Package gorsat.process

Class GorJavaUtilities

java.lang.Object

gorsat.process.GorJavaUtilities

public class GorJavaUtilities
extends 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 enum	GorJavaUtilities.Phenotypes
static class	GorJavaUtilities.PRPRPRValue
static class	GorJavaUtilities.PRPRValue
static class	GorJavaUtilities.VCFValue

Field Summary

Fields

Modifier and Type	Field	Description
static DecimalFormat	fd3
static final String	GORZ_META
static double[]	pArray
static String[]	prArray
static GorJavaUtilities.PRPRValue	prprFunction
static GorJavaUtilities.PRPRPRValue	prprprFunction

Constructor Summary

Constructors

Constructor	Description
GorJavaUtilities()

Method Summary

Modifier and Type	Method	Description
static String	clearHints(String query)
static String	createMapString(Map<String,String> createMap)
static void	createSymbolicLink(Path resultPath, Path cachePath)
static org.gorpipe.gor.model.GenomicIterator	getDbIteratorSource(String sqlQuery, boolean gortable, String source, boolean scoping)
static Optional<String>	getIgnoreCase(Collection<String> c, String str)
static GorJavaUtilities.PhenoInfo	getPhenotype(String phenoHeader, BufferedReader pheno)
static boolean	isGorCmd(String cmd)
static boolean	isPGorCmd(String cmd)
static String[]	mergeArrays(String[] array1, String[] array2)
static String	projectDataReplacement(String projectRoot, String myCommand)
static String	projectReplacement(String myCommand, String projectRoot, String requestId, String securityContext)
static String	projectReplacement(String myCommand, org.gorpipe.gor.session.GorSession session)
static Map<String,GorJavaUtilities.CmdParams>	readWhiteList(String cmdConfigFile)
static Map<String,GorJavaUtilities.CmdParams>	readWhiteList(Path cmdConfigPath)
static Path	resolveWhiteListFilePath(String whiteListFile, Path projectRoot)	Helper method to resolve whitelist file path (from config file) to full path.
static String	seekReplacement(String myCommand, String chr, int start, int stop)
static String[]	splitResourceHints(String query, String validStart)
static List<org.gorpipe.gor.model.Row>	stream2RowList(Stream<org.gorpipe.gor.model.Row> str)
static String[]	toUppercase(Collection<String> c)
static String	verifyLinkFileLastModified(org.gorpipe.gor.session.ProjectContext projectContext, String cacheFile)
static Stream<String>	wrapObjectArrayIterator(Iterator<Object[]> iterator)	Helper method for wrapping Object[] iterator to Stream.
static void	writeDictionaryFromMeta(org.gorpipe.gor.model.FileReader fileReader, String outfolderpath, String dictionarypath)

Methods inherited from class java.lang.Object

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

Field Details

GORZ_META

public static final String GORZ_META

See Also:

• Constant Field Values

fd3

public static DecimalFormat fd3

pArray

public static double[] pArray

prArray

public static String[] prArray

prprFunction

public static GorJavaUtilities.PRPRValue prprFunction

prprprFunction

public static GorJavaUtilities.PRPRPRValue prprprFunction

Constructor Details

GorJavaUtilities

public GorJavaUtilities()

Method Details

getPhenotype

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

clearHints

public static String clearHints(String query)

splitResourceHints

public static String[] splitResourceHints(String query,
 String validStart)

createMapString

public static String createMapString(Map<String,String> createMap)

stream2RowList

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

seekReplacement

public static String seekReplacement(String myCommand,
 String chr,
 int start,
 int stop)

projectReplacement

public static String projectReplacement(String myCommand,
 org.gorpipe.gor.session.GorSession session)
                                 throws IOException

Throws:

IOException

projectReplacement

public static String projectReplacement(String myCommand,
 String projectRoot,
 String requestId,
 String securityContext)
                                 throws IOException

Throws:

IOException

projectDataReplacement

public static String projectDataReplacement(String projectRoot,
 String myCommand)
                                     throws IOException

Throws:

IOException

getDbIteratorSource

public static org.gorpipe.gor.model.GenomicIterator getDbIteratorSource(String sqlQuery,
 boolean gortable,
 String source,
 boolean scoping)

wrapObjectArrayIterator

public static Stream<String> wrapObjectArrayIterator(Iterator<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 Map<String,GorJavaUtilities.CmdParams> readWhiteList(Path cmdConfigPath)

readWhiteList

public static Map<String,GorJavaUtilities.CmdParams> readWhiteList(String cmdConfigFile)
                                                            throws IOException

Throws:

IOException

resolveWhiteListFilePath

public static Path resolveWhiteListFilePath(String whiteListFile,
 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 Optional<String> getIgnoreCase(Collection<String> c,
 String str)

toUppercase

public static String[] toUppercase(Collection<String> c)

mergeArrays

public static String[] mergeArrays(String[] array1,
 String[] array2)

isGorCmd

public static boolean isGorCmd(String cmd)

isPGorCmd

public static boolean isPGorCmd(String cmd)

createSymbolicLink

public static void createSymbolicLink(Path resultPath,
 Path cachePath)
                               throws IOException

Throws:

IOException

verifyLinkFileLastModified

public static String verifyLinkFileLastModified(org.gorpipe.gor.session.ProjectContext projectContext,
 String cacheFile)

writeDictionaryFromMeta

public static void writeDictionaryFromMeta(org.gorpipe.gor.model.FileReader fileReader,
 String outfolderpath,
 String dictionarypath)
                                    throws IOException

Throws:

IOException