KBaseRelationEngine.spec

/*
A KBase module: KBaseRelationEngine
*/

module KBaseRelationEngine {
	typedef int boolean;
	
	typedef structure{
		int nodes_created;
		int nodes_deleted;		
		int relationships_created;
		int relationships_deleted;		
		int properties_set;		
	} GraphUpdateStat;

    typedef structure{
    	string taxonomy_guid;
    	string feature_guid;
    	string proteinSequence;
    	string nucleotideSequence;
    } FeatureSequence;

	/**
		One of guids should provided.
	*/
    typedef structure{
    	string taxonomy_guid;
    	string ortholog_guid;
    	string goterm_guid;
	}GetFeatureSequencesParams;

	funcdef getFeatureSequences(GetFeatureSequencesParams params) returns(list<FeatureSequence>) authentication required;
	
	typedef structure{
		string guid;
		string name;
		string data_type;
		string taxonomy_guid;
		string ws_ndarray_id;
	} CompendiumDescriptor;


	/**
		data_type - one of ["expression","fitness"]
	*/
    typedef structure{
    	string taxonomy_guid;
    	string data_type;
	}GetCompendiumDescriptorsParams;

	funcdef getCompendiumDescriptors(GetCompendiumDescriptorsParams params) returns(list<CompendiumDescriptor>) authentication required;
	
	typedef structure{
		string guid;
		string name;
		string version;
		int last_run_epoch;
		int nodes_created;
		int relations_created;
		int properties_set;
		
	} KEAppDescriptor;
	
	typedef structure{
		KEAppDescriptor app;
	}StoreKEAppDescriptorParams; 
	funcdef storeKEAppDescriptor(StoreKEAppDescriptorParams params) returns (GraphUpdateStat) authentication required; 
		
	typedef structure{
		string app_guid;
	}CleanKEAppResultsParams;	
	funcdef cleanKEAppResults(CleanKEAppResultsParams params) returns () authentication required;
	
	typedef structure{
		string app_guid;
	}GetKEAppDescriptorParams;	
	funcdef getKEAppDescriptor(GetKEAppDescriptorParams params) returns (KEAppDescriptor) authentication required;
	
	typedef structure{
		string guid; 
		string keapp_guid;
		string compendium_guid;
		string taxonomy_guid;
		list<string> feature_guids;
		list<string> condition_guids;
	} Bicluster;		
		
	typedef structure{
		list<Bicluster> biclusters;
	} StoreBiclustersParams; 		
	funcdef storeBiclusters(StoreBiclustersParams params) returns(GraphUpdateStat) authentication required;
				
	typedef structure{
		string keapp_guid;
		string taxonomy_guid;
		string compendium_guid;
	}GetBiclustersParams;	
	funcdef getBiclusters(GetBiclustersParams params) returns (list<Bicluster>) authentication required;

		
	typedef structure{
		string term_guid;
		string term_name;
		
    	int sample_count;
    	int total_count;
    	int expected_count;
		float p_value;		
	} TermEnrichment;
		
	typedef structure{
		string guid;
		string keapp_guid;
		string source_gene_set_guid;
		string source_gene_set_type;
		boolean with_expression;
		boolean with_fitness;				
		string term_namespace;
		list<TermEnrichment> terms; 
	} TermEnrichmentProfile;
	
	typedef structure{
		list<TermEnrichmentProfile> profiles;
	} StoreTermEnrichmentProfilesParams;		
	funcdef storeTermEnrichmentProfiles(StoreTermEnrichmentProfilesParams params) returns(GraphUpdateStat) authentication required;		
		
		
	typedef structure{
		string feature_guid;
		string feature_name;
		string ref_term_guid;
		string ref_term_name;
		list<TermEnrichmentProfile> profiles; 
	} GetWSFeatureTermEnrichmentProfilesOutput;
		
	typedef structure{
		string ws_feature_guid;
		boolean ortholog_profiles;
		list<string> keapp_guids;
	}GetWSFeatureTermEnrichmentProfilesParams;	
	funcdef getWSFeatureTermEnrichmentProfiles(GetWSFeatureTermEnrichmentProfilesParams params)	returns(GetWSFeatureTermEnrichmentProfilesOutput) authentication required;
		
		
	typedef structure{
		string feature_guid;
		string feature_name;
		string feature_function;
		list<string> feature_aliases;
		boolean with_expression;
		boolean with_fitness;		
		string ref_term_guid;
		string ref_term_name;
		string target_term_guid;
		string target_term_name;
	} WSFeatureTermPair;
	 
	typedef structure{
		string ws_genome_guid;
		string target_keapp_guid;		
	}GetWSFeatureTermPairsParams; 		
	funcdef getWSFeatureTermPairs(GetWSFeatureTermPairsParams params) returns(list<WSFeatureTermPair>) authentication required;
		
		
	typedef structure{
		string feature_guid;
		list<string> term_guids;
	} FeatureTerms;	
		
	typedef structure{
		string taxon_guid;
		string term_space;
	} GetFeatureTermsParams;
	funcdef getFeatureTerms(GetFeatureTermsParams params) returns (list<FeatureTerms>) authentication required;
			
			
	typedef structure{
		string guid;
		string name;
		string space;
	} Term;		
		
	typedef structure{
		list<string> term_guids;
	} GetTermsParams;
	funcdef getTerms(GetTermsParams params) returns(list<Term>) authentication required;
		
		
	typedef structure{
		boolean with_term_enrichmnet_profiles;
		list<string> app_guids;
	} GetOrthologGroupsParams;
		
	typedef structure{
		list<string> ortholog_group_guids;
	} GetOrthologGroupsOutput;	
	funcdef getOrthologGroups(GetOrthologGroupsParams params) returns(GetOrthologGroupsOutput) authentication required;
	
	
	typedef structure{
		mapping<string,list<TermEnrichmentProfile>> ortholog2profiles;
	} GetOrthologTermEnrichmentProfilesOutput;
	
	typedef structure{
		list<string> ortholog_group_guids;
		list<string> app_guids;
	}GetOrthologTermEnrichmentProfilesParams;		
	funcdef getOrthologTermEnrichmentProfiles(GetOrthologTermEnrichmentProfilesParams params) returns(GetOrthologTermEnrichmentProfilesOutput)	authentication required;	
		
		
	typedef string ws_genome_obj_ref;
	typedef string ws_feature_guid;
	typedef string ref_ontology_term_guid;

	typedef structure{
		ws_genome_obj_ref genome_ref;
		list<ws_feature_guid> feature_guids;				
	} StoreWSGenomeParams;	
	funcdef storeWSGenome(StoreWSGenomeParams params) returns (GraphUpdateStat) authentication required;


	typedef structure{
		string guid;
		string name;
		string function;
		list<string> aliases;		
		string ref_term_guid;
	} WSFeature;
	
	typedef structure{
		ws_genome_obj_ref genome_ref;
		list<WSFeature> features;				
		mapping<string,string> ws2ref_feature_guids;		
	} StoreRichWSGenomeParams;	
	funcdef storeRichWSGenome(StoreRichWSGenomeParams params) returns (GraphUpdateStat) authentication required;


	typedef structure{
		mapping<string,string> ws2ref_feature_guids;		
	} ConnectWSFeatures2RefOrthologsParams;
	funcdef connectWSFeatures2RefOrthologs(ConnectWSFeatures2RefOrthologsParams params) returns (GraphUpdateStat) authentication required;

	typedef structure{
		mapping<ws_feature_guid,list<ref_ontology_term_guid>> feature2term_list;		
	} ConnectWSFeatures2RefOTermsParams;
	funcdef connectWSFeatures2RefOTerms(ConnectWSFeatures2RefOTermsParams params) returns (GraphUpdateStat) authentication required;

	
	
};