ISA-tools/ISAconfigurator — Issue #25: failing to save configurations owing to malformed UTF-8 characters
Author: proccaserra
Created: 2012-02-28 07:04:42+00:00
State: open
Labels: Minor Bug, Priority Task

ISAcreator 1.5 prerelease:

How to reproduce:
open a configuration, alter it (possibly adding a unit fields and setting it to use Unit Ontology (served by NCBO bioportal)
Save.
Close without saving
Try to reopen the configuration
Tables and fields no longer show up in UI

Stack trace catches the following during the save process:
java.io.CharConversionException: Malformed UTF-8 character: 0xcd 0x73
at org.apache.xmlbeans.impl.piccolo.xml.UTF8XMLDecoder.decode(UTF8XMLDecoder.java:80)
at org.apache.xmlbeans.impl.piccolo.xml.XMLStreamReader$FastStreamDecoder.read(XMLStreamReader.java:762)
at org.apache.xmlbeans.impl.piccolo.xml.XMLStreamReader.read(XMLStreamReader.java:162)
at org.apache.xmlbeans.impl.piccolo.xml.PiccoloLexer.yy_refill(PiccoloLexer.java:3474)
at org.apache.xmlbeans.impl.piccolo.xml.PiccoloLexer.yylex(PiccoloLexer.java:3958)
at org.apache.xmlbeans.impl.piccolo.xml.Piccolo.yylex(Piccolo.java:1290)
at org.apache.xmlbeans.impl.piccolo.xml.Piccolo.yyparse(Piccolo.java:1400)
at org.apache.xmlbeans.impl.piccolo.xml.Piccolo.parse(Piccolo.java:714)
at org.apache.xmlbeans.impl.store.Locale$SaxLoader.load(Locale.java:3454)
at org.apache.xmlbeans.impl.store.Locale.parseToXmlObject(Locale.java:1276)
at org.apache.xmlbeans.impl.store.Locale.parseToXmlObject(Locale.java:1263)
at org.apache.xmlbeans.impl.schema.SchemaTypeLoaderBase.parse(SchemaTypeLoaderBase.java:345)
at org.apache.xmlbeans.impl.schema.SchemaTypeLoaderBase.parse(SchemaTypeLoaderBase.java:252)
at org.isatools.isatab.configurator.schema.IsatabConfigFileDocument$Factory.parse(Unknown Source)
at org.isatools.isacreator.configuration.io.ConfigXMLParser.parseFile(ConfigXMLParser.java:187)
at org.isatools.isacreator.configuration.io.ConfigXMLParser.getTableDefinitions(ConfigXMLParser.java:177)
at org.isatools.isacreator.configuration.io.ConfigXMLParser.loadConfiguration(ConfigXMLParser.java:90)
at org.isatools.isacreatorconfigurator.configui.MenuPanel.loadSession(MenuPanel.java:321)
at org.isatools.isacreatorconfigurator.configui.MenuPanel.access$800(MenuPanel.java:66)
at org.isatools.isacreatorconfigurator.configui.MenuPanel$CreateMenu$2$1.run(MenuPanel.java:190)
at java.lang.Thread.run(Thread.java:680)