[Treebase-guts] [ treebase-Bugs-2960840 ] PhyloWS API Issues Need Fixing

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Bugs item #2960840, was opened at 2010-02-28 20:05
Message generated for change (Comment added) made by rvos
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Category: ui
Group: None
Status: Open
Priority: 9
Private: No
Submitted By: William Piel (sfrgpiel)
>Assigned to: Rutger Vos (rvos)
Summary: PhyloWS API Issues Need Fixing

Initial Comment:
A couple of things should be fixed with PhyloWS, some are higher value than others. I would rank items 1 and 4 at level "9," with the other ones lower (but if they are low-hanging easy fixes, it would be great to fix them before the release).

1. Failure with Safari RSS browser: Originally we thought that this failed because RSS results are not delivered with <?xml version="1.0" encoding="utf-8"?> at the top -- but that's not the case. 

2. The initial url (e.g. http://purl.org/phylo/treebase/phylows/taxon/find?query=dcterms.title==%22Homo%20sapiens%22&recordSchema=study&format=rss1) uses purl.org but returns a list where the domains change from purl.org to nescent.org -- I'd rather that we not proliferate synonymous URIs that have different domains. Let's keep all "/phylows/" urls with the purl.org domain.

3. Let's add some verbiage to each RSS 1.0 result so that a minium synopsis of readable info is provided to users of RSS browsers. For studies, provide the citation; for matrices, provide matrix name and data type; for trees, provide tree name, tree title, tree type; for taxa, provide the taxon name. So, for example, while the current implementation looks like this:

<item rdf:about="http://treebase-dev.nescent.org:6666/treebase-web/phylows/study/TB2:S1925">
	<title>TB2:S1925</title>	<link>http://treebase-dev.nescent.org:6666/treebase-web/phylows/study/TB2:S1925</link>
	<description>TB2:S1925</description>
</item>

...We need to be more verbose, not only in the <description> so that the user reading the RSS feed has some idea what it is about, but also in the <prism> and <dc> contents, so that machines reading this feed can do something useful with it. In the case of a study, let's return this:

<item rdf:about="http://purl.org/phylo/treebase/phylows/study/TB2:S1925">
	<title><![CDATA[[Study] Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences]]></title>
	<link>http://purl.org/phylo/treebase/phylows/study/TB2:S1925</link>
	<description><![CDATA[Tanaka, E. and C. Tanaka. 2008. Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences. Mycoscience, 49(20): 115-125.]]></description>
	<dc:creator><![CDATA[Tanaka, E.; Tanaka, C.]]></dc:creator>
	<dc:date>2007-01-01</dc:date>
	<dc:subject><![CDATA[Phylogenies]]></dc:subject>
	<dc:title><![CDATA[[Study] Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences]]></dc:title>
	<dc:publisher>Mycoscience</dc:publisher>
	<prism:publicationName>Mycoscience</prism:publicationName>
	<prism:contributor>Tanaka, Eiji</prism:contributor>
	<prism:contributor>Tanaka, Chihiro</prism:contributor>
	<prism:volume>49</prism:volume>
	<prism:pageRange>115-125</prism:pageRange>
	<prism:startingPage>115</prism:startingPage>
	<prism:endingPage>125</prism:endingPage>
	<prism:doi>10.1007/s10267-007-0401-5</prism:doi>
	<dcterms:bibliographicCitation>Tanaka, E. and C. Tanaka. 2008. Phylogenetic study of clavicipitaceous fungi using acetaldehyde dehydrogenase gene sequences. Mycoscience, 49(20): 115-125.</dcterms:bibliographicCitation>
	<prism:publicationDate>2007-01-01</prism:publicationDate>
	<prism:section>Study</prism:section>
</item>

4. PhyloWS requests that search on taxa to return a list of trees are so slow as to be unusable. This problem may be fixed by Youjun, seeing as it is also slow in the web GUI interface and Youjun is tackling the problem there. 

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

5. My understanding is that our /phylows/study/find? queries do not support searching on the journal name of an article. It would be great if this were offered because that would let us give journal editors RSS feeds into their own data.

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>Comment By: Rutger Vos (rvos)
Date: 2010-03-01 16:09

Message:
Ok, I'll work on this.

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Comment By: Rutger Vos (rvos)
Date: 2010-03-01 16:09

Message:
Thanks for reporting this bug.  We'll look into it as soon as possible.

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