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Duplicate names for nested taxa with same input name #1

Closed chinchliff closed 11 years ago

chinchliff commented 11 years ago

Importing still seems to be keeping names the same in at least some cases where the parent and child have the same name. Not sure if this is confined to exact parent<-child relationships or cases where it is parent<-[intermediate nodes]<-child as well.

An example is the name Mus. There is a parent named "Mus" with a child also named "Mus".

blackrim commented 11 years ago

Did these cause problems with the import or it is functioning but there are still duplicated? I will check these out in a bit On Nov 4, 2012 2:47 PM, "chinchliff" notifications@github.com wrote:

Importing still seems to be keeping names the same in at least some cases where the parent and child have the same name. Not sure if this is confined to exact parent<-child relationships or cases where it is parent<-[intermediate nodes]<-child as well.

An example is the name Mus. There is a parent named "Mus" with a child also named "Mus".

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/opentree-taxomachine/issues/1.

chinchliff commented 11 years ago

The import seems to be working fine. The parent/child Mus nodes both get found by the TNRS.

blackrim commented 11 years ago

hm, this makes me think that you are pointing to a different place, because the one on http://opentree-dev.bio.ku.edu:7474 has both the mus correct and the preftaxchildof. Are you reprocessing or connecting to that one?

On Sun, Nov 4, 2012 at 4:11 PM, chinchliff notifications@github.com wrote:

The import seems to be working fine. The parent/child Mus nodes both get found by the TNRS.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/opentree-taxomachine/issues/1#issuecomment-10055475.

chinchliff commented 11 years ago

I was building it locally using inittaxsyn, but only with the ncbi info. I had a thought this morning that those preftax rels maybe probably don't get created until the add tax step, so that would be why they aren't there. Ah, and I just realized that I probably have an older version of the ncbi tax data before the nested mus got renamed. So that would explain it. I will update that and see if I can build it with add tax without running out of memory

On Monday, November 5, 2012, Stephen Smith wrote:

hm, this makes me think that you are pointing to a different place, because the one on http://opentree-dev.bio.ku.edu:7474 has both the mus correct and the preftaxchildof. Are you reprocessing or connecting to that one?

On Sun, Nov 4, 2012 at 4:11 PM, chinchliff <notifications@github.com<javascript:_e({}, 'cvml', 'notifications@github.com');>> wrote:

The import seems to be working fine. The parent/child Mus nodes both get found by the TNRS.

— Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/opentree-taxomachine/issues/1#issuecomment-10055475>.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/opentree-taxomachine/issues/1#issuecomment-10072433.

blackrim commented 11 years ago

sure thing. there are a number of potential issues, but at least my most recent builds seem to have done fine. actually the preftax dont get made until you do the makeottol command. but that is going to crash if there are parent child identical nodes, so best to make sure that is corrected before that command (that is where it gets in a loop, even if there is a taxon in between that doesn't have the same name)

Stephen

On Mon, Nov 5, 2012 at 9:53 AM, chinchliff notifications@github.com wrote:

I was building it locally using inittaxsyn, but only with the ncbi info. I had a thought this morning that those preftax rels maybe probably don't get created until the add tax step, so that would be why they aren't there. Ah, and I just realized that I probably have an older version of the ncbi tax data before the nested mus got renamed. So that would explain it. I will update that and see if I can build it with add tax without running out of memory

On Monday, November 5, 2012, Stephen Smith wrote:

hm, this makes me think that you are pointing to a different place, because the one on http://opentree-dev.bio.ku.edu:7474 has both the mus correct and the preftaxchildof. Are you reprocessing or connecting to that one?

On Sun, Nov 4, 2012 at 4:11 PM, chinchliff <notifications@github.com<javascript:_e({}, 'cvml', 'notifications@github.com');>> wrote:

The import seems to be working fine. The parent/child Mus nodes both get found by the TNRS.

— Reply to this email directly or view it on GitHub<

https://github.com/OpenTreeOfLife/opentree-taxomachine/issues/1#issuecomment-10055475>.

— Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/opentree-taxomachine/issues/1#issuecomment-10072433>.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/opentree-taxomachine/issues/1#issuecomment-10073062.