Standardizer exception

Getting an exception when starting up a Standardizer object in JChem 14.7.14.0:

Jul 17, 2014 3:36:47 PM chemaxon.naming.n2s.CASNumberConverter <clinit>

WARNING: Exception while loding cache

java.io.IOException: Cannot create parent directory

	at chemaxon.util.DotfileUtil.ensureParentExists(DotfileUtil.java:165)

	at chemaxon.util.DotfileUtil.getDotFileWithEnsuredPath(DotfileUtil.java:78)

	at chemaxon.naming.n2s.CASNumberConverter.<clinit>(CASNumberConverter.java:43)

	at chemaxon.formats.recognizer.NameRecognizer.isSurelyName(NameRecognizer.java:173)

	at chemaxon.formats.recognizer.NameRecognizer.evaluateName(NameRecognizer.java:111)

	at chemaxon.formats.recognizer.NameRecognizer.isNameLine(NameRecognizer.java:96)

	at chemaxon.formats.recognizer.NameRecognizer.tryToRecognize(NameRecognizer.java:57)

	at chemaxon.formats.recognizer.RecognitionSubsystem.processLine(RecognitionSubsystem.java:153)

	at chemaxon.formats.recognizer.RecognitionSubsystem.processLine(RecognitionSubsystem.java:114)

	at chemaxon.formats.MolInputStream.processLine(MolInputStream.java:334)

	at chemaxon.formats.MolInputStream.initTextFormat(MolInputStream.java:246)

	at chemaxon.formats.MolInputStream.init(MolInputStream.java:136)

	at chemaxon.formats.MolInputStream.<init>(MolInputStream.java:116)

	at chemaxon.formats.MolImporter.init(MolImporter.java:542)

	at chemaxon.formats.MolImporter.<init>(MolImporter.java:118)

	at chemaxon.standardizer.advancedactions.StripSaltsAction.readSaltDictionary(StripSaltsAction.java:309)

	at chemaxon.standardizer.advancedactions.StripSaltsAction.<clinit>(StripSaltsAction.java:65)

	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)

	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)

	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)

	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)

	at chemaxon.standardizer.StandardizerActionFactory.getStandardizerAction(StandardizerActionFactory.java:231)

	at chemaxon.standardizer.StandardizerActionFactory.getAvailableStandardizerActions(StandardizerActionFactory.java:184)

	at chemaxon.standardizer.configuration.reader.StandardizerSAXHandler.initializeMap(StandardizerSAXHandler.java:112)

	at chemaxon.standardizer.configuration.reader.StandardizerSAXHandler.<init>(StandardizerSAXHandler.java:101)

	at chemaxon.standardizer.configuration.reader.StandardizerSAXHandler.<init>(StandardizerSAXHandler.java:78)

	at chemaxon.standardizer.configuration.reader.StandardizerXMLReader.<init>(StandardizerXMLReader.java:77)

	at chemaxon.standardizer.Standardizer.<init>(Standardizer.java:204)

	at com.epoch.servlet.GroupLoader.loadAppConfig(GroupLoader.java:125)

The line of code that is eliciting the error is:

AppConfig.standardizer =

                    new Standardizer(new File(normalizeConfigFile));

The contents of normalizeConfigFile are:

<?xml version="1.0" encoding="UTF-8"?>

<!-- Standardizer configuration file -->



<StandardizerConfiguration Version ="0.1">

    <Actions>

        <Transformation ID="S_or_Se_ylide_double"

            Structure="[#16,#34;++:1]-[#34,#16,#8,#7,#6;-:2]>>[#16,#34;+:1]=[#34,#16,#8,#7,#6:2]"/>

        <Transformation ID="S_or_Se_ylide_double"

            Structure="[#16,#34;+:1]-[#34,#16,#8,#7,#6;-:2]>>[#16,#34;0:1]=[#34,#16,#8,#7,#6:2]"/>

        <Transformation ID="S_or_Se_ylide_triple"

            Structure="[#16,#34;++:1]=[#34,#16,#8,#7,#6;-:2]>>[#16,#34;+:1]#[#34,#16,#8,#7,#6:2]"/>

        <Transformation ID="S_or_Se_ylide_triple"

            Structure="[#16,#34;+:1]=[#34,#16,#8,#7,#6;-:2]>>[#16,#34;0:1]#[#34,#16,#8,#7,#6:2]"/>

        <Transformation ID="N_or_P_or_As_ylide_double"

            Structure="[#7,#15,#33;+:1]-[#34,#16,#8,#7,#6;-:2]>>[#7,#15,#33;0:1]=[#34,#16,#8,#7,#6:2]"/>

        <Transformation ID="N_or_P_or_As_ylide_triple"

            Structure="[#7,#15,#33;+:1]=[#34,#16,#8,#7,#6;-:2]>>[#7,#15,#33;0:1]#[#34,#16,#8,#7,#6:2]"/>

        <Transformation ID="N_or_P_or_As_dianion_ylide_double"

            Structure="[#7,#15,#33;+:1]-[#34,#16,#8,#7,#6;--:2]>>[#7,#15,#33;0:1]=[#34,#16,#8,#7,#6;-:2]"/>

    </Actions>

</StandardizerConfiguration>

Interestingly, when I change the code to try to catch the IOException, then when I compile, I get this error:

GroupLoader.java:127: exception java.io.IOException is never thrown in body of corresponding try statement

		} catch (IOException e) {

		  ^

GroupLoader.java:139: exception java.io.IOException is never thrown in body of corresponding try statement

		} catch (IOException e) {

		  ^

Seems pretty clear that the line is throwing an IOException, so why won't it let me catch it?.

So then I changed the code to catch a generic exception. It compiles now, but it still doesn't catch the exception when the program starts up.

I think I have done all I can do to solve this problem.

Bob, it's not an exception thrown from Standardizer code, it's a stack trace printed by chemaxon.naming.n2s.CASNumberConverter. Standardizer ignores it on purpose: it's absolutely not relevant there.

Just ignore this printed message. We will find less confusing ways to display such warnings.