Merge branch 'master' of git://git.code.sf.net/p/com-hfg/git into gradle_project
Merge branch 'master' of git://git.code.sf.net/p/com-hfg/git into gradle_project
Merge branch 'master' of git://git.code.sf.net/p/com-hfg/git into gradle_project
Merge branch 'master' of git://git.code.sf.net/p/com-hfg/git into gradle_project
Possible NPE fix in DigestFragment's toString().
Added MathUtil.round().
Merge remote-tracking branch 'origin/master'
Added a size check and reattempts to FileObjImpl's writeToLocalFile().
Added lessThan() and greaterThan() to NCBITaxonNodeRank.
Modified DatabaseCharField's setValueFromResultSet() to treat an empty string like a null value.
Added setNonce() to StyleTag.
Improved ProteinDigest behavior for complex digests.
Modified SimpleProteinProperty's getReturnType() to not match synthetic methods.
Merge branch 'master' of ssh://git.code.sf.net/p/com-hfg/git into gradle_project
Adding buildSrc Gradle magic directory for sharing build code.
More Element adjustments to allow mass value retrieval for any supported atomic weights version.
Modified KaSet.PATRICKIOS_SIMPLE to include null values for cys, tyr, and his.
Modified IsoelectricPoint so that it will use Ka values associated with an amino acid if the KaSet doesn't include values for that amino acid.
Merge branch 'master' of ssh://git.code.sf.net/p/com-hfg/git into gradle_project
Filter out test that have excluded classes
Added convertToUnicodeEscaped() and convertFromUnicodeEscaped() to StringUtil.
Added registerInvalidPathHandler() to ServletRequestDispatcher.
add testSubtractDaysFromDate() in DateUtil
Merge remote-tracking branch 'origin/master'
add Erinaceus europaeus to NCBITaxon
Merge remote-tracking branch 'origin/master'
Added Meta.CONTENT_SECURITY_POLICY.
Merge branch 'master' of ssh://git.code.sf.net/p/com-hfg/git
Adding methods for measuring response timing for SMB file obj
Added step syntax support to CronSchedule.
Additional syntax support added to CronSchedule.
Updated dependency versions in build.gradle.
Added AtomGroup, Locant, and OrbitalHybridizationGeometry.
Added AminoAcidLocant and StructureAtomGroup.
Changes to core chem classes to better support molecular models.
build.grade fix.
Merge remote-tracking branch 'origin/master'
add support for 128 barcodes and flexible width
Added set/getName() to Option.
Merge remote-tracking branch 'origin/master'
Quantity now implements Cloneable.
JS-2698 Adding ability to calculate the number of milliseconds to the next cronSchedule calendar event
JS-2707 Check if data exists before skipping line if it's a comment line
JS-2648 Fix issues with input data having forward slashes escaped.
Added TSV.write() version for DataRow.
Added an Other value to AuthenticationProvider.
Added rowCount() to AbstractSparseMatrix.
Adjusted the HTTPFileObj's URI constructor.
Added DataType.fromTypesValue().
Adding method DataTable.getFirstRowKey. Usecase is for panopticon using dataTables with a single row and the RowKey is not predictable. The RowKey is needed for searching column data
Adding new methods to create DataTable instances from DataRows and from searching a column for a particular value. Warning: Casting raws to generic type will need some refinements.
Minor cleanup of TestNonlinearColorScale.
Further native digest fixes in ProteinDigest.
Fixed how ProteinDigest deals with complex native digest by adding recursion.
Cleaned up TestColorScale's test2().
Merge remote-tracking branch 'origin/master'
Updated HTMLDoc's setMetaContentTypeAndEncoding() to avoid duplicate meta content type tags if one had previously been directly set.
Adding brittle SMBFileObj test to help debug SMBFileObj issues, basically was not setting credentials on new SmbFile Objects. Will only work on OSX and will need updates to run other users machines.
Merge branch 'master' of ssh://git.code.sf.net/p/com-hfg/git
Adding getDataColumn by string into the DataRow class. Will be used in corelabkey in constructors to populate assay Data instances.
Merge remote-tracking branch 'origin/master'
Added InputStream and CharSequence constructors to CSS.
Remove COPY_ATTRIBUTES from File.move method, no longer a valid parameter. Added test.
Merge branch 'master' of ssh://git.code.sf.net/p/com-hfg/git
Utilize URLEncoder to encode the file name and cast the + encoded space values to %20 values
Merge branch 'master' of ssh://git.code.sf.net/p/com-hfg/git
Escape any white spaces in the file name which will throw in Exception with trying to cast to URI
Adjusted XMLBasedDoc's toIndentedXML(OutputStream inStream, int inInitialIndentLevel, int inIndentSize) to use the Writer form of the method.
Added convertImagesToDataUrls() to HTMLDoc.
Added convertImagesToDataUrls() to HTMLDoc.
Fix DataRow.getString method. Return the string of the column value not the column name. Adding test for some DataRow Getters.
Adding helper methods to DataTable. Get all values for column, countUnique values in a column and boolean check to figure out if all the values in a column are the same.
Added Papain as a protease. Not sure if this should go to master.
Added QuadFunction.
Fixed x offset issue in PhylogeneticTree's toRectangularCladomgramSVG().
Added DisplayValue.
Modified ScaleColorist's normalizeValue() to map out of range values to the range limits to avoid throwing exceptions.
Added SQLUtil.setArray() and SQLUtil.setBytes().
Merge remote-tracking branch 'origin/master'
Added DataRow.
Adding method to convert LocalDate to Date object
Added a version of parseToDataTable() and parse() to DelimitedTextParser that take a list of lines.
Added FileSource interface.
Added new forms of DateUtil.getISO_8601_DateTime().
Merge remote-tracking branch 'origin/master'
Added SET as a SQLClauseType.
Set Exception message ingo JDBCException message.
update to file util convertSeparatorToUnix helper method
Fixed issue with unicode characters in ContentTransferEncoding's quotedPrintableEncode().
XMLTagReader, XMLTagDocHandler, and HTMLFragment now supports multiple root tags.
Updated gradle wrapper to v8.3.
Improved SaxyParser errors for missing end tags.
Fixed bug in SQLUtil.setTimestamp() where nulls wer being set to type BIGINT.
Merge remote-tracking branch 'origin/master'
Adjusted PooledJDBCConnection's checkout() to avoid the logging in SQLUtil.execute().
Adding couple more test to make sure Date obj with UTC timezone don't change the date when cast to localDate
Adding .gitignore file
Adding method to convert a Date obj to LocalDate object based on ZoneId.systemDefault. Will be used in Date Based Labkey queries
update SsmlTextRun test with working white space
Merge remote-tracking branch 'origin/master'