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OpenBEL / bel.rb

Process BEL (Biological Expression Language) with ruby.
Apache License 2.0
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Replace uri with prefixes for turtle format #115

Closed rumilbaybikov closed 8 years ago

abargnesi commented 8 years ago

@rumilbaybikov The relative path resolution seems the most problematic. Is it intended that this configuration file be provided by the user or included within the gem?

rumilbaybikov commented 8 years ago

@abargnesi Added a new option -p containing the path to custom user configuration file with prefixes. If option -p is not provided then default prefixes defined in config/namespaces_prefixes.yml will be used.

Usage: bel translate -i bel.rb/small_corpus.bel -p bel.rb/prefixes.yml bel turtle

abargnesi commented 8 years ago

Thanks @rumilbaybikov!

I merged manually due to conflicts applying the second commit. It is generally recommended to put work on a separate topic branch in git. This branch should then be offered in the PR.

Consult the contributing guide for details on branches in bel.rb. Also check out this terminalcast for an example of making a change on a topic branch.

abargnesi commented 8 years ago

This has been merged back to the next branch in a6cf83b.

abargnesi commented 8 years ago

@rumilbaybikov, @juliakozlovsky

Please read and fill out a CLA (individual or corporate) and submit to the OpenBEL/cla project. This is required once.

See here for steps.

juliakozlovsky commented 8 years ago

Hi Tony - I spoke to our (mine, Alexander's and Rumil's) manager, and he said he needs to run this through our Legal people, and it needs to be corporate-level thing from our end, not individual. We don't currently anticipate any specific issues with doing this per se, but we need some time to sort out our company policy.