com.github.jmchilton.blend4j.galaxy.ToolShedRepositoriesClientImpl Maven / Gradle / Ivy

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blend4j is a JVM partial reimplemenation of the Python library bioblend (http://bioblend.readthedocs.org/en/latest/) for interacting with Galaxy, CloudMan, and BioCloudCentral.

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package com.github.jmchilton.blend4j.galaxy;

import com.github.jmchilton.blend4j.galaxy.beans.InstallableRepositoryRevision;
import com.github.jmchilton.blend4j.galaxy.beans.InstalledRepository;
import com.github.jmchilton.blend4j.galaxy.beans.RepositoryInstall;
import com.github.jmchilton.blend4j.galaxy.beans.RepositoryWorkflow;
import com.github.jmchilton.blend4j.galaxy.beans.Workflow;
import com.sun.jersey.api.client.ClientResponse;
import com.sun.jersey.api.client.WebResource;
import java.util.HashMap;
import java.util.List;
import org.codehaus.jackson.type.TypeReference;

class ToolShedRepositoriesClientImpl extends Client implements ToolShedRepositoriesClient {
  private static final TypeReference> TOOL_SHED_REPOSITORY_LIST_TYPE_REFERENCE = new TypeReference>() {
  };
  private static final TypeReference> TOOL_SHED_REPOSITORY_WORKFLOW_LIST_TYPE_REFERENCE = 
    new TypeReference>() {
    };
  private static final TypeReference> WORKFLOW_LIST_TYPE_REFERENCE = 
    new TypeReference>() {
    };
  

  ToolShedRepositoriesClientImpl(GalaxyInstanceImpl galaxyInstance) {
    super(galaxyInstance, "tool_shed_repositories");
  }

  public List getRepositories() {
    return super.get(TOOL_SHED_REPOSITORY_LIST_TYPE_REFERENCE);
  }

  public InstalledRepository showRepository(final String toolShedId) {
    return super.show(toolShedId, InstalledRepository.class);
  }

  public ClientResponse installRepositoryRequest(final RepositoryInstall install) {
    final WebResource resource = super.webResource.path("new").path("install_repository_revision");
    return super.create(resource, install);
  }
  
  public List installRepository(final RepositoryInstall install) {
    final ClientResponse response = this.installRepositoryRequest(install);
    return super.read(response, TOOL_SHED_REPOSITORY_LIST_TYPE_REFERENCE);
  }
  
  public ClientResponse repairRepositoryRequest(final InstallableRepositoryRevision repositoryIdentifier) {
    final WebResource resource = super.webResource.path("repair_repository_revision");
    return super.create(resource, repositoryIdentifier);
  }

  public ClientResponse exportedWorkflowsRequest(String toolShedId) {
    final WebResource resource = super.webResource.path(toolShedId).path("exported_workflows");
    return resource.get(ClientResponse.class);
  }

  public List exportedWorkflows(String toolShedId) {
    return super.read(this.exportedWorkflowsRequest(toolShedId), 
                      TOOL_SHED_REPOSITORY_WORKFLOW_LIST_TYPE_REFERENCE);
  }

  public ClientResponse importWorkflowRequest(String toolShedId, int index) {
    final WebResource resource = super.webResource.path(toolShedId).path("import_workflow");
    final HashMap postObject = new HashMap();
    postObject.put("index", index);
    return super.create(resource, postObject);
  }

  public Workflow importWorkflow(String toolShedId, int index) {
    final ClientResponse response = this.importWorkflowRequest(toolShedId, index);
    return response.getEntity(Workflow.class);
  }

  public ClientResponse importWorkflowsRequest(String toolShedId) {
    final WebResource resource = super.webResource.path(toolShedId).path("import_workflows");
    return super.create(resource);
  }

  public List importWorkflows(String toolShedId) {
    return read(importWorkflowsRequest(toolShedId), WORKFLOW_LIST_TYPE_REFERENCE);
  }

}