{"action":"opened","number":109,"pull_request":{"url":"https://api.github.com/repos/OpenTreeOfLife/peyotl/pulls/109","id":28179750,"html_url":"https://github.com/OpenTreeOfLife/peyotl/pull/109","diff_url":"https://github.com/OpenTreeOfLife/peyotl/pull/109.diff","patch_url":"https://github.com/OpenTreeOfLife/peyotl/pull/109.patch","issue_url":"https://api.github.com/repos/OpenTreeOfLife/peyotl/issues/109","number":109,"state":"open","locked":false,"title":"better wrapping of OTT, improve API wrappers, and more tests. One bug fix for the (rare) case of newick strings that need unicode.","user":{"login":"mtholder","id":136067,"avatar_url":"https://avatars.githubusercontent.com/u/136067?v=3","gravatar_id":"","url":"https://api.github.com/users/mtholder","html_url":"https://github.com/mtholder","followers_url":"https://api.github.com/users/mtholder/followers","following_url":"https://api.github.com/users/mtholder/following{/other_user}","gists_url":"https://api.github.com/users/mtholder/gists{/gist_id}","starred_url":"https://api.github.com/users/mtholder/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mtholder/subscriptions","organizations_url":"https://api.github.com/users/mtholder/orgs","repos_url":"https://api.github.com/users/mtholder/repos","events_url":"https://api.github.com/users/mtholder/events{/privacy}","received_events_url":"https://api.github.com/users/mtholder/received_events","type":"User","site_admin":false},"body":"This was started as a branch to add some functionality to the OTT wrapper (peyotl/ott/__init__.py) for queries on a local copy of OTT. That code is not used in the peyotl-dependent infrastructure.\r\n\r\nWhile working on that, I noticed and cleaned up some issues with the wrappers around the API and the tutorials.  I should have put those on a separate branch. they also do not affect deployed services.\r\n\r\nThere was one bug fix (see nexson_syntax below)\r\n\r\nThe summary:\r\n\r\n  * peyotl/ott/__init__.py support for writing OTT subtrees in newick; looking up an OTT ID from an NCBI taxonomy ID; and the ability to detect taxa that match one of a set of flags.\r\n\r\n  * peyotl/api/{taxomachine | taxon | treemachine}.py reducing code duplication by a new TaxonHolder class\r\n\r\n  * peyotl/manip.py new function for iterating over otus in a study\r\n\r\n  * peyotl/nexson_syntax/__init__.py bug fix - now correctly emits newicks even if they have labels that require the use of unicode strings in python 2. Not many OTT IDs need this. I'm not sure if any of the studies in phylesystem map to those studies. So this may not have caused any problems. I discovered it while implementing the newick export of OTT\r\n\r\n  * peyotl/utility/dict_wrapper.py better formatting as string - this class is just used by API wrappers at this point.\r\n\r\n  * tutorials/* examples/* new example scripts\r\n\r\n  * maintainer-tests.sh and tutorial-tests.sh new tests that make sure the tutorials work. Called by the maintainer-tests 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