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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 12:48:58 UTC
[39/50] [abbrv] incubator-taverna-workbench-common-activities git
commit: taverna-wsdl-activity-ui/
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/440bbd62/src/test/resources/kegg.wsdl
----------------------------------------------------------------------
diff --git a/src/test/resources/kegg.wsdl b/src/test/resources/kegg.wsdl
deleted file mode 100644
index a62b707..0000000
--- a/src/test/resources/kegg.wsdl
+++ /dev/null
@@ -1,1889 +0,0 @@
-<?xml version="1.0"?>
-<definitions
- name="KEGG_v6.1"
- xmlns:typens="SOAP/KEGG"
- xmlns:xsd="http://www.w3.org/2001/XMLSchema"
- xmlns:soap="http://schemas.xmlsoap.org/wsdl/soap/"
- xmlns:soapenc="http://schemas.xmlsoap.org/soap/encoding/"
- xmlns:wsdl="http://schemas.xmlsoap.org/wsdl/"
- xmlns="http://schemas.xmlsoap.org/wsdl/"
- targetNamespace="SOAP/KEGG">
-
- <types>
- <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" targetNamespace="SOAP/KEGG">
- <xsd:import namespace="http://schemas.xmlsoap.org/soap/encoding/"/>
- <xsd:import namespace="http://schemas.xmlsoap.org/wsdl/"/>
-<!-- common variable -->
- <xsd:complexType name="ArrayOfint">
- <xsd:complexContent>
- <xsd:restriction base="soapenc:Array">
-
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="xsd:int[]"/>
- </xsd:restriction>
- </xsd:complexContent>
- </xsd:complexType>
- <xsd:complexType name="ArrayOfstring">
- <xsd:complexContent>
- <xsd:restriction base="soapenc:Array">
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="xsd:string[]"/>
- </xsd:restriction>
-
- </xsd:complexContent>
- </xsd:complexType>
-<!-- SSDB -->
- <xsd:complexType name="SSDBRelation">
- <xsd:all>
- <xsd:element name="genes_id1" type="xsd:string"/>
- <xsd:element name="genes_id2" type="xsd:string"/>
- <xsd:element name="sw_score" type="xsd:int"/>
- <xsd:element name="bit_score" type="xsd:float"/>
-
- <xsd:element name="identity" type="xsd:float"/>
- <xsd:element name="overlap" type="xsd:int"/>
- <xsd:element name="start_position1" type="xsd:int"/>
- <xsd:element name="end_position1" type="xsd:int"/>
- <xsd:element name="start_position2" type="xsd:int"/>
- <xsd:element name="end_position2" type="xsd:int"/>
- <xsd:element name="best_flag_1to2" type="xsd:boolean"/>
- <xsd:element name="best_flag_2to1" type="xsd:boolean"/>
- <xsd:element name="definition1" type="xsd:string"/>
-
- <xsd:element name="definition2" type="xsd:string"/>
- <xsd:element name="length1" type="xsd:int"/>
- <xsd:element name="length2" type="xsd:int"/>
- </xsd:all>
- </xsd:complexType>
- <xsd:complexType name="ArrayOfSSDBRelation">
- <xsd:complexContent>
- <xsd:restriction base="soapenc:Array">
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:SSDBRelation[]"/>
-
- </xsd:restriction>
- </xsd:complexContent>
- </xsd:complexType>
-<!-- MOTIF -->
- <xsd:complexType name="MotifResult">
- <xsd:all>
- <xsd:element name="motif_id" type="xsd:string"/>
- <xsd:element name="definition" type="xsd:string"/>
- <xsd:element name="genes_id" type="xsd:string"/>
-
- <xsd:element name="start_position" type="xsd:int"/>
- <xsd:element name="end_position" type="xsd:int"/>
- <xsd:element name="score" type="xsd:float"/>
- <xsd:element name="evalue" type="xsd:double"/>
- </xsd:all>
- </xsd:complexType>
- <xsd:complexType name="ArrayOfMotifResult">
- <xsd:complexContent>
- <xsd:restriction base="soapenc:Array">
-
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:MotifResult[]"/>
- </xsd:restriction>
- </xsd:complexContent>
- </xsd:complexType>
-<!-- DEFINITION -->
- <xsd:complexType name="Definition">
- <xsd:all>
- <xsd:element name="entry_id" type="xsd:string"/>
- <xsd:element name="definition" type="xsd:string"/>
-
- </xsd:all>
- </xsd:complexType>
- <xsd:complexType name="ArrayOfDefinition">
- <xsd:complexContent>
- <xsd:restriction base="soapenc:Array">
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:Definition[]"/>
- </xsd:restriction>
- </xsd:complexContent>
- </xsd:complexType>
-
-<!-- LinkDB -->
- <xsd:complexType name="LinkDBRelation">
- <xsd:all>
- <xsd:element name="entry_id1" type="xsd:string"/>
- <xsd:element name="entry_id2" type="xsd:string"/>
- <xsd:element name="type" type="xsd:string"/>
- <xsd:element name="path" type="xsd:string"/>
- </xsd:all>
- </xsd:complexType>
-
- <xsd:complexType name="ArrayOfLinkDBRelation">
- <xsd:complexContent>
- <xsd:restriction base="soapenc:Array">
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:LinkDBRelation[]"/>
- </xsd:restriction>
- </xsd:complexContent>
- </xsd:complexType>
-<!-- Pathway -->
- <xsd:complexType name="PathwayElement">
-
- <xsd:all>
- <xsd:element name="element_id" type="xsd:int"/>
- <xsd:element name="type" type="xsd:string"/>
- <xsd:element name="names" type="typens:ArrayOfstring"/>
- <xsd:element name="components" type="typens:ArrayOfint"/>
- </xsd:all>
- </xsd:complexType>
- <xsd:complexType name="ArrayOfPathwayElement">
- <xsd:complexContent>
-
- <xsd:restriction base="soapenc:Array">
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:PathwayElement[]"/>
- </xsd:restriction>
- </xsd:complexContent>
- </xsd:complexType>
- <xsd:complexType name="PathwayElementRelation">
- <xsd:all>
- <xsd:element name="element_id1" type="xsd:int"/>
- <xsd:element name="element_id2" type="xsd:int"/>
-
- <xsd:element name="type" type="xsd:string"/>
- <!--xsd:element name="name" type="xsd:string"/-->
- <xsd:element name="subtypes" type="typens:ArrayOfSubtype"/>
- </xsd:all>
- </xsd:complexType>
- <xsd:complexType name="ArrayOfPathwayElementRelation">
- <xsd:complexContent>
- <xsd:restriction base="soapenc:Array">
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:PathwayElementRelation[]"/>
-
- </xsd:restriction>
- </xsd:complexContent>
- </xsd:complexType>
- <xsd:complexType name="Subtype">
- <xsd:all>
- <xsd:element name="relation" type="xsd:string"/>
- <xsd:element name="element_id" type="xsd:int"/>
- <xsd:element name="type" type="xsd:string"/>
- </xsd:all>
-
- </xsd:complexType>
- <xsd:complexType name="ArrayOfSubtype">
- <xsd:complexContent>
- <xsd:restriction base="soapenc:Array">
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:Subtype[]"/>
- </xsd:restriction>
- </xsd:complexContent>
- </xsd:complexType>
-<!-- v6.0 -->
-
- <xsd:complexType name="StructureAlignment">
- <xsd:all>
- <xsd:element name="target_id" type="xsd:string"/>
- <xsd:element name="score" type="xsd:float"/>
- <xsd:element name="query_nodes" type="typens:ArrayOfint"/>
- <xsd:element name="target_nodes" type="typens:ArrayOfint"/>
- </xsd:all>
- </xsd:complexType>
- <xsd:complexType name="ArrayOfStructureAlignment">
-
- <xsd:complexContent>
- <xsd:restriction base="soapenc:Array">
- <xsd:attribute ref="soapenc:arrayType" wsdl:arrayType="typens:StructureAlignment[]"/>
- </xsd:restriction>
- </xsd:complexContent>
- </xsd:complexType>
-
- </xsd:schema>
- </types>
-
-<!-- KEGG information -->
-<!-- list_databases -->
- <message name="list_databasesRequest"/>
- <message name="list_databasesResponse">
- <part name="return" type="typens:ArrayOfDefinition"/>
- </message>
-<!-- list_organisms -->
- <message name="list_organismsRequest"/>
- <message name="list_organismsResponse">
- <part name="return" type="typens:ArrayOfDefinition"/>
-
- </message>
-<!-- list_pathways -->
- <message name="list_pathwaysRequest">
- <part name="org" type="xsd:string"/>
- </message>
- <message name="list_pathwaysResponse">
- <part name="return" type="typens:ArrayOfDefinition"/>
- </message>
-<!-- list_ko_classes -->
- <message name="list_ko_classesRequest">
-
- <part name="class_id" type="xsd:string"/>
- </message>
- <message name="list_ko_classesResponse">
- <part name="return" type="typens:ArrayOfDefinition"/>
- </message>
-<!-- DBGET -->
-<!-- binfo -->
- <message name="binfoRequest">
- <part name="db" type="xsd:string"/>
- </message>
-
- <message name="binfoResponse">
- <part name="return" type="xsd:string"/>
- </message>
-<!-- bget -->
- <message name="bgetRequest">
- <part name="string" type="xsd:string"/>
- </message>
- <message name="bgetResponse">
- <part name="return" type="xsd:string"/>
-
- </message>
-<!-- bfind -->
- <message name="bfindRequest">
- <part name="string" type="xsd:string"/>
- </message>
- <message name="bfindResponse">
- <part name="return" type="xsd:string"/>
- </message>
-<!-- btit -->
- <message name="btitRequest">
-
- <part name="string" type="xsd:string"/>
- </message>
- <message name="btitResponse">
- <part name="return" type="xsd:string"/>
- </message>
-<!-- bconv -->
- <message name="bconvRequest">
- <part name="string" type="xsd:string"/>
- </message>
-
- <message name="bconvResponse">
- <part name="return" type="xsd:string"/>
- </message>
-<!-- LinkDB -->
- <message name="get_linkdb_by_entryRequest">
- <part name="entry_id" type="xsd:string"/>
- <part name="db" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
-
- </message>
- <message name="get_linkdb_by_entryResponse">
- <part name="return" type="typens:ArrayOfLinkDBRelation"/>
- </message>
-<!-- SSDB -->
-<!-- get_best_neighbors_by_gene -->
- <message name="get_best_neighbors_by_geneRequest">
- <part name="genes_id" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
-
- </message>
- <message name="get_best_neighbors_by_geneResponse">
- <part name="return" type="typens:ArrayOfSSDBRelation"/>
- </message>
-<!-- get_best_best_neighbors_by_gene -->
- <message name="get_best_best_neighbors_by_geneRequest">
- <part name="genes_id" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
-
- </message>
- <message name="get_best_best_neighbors_by_geneResponse">
- <part name="return" type="typens:ArrayOfSSDBRelation"/>
- </message>
-<!-- get_reverse_best_neighbors_by_gene -->
- <message name="get_reverse_best_neighbors_by_geneRequest">
- <part name="genes_id" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
-
- </message>
- <message name="get_reverse_best_neighbors_by_geneResponse">
- <part name="return" type="typens:ArrayOfSSDBRelation"/>
- </message>
-<!-- get_paralogs_by_geneRequest -->
- <message name="get_paralogs_by_geneRequest">
- <part name="genes_id" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
-
- </message>
- <message name="get_paralogs_by_geneResponse">
- <part name="return" type="typens:ArrayOfSSDBRelation"/>
- </message>
-<!-- MOTIF -->
-<!-- get_motifs_by_gene -->
- <message name="get_motifs_by_geneRequest">
- <part name="genes_id" type="xsd:string"/>
- <part name="db" type="xsd:string"/>
- </message>
-
- <message name="get_motifs_by_geneResponse">
- <part name="return" type="typens:ArrayOfMotifResult"/>
- </message>
-<!-- get_genes_by_motifs -->
- <message name="get_genes_by_motifsRequest">
- <part name="motif_id_list" type="typens:ArrayOfstring"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
- </message>
-
- <message name="get_genes_by_motifsResponse">
- <part name="return" type="typens:ArrayOfDefinition"/>
- </message>
-<!-- KO,OC,PC -->
-<!-- get_ko_by_gene -->
- <message name="get_ko_by_geneRequest">
- <part name="genes_id" type="xsd:string"/>
- </message>
- <message name="get_ko_by_geneResponse">
- <part name="return" type="typens:ArrayOfstring"/>
-
- </message>
-<!-- get_ko_by_ko_class -->
- <message name="get_ko_by_ko_classRequest">
- <part name="class_id" type="xsd:string"/>
- </message>
- <message name="get_ko_by_ko_classResponse">
- <part name="return" type="typens:ArrayOfDefinition"/>
- </message>
-<!-- get_genes_by_ko -->
- <message name="get_genes_by_koRequest">
-
- <part name="ko_id" type="xsd:string"/>
- <part name="org" type="xsd:string"/>
- </message>
- <message name="get_genes_by_koResponse">
- <part name="return" type="typens:ArrayOfDefinition"/>
- </message>
-<!-- get_genes_by_ko_class -->
- <message name="get_genes_by_ko_classRequest">
- <part name="class_id" type="xsd:string"/>
-
- <part name="org" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
- </message>
- <message name="get_genes_by_ko_classResponse">
- <part name="return" type="typens:ArrayOfDefinition"/>
- </message>
-<!-- get_oc_members_by_gene -->
-<!--
- <message name="get_oc_members_by_geneRequest">
- <part name="genes_id" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
- </message>
- <message name="get_oc_members_by_geneResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
--->
-<!-- get_pc_members_by_gene -->
-
-<!--
- <message name="get_pc_members_by_geneRequest">
- <part name="genes_id" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
- </message>
- <message name="get_pc_members_by_geneResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
--->
-<!-- PATHWAY -->
-<!-- Coloring pathways -->
-<!-- mark_pathway_by_objects -->
- <message name="get_elements_by_pathwayRequest">
- <part name="pathway_id" type="xsd:string"/>
- </message>
- <message name="get_elements_by_pathwayResponse">
- <part name="return" type="typens:ArrayOfPathwayElement"/>
- </message>
- <message name="get_element_relations_by_pathwayRequest">
-
- <part name="pathway_id" type="xsd:string"/>
- </message>
- <message name="get_element_relations_by_pathwayResponse">
- <part name="return" type="typens:ArrayOfPathwayElementRelation"/>
- </message>
- <message name="color_pathway_by_elementsRequest">
- <part name="pathway_id" type="xsd:string"/>
- <part name="element_list" type="typens:ArrayOfint"/>
- <part name="fg_color_list" type="typens:ArrayOfstring"/>
-
- <part name="bg_color_list" type="typens:ArrayOfstring"/>
- </message>
- <message name="color_pathway_by_elementsResponse">
- <part name="return" type="xsd:string"/>
- </message>
- <message name="get_html_of_colored_pathway_by_elementsRequest">
- <part name="pathway_id" type="xsd:string"/>
- <part name="element_list" type="typens:ArrayOfint"/>
- <part name="fg_color_list" type="typens:ArrayOfstring"/>
-
- <part name="bg_color_list" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_html_of_colored_pathway_by_elementsResponse">
- <part name="return" type="xsd:string"/>
- </message>
-
- <message name="mark_pathway_by_objectsRequest">
- <part name="pathway_id" type="xsd:string"/>
- <part name="object_id_list" type="typens:ArrayOfstring"/>
-
- </message>
- <message name="mark_pathway_by_objectsResponse">
- <part name="return" type="xsd:string"/>
- </message>
-<!-- color_pathway_by_objects -->
- <message name="color_pathway_by_objectsRequest">
- <part name="pathway_id" type="xsd:string"/>
- <part name="object_id_list" type="typens:ArrayOfstring"/>
- <part name="fg_color_list" type="typens:ArrayOfstring"/>
-
- <part name="bg_color_list" type="typens:ArrayOfstring"/>
- </message>
- <message name="color_pathway_by_objectsResponse">
- <part name="return" type="xsd:string"/>
- </message>
-<!-- get_html_org_marked_pathway_by_objects -->
- <message name="get_html_of_marked_pathway_by_objectsRequest">
- <part name="pathway_id" type="xsd:string"/>
- <part name="object_id_list" type="typens:ArrayOfstring"/>
-
- </message>
- <message name="get_html_of_marked_pathway_by_objectsResponse">
- <part name="return" type="xsd:string"/>
- </message>
-<!-- get_html_of_colored_pathway_by_objects -->
- <message name="get_html_of_colored_pathway_by_objectsRequest">
- <part name="pathway_id" type="xsd:string"/>
- <part name="object_id_list" type="typens:ArrayOfstring"/>
- <part name="fg_color_list" type="typens:ArrayOfstring"/>
-
- <part name="bg_color_list" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_html_of_colored_pathway_by_objectsResponse">
- <part name="return" type="xsd:string"/>
- </message>
-<!-- Objects on the pathway -->
-<!-- get_genes_by_pathway -->
- <message name="get_genes_by_pathwayRequest">
- <part name="pathway_id" type="xsd:string"/>
- </message>
-
- <message name="get_genes_by_pathwayResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-<!-- get_enzymes_by_pathway -->
- <message name="get_enzymes_by_pathwayRequest">
- <part name="pathway_id" type="xsd:string"/>
- </message>
- <message name="get_enzymes_by_pathwayResponse">
- <part name="return" type="typens:ArrayOfstring"/>
-
- </message>
-<!-- get_reactions_by_pathway -->
- <message name="get_reactions_by_pathwayRequest">
- <part name="pathway_id" type="xsd:string"/>
- </message>
- <message name="get_reactions_by_pathwayResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-<!-- Pathways by objects -->
-<!-- get_pathways_by_genes -->
-
- <message name="get_pathways_by_genesRequest">
- <part name="genes_id_list" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_pathways_by_genesResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-<!-- get_pathways_by_enzymes -->
- <message name="get_pathways_by_enzymesRequest">
- <part name="enzyme_id_list" type="typens:ArrayOfstring"/>
-
- </message>
- <message name="get_pathways_by_enzymesResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-<!-- get_pathways_by_reactions -->
- <message name="get_pathways_by_reactionsRequest">
- <part name="reaction_id_list" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_pathways_by_reactionsResponse">
-
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-<!-- Mutual transformation of objects -->
-<!-- Relation among pathways -->
-<!-- get_linked_pathways -->
- <message name="get_linked_pathwaysRequest">
- <part name="pathway_id" type="xsd:string"/>
- </message>
- <message name="get_linked_pathwaysResponse">
- <part name="return" type="typens:ArrayOfstring"/>
-
- </message>
-<!-- Relation among genes and enzymes -->
-<!-- get_genes_by_enzyme -->
- <message name="get_genes_by_enzymeRequest">
- <part name="enzyme_id" type="xsd:string"/>
- <part name="org" type="xsd:string"/>
- </message>
- <message name="get_genes_by_enzymeResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-
-<!-- get_enzymes_by_gene -->
- <message name="get_enzymes_by_geneRequest">
- <part name="genes_id" type="xsd:string"/>
- </message>
- <message name="get_enzymes_by_geneResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-<!-- Relation among enzymes, compounds and reactions -->
-<!-- get_enzymes_by_reaction -->
- <message name="get_enzymes_by_reactionRequest">
-
- <part name="reaction_id" type="xsd:string"/>
- </message>
- <message name="get_enzymes_by_reactionResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-<!-- get_reactions_by_enzyme -->
- <message name="get_reactions_by_enzymeRequest">
- <part name="enzyme_id" type="xsd:string"/>
- </message>
-
- <message name="get_reactions_by_enzymeResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-<!-- GENES -->
-<!-- get_genes_by_organism -->
- <message name="get_genes_by_organismRequest">
- <part name="org" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
- </message>
-
- <message name="get_genes_by_organismResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-<!-- GENOME -->
-<!-- get_number_of_genes_by_organism -->
- <message name="get_number_of_genes_by_organismRequest">
- <part name="abbr" type="xsd:string"/>
- </message>
- <message name="get_number_of_genes_by_organismResponse">
- <part name="return" type="xsd:int"/>
-
- </message>
-<!-- LIGAND -->
- <message name="get_reactions_by_glycanRequest">
- <part name="glycan_id" type="xsd:string"/>
- </message>
- <message name="get_reactions_by_glycanResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_reactions_by_compoundRequest">
-
- <part name="compound_id" type="xsd:string"/>
- </message>
- <message name="get_reactions_by_compoundResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_enzymes_by_glycanRequest">
- <part name="glycan_id" type="xsd:string"/>
- </message>
- <message name="get_enzymes_by_glycanResponse">
-
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_enzymes_by_compoundRequest">
- <part name="compound_id" type="xsd:string"/>
- </message>
- <message name="get_enzymes_by_compoundResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_pathways_by_compoundsRequest">
-
- <part name="compound_id_list" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_pathways_by_compoundsResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_pathways_by_glycansRequest">
- <part name="glycan_id_list" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_pathways_by_glycansResponse">
-
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_compounds_by_pathwayRequest">
- <part name="pathway_id" type="xsd:string"/>
- </message>
- <message name="get_compounds_by_pathwayResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_compounds_by_enzymeRequest">
-
- <part name="enzyme_id" type="xsd:string"/>
- </message>
- <message name="get_compounds_by_enzymeResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_glycans_by_enzymeRequest">
- <part name="enzyme_id" type="xsd:string"/>
- </message>
- <message name="get_glycans_by_enzymeResponse">
-
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_glycans_by_pathwayRequest">
- <part name="pathway_id" type="xsd:string"/>
- </message>
- <message name="get_glycans_by_pathwayResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_compounds_by_reactionRequest">
-
- <part name="reaction_id" type="xsd:string"/>
- </message>
- <message name="get_compounds_by_reactionResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_glycans_by_reactionRequest">
- <part name="reaction_id" type="xsd:string"/>
- </message>
- <message name="get_glycans_by_reactionResponse">
-
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="convert_mol_to_kcfRequest">
- <part name="mol_text" type="xsd:string"/>
- </message>
- <message name="convert_mol_to_kcfResponse">
- <part name="return" type="xsd:string"/>
- </message>
- <message name="get_kos_by_pathwayRequest">
-
- <part name="pathway_id" type="xsd:string"/>
- </message>
- <message name="get_kos_by_pathwayResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
- <message name="get_pathways_by_kosRequest">
- <part name="ko_id_list" type="typens:ArrayOfstring"/>
- <part name="org" type="xsd:string"/>
- </message>
-
- <message name="get_pathways_by_kosResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-
-<!-- v6.0 -->
- <message name="search_compounds_by_nameRequest">
- <part name="name" type="xsd:string"/>
- </message>
- <message name="search_compounds_by_nameResponse">
- <part name="return" type="typens:ArrayOfstring"/>
-
- </message>
-
- <message name="search_glycans_by_nameRequest">
- <part name="name" type="xsd:string"/>
- </message>
- <message name="search_glycans_by_nameResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-
- <message name="search_compounds_by_compositionRequest">
-
- <part name="composition" type="xsd:string"/>
- </message>
- <message name="search_compounds_by_compositionResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-
- <message name="search_compounds_by_massRequest">
- <part name="mass" type="xsd:float"/>
- <part name="range" type="xsd:float"/>
-
- </message>
- <message name="search_compounds_by_massResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-
- <message name="search_glycans_by_massRequest">
- <part name="mass" type="xsd:float"/>
- <part name="range" type="xsd:float"/>
- </message>
-
- <message name="search_glycans_by_massResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-
- <message name="search_glycans_by_compositionRequest">
- <part name="composition" type="xsd:string"/>
- </message>
- <message name="search_glycans_by_compositionResponse">
- <part name="return" type="typens:ArrayOfstring"/>
-
- </message>
-
- <message name="search_compounds_by_subcompRequest">
- <part name="mol" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
- </message>
- <message name="search_compounds_by_subcompResponse">
- <part name="return" type="typens:ArrayOfStructureAlignment"/>
-
- </message>
-
- <message name="search_glycans_by_kcamRequest">
- <part name="kcf" type="xsd:string"/>
- <part name="program" type="xsd:string"/>
- <part name="option" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
- </message>
-
- <message name="search_glycans_by_kcamResponse">
- <part name="return" type="typens:ArrayOfStructureAlignment"/>
- </message>
-
- <message name="get_linkdb_between_databasesRequest">
- <part name="from_db" type="xsd:string"/>
- <part name="to_db" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
-
- </message>
- <message name="get_linkdb_between_databasesResponse">
- <part name="return" type="typens:ArrayOfLinkDBRelation"/>
- </message>
-
-<!-- v6.1 -->
- <message name="search_drugs_by_nameRequest">
- <part name="name" type="xsd:string"/>
- </message>
- <message name="search_drugs_by_nameResponse">
-
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-
- <message name="search_drugs_by_compositionRequest">
- <part name="composition" type="xsd:string"/>
- </message>
- <message name="search_drugs_by_compositionResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-
- <message name="search_drugs_by_massRequest">
- <part name="mass" type="xsd:float"/>
- <part name="range" type="xsd:float"/>
- </message>
- <message name="search_drugs_by_massResponse">
- <part name="return" type="typens:ArrayOfstring"/>
- </message>
-
- <message name="search_drugs_by_subcompRequest">
-
- <part name="mol" type="xsd:string"/>
- <part name="offset" type="xsd:int"/>
- <part name="limit" type="xsd:int"/>
- </message>
- <message name="search_drugs_by_subcompResponse">
- <part name="return" type="typens:ArrayOfStructureAlignment"/>
- </message>
-
- <portType name="KEGGPortType">
-
-<!-- KEGG information -->
- <operation name="list_databases">
- <input message="typens:list_databasesRequest"/>
- <output message="typens:list_databasesResponse"/>
- </operation>
- <operation name="list_organisms">
- <input message="typens:list_organismsRequest"/>
- <output message="typens:list_organismsResponse"/>
- </operation>
-
- <operation name="list_pathways">
- <input message="typens:list_pathwaysRequest"/>
- <output message="typens:list_pathwaysResponse"/>
- </operation>
- <operation name="list_ko_classes">
- <input message="typens:list_ko_classesRequest"/>
- <output message="typens:list_ko_classesResponse"/>
- </operation>
-<!-- DBGET -->
-
- <operation name="binfo">
- <input message="typens:binfoRequest"/>
- <output message="typens:binfoResponse"/>
- </operation>
- <operation name="bget">
- <input message="typens:bgetRequest"/>
- <output message="typens:bgetResponse"/>
- </operation>
- <operation name="bfind">
-
- <input message="typens:bfindRequest"/>
- <output message="typens:bfindResponse"/>
- </operation>
- <operation name="btit">
- <input message="typens:btitRequest"/>
- <output message="typens:btitResponse"/>
- </operation>
- <operation name="bconv">
- <input message="typens:bconvRequest"/>
-
- <output message="typens:bconvResponse"/>
- </operation>
-<!-- LinkDB -->
- <operation name="get_linkdb_by_entry">
- <input message="typens:get_linkdb_by_entryRequest"/>
- <output message="typens:get_linkdb_by_entryResponse"/>
- </operation>
-<!-- SSDB -->
- <operation name="get_best_neighbors_by_gene">
- <input message="typens:get_best_neighbors_by_geneRequest"/>
-
- <output message="typens:get_best_neighbors_by_geneResponse"/>
- </operation>
- <operation name="get_best_best_neighbors_by_gene">
- <input message="typens:get_best_best_neighbors_by_geneRequest"/>
- <output message="typens:get_best_best_neighbors_by_geneResponse"/>
- </operation>
- <operation name="get_reverse_best_neighbors_by_gene">
- <input message="typens:get_reverse_best_neighbors_by_geneRequest"/>
- <output message="typens:get_reverse_best_neighbors_by_geneResponse"/>
-
- </operation>
- <operation name="get_paralogs_by_gene">
- <input message="typens:get_paralogs_by_geneRequest"/>
- <output message="typens:get_paralogs_by_geneResponse"/>
- </operation>
-<!-- MOTIF -->
- <operation name="get_motifs_by_gene">
- <input message="typens:get_motifs_by_geneRequest"/>
- <output message="typens:get_motifs_by_geneResponse"/>
-
- </operation>
- <operation name="get_genes_by_motifs">
- <input message="typens:get_genes_by_motifsRequest"/>
- <output message="typens:get_genes_by_motifsResponse"/>
- </operation>
-<!-- KO,OC,PC -->
- <operation name="get_ko_by_gene">
- <input message="typens:get_ko_by_geneRequest"/>
- <output message="typens:get_ko_by_geneResponse"/>
-
- </operation>
- <operation name="get_ko_by_ko_class">
- <input message="typens:get_ko_by_ko_classRequest"/>
- <output message="typens:get_ko_by_ko_classResponse"/>
- </operation>
- <operation name="get_genes_by_ko">
- <input message="typens:get_genes_by_koRequest"/>
- <output message="typens:get_genes_by_koResponse"/>
- </operation>
-
- <operation name="get_genes_by_ko_class">
- <input message="typens:get_genes_by_ko_classRequest"/>
- <output message="typens:get_genes_by_ko_classResponse"/>
- </operation>
-<!--
- <operation name="get_oc_members_by_gene">
- <input message="typens:get_oc_members_by_geneRequest"/>
- <output message="typens:get_oc_members_by_geneResponse"/>
- </operation>
--->
-<!--
- <operation name="get_pc_members_by_gene">
- <input message="typens:get_pc_members_by_geneRequest"/>
- <output message="typens:get_pc_members_by_geneResponse"/>
- </operation>
--->
-<!-- PATHWAY -->
-<!-- Coloring pathways -->
- <operation name="get_elements_by_pathway">
- <input message="typens:get_elements_by_pathwayRequest"/>
- <output message="typens:get_elements_by_pathwayResponse"/>
-
- </operation>
- <operation name="get_element_relations_by_pathway">
- <input message="typens:get_element_relations_by_pathwayRequest"/>
- <output message="typens:get_element_relations_by_pathwayResponse"/>
- </operation>
- <operation name="color_pathway_by_elements">
- <input message="typens:color_pathway_by_elementsRequest"/>
- <output message="typens:color_pathway_by_elementsResponse"/>
- </operation>
-
- <operation name="get_html_of_colored_pathway_by_elements">
- <input message="typens:get_html_of_colored_pathway_by_elementsRequest"/>
- <output message="typens:get_html_of_colored_pathway_by_elementsResponse"/>
- </operation>
-
- <operation name="mark_pathway_by_objects">
- <input message="typens:mark_pathway_by_objectsRequest"/>
- <output message="typens:mark_pathway_by_objectsResponse"/>
- </operation>
-
- <operation name="color_pathway_by_objects">
- <input message="typens:color_pathway_by_objectsRequest"/>
- <output message="typens:color_pathway_by_objectsResponse"/>
- </operation>
- <operation name="get_html_of_marked_pathway_by_objects">
- <input message="typens:get_html_of_marked_pathway_by_objectsRequest"/>
- <output message="typens:get_html_of_marked_pathway_by_objectsResponse"/>
- </operation>
- <operation name="get_html_of_colored_pathway_by_objects">
-
- <input message="typens:get_html_of_colored_pathway_by_objectsRequest"/>
- <output message="typens:get_html_of_colored_pathway_by_objectsResponse"/>
- </operation>
-<!-- Objects on the pathway -->
- <operation name="get_genes_by_pathway">
- <input message="typens:get_genes_by_pathwayRequest"/>
- <output message="typens:get_genes_by_pathwayResponse"/>
- </operation>
- <operation name="get_enzymes_by_pathway">
-
- <input message="typens:get_enzymes_by_pathwayRequest"/>
- <output message="typens:get_enzymes_by_pathwayResponse"/>
- </operation>
- <operation name="get_reactions_by_pathway">
- <input message="typens:get_reactions_by_pathwayRequest"/>
- <output message="typens:get_reactions_by_pathwayResponse"/>
- </operation>
-<!-- Pathways by objects -->
- <operation name="get_pathways_by_genes">
-
- <input message="typens:get_pathways_by_genesRequest"/>
- <output message="typens:get_pathways_by_genesResponse"/>
- </operation>
- <operation name="get_pathways_by_enzymes">
- <input message="typens:get_pathways_by_enzymesRequest"/>
- <output message="typens:get_pathways_by_enzymesResponse"/>
- </operation>
- <operation name="get_pathways_by_reactions">
- <input message="typens:get_pathways_by_reactionsRequest"/>
-
- <output message="typens:get_pathways_by_reactionsResponse"/>
- </operation>
-<!-- Mutual transformation of objects -->
-<!-- Realtion among pathways -->
- <operation name="get_linked_pathways">
- <input message="typens:get_linked_pathwaysRequest"/>
- <output message="typens:get_linked_pathwaysResponse"/>
- </operation>
-<!-- Realtion among genes and enzymes -->
- <operation name="get_genes_by_enzyme">
-
- <input message="typens:get_genes_by_enzymeRequest"/>
- <output message="typens:get_genes_by_enzymeResponse"/>
- </operation>
- <operation name="get_enzymes_by_gene">
- <input message="typens:get_enzymes_by_geneRequest"/>
- <output message="typens:get_enzymes_by_geneResponse"/>
- </operation>
-<!-- Realtion among enzymes, compounds and reactions -->
- <operation name="get_enzymes_by_reaction">
-
- <input message="typens:get_enzymes_by_reactionRequest"/>
- <output message="typens:get_enzymes_by_reactionResponse"/>
- </operation>
- <operation name="get_reactions_by_enzyme">
- <input message="typens:get_reactions_by_enzymeRequest"/>
- <output message="typens:get_reactions_by_enzymeResponse"/>
- </operation>
-<!-- GENES -->
- <operation name="get_genes_by_organism">
-
- <input message="typens:get_genes_by_organismRequest"/>
- <output message="typens:get_genes_by_organismResponse"/>
- </operation>
-<!-- GENOME -->
- <operation name="get_number_of_genes_by_organism">
- <input message="typens:get_number_of_genes_by_organismRequest"/>
- <output message="typens:get_number_of_genes_by_organismResponse"/>
- </operation>
-<!-- LIGAND -->
- <operation name="get_reactions_by_glycan">
-
- <input message="typens:get_reactions_by_glycanRequest"/>
- <output message="typens:get_reactions_by_glycanResponse"/>
- </operation>
- <operation name="get_reactions_by_compound">
- <input message="typens:get_reactions_by_compoundRequest"/>
- <output message="typens:get_reactions_by_compoundResponse"/>
- </operation>
- <operation name="get_enzymes_by_glycan">
- <input message="typens:get_enzymes_by_glycanRequest"/>
-
- <output message="typens:get_enzymes_by_glycanResponse"/>
- </operation>
- <operation name="get_enzymes_by_compound">
- <input message="typens:get_enzymes_by_compoundRequest"/>
- <output message="typens:get_enzymes_by_compoundResponse"/>
- </operation>
- <operation name="get_pathways_by_compounds">
- <input message="typens:get_pathways_by_compoundsRequest"/>
- <output message="typens:get_pathways_by_compoundsResponse"/>
-
- </operation>
- <operation name="get_pathways_by_glycans">
- <input message="typens:get_pathways_by_glycansRequest"/>
- <output message="typens:get_pathways_by_glycansResponse"/>
- </operation>
- <operation name="get_compounds_by_pathway">
- <input message="typens:get_compounds_by_pathwayRequest"/>
- <output message="typens:get_compounds_by_pathwayResponse"/>
- </operation>
-
- <operation name="get_glycans_by_pathway">
- <input message="typens:get_glycans_by_pathwayRequest"/>
- <output message="typens:get_glycans_by_pathwayResponse"/>
- </operation>
- <operation name="get_compounds_by_reaction">
- <input message="typens:get_compounds_by_reactionRequest"/>
- <output message="typens:get_compounds_by_reactionResponse"/>
- </operation>
- <operation name="get_glycans_by_reaction">
-
- <input message="typens:get_glycans_by_reactionRequest"/>
- <output message="typens:get_glycans_by_reactionResponse"/>
- </operation>
- <operation name="get_compounds_by_enzyme">
- <input message="typens:get_compounds_by_enzymeRequest"/>
- <output message="typens:get_compounds_by_enzymeResponse"/>
- </operation>
- <operation name="get_glycans_by_enzyme">
- <input message="typens:get_glycans_by_enzymeRequest"/>
-
- <output message="typens:get_glycans_by_enzymeResponse"/>
- </operation>
- <operation name="convert_mol_to_kcf">
- <input message="typens:convert_mol_to_kcfRequest"/>
- <output message="typens:convert_mol_to_kcfResponse"/>
- </operation>
- <operation name="get_kos_by_pathway">
- <input message="typens:get_kos_by_pathwayRequest"/>
- <output message="typens:get_kos_by_pathwayResponse"/>
-
- </operation>
- <operation name="get_pathways_by_kos">
- <input message="typens:get_pathways_by_kosRequest"/>
- <output message="typens:get_pathways_by_kosResponse"/>
- </operation>
-<!-- v6.0 -->
- <operation name="search_compounds_by_name">
- <input message="typens:search_compounds_by_nameRequest"/>
- <output message="typens:search_compounds_by_nameResponse"/>
-
- </operation>
- <operation name="search_glycans_by_name">
- <input message="typens:search_glycans_by_nameRequest"/>
- <output message="typens:search_glycans_by_nameResponse"/>
- </operation>
- <operation name="search_compounds_by_composition">
- <input message="typens:search_compounds_by_compositionRequest"/>
- <output message="typens:search_compounds_by_compositionResponse"/>
- </operation>
-
- <operation name="search_compounds_by_mass">
- <input message="typens:search_compounds_by_massRequest"/>
- <output message="typens:search_compounds_by_massResponse"/>
- </operation>
- <operation name="search_glycans_by_mass">
- <input message="typens:search_glycans_by_massRequest"/>
- <output message="typens:search_glycans_by_massResponse"/>
- </operation>
- <operation name="search_glycans_by_composition">
-
- <input message="typens:search_glycans_by_compositionRequest"/>
- <output message="typens:search_glycans_by_compositionResponse"/>
- </operation>
- <operation name="search_compounds_by_subcomp">
- <input message="typens:search_compounds_by_subcompRequest"/>
- <output message="typens:search_compounds_by_subcompResponse"/>
- </operation>
- <operation name="search_glycans_by_kcam">
- <input message="typens:search_glycans_by_kcamRequest"/>
-
- <output message="typens:search_glycans_by_kcamResponse"/>
- </operation>
- <operation name="get_linkdb_between_databases">
- <input message="typens:get_linkdb_between_databasesRequest"/>
- <output message="typens:get_linkdb_between_databasesResponse"/>
- </operation>
-
-<!-- v6.1 -->
- <operation name="search_drugs_by_name">
- <input message="typens:search_drugs_by_nameRequest"/>
-
- <output message="typens:search_drugs_by_nameResponse"/>
- </operation>
- <operation name="search_drugs_by_composition">
- <input message="typens:search_drugs_by_compositionRequest"/>
- <output message="typens:search_drugs_by_compositionResponse"/>
- </operation>
- <operation name="search_drugs_by_mass">
- <input message="typens:search_drugs_by_massRequest"/>
- <output message="typens:search_drugs_by_massResponse"/>
-
- </operation>
- <operation name="search_drugs_by_subcomp">
- <input message="typens:search_drugs_by_subcompRequest"/>
- <output message="typens:search_drugs_by_subcompResponse"/>
- </operation>
-
- </portType>
-
-
- <binding name="KEGGBinding" type="typens:KEGGPortType">
-
- <soap:binding style="rpc" transport="http://schemas.xmlsoap.org/soap/http"/>
-<!-- KEGG information -->
- <operation name="list_databases">
- <soap:operation soapAction="SOAP/KEGG#list_databases"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
- <operation name="list_organisms">
- <soap:operation soapAction="SOAP/KEGG#list_organisms"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
- <operation name="list_pathways">
- <soap:operation soapAction="SOAP/KEGG#list_pathways"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
- <operation name="list_ko_classes">
- <soap:operation soapAction="SOAP/KEGG#list_ko_classes"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
-<!-- DBGET -->
- <operation name="binfo">
- <soap:operation soapAction="SOAP/KEGG#binfo"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="bget">
- <soap:operation soapAction="SOAP/KEGG#bget"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="bfind">
- <soap:operation soapAction="SOAP/KEGG#bfind"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="btit">
- <soap:operation soapAction="SOAP/KEGG#btit"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="bconv">
- <soap:operation soapAction="SOAP/KEGG#bconv"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!-- LinkDB -->
- <operation name="get_linkdb_by_entry">
- <soap:operation soapAction="SOAP/KEGG#get_linkdb_by_entry"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
-
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!-- SSDB -->
- <operation name="get_best_neighbors_by_gene">
- <soap:operation soapAction="SOAP/KEGG#get_best_neighbors_by_gene"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_best_best_neighbors_by_gene">
- <soap:operation soapAction="SOAP/KEGG#get_best_best_neighbors_by_gene"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_reverse_best_neighbors_by_gene">
- <soap:operation soapAction="SOAP/KEGG#get_reverse_best_neighbors_by_gene"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_paralogs_by_gene">
- <soap:operation soapAction="SOAP/KEGG#get_paralogs_by_gene"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!-- MOTIF -->
- <operation name="get_motifs_by_gene">
- <soap:operation soapAction="SOAP/KEGG#get_motifs_by_gene"/>
- <input>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_genes_by_motifs">
- <soap:operation soapAction="SOAP/KEGG#get_genes_by_motifs"/>
- <input>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!-- KO,OC,PC -->
- <operation name="get_ko_by_gene">
- <soap:operation soapAction="SOAP/KEGG#get_ko_by_gene"/>
-
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_ko_by_ko_class">
- <soap:operation soapAction="SOAP/KEGG#get_ko_by_ko_class"/>
-
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_genes_by_ko">
- <soap:operation soapAction="SOAP/KEGG#get_genes_by_ko"/>
-
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_genes_by_ko_class">
- <soap:operation soapAction="SOAP/KEGG#get_genes_by_ko_class"/>
-
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!--
- <operation name="get_oc_members_by_gene">
- <soap:operation soapAction="SOAP/KEGG#get_oc_members_by_gene"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
--->
-<!--
- <operation name="get_pc_members_by_gene">
- <soap:operation soapAction="SOAP/KEGG#get_pc_members_by_gene"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
--->
-<!-- PATHWAY -->
-
-<!-- Coloring pathways -->
- <operation name="get_elements_by_pathway">
- <soap:operation soapAction="SOAP/KEGG#get_elements_by_pathway"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="get_element_relations_by_pathway">
- <soap:operation soapAction="SOAP/KEGG#get_element_relations_by_pathway"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="color_pathway_by_elements">
- <soap:operation soapAction="SOAP/KEGG#color_pathway_by_elements"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="get_html_of_colored_pathway_by_elements">
- <soap:operation soapAction="SOAP/KEGG#get_html_of_colored_pathway_by_elements"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
-
- <operation name="mark_pathway_by_objects">
- <soap:operation soapAction="SOAP/KEGG#mark_pathway_by_objects"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
- <operation name="color_pathway_by_objects">
- <soap:operation soapAction="SOAP/KEGG#color_pathway_by_objects"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
- <operation name="get_html_of_marked_pathway_by_objects">
- <soap:operation soapAction="SOAP/KEGG#get_html_of_marked_pathway_by_objects"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
- <operation name="get_html_of_colored_pathway_by_objects">
- <soap:operation soapAction="SOAP/KEGG#get_html_of_colored_pathway_by_objects"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
-<!-- Objects on the pathway -->
- <operation name="get_genes_by_pathway">
- <soap:operation soapAction="SOAP/KEGG#get_genes_by_pathway"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_enzymes_by_pathway">
- <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_pathway"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_reactions_by_pathway">
- <soap:operation soapAction="SOAP/KEGG#get_reactions_by_pathway"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!-- Pathways by object -->
- <operation name="get_pathways_by_genes">
- <soap:operation soapAction="SOAP/KEGG#get_pathways_by_genes"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
-
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_pathways_by_enzymes">
- <soap:operation soapAction="SOAP/KEGG#get_pathways_by_enzymes"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
-
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_pathways_by_reactions">
- <soap:operation soapAction="SOAP/KEGG#get_pathways_by_reactions"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
-
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!-- Mutual transformation of objects -->
- <operation name="get_linked_pathways">
- <soap:operation soapAction="SOAP/KEGG#get_linked_pathways"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_genes_by_enzyme">
- <soap:operation soapAction="SOAP/KEGG#get_genes_by_enzyme"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_enzymes_by_gene">
- <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_gene"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_enzymes_by_reaction">
- <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_reaction"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_reactions_by_enzyme">
- <soap:operation soapAction="SOAP/KEGG#get_reactions_by_enzyme"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!-- GENES -->
- <operation name="get_genes_by_organism">
- <soap:operation soapAction="SOAP/KEGG#get_genes_by_organism"/>
- <input>
-
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!-- GENOME -->
- <operation name="get_number_of_genes_by_organism">
- <soap:operation soapAction="SOAP/KEGG#get_number_of_genes_by_organism"/>
-
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-<!-- LIGAND -->
- <operation name="get_reactions_by_glycan">
-
- <soap:operation soapAction="SOAP/KEGG#get_reactions_by_glycan"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_reactions_by_compound">
-
- <soap:operation soapAction="SOAP/KEGG#get_reactions_by_compound"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_enzymes_by_glycan">
-
- <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_glycan"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_enzymes_by_compound">
-
- <soap:operation soapAction="SOAP/KEGG#get_enzymes_by_compound"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_pathways_by_compounds">
-
- <soap:operation soapAction="SOAP/KEGG#get_pathways_by_compounds"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_pathways_by_glycans">
-
- <soap:operation soapAction="SOAP/KEGG#get_pathways_by_glycans"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_compounds_by_pathway">
-
- <soap:operation soapAction="SOAP/KEGG#get_compounds_by_pathway"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_glycans_by_pathway">
-
- <soap:operation soapAction="SOAP/KEGG#get_glycans_by_pathway"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_compounds_by_reaction">
-
- <soap:operation soapAction="SOAP/KEGG#get_compounds_by_reaction"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_glycans_by_reaction">
-
- <soap:operation soapAction="SOAP/KEGG#get_glycans_by_reaction"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_compounds_by_enzyme">
-
- <soap:operation soapAction="SOAP/KEGG#get_compounds_by_enzyme"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_glycans_by_enzyme">
-
- <soap:operation soapAction="SOAP/KEGG#get_glycans_by_enzyme"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="convert_mol_to_kcf">
-
- <soap:operation soapAction="SOAP/KEGG#convert_mol_to_kcf"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_kos_by_pathway">
-
- <soap:operation soapAction="SOAP/KEGG#get_kos_by_pathway"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
- <operation name="get_pathways_by_kos">
-
- <soap:operation soapAction="SOAP/KEGG#get_pathways_by_kos"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
- </operation>
-
-<!-- v6.0 -->
- <operation name="search_compounds_by_name">
- <soap:operation soapAction="SOAP/KEGG#search_compounds_by_name"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="search_glycans_by_name">
- <soap:operation soapAction="SOAP/KEGG#search_glycans_by_name"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="search_compounds_by_composition">
- <soap:operation soapAction="SOAP/KEGG#search_compounds_by_composition"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="search_compounds_by_mass">
- <soap:operation soapAction="SOAP/KEGG#search_compounds_by_mass"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="search_glycans_by_mass">
- <soap:operation soapAction="SOAP/KEGG#search_glycans_by_mass"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="search_glycans_by_composition">
- <soap:operation soapAction="SOAP/KEGG#search_glycans_by_composition"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="search_compounds_by_subcomp">
- <soap:operation soapAction="SOAP/KEGG#search_compounds_by_subcomp"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="search_glycans_by_kcam">
- <soap:operation soapAction="SOAP/KEGG#search_glycans_by_kcam"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
- <operation name="get_linkdb_between_databases">
- <soap:operation soapAction="SOAP/KEGG#get_linkdb_between_databases"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </output>
-
- </operation>
-
-<!-- v6.1 -->
- <operation name="search_drugs_by_name">
- <soap:operation soapAction="SOAP/KEGG#search_drugs_by_name"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
- <operation name="search_drugs_by_composition">
- <soap:operation soapAction="SOAP/KEGG#search_drugs_by_composition"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
- <operation name="search_drugs_by_mass">
- <soap:operation soapAction="SOAP/KEGG#search_drugs_by_mass"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
- <operation name="search_drugs_by_subcomp">
- <soap:operation soapAction="SOAP/KEGG#search_drugs_by_subcomp"/>
- <input>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
- </input>
- <output>
- <soap:body use="encoded" namespace="SOAP/KEGG" encodingStyle="http://schemas.xmlsoap.org/soap/encoding/"/>
-
- </output>
- </operation>
-
- </binding>
-
- <service name="KEGG">
- <port name="KEGGPort" binding="typens:KEGGBinding">
- <soap:address location="http://soap.genome.jp/keggapi/request_v6.1.cgi"/>
- </port>
- </service>
-
-</definitions>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/440bbd62/taverna-wsdl-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/pom.xml b/taverna-wsdl-activity-ui/pom.xml
new file mode 100644
index 0000000..be2d224
--- /dev/null
+++ b/taverna-wsdl-activity-ui/pom.xml
@@ -0,0 +1,95 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+ <modelVersion>4.0.0</modelVersion>
+ <parent>
+ <groupId>net.sf.taverna</groupId>
+ <artifactId>taverna-parent</artifactId>
+ <version>3.0.1-SNAPSHOT</version>
+ </parent>
+ <groupId>net.sf.taverna.t2.ui-activities</groupId>
+ <artifactId>wsdl-activity-ui</artifactId>
+ <version>2.0-SNAPSHOT</version>
+ <packaging>bundle</packaging>
+ <name>Taverna 2 WSDL Activity UI</name>
+ <build>
+ <plugins>
+ <plugin>
+ <groupId>org.apache.felix</groupId>
+ <artifactId>maven-bundle-plugin</artifactId>
+ <extensions>true</extensions>
+ <configuration>
+ <instructions>
+ <!-- Use the java version instead of xmlcommons for javax.* packages -->
+ <Import-Package>javax.xml.namespace;version="0.0.0",javax.xml.parsers;version="0.0.0",org.w3c.dom;version="0.0.0",org.xml.sax;version="0.0.0",*</Import-Package>
+ </instructions>
+ </configuration>
+ </plugin>
+ </plugins>
+ </build>
+ <dependencies>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-icons-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-palette-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.activities</groupId>
+ <artifactId>wsdl-activity</artifactId>
+ <version>${t2.activities.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-components</groupId>
+ <artifactId>credential-manager-ui</artifactId>
+ <version>${t2.ui.components.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>contextual-views-api</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.ui-api</groupId>
+ <artifactId>activity-tools</artifactId>
+ <version>${t2.ui.api.version}</version>
+ </dependency>
+ <dependency>
+ <groupId>net.sf.taverna.t2.lang</groupId>
+ <artifactId>ui</artifactId>
+ <version>${t2.lang.version}</version>
+ </dependency>
+
+ <dependency>
+ <groupId>junit</groupId>
+ <artifactId>junit</artifactId>
+ <version>${junit.version}</version>
+ <scope>test</scope>
+ </dependency>
+ </dependencies>
+ <repositories>
+ <repository>
+ <releases />
+ <snapshots>
+ <enabled>false</enabled>
+ </snapshots>
+ <id>mygrid-repository</id>
+ <name>myGrid Repository</name>
+ <url>http://www.mygrid.org.uk/maven/repository
+ </url>
+ </repository>
+ <repository>
+ <releases>
+ <enabled>false</enabled>
+ </releases>
+ <snapshots />
+ <id>mygrid-snapshot-repository</id>
+ <name>myGrid Snapshot Repository</name>
+ <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
+ </repository>
+ </repositories>
+</project>
+
http://git-wip-us.apache.org/repos/asf/incubator-taverna-workbench-common-activities/blob/440bbd62/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java
----------------------------------------------------------------------
diff --git a/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java
new file mode 100644
index 0000000..d92dab9
--- /dev/null
+++ b/taverna-wsdl-activity-ui/src/main/java/net/sf/taverna/t2/activities/wsdl/actions/AbstractAddXMLSplitterAction.java
@@ -0,0 +1,156 @@
+package net.sf.taverna.t2.activities.wsdl.actions;
+/*******************************************************************************
+ * Copyright (C) 2008 The University of Manchester
+ *
+ * Modifications to the initial code base are copyright of their
+ * respective authors, or their employers as appropriate.
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1 of
+ * the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with this program; if not, write to the Free Software
+ * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
+ ******************************************************************************/
+
+import java.awt.event.ActionEvent;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+
+import javax.swing.AbstractAction;
+import javax.swing.JComponent;
+import javax.swing.JOptionPane;
+import javax.wsdl.WSDLException;
+import javax.xml.parsers.ParserConfigurationException;
+
+import net.sf.taverna.t2.workbench.edits.EditException;
+import net.sf.taverna.t2.workbench.edits.EditManager;
+import net.sf.taverna.t2.workbench.selection.SelectionManager;
+import net.sf.taverna.wsdl.parser.ArrayTypeDescriptor;
+import net.sf.taverna.wsdl.parser.ComplexTypeDescriptor;
+import net.sf.taverna.wsdl.parser.TypeDescriptor;
+import net.sf.taverna.wsdl.parser.UnknownOperationException;
+
+import org.apache.log4j.Logger;
+import org.jdom.JDOMException;
+import org.xml.sax.SAXException;
+
+import uk.org.taverna.scufl2.api.activity.Activity;
+import uk.org.taverna.scufl2.api.common.Scufl2Tools;
+import uk.org.taverna.scufl2.api.core.Workflow;
+import uk.org.taverna.scufl2.api.profiles.Profile;
+
+/**
+ * Abstract superclass of {@link AddXMLOutputSplitterAction} and
+ * {@link AddXMLInputSplitterAction}.
+ * <p>
+ * Pops up a {@link JOptionPane} with the names of all the wsdl ports. The one
+ * that is selected is added as an input/output splitter to the currently open
+ * dataflow using the {@link AddXMLSplitterEdit}
+ *
+ * @author Ian Dunlop
+ * @author Stian Soiland-Reyes
+ * @author Stuart Owen
+ *
+ */
+@SuppressWarnings("serial")
+public abstract class AbstractAddXMLSplitterAction extends AbstractAction {
+
+ private static Logger logger = Logger.getLogger(AddXMLOutputSplitterAction.class);
+
+ protected Scufl2Tools scufl2Tools = new Scufl2Tools();
+
+ protected JComponent owner;
+ protected final Activity activity;
+ protected final EditManager editManager;
+ protected final SelectionManager selectionManager;
+
+ public AbstractAddXMLSplitterAction(Activity activity,
+ JComponent owner, EditManager editManager, SelectionManager selectionManager) {
+ this.activity = activity;
+ this.owner = owner;
+ this.editManager = editManager;
+ this.selectionManager = selectionManager;
+ }
+
+ public void actionPerformed(ActionEvent ev) {
+ List<String> possibilities;
+ Map<String, TypeDescriptor> typeDescriptors;
+ try {
+ typeDescriptors = getTypeDescriptors();
+ } catch (UnknownOperationException ex) {
+ logger.error("Can't find operation for activity "
+ + activity, ex);
+ return;
+ } catch (IOException | ParserConfigurationException | WSDLException | SAXException | JDOMException ex) {
+ logger.error("Can't read definition for activity "
+ + activity, ex);
+ return;
+ }
+
+ typeDescriptors = filterDescriptors(typeDescriptors);
+
+ possibilities = new ArrayList<String>(typeDescriptors.keySet());
+ if (possibilities.isEmpty()) {
+ logger.warn("No type descriptors found for activity " + activity);
+ return;
+ }
+ Collections.sort(possibilities);
+
+ String portName = (String) JOptionPane.showInputDialog(owner,
+ "Select the port to add the splitter to",
+ "Add output XML splitter", JOptionPane.PLAIN_MESSAGE, null,
+ possibilities.toArray(), possibilities.get(0));
+
+ Workflow workflow = selectionManager.getSelectedWorkflow();
+ Profile profile = selectionManager.getSelectedProfile();
+ TypeDescriptor typeDescriptorForPort = typeDescriptors
+ .get(portName);
+
+ if (typeDescriptorForPort instanceof ArrayTypeDescriptor
+ || typeDescriptorForPort instanceof ComplexTypeDescriptor) {
+ AddXMLSplitterEdit edit = new AddXMLSplitterEdit(workflow, profile,
+ activity, typeDescriptorForPort, portName, isInput());
+ try {
+ editManager.doDataflowEdit(workflow.getParent(), edit);
+ } catch (EditException ex) {
+ logger.error("Could not perform edit to add " + portName, ex);
+ }
+ } else {
+ logger.warn("Unknown typedescriptor for " + portName);
+ }
+ }
+
+ public static Map<String, TypeDescriptor> filterDescriptors(
+ Map<String, TypeDescriptor> descriptors) {
+ Map<String, TypeDescriptor> filtered = new HashMap<String, TypeDescriptor>();
+ for (Entry<String, TypeDescriptor> entry : descriptors.entrySet()) {
+ TypeDescriptor descriptor = entry.getValue();
+ if (descriptor.getMimeType().contains("'text/xml'")) {
+ filtered.put(entry.getKey(), descriptor);
+ }
+ }
+ return filtered;
+ }
+
+ protected abstract boolean isInput();
+
+ public abstract Map<String, TypeDescriptor> getTypeDescriptors()
+ throws UnknownOperationException, IOException, ParserConfigurationException, WSDLException, SAXException, JDOMException;
+
+ public void setOwner(JComponent owner) {
+ this.owner = owner;
+ }
+}
\ No newline at end of file