 Stephen Ficklin
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eb1470667f
Fix for issue raised by sean on GFF3 loader
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%!s(int64=3) %!d(string=hai) anos |
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Stephen Ficklin
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2811ee8220
Fixed bug with GFF3 loader when adding relationships for children that start at the same coordinate
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%!s(int64=3) %!d(string=hai) anos |
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Stephen Ficklin
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a54dc85953
PHP 7.0 bug fix
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%!s(int64=3) %!d(string=hai) anos |
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Stephen Ficklin
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a4be52db49
Added a fix in case the Target feature is also a feature in the GFF3 file but was introduced before the actual feature
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%!s(int64=3) %!d(string=hai) anos |
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Stephen Ficklin
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a46f306134
Fix for match/target features
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%!s(int64=3) %!d(string=hai) anos |
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Stephen Ficklin
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34f161ac8e
Fixes to GFF3 loader
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%!s(int64=3) %!d(string=hai) anos |
 Risharde Ramnath
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70858e9b53
Remove unnecessary urldecoding for parent attribute
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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27de73ff9b
Remove validation for tag and tag values. Remove additional output code for logMessage.
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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dcfd25d186
Modified TripalImporter logmessage function to output log messages to terminal / command line when code is executed on command line
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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ac790a4eeb
Unit test for escaped characters with tag values
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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541d67099e
Fix merge
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%!s(int64=4) %!d(string=hai) anos |
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Stephen Ficklin
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bf8a978bb2
Fixed warning messags when submitting form and bug when adding proteins
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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5260a06a06
This latest commit detects a bug using the testGFFImporterEscapedTagValueWithComma unit test
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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2f66751d03
2 validation checks for attribute tag name and attribute tag value plus unit test for tag name that contains a comma
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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bba096323a
Fixed a mix up of validation for ID which should have been for seqid. Removed validation for ID. Altered tests to properly work. Added new test for invalid character in seqid/landmark id
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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5278d2a50b
Fix for GFF if phase value is invalid + unit tests for the gff phase column that checks for valid and invalid characters
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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d25737f6e4
GFF loader modification to throw error if strand character is invalid. Added unit test with an invalid strand gff to confirm it works.
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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ea8b4a0b58
GFF fix for strands that are specified as question marks + finish php unit test for strands
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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da939901ea
Fixed ID regular expression check in GFF loader, added new test for invalid start end values and corresponding test gff file
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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49651d6c8a
Better ID validation check within the GFF3 loader
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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fefe37536c
Minor fix regarding whitespace detection in GFF3 importer ID validation
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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5e98649061
2 additional unit tests and corresponding gff files related to ID validations for unescaped whitespaces and IDs beginning with right arrow character
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%!s(int64=4) %!d(string=hai) anos |
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Stephen Ficklin
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8b0cfedbe4
Added check for Gap in the GFF
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%!s(int64=4) %!d(string=hai) anos |
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Risharde Ramnath
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bde6690233
Bug fix that makes GFFImporter caching of features work correctly
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%!s(int64=4) %!d(string=hai) anos |
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Stephen Ficklin
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4ef5653ee0
Fixed caching bug and cleaned up memory leaks
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%!s(int64=4) %!d(string=hai) anos |
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Stephen Ficklin
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0ab2db8eb1
Now FASTA sequences are being added... all done except testing!
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%!s(int64=4) %!d(string=hai) anos |
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Stephen Ficklin
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2a7510c736
Now supports creation of proteins and tarets
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%!s(int64=4) %!d(string=hai) anos |
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Stephen Ficklin
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dbedaf88b0
GFF3 loader: Added file caching to reduce memory requirements. Added insert to analyisfeature table
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%!s(int64=4) %!d(string=hai) anos |
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Stephen Ficklin
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f2bd2bb030
Fixed bugs in GFF loader when landmarks are present and with finding feature property CV terms
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%!s(int64=4) %!d(string=hai) anos |
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Stephen Ficklin
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d14083521c
minor updates
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%!s(int64=4) %!d(string=hai) anos |
