autocompiles GFF3 to NCList

[nathandunn]

Fixes #2084

• clean out
• restrict upload name to have no spaces
• test against demo site
• retest against new directory
• retest against existing directory (extendedTrackList.json)
• test against a refresh after data is uploaded (or block)
• revert gzip code
• retest against new directory
• retest against existing directory (extendedTrackList.json)
  • if temp directory exists, then we need to create and add to extendedTrackList (do we need to remove?)
• allow gzipped gff3 (writes to the wrong directory currently) add gzip compression upload for GFF3 / JSON #2092
• test against very large data
• remove topLevelFeatures or compile without --type=mRNA

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related to #2084 and #2073

[nathandunn]

Getting this error when creating a new track from an existing:

execitugin /Users/nathandunn/repositories/nathanApolloMaster/web-app/jbrowse/bin/flatfile-to-json.pl --gff /opt/temporary/apollo/16538-Official Volvox/raw/TEst1.gff --compress --type mRNA --trackLabel TEst1 --out /opt/temporary/apollo/16538-Official Volvox err3: No such file or directory opening '/opt/temporary/apollo/16538-Official' for reading at /Users/nathandunn/repositories/nathanApolloMaster/web-app/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm line 144. at /Users/nathandunn/repositories/nathanApolloMaster/web-app/jbrowse/bin/../src/perl5/Bio/JBrowse/ConfigurationManager.pm line 7. Bio::JBrowse::ConfigurationManager::__ANON__("No such file or directory opening '/opt/temporary/apollo/1653"...) called at /usr/local/Cellar/perl/5.28.1/lib/perl5/5.28.1/Carp.pm line 291 Carp::croak("No such file or directory opening '/opt/temporary/apollo/1653"...) called at /usr/local/Cellar/perl/5.28.1/lib/perl5/site_perl/5.28.1/Bio/GFF3/LowLevel/Parser.pm line 51 Bio::GFF3::LowLevel::Parser::_open("Bio::GFF3::LowLevel::Parser", "/opt/temporary/apollo/16538-Official") called at /usr/local/Cellar/perl/5.28.1/lib/perl5/site_perl/5.28.1/Bio/GFF3/LowLevel/Parser.pm line 25 Bio::GFF3::LowLevel::Parser::open(undef, "/opt/temporary/apollo/16538-Official") called at /Users/nathandunn/repositories/nathanApolloMaster/web-app/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm line 144 Bio::JBrowse::Cmd::FlatFileToJson::make_gff_stream(Bio::JBrowse::Cmd::FlatFileToJson=HASH(0x7f9f54b40d10)) called at /Users/nathandunn/repositories/nathanApolloMaster/web-app/jbrowse/bin/../src/perl5/Bio/JBrowse/Cmd/FlatFileToJson.pm line 118 Bio::JBrowse::Cmd::FlatFileToJson::run(Bio::JBrowse::Cmd::FlatFileToJson=HASH(0x7f9f54b40d10)) called at /Users/nathandunn/repositories/nathanApolloMaster/web-app/jbrowse/bin/flatfile-to-json.pl line 9