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problems on generate-names.pl #1061

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billzt opened this Issue May 26, 2018 · 1 comment

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billzt commented May 26, 2018

When I use generate-names.pl in the same method as I did in the 1.12.X version, it runs error like this:

malformed JSON string, neither tag, array, object, number, string or atom, at character offset 1902 (before "]\n}") at /opt/JBrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 32.
 at /opt/JBrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7.
	Bio::JBrowse::ConfigurationManager::__ANON__("malformed JSON string, neither tag, array, object, number, st"...) called at /opt/JBrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 32
	Bio::JBrowse::ConfigurationManager::slurpJSON("/home/JBrowse_data/Garb-CRI/trackList.json") called at /opt/JBrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 143
	Bio::JBrowse::ConfigurationManager::_load_include(Bio::JBrowse::ConfigurationManager=HASH(0x3046838), HASH(0x30468b0), "/home/JBrowse_data/Garb-CRI/") called at /opt/JBrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 69
	Bio::JBrowse::ConfigurationManager::_load_includes(Bio::JBrowse::ConfigurationManager=HASH(0x3046838), HASH(0x2394658)) called at /opt/JBrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 39
	Bio::JBrowse::ConfigurationManager::get_final_config(Bio::JBrowse::ConfigurationManager=HASH(0x3046838)) called at /opt/JBrowse/bin/../src/perl5/GenomeDB.pm line 286
	GenomeDB::trackList(GenomeDB=HASH(0x23945c8)) called at /opt/JBrowse/bin/../src/perl5/Bio/JBrowse/Cmd/IndexNames.pm line 82
	Bio::JBrowse::Cmd::IndexNames::run(Bio::JBrowse::Cmd::IndexNames=HASH(0x242e238)) called at /opt/JBrowse/bin/generate-names.pl line 8

What does this mean?

@rbuels

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rbuels commented May 27, 2018

It sounds like there is a syntax error in one of your included configuration files. generate-names.pl now traverses all the included configs, which it didn't before.

We need to fix this to have better error output though, like telling you which config file has the syntax error in it!

@rbuels rbuels added this to the 1.14.2 milestone May 28, 2018

@rbuels rbuels closed this in 0405097 May 31, 2018

cmdcolin added a commit that referenced this issue Jun 2, 2018

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