Created script to resolve phylorefs using the Open Tree of Life APIs

[gaurav]

Added a script that can be used to resolve multiple Phyx files against the Open Tree of Life using their updated MRCA API (#45). Also fixes Travis CI testing, which broke unexpectedly.

[hlapp]

I might be missing something but it doesn't seem like you're testing non-resolving phylorefs, nor malformed queries raising the expected error.

[gaurav]

I might be missing something but it doesn't seem like you're testing non-resolving phylorefs, nor malformed queries raising the expected error.

Thanks for pointing this out, @hlapp! I've added four additional tests:

• A test for phylorefs with a specifier that is present in the Open Tree Taxonomy, but not on the synthetic tree, such as Diplocynodon ratelii, which produces a 400 error from the Open Tree of Life.
• A test for phylorefs with a single internal specifier (which cannot be resolved).
• A test for phylorefs that contain specifiers that are not present in the Open Tree Taxonomy (which was not being handled correctly).

Are there any other cases we should test for?

[hlapp]

@gaurav as commented in a previous PR, can I please ask you to rebase first for merge ability so that you are asking me to review what would actually get merged. Right now as a reviewer I can't know that.

[gaurav]

Sorry, Github said that "This branch has no conflicts with the base branch", which I assumed meant that it was mergeable. I've now run git rebase master and force-updated this PR so that all the changes from master are present here as well.

[hlapp]

I'm approving this though please consider the one in-line comment I left.

[gaurav]

Github/Travis CI integration seems to be acting up right now, but the final commit (f03a1f6) has passed testing on TravisCI at https://travis-ci.org/github/phyloref/phyx.js/builds/742347928. I'm going to go ahead and merge it.