@hra-api/js-client

HraApiJsClient - JavaScript client for @hra-api/js-client This API provides programmatic access to data registered to the Human Reference Atlas (HRA). See the HuBMAP HRA Portal for details.

This SDK is automatically generated by the OpenAPI Generator project:

• API version: 0.11.0
• Package version: 0.11.0
• Generator version: 7.7.0
• Build package: org.openapitools.codegen.languages.JavascriptClientCodegen

Installation

For Node.js

npm

To publish the library as a npm, please follow the procedure in "Publishing npm packages".

Then install it via:

npm install @hra-api/js-client --save

Finally, you need to build the module:

npm run build

Local development

To use the library locally without publishing to a remote npm registry, first install the dependencies by changing into the directory containing package.json (and this README). Let's call this JAVASCRIPT_CLIENT_DIR. Then run:

npm install

Next, link it globally in npm with the following, also from JAVASCRIPT_CLIENT_DIR:

npm link

To use the link you just defined in your project, switch to the directory you want to use your @hra-api/js-client from, and run:

npm link /path/to/<JAVASCRIPT_CLIENT_DIR>

Finally, you need to build the module:

npm run build

git

If the library is hosted at a git repository, e.g.https://github.com/GIT_USER_ID/GIT_REPO_ID then install it via:

    npm install GIT_USER_ID/GIT_REPO_ID --save

For browser

The library also works in the browser environment via npm and browserify. After following the above steps with Node.js and installing browserify with npm install -g browserify, perform the following (assuming main.js is your entry file):

browserify main.js > bundle.js

Then include bundle.js in the HTML pages.

Webpack Configuration

Using Webpack you may encounter the following error: "Module not found: Error: Cannot resolve module", most certainly you should disable AMD loader. Add/merge the following section to your webpack config:

module: {
  rules: [
    {
      parser: {
        amd: false
      }
    }
  ]
}

Getting Started

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

var HraApiJsClient = require('@hra-api/js-client');


var api = new HraApiJsClient.DsGraphApi()
var opts = {
  'token': "token_example" // {String} Authentication token to use for authenticated searches
};
api.atlasD2k(opts).then(function(data) {
  console.log('API called successfully. Returned data: ' + data);
}, function(error) {
  console.error(error);
});

Documentation for API Endpoints

All URIs are relative to https://apps.humanatlas.io/api

Class | Method | HTTP request | Description ------------ | ------------- | ------------- | ------------- HraApiJsClient.DsGraphApi | atlasD2k | GET /ds-graph/atlas-d2k | Get Atlas D2K Dataset Graph HraApiJsClient.DsGraphApi | gtex | GET /ds-graph/gtex | Get GTEx Dataset Graph HraApiJsClient.DsGraphApi | hubmap | GET /ds-graph/hubmap | Get HuBMAP Dataset Graph HraApiJsClient.DsGraphApi | sennet | GET /ds-graph/sennet | Get SenNet Dataset Graph HraApiJsClient.HraPopApi | cellSummaryReport | POST /hra-pop/cell-summary-report | Given a cell summary in csv format, retrieve a predicted cell summary report from HRApop showing relative anatomical structures, datasets, and rui locations. HraApiJsClient.HraPopApi | ruiLocationCellSummary | POST /hra-pop/rui-location-cell-summary | Given a SpatialEntity already placed relative to a reference SpatialEntity, retrieve a predicted cell summary from HRApop HraApiJsClient.HraPopApi | supportedOrgans | GET /hra-pop/supported-organs | Get all organs supported by HRApop HraApiJsClient.HraPopApi | supportedReferenceOrgans | GET /hra-pop/supported-reference-organs | Get all reference organs supported by HRApop HraApiJsClient.HraPopApi | supportedTools | GET /hra-pop/supported-tools | Get all tools supported by HRApop HraApiJsClient.V1Api | aggregateResults | GET /v1/aggregate-results | Get aggregate results / statistics HraApiJsClient.V1Api | anatomicalSystemsTreeModel | GET /v1/anatomical-systems-tree-model | Get anatomical systems partonomy tree nodes HraApiJsClient.V1Api | biomarkerTermOccurences | GET /v1/biomarker-term-occurences | Get number of biomarker type term occurrences for a search HraApiJsClient.V1Api | biomarkerTreeModel | GET /v1/biomarker-tree-model | Get biomarker tree nodes HraApiJsClient.V1Api | cellTypeTermOccurences | GET /v1/cell-type-term-occurences | Get number of cell type term occurrences for a search HraApiJsClient.V1Api | cellTypeTreeModel | GET /v1/cell-type-tree-model | Get cell type tree nodes HraApiJsClient.V1Api | collisions | POST /v1/collisions | Given an extraction site, get mesh-based collisions with the reference organ. HraApiJsClient.V1Api | corridor | POST /v1/corridor | Given an extraction site, generate a corridor with the reference organ. HraApiJsClient.V1Api | dbStatus | GET /v1/db-status | Get current status of database HraApiJsClient.V1Api | dsGraph | GET /v1/ds-graph | Get dataset graph HraApiJsClient.V1Api | extractionSite | GET /v1/extraction-site | Lookup Extraction Site HraApiJsClient.V1Api | getSpatialPlacement | POST /v1/get-spatial-placement | Given a SpatialEntity already placed relative to a reference SpatialEntity, retrieve a new direct SpatialPlacement to the given SpatialEntity IRI HraApiJsClient.V1Api | gtexRuiLocations | GET /v1/gtex/rui_locations.jsonld | Get all GTEx rui locations (if enabled) HraApiJsClient.V1Api | hubmapRuiLocations | GET /v1/hubmap/rui_locations.jsonld | Get all hubmap rui locations (if enabled) HraApiJsClient.V1Api | mesh3dCellPopulation | POST /v1/mesh-3d-cell-population | Given a reference organ, 3d scene node, and cell population, generate cells in that distribution to fit in that 3d scene node. HraApiJsClient.V1Api | ontologyTermOccurences | GET /v1/ontology-term-occurences | Get number of ontology term occurrences for a search HraApiJsClient.V1Api | ontologyTreeModel | GET /v1/ontology-tree-model | Get ontology term tree nodes HraApiJsClient.V1Api | providerNames | GET /v1/provider-names | Get tissue provider names (for filtering) HraApiJsClient.V1Api | referenceOrganScene | GET /v1/reference-organ-scene | Get all nodes to form the 3D scene for an organ HraApiJsClient.V1Api | referenceOrgans | GET /v1/reference-organs | Get all reference organs HraApiJsClient.V1Api | ruiReferenceData | GET /v1/rui-reference-data | Get reference data for the RUI tool HraApiJsClient.V1Api | scene | GET /v1/scene | Get all nodes to form the 3D scene of reference body, organs, and tissues HraApiJsClient.V1Api | sennetRuiLocations | GET /v1/sennet/rui_locations.jsonld | Get all sennet rui locations (if enabled) HraApiJsClient.V1Api | sessionToken | POST /v1/session-token | Get a session token HraApiJsClient.V1Api | sparql | GET /v1/sparql | Run a SPARQL query HraApiJsClient.V1Api | sparqlPost | POST /v1/sparql | Run a SPARQL query (POST) HraApiJsClient.V1Api | technologyNames | GET /v1/technology-names | Get technology names (for filtering) HraApiJsClient.V1Api | tissueBlocks | GET /v1/tissue-blocks | Get Tissue Block Results

Documentation for Models

• HraApiJsClient.AggregateCount
• HraApiJsClient.DatabaseStatus
• HraApiJsClient.ErrorMessage
• HraApiJsClient.Filter
• HraApiJsClient.FlatSpatialPlacement
• HraApiJsClient.GetSpatialPlacementRequest
• HraApiJsClient.IdLabelPair
• HraApiJsClient.Mesh3dCellPopulationRequest
• HraApiJsClient.MinMax
• HraApiJsClient.OntologyTree
• HraApiJsClient.OntologyTreeNode
• HraApiJsClient.SessionToken
• HraApiJsClient.SessionTokenRequest
• HraApiJsClient.SparqlQueryRequest
• HraApiJsClient.SpatialEntity
• HraApiJsClient.SpatialEntityCommon
• HraApiJsClient.SpatialEntityCreator
• HraApiJsClient.SpatialEntityDimensions
• HraApiJsClient.SpatialObjectReference
• HraApiJsClient.SpatialPlacement
• HraApiJsClient.SpatialPlacementCommon
• HraApiJsClient.SpatialPlacementRotation
• HraApiJsClient.SpatialPlacementScaling
• HraApiJsClient.SpatialPlacementTranslation
• HraApiJsClient.SpatialSceneNode
• HraApiJsClient.SpatialSearch
• HraApiJsClient.TissueBlock
• HraApiJsClient.TissueCommon
• HraApiJsClient.TissueDataset
• HraApiJsClient.TissueDonor
• HraApiJsClient.TissueSampleCommon
• HraApiJsClient.TissueSection

Documentation for Authorization

Endpoints do not require authorization.