preston match throw java.lang.IllegalArgumentException on archive entry zip:hash://sha256/a6d67e8404218dcb06aea0271a61207e51ec3207a09bc419c672c3a777c9700b!/iczn-lists-master/opinions/google-sheets/Official List Publications - Sheet1.tsv

[jhpoelen]

Preston match stopped early when running preston match on a local copy of https://deeplinker.bio , with the following exception:

$ preston ls | pv -l | preston match -l tsv 'http://arctos.database.museum/guid/[a-zA-Z]+:[a-zA-Z]+:[^ \t\n,?;]+' | cut -f1,3 | grep -E '\shttp://arctos.database.museum/guid/[a-zA-Z]+:[a-zA-Z]+:[^ \t\n,?;]+' 
Oct 20, 2020 6:31:39 PM bio.guoda.preston.cmd.CmdLine run                                                                                ]
SEVERE: unexpected exception
java.lang.IllegalArgumentException: Illegal character in opaque part at index 133: zip:hash://sha256/a6d67e8404218dcb06aea0271a61207e51ec3207a09bc419c672c3a777c9700b!/iczn-lists-master/opinions/google-sheets/Official List Publications - Sheet1.tsv
	at java.net.URI.create(URI.java:852)
	at org.apache.commons.rdf.simple.IRIImpl.<init>(IRIImpl.java:33)
	at org.apache.commons.rdf.simple.SimpleRDF.createIRI(SimpleRDF.java:82)
	at bio.guoda.preston.model.RefNodeFactory.toIRI(RefNodeFactory.java:26)
	at bio.guoda.preston.process.TextMatcher.getEntryIri(TextMatcher.java:255)
	at bio.guoda.preston.process.TextMatcher.parseAsArchive(TextMatcher.java:148)
	at bio.guoda.preston.process.TextMatcher.attemptToParseAsArchive(TextMatcher.java:100)
	at bio.guoda.preston.process.TextMatcher.attemptToParse(TextMatcher.java:92)
	at bio.guoda.preston.process.TextMatcher.on(TextMatcher.java:80)
	at bio.guoda.preston.cmd.CmdMatch$1.emit(CmdMatch.java:51)
	at bio.guoda.preston.process.EmittingStreamRDF.copyOnEmit(EmittingStreamRDF.java:51)
	at bio.guoda.preston.process.EmittingStreamRDF.parseAndEmit(EmittingStreamRDF.java:40)
	at bio.guoda.preston.cmd.CmdMatch.run(CmdMatch.java:56)
	at bio.guoda.preston.cmd.CmdMatch.run(CmdMatch.java:36)
	at bio.guoda.preston.cmd.CmdLine.run(CmdLine.java:18)
	at bio.guoda.preston.cmd.CmdLine.run(CmdLine.java:26)
	at bio.guoda.preston.Preston.main(Preston.java:19)
Caused by: java.net.URISyntaxException: Illegal character in opaque part at index 133: zip:hash://sha256/a6d67e8404218dcb06aea0271a61207e51ec3207a09bc419c672c3a777c9700b!/iczn-lists-master/opinions/google-sheets/Official List Publications - Sheet1.tsv
	at java.net.URI$Parser.fail(URI.java:2848)
	at java.net.URI$Parser.checkChars(URI.java:3021)
	at java.net.URI$Parser.parse(URI.java:3058)
	at java.net.URI.<init>(URI.java:588)
	at java.net.URI.create(URI.java:850)
	... 16 more

Suspect that the whitespaces in URI needs to be escaped using customary escape commands like %20 (for whitespace). Can be done with built in new URI(...) constructor.

[mielliott]

Ah, makes sense. I'll try to fix it real quick. Please holler if you're already working on it.

[mielliott]

It should be fixed now.

[jhpoelen]

Confirmed fixed! @mielliott thanks!