Package org.intermine.bio.webservice

Class GenomicRegionSearchService

  • Direct Known Subclasses:
    AbstractRegionExportService
    public class GenomicRegionSearchService
extends org.intermine.webservice.server.lists.ListMakerService
    A web service resource to expose the Region Search functionality.

    • Field Summary

      • Fields inherited from class org.intermine.webservice.server.lists.ListMakerService

        LIST_TYPE_KEY

      • Fields inherited from class org.intermine.webservice.server.lists.AbstractListService

        LIST_DESCRIPTION_KEY, LIST_ID_KEY, LIST_NAME_KEY, LIST_SIZE_KEY

      • Fields inherited from class org.intermine.webservice.server.core.JSONService

        bagManager, model

      • Fields inherited from class org.intermine.webservice.server.WebService

        dataPackageOutput, DEFAULT_CALLBACK, im, os, out, output, request, response, webProperties

    • Constructor Summary

      Constructors 
      Constructor Description
      GenomicRegionSearchService​(org.intermine.api.InterMineAPI im)
      Constructor.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      protected java.util.Map<GenomicRegion,​org.intermine.objectstore.query.Query> createQueries​(GenomicRegionSearchListInput.GenomicRegionSearchInfo info)
      Create the queries used to run the genomic region search.
      protected org.intermine.api.profile.InterMineBag doListCreation​(GenomicRegionSearchListInput input, org.intermine.api.profile.Profile profile, java.lang.String type)
      Create the list specified by the region search input.
      protected java.util.Map<java.lang.String,​java.lang.Object> getHeaderAttributes()
      Gets the header attributes on the output object.
      protected org.intermine.webservice.server.lists.ListInput getInput()  
      protected java.lang.String getNewListType​(org.intermine.webservice.server.lists.ListInput input)  
      protected void makeList​(org.intermine.webservice.server.lists.ListInput input, java.lang.String type, org.intermine.api.profile.Profile profile, java.util.Set<java.lang.String> temporaryBagNamesAccumulator)  

      • Methods inherited from class org.intermine.webservice.server.lists.ListMakerService

        canServe, execute, getDefaultFormat, initialiseDelendumAccumulator, validateState

      • Methods inherited from class org.intermine.webservice.server.lists.AbstractListService

        getClassesForBags

      • Methods inherited from class org.intermine.webservice.server.core.JSONService

        addOutputInfo, addResultEntries, addResultEntries, addResultEntry, addResultEntry, addResultItem, addResultItem, addResultValue, addResultValue, addResultValue, getResultsKey, lazyList, postInit

      • Methods inherited from class org.intermine.webservice.server.WebService

        cleanUp, formatIsFlatFile, formatIsJSON, formatIsJSONP, formatIsXML, getAuthenticatedUser, getCallback, getColumnHeaderStyle, getDefaultFileName, getDefaultOutput, getDefaultOutput, getExtension, getFormat, getIntParameter, getIntParameter, getLineBreak, getListManager, getOptionalParameter, getOptionalParameter, getPermission, getProperty, getRawOutput, getRequestFileName, getRequiredParameter, hasCallback, initState, isAuthenticated, isGzip, isUncompressed, isZip, makeJSONOutput, makeXMLOutput, service, setFormat, setNameSpace, wantsColumnHeaders, wantsDataPackage

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • GenomicRegionSearchService

        public GenomicRegionSearchService​(org.intermine.api.InterMineAPI im)
        Constructor.
        Parameters:
        im - The InterMine state and settings object.

    • Method Detail

      • getNewListType

        protected java.lang.String getNewListType​(org.intermine.webservice.server.lists.ListInput input)
        Specified by:
        getNewListType in class org.intermine.webservice.server.lists.ListMakerService

      • makeList

        protected void makeList​(org.intermine.webservice.server.lists.ListInput input,
                        java.lang.String type,
                        org.intermine.api.profile.Profile profile,
                        java.util.Set<java.lang.String> temporaryBagNamesAccumulator)
                 throws java.lang.Exception
        Specified by:
        makeList in class org.intermine.webservice.server.lists.ListMakerService
        Throws:
        java.lang.Exception

      • doListCreation

        protected org.intermine.api.profile.InterMineBag doListCreation​(GenomicRegionSearchListInput input,
                                                                org.intermine.api.profile.Profile profile,
                                                                java.lang.String type)
                                                         throws org.intermine.objectstore.ObjectStoreException,
                                                                org.intermine.api.bag.ClassKeysNotFoundException,
                                                                org.intermine.api.bag.UnknownBagTypeException
        Create the list specified by the region search input.
        Parameters:
        input - The input object, containing the values specified by the user.
        profile - The user's profile
        type - The unqualified name of the class of object in the new list.
        Returns:
        A new list
        Throws:
        org.intermine.objectstore.ObjectStoreException - if there is an error running the queries.
        org.intermine.api.bag.UnknownBagTypeException - if bad bag type
        org.intermine.api.bag.ClassKeysNotFoundException - no class keys

      • getHeaderAttributes

        protected java.util.Map<java.lang.String,​java.lang.Object> getHeaderAttributes()
        Gets the header attributes on the output object.
        Overrides:
        getHeaderAttributes in class org.intermine.webservice.server.lists.ListMakerService
        Returns:
        A map of header attributes for JSON output.

      • getInput

        protected org.intermine.webservice.server.lists.ListInput getInput()
        Overrides:
        getInput in class org.intermine.webservice.server.lists.AbstractListService

      • createQueries

        protected java.util.Map<GenomicRegion,​org.intermine.objectstore.query.Query> createQueries​(GenomicRegionSearchListInput.GenomicRegionSearchInfo info)
        Create the queries used to run the genomic region search.
        Parameters:
        info - The options input object.
        Returns:
        A map from a region to the query needed to find objects in that region.