Package org.intermine.bio.webservice

Class BioQueryService

    • Field Summary

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

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

    • Constructor Summary

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

    • Method Summary

      All Methods Static Methods Instance Methods Abstract Methods Concrete Methods 
      Modifier and Type Method Description
      protected void checkPathQuery​(org.intermine.pathquery.PathQuery pq)
      No-op stub.
      protected void execute()  
      protected abstract java.lang.String getContentType()  
      protected java.lang.String getDefaultFileName()  
      org.intermine.webservice.server.Format getDefaultFormat()  
      protected org.intermine.webservice.server.output.Output getDefaultOutput​(java.io.PrintWriter out, java.io.OutputStream outputstream, java.lang.String sep)  
      protected abstract org.intermine.web.logic.export.Exporter getExporter​(org.intermine.pathquery.PathQuery pq)  
      java.io.OutputStream getOutputStream()  
      protected static java.util.List<java.lang.String> getPathQueryViews​(java.lang.String[] views)
      Parse path query views from request parameter "view" comma-separated
      java.io.PrintWriter getPrintWriter()  
      protected org.intermine.pathquery.PathQuery getQuery()
      Return the query specified in the request, shorn of all duplicate classes in the view.
      protected java.util.List<org.intermine.pathquery.Path> getQueryPaths​(org.intermine.pathquery.PathQuery pq)
      Parse view strings to Path objects
      protected abstract java.lang.String getSuffix()  

      • Methods inherited from class org.intermine.webservice.server.query.AbstractQueryService

        formatIsJsonObj, formatIsNTriples, formatIsRDF, getQueryBuilder, getSchemaLocation, getSchemaUrl

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

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

      • Methods inherited from class java.lang.Object

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

    • Constructor Detail

      • BioQueryService

        public BioQueryService​(org.intermine.api.InterMineAPI im)
        Constructor.
        Parameters:
        im - A reference to an InterMine API settings bundle.

    • Method Detail

      • getPrintWriter

        public java.io.PrintWriter getPrintWriter()
        Returns:
        print writer

      • getOutputStream

        public java.io.OutputStream getOutputStream()
        Returns:
        output stream

      • getDefaultFileName

        protected java.lang.String getDefaultFileName()
        Overrides:
        getDefaultFileName in class org.intermine.webservice.server.WebService

      • getSuffix

        protected abstract java.lang.String getSuffix()
        Returns:
        suffix

      • getContentType

        protected abstract java.lang.String getContentType()
        Returns:
        content type

      • getDefaultOutput

        protected org.intermine.webservice.server.output.Output getDefaultOutput​(java.io.PrintWriter out,
                                                                         java.io.OutputStream outputstream,
                                                                         java.lang.String sep)
        Overrides:
        getDefaultOutput in class org.intermine.webservice.server.WebService

      • getDefaultFormat

        public org.intermine.webservice.server.Format getDefaultFormat()
        Overrides:
        getDefaultFormat in class org.intermine.webservice.server.WebService

      • getQuery

        protected org.intermine.pathquery.PathQuery getQuery()
        Return the query specified in the request, shorn of all duplicate classes in the view. Note, it is the users responsibility to ensure that there are only SequenceFeatures in the view.
        Returns:
        A query.

      • getExporter

        protected abstract org.intermine.web.logic.export.Exporter getExporter​(org.intermine.pathquery.PathQuery pq)
        Parameters:
        pq - pathquery
        Returns:
        exporter

      • checkPathQuery

        protected void checkPathQuery​(org.intermine.pathquery.PathQuery pq)
                       throws java.lang.Exception
        No-op stub. Put query validation here.
        Parameters:
        pq - pathquery
        Throws:
        java.lang.Exception - if something goes wrong

      • execute

        protected void execute()
                throws java.lang.Exception
        Specified by:
        execute in class org.intermine.webservice.server.WebService
        Throws:
        java.lang.Exception

      • getPathQueryViews

        protected static java.util.List<java.lang.String> getPathQueryViews​(java.lang.String[] views)
        Parse path query views from request parameter "view" comma-separated
        Parameters:
        views - views in pathquery
        Returns:
        a list of query view as string

      • getQueryPaths

        protected java.util.List<org.intermine.pathquery.Path> getQueryPaths​(org.intermine.pathquery.PathQuery pq)
        Parse view strings to Path objects
        Parameters:
        pq - pathquery
        Returns:
        a list of query path