Add rename command

[beckyjackson]

See #293

usage: robot rename --input <file> --mapping <file> --output <file>
 -A,--add-prefix <arg>      add a new prefix to ontology file header
    --catalog <arg>         use catalog from provided file
 -f,--full <arg>            table of mappings for renaming
 -h,--help                  print usage information
 -i,--input <arg>           load ontology from a file
 -I,--input-iri <arg>       load ontology from an IRI
 -noprefixes                do not use default prefixes
 -o,--output <arg>          save ontology to a file
 -p,--prefix <arg>          add a prefix 'foo: http://bar'
 -P,--prefixes <arg>        use prefixes from JSON-LD file
 -r,--partial <arg>         table of partial mappings for renaming
 -V,--version               print version information
 -v,--verbose               increased logging
 -vv,--very-verbose         high logging
 -vvv,--very-very-verbose   maximum logging, including stack traces
 -x,--xml-entities          use entity substitution with ontology XML
                            output

The --add-prefix option makes sure that the prefix appears in the final output file, which does not happen if you just use --prefix.

Right now, the --full and --partial files expect a header - should this be assumed? Or should we do no headers?

[jamesaoverton]

Hey everyone. We think this one is ready to go. Please try it out and give us some feedback.

[jamesaoverton]

I'd like one change, please.

[jamesaoverton]

I given this some thought, and I've decided that promtping for user input is a bad idea. ROBOT is meant to be used for automation. None of our other commands are interactive. make will get stuck forever if it hits this warning, which will surprise and annoy our users.

I think the better alternatives are:

1. just log a warning
2. add a --fail-on-duplicates true/false option

[jamesaoverton]

--allow-duplicates is a better name, but now “f” is not a good short name. Maybe “a” or “d”, or no short name.