nexson export @rel, string booleans, ot:ottTaxonName

[mtholder]

This should be 3 issues; I think there may be issues for some/all of these. Sorry I did not want this to fall through the cracks, and I was afraid that I'd forget...

1. I think that meta tags of type "@xsi:type": "nex:ResourceMeta" should be using "@rel" rather than "$" for their content.
2. I think we decided to use true rather than "true" for booleans. I'm seeing "true" for ot:isLeaf and the '@root' property.
3. We decided that ot:ottTaxonName should be in otu objects not node objects.

[mtholder]

FWIW, I'm using the workaround_phylografter_export_diffs function in https://github.com/OpenTreeOfLife/peyotl/blob/master/peyotl/nexson_validation/phylografter_workaround.py when importing (on my private testing repos).

[pmidford]

Mark, I can deal with these tomorrow, or are you planning to do these today?
-Peter

On Monday, March 24, 2014, Mark T. Holder notifications@github.com wrote:

FWIW, I'm using the workaround_phylografter_export_diffs function in
https://github.com/OpenTreeOfLife/peyotl/blob/master/peyotl/nexson_validation/phylografter_workaround.pywhen importing (on my private testing repos).

Reply to this email directly or view it on GitHubhttps://github.com//issues/103#issuecomment-38439642
.

[mtholder]

Hi. Tomorrow is fine. There is no real rush. My workaround script means that these issues are not holding me up.

[pmidford]

Mark - Item 1 says use "@rel" rather than $, but I only find "@href" for specifying the value of these tags. No problem changing @href to @rel, but am I missing something here?

[mtholder]

Sorry. I meant @rel instead of @Property for those meta elements that use
@href.
sorry for the confusion.

mark

On Thu, Mar 27, 2014 at 5:46 PM, Peter Midford notifications@github.comwrote:

Mark - Item 1 says use "@rel https://github.com/rel" rather than $, but
I only find "@href https://github.com/href" for specifying the value of
these tags. No problem changing @href https://github.com/href to @relhttps://github.com/rel,
but am I missing something here?

—
Reply to this email directly or view it on GitHubhttps://github.com//issues/103#issuecomment-38870522
.

Mark Holder

mtholder@gmail.com
mtholder@ku.edu
http://phylo.bio.ku.edu/mark-holder

Department of Ecology and Evolutionary Biology
University of Kansas
6031 Haworth Hall
1200 Sunnyside Avenue
Lawrence, Kansas 66045

lab phone: 785.864.5789

fax (shared): 785.864.5860

[mtholder]

At least that is how I read https://github.com/nexml/nexml/wiki/NeXML-Manual#How_Metadata_are_Represented_using_the_ltmetagt_Element

[pmidford]

Should be fixed - @mtholder could you verify this is what you want.

[rhr]

Won't be live until I restart the app, which I'm waiting on as there's
quite a bit of user activity at the moment.

On Thu, Apr 3, 2014 at 3:23 PM, Peter Midford notifications@github.comwrote:

Should be fixed - @mtholder https://github.com/mtholder could you
verify this is what you want.

Reply to this email directly or view it on GitHubhttps://github.com//issues/103#issuecomment-39500148
.

[rhr]

Restarted - now live

On Thu, Apr 3, 2014 at 3:43 PM, Richard Ree rree@fieldmuseum.org wrote:

Won't be live until I restart the app, which I'm waiting on as there's
quite a bit of user activity at the moment.

On Thu, Apr 3, 2014 at 3:23 PM, Peter Midford notifications@github.comwrote:

Should be fixed - @mtholder https://github.com/mtholder could you
verify this is what you want.

Reply to this email directly or view it on GitHubhttps://github.com//issues/103#issuecomment-39500148
.

[josephwb]

We on the treemachine side were not keeping up with this, so treemachine cannot currently read these nexsons. I am working on updating NexsonReader.