Skip to content

biolink/biolink-java-client

BranchesTags

Repository files navigation

swagger-java-client

Requirements

Building the API client library requires Maven to be installed.

Installation

To install the API client library to your local Maven repository, simply execute:

mvn install

To deploy it to a remote Maven repository instead, configure the settings of the repository and execute:

mvn deploy

Refer to the official documentation for more information.

Maven users

Add this dependency to your project's POM:

<dependency>
    <groupId>io.swagger</groupId>
    <artifactId>swagger-java-client</artifactId>
    <version>1.0.0</version>
    <scope>compile</scope>
</dependency>

Gradle users

Add this dependency to your project's build file:

compile "io.swagger:swagger-java-client:1.0.0"

Others

At first generate the JAR by executing:

mvn package

Then manually install the following JARs:

  • target/swagger-java-client-1.0.0.jar
  • target/lib/*.jar

Getting Started

Please follow the installation instruction and execute the following Java code:

import io.swagger.client.*;
import io.swagger.client.auth.*;
import io.swagger.client.model.*;
import io.swagger.client.api.AssociationApi;

import java.io.File;
import java.util.*;

public class AssociationApiExample {

    public static void main(String[] args) {
        
        AssociationApi apiInstance = new AssociationApi();
        String id = "id_example"; // String | 
        Integer rows = 10; // Integer | number of rows
        Boolean flExcludesEvidence = true; // Boolean | If set, excludes evidence objects in response
        String evidence = "evidence_example"; // String | Object id, e.g. ECO:0000501 (for IEA; Includes inferred by default)                     or a specific publication or other supporting ibject, e.g. ZFIN:ZDB-PUB-060503-2.                     
        Integer page = 1; // Integer | Page number
        String object = "object_example"; // String | OBJECT id, e.g. HP:0011927. Includes inferred by default
        String subject = "subject_example"; // String | SUBJECT id, e.g. NCBIGene:84570, ZFIN:ZDB-GENE-050417-357. Includes inferred by default
        String subjectTaxon = "subjectTaxon_example"; // String | SUBJECT TAXON id, e.g. NCBITaxon:9606. Includes inferred by default
        Boolean graphize = true; // Boolean | If set, includes graph object in response
        String mapIdentifiers = "mapIdentifiers_example"; // String | Prefix to map all IDs to. E.g. NCBIGene
        try {
            List<Association> result = apiInstance.getAssociationObject(id, rows, flExcludesEvidence, evidence, page, object, subject, subjectTaxon, graphize, mapIdentifiers);
            System.out.println(result);
        } catch (ApiException e) {
            System.err.println("Exception when calling AssociationApi#getAssociationObject");
            e.printStackTrace();
        }
    }
}

Documentation for API Endpoints

All URIs are relative to https://localhost/api

Class Method HTTP request Description
AssociationApi getAssociationObject GET /association/{id} Returns the association with a given identifier
AssociationApi getAssociationSearch GET /association/find/ Returns list of matching associations
AssociationApi getAssociationSearch_0 GET /association/find/{subject_category}/ Returns list of matching associations
AssociationApi getAssociationSearch_1 GET /association/find/{subject_category}/{object_category}/ Returns list of matching associations
AssociationApi getAssociationsFrom GET /association/between/{subject}/{object} Returns associations connecting two entities
AssociationApi getAssociationsFrom_0 GET /association/from/{subject} Returns list of matching associations
AssociationApi getAssociationsTo GET /association/to/{object} Returns list of matching associations
BioentityApi getAlleleObject GET /bioentity/allele/{id} TODO Returns allele object
BioentityApi getAnatomyGeneAssociations GET /bioentity/anatomy/{id}/genes/ TODO Returns associations between anatomical entity and genes
BioentityApi getAnatomyObject GET /bioentity/anatomy/{id} TODO Returns anatomical entity
BioentityApi getAnatomyPhenotypeAssociations GET /bioentity/anatomy/{id}/phenotypes/ TODO Returns associations between anatomical entity and phenotypes
BioentityApi getDiseaseAnatomyAssociations GET /bioentity/disease/{id}/anatomy/ TODO Returns anatomical locations associated with a disease
BioentityApi getDiseaseFunctionAssociations GET /bioentity/disease/{id}/function/ TODO Returns biological functions associated with a disease
BioentityApi getDiseaseGeneAssociations GET /bioentity/disease/{id}/genes/ Returns genes associated with a disease
BioentityApi getDiseaseModelAssociations GET /bioentity/disease/{id}/models/ Returns associations to models of the disease
BioentityApi getDiseaseModelTaxonAssociations GET /bioentity/disease/{id}/models/{taxon} Same as `/disease/<id>/models` but constrain models by taxon
BioentityApi getDiseaseObject GET /bioentity/disease/{id} TODO Returns disease object
BioentityApi getDiseasePhenotypeAssociations GET /bioentity/disease/{id}/phenotypes/ Returns phenotypes associated with disease
BioentityApi getDiseaseSubstanceAssociations GET /bioentity/disease/{id}/substance/ Returns substances associated with a disease
BioentityApi getDiseaseSubstanceAssociations_0 GET /bioentity/substance/{id}/treats/ Returns substances associated with a disease
BioentityApi getEnvironmentObject GET /bioentity/environment/{id} TODO Returns environment entity
BioentityApi getEnvironmentPhenotypeAssociations GET /bioentity/environment/{id}/phenotypes/ TODO Returns list of associations
BioentityApi getGeneExpressionAssociations GET /bioentity/gene/{id}/expressed/ TODO Returns expression events for a gene
BioentityApi getGeneFunctionAssociations GET /bioentity/gene/{id}/function/ Returns function associations for a gene
BioentityApi getGeneHomologAssociations GET /bioentity/gene/{id}/homologs/ Returns homologs for a gene
BioentityApi getGeneInteractions GET /bioentity/gene/{id}/interactions/ Returns interactions for a gene
BioentityApi getGeneObject GET /bioentity/gene/{id} Returns gene object
BioentityApi getGenePhenotypeAssociations GET /bioentity/gene/{id}/phenotypes/ Returns phenotypes associated with gene
BioentityApi getGenePublicationList GET /bioentity/gene/{id}/pubs/ TODO Returns expression events for a gene
BioentityApi getGeneproductObject GET /bioentity/geneproduct/{id} TODO Returns gene product object
BioentityApi getGenericAssociations GET /bioentity/{id}/associations/ Returns associations for an entity regardless of the type
BioentityApi getGenericObject GET /bioentity/{id} TODO Returns object of any type
BioentityApi getGenotypeDiseaseAssociations GET /bioentity/genotype/{id}/diseases/ Returns diseases associated with a genotype
BioentityApi getGenotypeGeneAssociations GET /bioentity/genotype/{id}/genes/ Returns genes associated with a genotype
BioentityApi getGenotypeGenotypeAssociations GET /bioentity/genotype/{id}/genotypes/ Returns genotypes-genotype associations
BioentityApi getGenotypeObject GET /bioentity/genotype/{id} Returns genotype object
BioentityApi getGenotypePhenotypeAssociations GET /bioentity/genotype/{id}/phenotypes/ Returns phenotypes associated with a genotype
BioentityApi getGotermGeneAssociations GET /bioentity/goterm/{id}/genes/ TODO Returns associated phenotypes
BioentityApi getGotermObject GET /bioentity/goterm/{id} TODO Returns GO class object
BioentityApi getGotermPhenotypeAssociations GET /bioentity/goterm/{id}/phenotype/ TODO Returns associated phenotypes
BioentityApi getLiteratureDiseaseAssociations GET /bioentity/literature/{id}/diseases/ Returns associations between a lit entity and a disease
BioentityApi getLiteratureGeneAssociations GET /bioentity/literature/{id}/genes/ Returns associations between a lit entity and a gene
BioentityApi getLiteratureGenotypeAssociations GET /bioentity/literature/{id}/genotypes/ Returns associations between a lit entity and a genotype
BioentityApi getParentObject GET /bioentity/individual/{id} TODO Returns individual
BioentityApi getParentObject_0 GET /bioentity/investigation/{id} TODO Returns investigation object
BioentityApi getPathwayGeneAssociations GET /bioentity/pathway/{id}/genes/ TODO Returns list of genes associated with a pathway
BioentityApi getPathwayObject GET /bioentity/pathway/{id} TODO Returns pathway object
BioentityApi getPathwayParticipantAssociations GET /bioentity/pathway/{id}/participants/ TODO Returns associations to participants (molecules, etc) for a pathway
BioentityApi getPhenotypeAnatomyAssociations GET /bioentity/phenotype/{id}/anatomy/ Returns anatomical entities associated with a phenotype
BioentityApi getPhenotypeFunctionAssociations GET /bioentity/phenotype/{id}/function/ TODO Returns biological functions associated with a Phenotype
BioentityApi getPhenotypeGeneAssociations GET /bioentity/phenotype/{id}/gene/{taxid}/ids Returns gene ids for all genes for a particular phenotype in a taxon
BioentityApi getPhenotypeGeneAssociations_0 GET /bioentity/phenotype/{id}/genes/ TODO Returns associated phenotypes
BioentityApi getPhenotypeObject GET /bioentity/phenotype/{id} TODO Returns phenotype class object
BioentityApi getPhenotypePhenotypeAssociations GET /bioentity/phenotype/{id}/phenotype/ TODO Returns associated phenotypes
BioentityApi getPubObject GET /bioentity/literature/{id} TODO Returns publication object
BioentityApi getSequenceFeatureObject GET /bioentity/sequence_feature/{id} TODO Returns seqfeature
BioentityApi getSubstanceExposures GET /bioentity/substance/{id}/exposures/ TODO Returns associations between a substance and related exposures
BioentityApi getSubstanceInteractions GET /bioentity/substance/{id}/interactions/ TODO Returns associations between given drug and interactions
BioentityApi getSubstanceObject GET /bioentity/substance/{id} TODO Returns substance entity
BioentityApi getSubstanceParticipantInAssociations GET /bioentity/substance/{id}/participant_in/ Returns associations between an activity and process and the specified substance
BioentityApi getSubstanceRelationships GET /bioentity/substance/{id}/substances/ TODO Returns associations between a substance and other substances
BioentityApi getSubstanceRoleAssociations GET /bioentity/substance/{id}/roles/ Returns associations between given drug and roles
BioentityApi getSubstanceTargetAssociations GET /bioentity/substance/{id}/targets/ TODO Returns associations between given drug and targets
BioentityApi getVariantGeneAssociations GET /bioentity/variant/{id}/genes/ Returns genes associated with a variant
BioentityApi getVariantGenotypeAssociations GET /bioentity/variant/{id}/genotypes/ Returns genotypes associated with a variant
BioentityApi getVariantObject GET /bioentity/variant/{id} TODO Returns sequence variant entity
BioentityApi getVariantPhenotypeAssociations GET /bioentity/variant/{id}/phenotypes/ Returns phenotypes associated with a variant
BioentitysetApi getEntitySetAssociations GET /bioentityset/associations/ Returns compact associations for a given input set
BioentitysetApi getEntitySetGraphResource GET /bioentityset/graph/ TODO Graph object spanning all entities
BioentitysetApi getEntitySetHomologsDeprecated GET /bioentityset/DEPRECATEDhomologs/ Returns homology associations for a given input set of genes
BioentitysetApi getEntitySetOverRepresentationAnalysis GET /bioentityset/ora/ TODO Over-representation analysis
BioentitysetApi getEntitySetOverRepresentationAnalysis_0 GET /bioentityset/ora/{object_category}/ TODO Over-representation analysis
BioentitysetApi getEntitySetSummary GET /bioentityset/descriptor/counts/ Summary statistics for objects associated
BioentitysethomologsApi getEntitySetHomologs GET /bioentityset/homologs/homologs/ Returns homology associations for a given input set of genes
CamApi getActivityCollection GET /cam/activity/ Returns list of models
CamApi getInstance GET /cam/instance/{id} Returns list of matches
CamApi getModel GET /cam/model/{id} Returns a complete model
CamApi getModelCollection GET /cam/model/ Returns list of ALL models
CamApi getModelCollection_0 GET /cam/model/properties/ Returns list of all properties used across all models
CamApi getModelCollection_1 GET /cam/model/property_values/ Returns list property-values for all models
CamApi getModelCollection_2 GET /cam/model/query/ Returns list of models matching query
CamApi getModelContibutors GET /cam/instances/ Returns list of all instances
CamApi getModelContibutors_0 GET /cam/model/contributors/ Returns list of all contributors across all models
CamApi getPhysicalInteraction GET /cam/physical_interaction/ Returns list of models
EvidencegraphApi getAssociationObject GET /evidence/graph/{id} Returns evidence graph object for a given association
EvidencegraphApi getAssociationObject_0 GET /evidence/graph/{id}/image Returns evidence graph as a png
GenomefeaturesApi getFeaturesWithinResource GET /genome/features/within/{build}/{reference}/{begin}/{end} Returns list of matches
GraphApi getEdgeResource GET /graph/edges/from/{id} Returns edges emanating from a node
GraphApi getNodeResource GET /graph/node/{id} Returns a graph node
IdentifiermapperApi getPrefixCollection GET /identifier/mapper/{source}/{target}/ TODO maps a list of identifiers from a source to a target
IdentifierprefixesApi getPrefixCollection GET /identifier/prefixes/ Returns list of prefixes
IdentifierprefixesApi getPrefixCollection_0 GET /identifier/prefixes/contract/{uri} Returns contracted URI
IdentifierprefixesApi getPrefixCollection_1 GET /identifier/prefixes/expand/{id} Returns expanded URI
IndividualApi getIndividual GET /individual/{id} Returns list of matches
IndividualApi getPedigree GET /individual/pedigree/{id} Returns list of matches
NlpannotateApi getAnnotate GET /nlp/annotate/{text} Returns list of matches
OntolApi getInformationContentResource GET /ontol/information_content/{subject_category}/{object_category}/{subject_taxon} Calculates information content
OntolslimmerApi getFoo GET /ontol/slimmer/{subset} Maps to slim
OwlontologyApi getDlQuery GET /owl/ontology/dlquery/{query} Returns list of matches
OwlontologyApi getDlQuery_0 GET /owl/ontology/sparql/{query} Returns list of matches
PairsimApi getPairSimJaccardResource GET /pair/sim/jaccard/{id1}/{id2}/ Get pairwise similarity
PubpubsApi getFoo GET /pub/pubs/{term} Returns list of matches
RelationusageApi getRelationUsageBetweenResource GET /relation/usage/between/{subject_category}/{object_category} All relations used plus count of associations
RelationusageApi getRelationUsagePivotLabelResource GET /relation/usage/pivot/label Relation usage count for all subj x obj category combinations, showing label
RelationusageApi getRelationUsagePivotResource GET /relation/usage/pivot/ Relation usage count for all subj x obj category combinations
RelationusageApi getRelationUsageResource GET /relation/usage/ All relations used plus count of associations
SearchentityApi getAuthocomplete GET /search/entity/autocomplete/{term} Returns list of matches
SearchentityApi getAuthocomplete_0 GET /search/entity/query/ Returns list of matches
SearchentityApi getSearchEntities GET /search/entity/{term} Returns list of matches
VariationsetApi deleteVariantSetItem DELETE /variation/set/{id} Deletes variant set
VariationsetApi getAnalyze GET /variation/set/analyze/{id} Returns list of matches
VariationsetApi getVariantSetItem GET /variation/set/{id} Returns a variant set
VariationsetApi getVariantSetsArchiveCollection GET /variation/set/archive/{year}/{month}/{day}/ Returns list of variant sets from a specified time period
VariationsetApi getVariantSetsCollection GET /variation/set/ Returns list of variant sets
VariationsetApi postVariantSetsCollection POST /variation/set/ Creates a new variant set
VariationsetApi putVariantSetItem PUT /variation/set/{id} Updates a variant set

Documentation for Models

Documentation for Authorization

All endpoints do not require authorization. Authentication schemes defined for the API:

Recommendation

It's recommended to create an instance of ApiClient per thread in a multithreaded environment to avoid any potential issue.

Author

About

No description, website, or topics provided.

Resources

Readme

License

Apache-2.0 license
Activity
Custom properties

Stars

1 star

Watchers

3 watching

Forks

0 forks
Report repository

Releases

No releases published

Packages

No packages published

Languages