[MOBY-guts] biomoby commit

[Mark Wilkinson]

mwilkinson
Tue Dec 16 15:46:40 EST 2003
Update of /home/repository/moby/moby-live/Perl/scripts/Services
In directory pub.open-bio.org:/tmp/cvs-serv665/scripts/Services

Modified Files:
	LocalServices.pm 
Log Message:
corrected the SeqHound call for EMBL accession numbers  Added a new service that wraps the SeqHound SHoundGetTaxParent function to retrieve the taxonomic parents of a given taxon id.

moby-live/Perl/scripts/Services LocalServices.pm,1.48,1.49
===================================================================
RCS file: /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm,v
retrieving revision 1.48
retrieving revision 1.49
diff -u -r1.48 -r1.49
--- /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/12/11 22:30:53	1.48
+++ /home/repository/moby/moby-live/Perl/scripts/Services/LocalServices.pm	2003/12/16 20:46:40	1.49
@@ -17,15 +17,31 @@
 use MIME::Base64;
 use XML::DOM;
 use MOBY::Client::OntologyServer;
-use MOBY::CommonSubs qw(:all);  # this provides the
-# subroutines:
-#getSimpleArticleIDs
-#getSimpleArticleNamespaceURI
-#simpleResponse
-#responseHeader
-#responseFooter
-#getInputArticles
-#getNodeContentWithArticle
+use MOBY::CommonSubs qw(:all);  # this provides the following vars and functions
+    #getSimpleArticleIDs
+    #getSimpleArticleNamespaceURI
+    #simpleResponse
+    #responseHeader
+    #responseFooter
+    #getInputArticles
+    #getInputs
+    #getInputID
+    #getArticles
+    #getCollectedSimples
+    #getNodeContentWithArticle
+    #extractRawContent
+    #collectionResponse
+    #validateNamespaces
+    #validateThisNamespace
+    #isSimpleArticle
+    #isCollectionArticle
+    #extractResponseArticles
+    #getResponseArticles
+    #getCrossReferences
+    #genericServiceInputParser
+    #COLLECTION
+    #SIMPLE
+
 my $debug = 1;
 
 use vars qw(@ISA);
@@ -103,7 +119,7 @@
     return SOAP::Data->type('base64' => (responseHeader("illuminae.com") . $MOBY_RESPONSE . responseFooter));    
 }
 
-sub getTaxParent { # DOES NOT WORK - SHound call doesn't exist
+sub getTaxParent { # now it works.
     my ($caller, $data) = @_;
     my $MOBY_RESPONSE;
     my (@inputs)= genericServiceInputParser($data); # ([SIMPLE, $queryID, $simple],...)
@@ -327,14 +343,6 @@
 #  ===============================================
 #  =    Genbank Retrieval Scripts                =
 #  =                                             =
-#  = Note:  The two VirtualSequenceRetrieve's    =
-#  =        and two SequenceRetrieves below could=
-#  =        have been registered as two services =
-#  =        instead of four, by simply           =
-#  =        registering each under two different =
-#  =        namespaces (Acc and gi) instead of   =
-#  =        having a single service for each     =
-#  =        namespace                            =
 #  ===============================================
 
 
@@ -369,7 +377,7 @@
 				my $gb = SHoundGetGenBankff($identifier);
 	            (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
 				$MOBY_RESPONSE .= simpleResponse("<genbank-flatfile namespace='NCBI_gi' id='$identifier'><![CDATA[$gb]]></genbank-flatfile>", "", $qID);
-			} elsif ($ns eq $validNS{'NCBI_Acc'}){  # THIS ONE DOESN'T WORK YET????
+			} elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
 				my $gi = SHoundFindAcc($identifier);
 				(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
 				my $gb = SHoundGetGenBankff($gi);
@@ -458,7 +466,7 @@
 				$tempresponse .="</CrossReference>\n<Integer namespace='' id='' articleName='Length'>".($SEQ->length)."</Integer>
 												 </VirtualSequence>";
 				$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
-			} elsif ($ns eq $validNS{'NCBI_Acc'}){  # THIS ONE DOESN'T WORK YET????
+			} elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
 				my $gi = SHoundFindAcc($identifier);
 				(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
 				my ($SEQ, $length, $seq) = _makeSeqObj($gi);
@@ -541,7 +549,7 @@
 												 <String namespace='' id='' articleName='SequenceString'>".($SEQ->seq)."</String>
 												 </$objType>";
 				$MOBY_RESPONSE .= simpleResponse($tempresponse, "", $qID);
-			} elsif ($ns eq $validNS{'NCBI_Acc'}){  # THIS ONE DOESN'T WORK YET????
+			} elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
 				my $gi = SHoundFindAcc($identifier);
 				(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
 				my ($SEQ, $length, $seq) = _makeSeqObj($gi);
@@ -617,7 +625,7 @@
 				my $gb = SHoundGetFasta($identifier);
 	            (($MOBY_RESPONSE .= simpleResponse("", "No_genbank_record_found", $qID)) && next) unless $gb;
 				$MOBY_RESPONSE .= simpleResponse("<FASTA namespace='NCBI_gi' id='$identifier'><![CDATA[$gb]]></FASTA>", "", $qID);
-			} elsif ($ns eq $validNS{'NCBI_Acc'}){  # THIS ONE DOESN'T WORK YET????
+			} elsif (($ns eq $validNS{'NCBI_Acc'}) || ($ns eq $validNS{'EMBL'})){
 				my $gi = SHoundFindAcc($identifier);
 				(($MOBY_RESPONSE .= simpleResponse("", "No_gi_found_for_accession", $qID)) && next) unless $gi;
 				my $gb = SHoundGetFasta($gi);