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.PhenoInfo
static class	GorJavaUtilities.Phenotypes
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 java.lang.String	GORZ_META
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	clearHints(java.lang.String query)
static java.lang.String	createMapString(java.util.Map<java.lang.String,java.lang.String> createMap)
static org.gorpipe.gor.model.GenomicIterator	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 GorJavaUtilities.PhenoInfo	getPhenotype(java.lang.String phenoHeader, java.io.BufferedReader pheno)
static boolean	isGorCmd(java.lang.String cmd)
static boolean	isPGorCmd(java.lang.String cmd)
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.lang.String[]	splitResourceHints(java.lang.String query, java.lang.String validStart)
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.
static void	writeDictionaryFromMeta(java.nio.file.Path outfolderpath, java.nio.file.Path dictionarypath)

Methods inherited from class java.lang.Object

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

Field Detail

GORZ_META

public static final java.lang.String GORZ_META

See Also:

Constant Field Values

fd3

public static java.text.DecimalFormat fd3

pArray

public static double[] pArray

prArray

public static java.lang.String[] prArray

prprFunction

public static GorJavaUtilities.PRPRValue prprFunction

prprprFunction

public static GorJavaUtilities.PRPRPRValue prprprFunction

Constructor Detail

GorJavaUtilities

public GorJavaUtilities()

Method Detail

getPhenotype

public static GorJavaUtilities.PhenoInfo getPhenotype(java.lang.String phenoHeader,
                                                      java.io.BufferedReader pheno)

clearHints

public static java.lang.String clearHints(java.lang.String query)

splitResourceHints

public static java.lang.String[] splitResourceHints(java.lang.String query,
                                                    java.lang.String validStart)

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.gor.model.GenomicIterator 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)

isGorCmd

public static boolean isGorCmd(java.lang.String cmd)

isPGorCmd

public static boolean isPGorCmd(java.lang.String cmd)

writeDictionaryFromMeta

public static void writeDictionaryFromMeta(java.nio.file.Path outfolderpath,
                                           java.nio.file.Path dictionarypath)
                                    throws java.io.IOException

Throws:

java.io.IOException