synth tree "version 4.0"

[Joseph Brown]

Y'All,

This happened somewhat quietly on Friday, so I thought I'd email to make things explicit.

On dev now is "version 4.0" of the synthetic tree. For those not in the loop, the only change is the version of the taxonomy (update from 2.8draft5 from the PNAS paper to 2.9draft12). To be clear, this tree has all of the same source input trees as the published tree.

So, yeah, um... that is it.

Maybe people off of this list might want to scrutinize things to see if the taxonomy update has fixed their favourite clade? Karen?

JWB.

[Jonathan A Rees]

That's great. Did you run the germinator/taxa tests?

A detail on what's on dev: Unfortunately the TNRS has not yet been updated to OTT 2.9. (There's an as yet undiagnosed taxomachine failure.) The tree browser should work fine, but you won't be able to search for taxa that are new in OTT 2.9, even when they are in the synthetic tree.

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[Karen Cranston]

Thanks, Joseph!

Stephtn - speaking of taxomachine... can I ask you to take a look at the taxomachine load / indexing / deployment? It's not working, but there is very little output and no up-to-date tests, so it is really hard to tell what's happening. Jonathan and I are stymied, and at this point, we don't know enough about neo4j / taxomachine to debug (and it doesn't really make sense for us to learn this stuff, since it looks like we are reducing the use of neo4j in the future).

Cheers,

Karen

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[Karen Cranston]

Stephtn = Stephen. Argh.

[Peter Midford]

As I indicated to Jonathan, taxonomy loading has worked for me several
times in the past few weeks. I agree that updating tests/adding some
unit tests would a good idea.

> <https://devtree.opentreeoflife.org/opentree/argus/opentree4.0@1>.
> For those not in the loop, the /only/ change is the version

> of the taxonomy (update from 2.8draft5 from the PNAS paper
> to 2.9draft12). To be clear, this tree has all of the same
> source input trees as the published tree.
>
> So, yeah, um... that is it.
>
> Maybe people off of this list might want to scrutinize
> things to see if the taxonomy update has fixed their
> favourite clade? Karen?
>
> JWB.
>
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[Jonathan A Rees]

Taxomachine works just fine with OTT 2.8.  But it is failing on OTT 2.9 draft 12. Which taxonomies did you try, and how did you assess "working"?

I've created https://github.com/OpenTreeOfLife/taxomachine/issues/104

so we can continue discussion of this particular issue there.

[Peter Midford]

Ok, I haven't tried 2.9. For the record, 2.8 and 2.6 and Asterales,
with both standalone and the neo4j plugin.

[Joseph Brown]

I put a summary of the germinator tests here.

JWB

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[Jonathan A Rees]

It would be great to see these as regression tests:  which tests succeeded in old & new versions, which failed, which succeeded in old but failed in new (could be introduction of a bug), which failed in old but succeeded in new (could be that something got fixed).

One way to address this: We could add a column to the test list for "last version of synthetic tree in which this test passed".

[Joseph Brown]

Agreed.

JWB

[Jonathan A Rees]

Where can I find a Newick file for the draftversion4 ?

(if you like you can upload it to ~opentree/downloads/ on ot10)

[Joseph Brown]

I'll upload it there shortly.

JWB

On 23 October 2015 at 18:14, Jonathan A Rees <re...@mumble.net> wrote:

Where can I find a Newick file for the draftversion4 ?

(if you like you can upload it to ~opentree/downloads/ on ot10)

[Joseph Brown]

Ok, it is there now, named "Life_v4.0_ott2.9draft12_synth_15October2015.tre".

JWB.