[Treebase-guts] [ treebase-Bugs-3413049 ] Download selection of trees

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Bugs item #3413049, was opened at 2011-09-22 16:50
Message generated for change (Tracker Item Submitted) made by sfrgpiel
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Category: ui
Group: None
Status: Open
Priority: 7
Private: No
Submitted By: William Piel (sfrgpiel)
Assigned to: hshyket (hshyket)
Summary: Download selection of trees

Initial Comment:
As discussed, it would be valuable to have a button to download the current selection of trees. At a minimum, this generates a NEXUS file with the trees all in the same tree block and with the name of each tree being the tree_id. Ideally, it would build a distinct list of all taxon labels in the trees and use that to generate a taxon block and a translation table in the tree block (as in treeBlock.generateAFileDynamically). But this may prove too slow for large collections of trees, in which case it is better just to dump the nexickstring inside a trees block. Perhaps do a "number of trees" test, where fewer than 100 trees can use the TAXA BLOCK and TRANSLATION table, while more than 100 trees would just dump the newickstring. 

Also ideally a parallel download option would also be available if getFormat(request) == FORMAT_NEXML -- but if too hard to implement, then never mind. For a NeXML download, the tree name does not need to be substituted with the tree_id because this can be supplied as metadata. e.g. for tree_id 4105 and study_id 1000, express like so:

<tree about="#Tr4105" id="Tr4105" label="ML tree" xsi:type="nex:FloatTree">
<meta href="http://purl.org/phylo/treebase/phylows/study/TB2:S1000" id="meta60715" rel="rdfs:isDefinedBy" xsi:type="nex:ResourceMeta"/>

The priority is for the NEXUS download button (or the NeXML download button) to be used in the UI. But ultimately it would be great if our API had the same functionality. For example, currently a set of trees can only be viewed in RSS:

http://purl.org/phylo/treebase/phylows/taxon/find?query=dcterms.title==%22Homo%20sapiens%22&format=rss1&recordSchema=tree

but ideally the same query (get me all trees with humans) would be downloadable as a single NEXUS file like so:

http://purl.org/phylo/treebase/phylows/taxon/find?query=dcterms.title==%22Homo%20sapiens%22&format=nexus&recordSchema=tree

or NeXML like so:

http://purl.org/phylo/treebase/phylows/taxon/find?query=dcterms.title==%22Homo%20sapiens%22&format=nexml&recordSchema=tree

bp


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