Package gorsat.process

Class GorJavaUtilities

java.lang.Object
gorsat.process.GorJavaUtilities
public class GorJavaUtilities
extends java.lang.Object
Created by sigmar on 21/12/15.

  • Nested Class Summary

    Nested Classes 
    Modifier and Type Class Description
    static class  GorJavaUtilities.CmdParams  
    static class  GorJavaUtilities.PRPRPRValue  
    static class  GorJavaUtilities.PRPRValue  
    static class  GorJavaUtilities.VCFValue  

  • Field Summary

    Fields 
    Modifier and Type Field Description
    static java.text.DecimalFormat fd3  
    static double[] pArray  
    static java.lang.String[] prArray  
    static GorJavaUtilities.PRPRValue prprFunction  
    static GorJavaUtilities.PRPRPRValue prprprFunction  

  • Constructor Summary

    Constructors 
    Constructor Description
    GorJavaUtilities()  

  • Method Summary

    Modifier and Type Method Description
    static java.lang.String createMapString​(java.util.Map<java.lang.String,​java.lang.String> createMap)  
    static org.gorpipe.model.gor.iterators.RowSource getDbIteratorSource​(java.lang.String sqlQuery, boolean gortable, java.lang.String source, boolean scoping)  
    static java.util.Optional<java.lang.String> getIgnoreCase​(java.util.Collection<java.lang.String> c, java.lang.String str)  
    static java.lang.String[] mergeArrays​(java.lang.String[] array1, java.lang.String[] array2)  
    static java.lang.String projectDataReplacement​(java.lang.String projectRoot, java.lang.String myCommand)  
    static java.lang.String projectReplacement​(java.lang.String myCommand, java.lang.String projectRoot, java.lang.String requestId, java.lang.String securityContext)  
    static java.lang.String projectReplacement​(java.lang.String myCommand, org.gorpipe.gor.session.GorSession session)  
    static java.util.Map<java.lang.String,​GorJavaUtilities.CmdParams> readWhiteList​(java.lang.String cmdConfigFile)  
    static java.util.Map<java.lang.String,​GorJavaUtilities.CmdParams> readWhiteList​(java.nio.file.Path cmdConfigPath)  
    static java.nio.file.Path resolveWhiteListFilePath​(java.lang.String whiteListFile, java.nio.file.Path projectRoot)
    Helper method to resolve whitelist file path (from config file) to full path.
    static java.lang.String seekReplacement​(java.lang.String myCommand, java.lang.String chr, int start, int stop)  
    static java.util.List<org.gorpipe.gor.model.Row> stream2RowList​(java.util.stream.Stream<org.gorpipe.gor.model.Row> str)  
    static java.lang.String[] toUppercase​(java.util.Collection<java.lang.String> c)  
    static java.util.stream.Stream<java.lang.String> wrapObjectArrayIterator​(java.util.Iterator<java.lang.Object[]> iterator)
    Helper method for wrapping Object[] iterator to Stream.

    Methods inherited from class java.lang.Object

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

  • Field Details

  • Constructor Details

  • Method Details

    • createMapString

      public static java.lang.String createMapString​(java.util.Map<java.lang.String,​java.lang.String> createMap)

    • stream2RowList

      public static java.util.List<org.gorpipe.gor.model.Row> stream2RowList​(java.util.stream.Stream<org.gorpipe.gor.model.Row> str)

    • seekReplacement

      public static java.lang.String seekReplacement​(java.lang.String myCommand, java.lang.String chr, int start, int stop)

    • projectReplacement

      public static java.lang.String projectReplacement​(java.lang.String myCommand, org.gorpipe.gor.session.GorSession session) throws java.io.IOException
      Throws:
      java.io.IOException

    • projectReplacement

      public static java.lang.String projectReplacement​(java.lang.String myCommand, java.lang.String projectRoot, java.lang.String requestId, java.lang.String securityContext) throws java.io.IOException
      Throws:
      java.io.IOException

    • projectDataReplacement

      public static java.lang.String projectDataReplacement​(java.lang.String projectRoot, java.lang.String myCommand) throws java.io.IOException
      Throws:
      java.io.IOException

    • getDbIteratorSource

      public static org.gorpipe.model.gor.iterators.RowSource getDbIteratorSource​(java.lang.String sqlQuery, boolean gortable, java.lang.String source, boolean scoping)

    • wrapObjectArrayIterator

      public static java.util.stream.Stream<java.lang.String> wrapObjectArrayIterator​(java.util.Iterator<java.lang.Object[]> iterator)
      Helper method for wrapping Object[] iterator to Stream.
      Parameters:
      iterator -
      Returns:
      Stream where iterator elements are represented as string joined with tab delimiter

    • readWhiteList

      public static java.util.Map<java.lang.String,​GorJavaUtilities.CmdParams> readWhiteList​(java.nio.file.Path cmdConfigPath)

    • readWhiteList

      public static java.util.Map<java.lang.String,​GorJavaUtilities.CmdParams> readWhiteList​(java.lang.String cmdConfigFile) throws java.io.IOException
      Throws:
      java.io.IOException

    • resolveWhiteListFilePath

      public static java.nio.file.Path resolveWhiteListFilePath​(java.lang.String whiteListFile, java.nio.file.Path projectRoot)
      Helper method to resolve whitelist file path (from config file) to full path.

      If whitelist path is resolved as follows: 1. If input is absolute or empty then it is returned. 2. Search relative for the project directory. 3. If nothing is found we return the input.

      Parameters:
      whiteListFile - white list file path, can not be null or emtpy.
      projectRoot - project root for the current project.
      Returns:
      fully resolved path to the whitelist file.

    • getIgnoreCase

      public static java.util.Optional<java.lang.String> getIgnoreCase​(java.util.Collection<java.lang.String> c, java.lang.String str)

    • toUppercase

      public static java.lang.String[] toUppercase​(java.util.Collection<java.lang.String> c)

    • mergeArrays

      public static java.lang.String[] mergeArrays​(java.lang.String[] array1, java.lang.String[] array2)