Method for reading Nexson and adding to graph

[jar398]

Method for reading Nexson and adding to graph

[josephwb]

Nexson file can now be read into MainRunner (either using "justtrees" or "addtree"). Uses a 'peek', so user does not have to specify whether tree file is newick or nexson format. Works fine for single tree nexson example file, but dies on the two-tree file with error:
Exception in thread "main" java.lang.RuntimeException: missing value for ot:studyPublication

[pmidford]

Hi Joseph,
I checked, ot:studyPublication is present in the JSON file, so there isn't an obvious problem with the file.

-Peter

On Mar 13, 2013, at 4:25 PM, "Joseph W. Brown" [email protected] wrote:

Nexson file can now be read into MainRunner (either using "justtrees" or "addtree"). Uses a 'peek', so user does not have to specify whether tree file is newick or nexson format. Works fine for single tree nexson example file, but dies on the two-tree file with error:
Exception in thread "main" java.lang.RuntimeException: missing value for ot:studyPublication

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[josephwb]

Weird. It has both "ot:studyPublicationReference" and "ot:studyPublication", while the single tree file has only the former. I deleted the latter from the two-tree file, and everything works nicely. Perhaps NexsonReader isn't expecting this field? I'll check.

[pmidford]

If you look in phylografter, study 15 doesn't have a recorded DOI (actually there is a DOI, but it's embedded in the reference string). The ot:studyPublication is only written when a DOI or other suitable URI (e.g., jstor) is available in the right field. Jonathan has a task to track down the missing DOI's in phylografter, but until that's done, there will be quite a few studies without studyPublication fields, but some do.

On Mar 13, 2013, at 4:54 PM, Joseph W. Brown [email protected] wrote:

Weird. It has both "ot:studyPublicationReference" and "ot:studyPublication", while the single tree file has only the former. I deleted the latter from the two-tree file, and everything works nicely. Perhaps NexsonReader isn't expecting this field? I'll check.

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[blackrim]

Can this be closed? I am working on the plugin and updating bits and wondering if more needs to be done here before moving on that

[josephwb]

Trees read in with properties. Moving "add properties to graph" in a separate issue.