1.61 -r1.62
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2004/02/10 01:17:04 1.61
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm 2004/02/23 21:31:53 1.62
@@ -92,10 +92,10 @@
my ($caller, $data) = @_;
my $MOBY_RESPONSE;
my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
- return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs));
+ return SOAP::Data->type('base64' => responseHeader("illuminae.com") . responseFooter()) unless (scalar(@inputs)); # invalid - return empty
my ($validNS) = validateNamespaces("taxon"); # ONLY do this if you are intending to be namespace aware!
- return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS;
+ return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . responseFooter)) unless $validNS; # invalid - return empty
foreach (@inputs){
my ($articleType, $qID, $input) = @{$_};
@@ -118,7 +118,6 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -153,7 +152,6 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -187,7 +185,6 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -222,7 +219,6 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -257,7 +253,6 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -295,7 +290,6 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -333,7 +327,6 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -367,7 +360,6 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -401,7 +393,6 @@
$MOBY_RESPONSE .= collectionResponse(\@simples, "", $qID);
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -428,7 +419,6 @@
$parent && ($MOBY_RESPONSE .= simpleResponse("<Object namespace='taxon' id='$parent'/>", "", $qID));
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -453,13 +443,12 @@
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless ($namespace eq $validNS);
my $name = SHoundGetTaxNameFromTaxID($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless ($name);
- $name && ($MOBY_RESPONSE .= simpleResponse("<String namespace='taxon' id='$identifier'>
- <CrossReference>
- <Object namespace='Global_Keyword' id='$name'/>
- </CrossReference>$name</String>", "", $qID));
+ $name && ($MOBY_RESPONSE .= simpleResponse("<String namespace='taxon' id='$identifier'>".
+ "<CrossReference>".
+ "<Object namespace='Global_Keyword' id='$name'/>".
+ "</CrossReference>$name</String>", "", $qID));
}
}
- print STDERR responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter;
return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));
}
@@ -668,22 +657,22 @@
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $gi;
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("<genbank-flatfile namespace='NCBI_gi' id='$gi'>
- <CrossReference>
- <Object namespace='$ns' id='$identifier'/>
- </CrossReference>
- <![CDATA[$gb]]></genbank-flatfile>",
+ $MOBY_RESPONSE .= simpleResponse("<genbank-flatfile namespace='NCBI_gi' id='$gi'>".
+ "<CrossReference>".
+ "<Object namespace='$ns' id='$identifier'/>".
+ "</CrossReference>".
+ "<![CDATA[$gb]]></genbank-flatfile>",
"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $gi;
my $gb = SHoundGetGenBankff($gi);
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("<genbank-flatfile namespace='NCBI_gi' id='$gi'>
- <CrossReference>
- <Object namespace='$ns' id='$identifier'/>
- </CrossReference>
- <![CDATA[$gb]]></genbank-flatfile>",
+ $MOBY_RESPONSE .= simpleResponse("<genbank-flatfile namespace='NCBI_gi' id='$gi'>".
+ "<CrossReference>".
+ "<Object namespace='$ns' id='$identifier'/>".
+ "</CrossReference>".
+ "<![CDATA[$gb]]></genbank-flatfile>",
"", $qID);
}
}
@@ -916,22 +905,22 @@
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $gi;
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("<FASTA namespace='NCBI_gi' id='$gi'>
- <CrossReference>
- <Object namespace='$ns' id='$identifier'/>
- </CrossReference>
- <![CDATA[$gb]]></FASTA>",
+ $MOBY_RESPONSE .= simpleResponse("<FASTA namespace='NCBI_gi' id='$gi'>".
+ "<CrossReference>".
+ "<Object namespace='$ns' id='$identifier'/>".
+ "</CrossReference>".
+ "<![CDATA[$gb]]></FASTA>",
"", $qID);
} else {
my $gi = SHoundFindName($identifier);
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $gi;
my $gb = SHoundGetFasta($gi);
(($MOBY_RESPONSE .= simpleResponse("", "", $qID)) && next) unless $gb;
- $MOBY_RESPONSE .= simpleResponse("<FASTA namespace='NCBI_gi' id='$gi'>
- <CrossReference>
- <Object namespace='$ns' id='$identifier'/>
- </CrossReference>
- <![CDATA[$gb]]></FASTA>",
+ $MOBY_RESPONSE .= simpleResponse("<FASTA namespace='NCBI_gi' id='$gi'>".
+ "<CrossReference>".
+ "<Object namespace='$ns' id='$identifier'/>".
+ "</CrossReference>".
+ "<![CDATA[$gb]]></FASTA>",
"", $qID);
}
}
@@ -991,11 +980,11 @@
if ($res->is_success) { # if successful, then base64 encide the data
my $image_data = encode_base64($res->content); # and create the simple image object
# push @simples, "<moby:b64_encoded_jpeg namespace='$namespace_LSID' id='$Allele'>$image_data</moby:b64_encoded_jpeg>"; # push it onto the collection list
- push @simples, qq{<SimpleAnnotatedJPEGImage namespace="DragonDB_Allele" id="$identifier">
- <CrossReference>
- <Object namespace="DragonDB_Gene" id="$Locus"/>
- </CrossReference>$image_data<String namespace="" id="" articleName="Description">$picdesc</String>
- </SimpleAnnotatedJPEGImage>};
+ push @simples, "<SimpleAnnotatedJPEGImage namespace='DragonDB_Allele' id='$identifier'>".
+ "<CrossReference>".
+ "<Object namespace='DragonDB_Gene' id='$Locus'/>".
+ "</CrossReference>$image_data<String namespace='' id='' articleName='Description'>$picdesc</String>".
+ "</SimpleAnnotatedJPEGImage>";
} # no else
}
}
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