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:

shell mvn install

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

shell mvn deploy

Refer to the official documentation for more information.

Maven users

Add this dependency to your project's POM:

xml <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:

groovy 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:

```java

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/{subjectcategory}/ | Returns list of matching associations AssociationApi | getAssociationSearch_1 | GET /association/find/{subjectcategory}/{objectcategory}/ | 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/sequencefeature/{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}/participantin/ | 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/{objectcategory}/ | 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/propertyvalues/ | 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/physicalinteraction/ | 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/informationcontent/{subjectcategory}/{objectcategory}/{subjecttaxon} | 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/{subjectcategory}/{objectcategory} | 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

• APageOfResults
• AbstractPropertyValue
• Allele
• AnnotationExtension
• Association
• AssociationPropertyValue
• AssociationResults
• BioObject
• Chromosome
• CompactAssociationSet
• Edge
• Exon
• Gene
• Genotype
• Graph
• NamedObject
• Node
• PageOfVariantSets
• Publication
• Relation
• SearchResult
• Seq
• SequenceFeature
• SequenceLocation
• SequencePosition
• Substance
• SummaryPropertyValue
• Taxon
• Transcript
• VariantSet

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