{"action":"opened","issue":{"url":"https://api.github.com/repos/D-PLACE/dplace/issues/362","repository_url":"https://api.github.com/repos/D-PLACE/dplace","labels_url":"https://api.github.com/repos/D-PLACE/dplace/issues/362/labels{/name}","comments_url":"https://api.github.com/repos/D-PLACE/dplace/issues/362/comments","events_url":"https://api.github.com/repos/D-PLACE/dplace/issues/362/events","html_url":"https://github.com/D-PLACE/dplace/issues/362","id":162355070,"number":362,"title":"Revise phylogeny loading code. ","user":{"login":"SimonGreenhill","id":220169,"avatar_url":"https://avatars.githubusercontent.com/u/220169?v=3","gravatar_id":"","url":"https://api.github.com/users/SimonGreenhill","html_url":"https://github.com/SimonGreenhill","followers_url":"https://api.github.com/users/SimonGreenhill/followers","following_url":"https://api.github.com/users/SimonGreenhill/following{/other_user}","gists_url":"https://api.github.com/users/SimonGreenhill/gists{/gist_id}","starred_url":"https://api.github.com/users/SimonGreenhill/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SimonGreenhill/subscriptions","organizations_url":"https://api.github.com/users/SimonGreenhill/orgs","repos_url":"https://api.github.com/users/SimonGreenhill/repos","events_url":"https://api.github.com/users/SimonGreenhill/events{/privacy}","received_events_url":"https://api.github.com/users/SimonGreenhill/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/D-PLACE/dplace/labels/data","name":"data","color":"fbca04"}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/D-PLACE/dplace/milestones/1","html_url":"https://github.com/D-PLACE/dplace/milestones/First%20Release","labels_url":"https://api.github.com/repos/D-PLACE/dplace/milestones/1/labels","id":1164758,"number":1,"title":"First Release","description":"Required features/fixes for release of D-PLACE web portal and submission of database paper.","creator":{"login":"SimonGreenhill","id":220169,"avatar_url":"https://avatars.githubusercontent.com/u/220169?v=3","gravatar_id":"","url":"https://api.github.com/users/SimonGreenhill","html_url":"https://github.com/SimonGreenhill","followers_url":"https://api.github.com/users/SimonGreenhill/followers","following_url":"https://api.github.com/users/SimonGreenhill/following{/other_user}","gists_url":"https://api.github.com/users/SimonGreenhill/gists{/gist_id}","starred_url":"https://api.github.com/users/SimonGreenhill/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/SimonGreenhill/subscriptions","organizations_url":"https://api.github.com/users/SimonGreenhill/orgs","repos_url":"https://api.github.com/users/SimonGreenhill/repos","events_url":"https://api.github.com/users/SimonGreenhill/events{/privacy}","received_events_url":"https://api.github.com/users/SimonGreenhill/received_events","type":"User","site_admin":false},"open_issues":21,"closed_issues":56,"state":"open","created_at":"2015-06-15T12:03:49Z","updated_at":"2016-06-27T00:03:54Z","due_on":null,"closed_at":null},"comments":0,"created_at":"2016-06-27T00:03:54Z","updated_at":"2016-06-27T00:03:54Z","closed_at":null,"body":"We need to modify the phylogeny loading code for #344 to add source information for where the trees came from, and link the language *labels* in the tree to glottolog ids.\r\n\r\nAt the moment we have the various phylogenies stored as a text/nexus file. Some are labelled by ISOcode (e.g. austroasiatic.trees), some by the label in the publication (e.g. bantu.trees, austronesian.trees, indoeuropean.trees, semitic.trees, utoaztecan.trees) or something that might be an ISO code but could just be a three letter code (e.g. tukanoan.trees). \r\n\r\nWe need to be able to (a) store and display which source the trees come from, (b) recover what matchings we have for language label in the nexus file to the tree file, (c) standardise this so the import code can load the languagetreelabels table properly.\r\n\r\n**Suggestion:**\r\n\r\nMove phylogenies to their own top-level directory ./phylogeny/\r\n\r\nFor every phylogeny we have 3 files labelled as <...>.{trees, bib, txt}:\r\n\r\n- Each tree file is stored as-is in a .trees file with labels from the publication\r\n- Each tree file has a .txt file which stores a 2 column tab-delimited file of PublicationLabel \\t Glottolog code. \r\n- Each tree file has BibTex file in .bib providing the reference details which is loaded into the Source Table.\r\n\r\nThoughts? @Bibiko @xrotwang @stefelisabeth @kirbykat "}}
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