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  • Apr 03 19:08

    mtholder on no-nexson

    relying on peyutil and nexson (compare)

  • Apr 02 05:39

    jimallman on master

    Trying updated GitHub App IDs o… (compare)

  • Apr 02 03:26

    mtholder on no-nexson

    working toward depending on uti… (compare)

  • Apr 01 23:44

    bredelings on finish-tnrs

    Use structured binding. Fix lcase_match_prefix( ). Move functions out of header fi… (compare)

  • Apr 01 22:59

    mtholder on no-nexson

    ignore test output depending on nexson standalone (compare)

  • Mar 31 20:23
    bredelings review_requested #93
  • Mar 31 20:23
    bredelings opened #93
  • Mar 31 20:22
    bredelings review_requested #92
  • Mar 26 15:58

    mtholder on highlight-extinct-nodes-in-synth-view

    (compare)

  • Mar 26 15:58
    mtholder closed #1221
  • Mar 26 15:58

    mtholder on master

    Mark all extinct nodes in synth… Add dagger before extinct name … Detect extinct unnamed nodes be… and 3 more (compare)

  • Mar 24 20:47

    bredelings on phylesystem-no-checkout

    Take a --script-managed-trees a… Compute the paths for the scrip… Add a function to newick_to_nex… and 2 more (compare)

  • Mar 19 20:06
    jimallman review_requested #152
  • Mar 19 20:06
    jimallman review_requested #152
  • Mar 19 20:05
    jimallman opened #152
  • Mar 19 20:03

    jimallman on handle-multiple-installed-python-headers

    Correctly handle multiple insta… (compare)

  • Mar 19 16:33
    snacktavish commented #1193
  • Mar 19 15:48
    jimallman labeled #1177
  • Mar 19 15:46
    jimallman commented #1193
  • Mar 19 15:45
    jimallman commented #1193
Emily Jane McTavish
@snacktavish
For getting subtrees from large phylogenies
we should check if we have these trees, and add them! Probably have decently mapped tip labels.
I was working on OTU mapping for that Hug et all new candidate phylum tree, might be better to use this version.
Yan Wong
@hyanwong
:thumbsup:
Jim Allman
@jimallman
fyi, the curation refinements we talked about last week (https://github.com/OpenTreeOfLife/opentree/pull/1223#issuecomment-598244130) are available for review on devtree. Here's a preview:
Screen Shot 2020-03-12 at 11.11.38 AM.png
Emily Jane McTavish
@snacktavish
Hmm looks like our weird DOI switching issues have corpped back up and I'm confused about why!
Jim Allman
@jimallman
ok, chasing this now. (hopefully just a merge or branch glitch on dev)
Jim Allman
@jimallman
@snacktavish Looks like someone has deployed a branch of phylesystem-api called streamline-update. I can't find this branch locally or on github, but it's listed in deployed-systems as the active branch on devapi. :confused: In any case, behavior on production is normal.
ah, it looks like we're the culprits! :D the branch is gone, but the commits are mine and yours @snacktavish . i'll reset devapi to use the current master branch and deploy in a minute...
Jim Allman
@jimallman
OK, that fixed the new-study problem above and correctly found the sabretooth study. (I wouldn't be surprised if it fixes other quirks as well.)
Emily Jane McTavish
@snacktavish
hahah I got a guilty feeling when I saw that - despite having no recollection of this branch!! Whooopsies.
Emily Jane McTavish
@snacktavish
Glad you caught and fixed!
Emily Jane McTavish
@snacktavish
I was editing this tree https://tree.opentreeoflife.org/curator/study/edit/ot_350?tab=trees, and wanted to check the MRCA in the synth tree via the tree viewer - but I get an error that ""ott5308896": "invalid_ott_id"," but I'm not actually sure how to figure out which tip in the tree that is, which out searching backwards through taxonomies.
I clicked on the taxa in teh OTU mapping until I discovered the culprit
image.png
So, two part question - 1) should we return more info when we try to get the MRCA of a tree and can't 2) should we somehow flag ottids that are no longer valid in the OTU mapping page?
How does otcetera handle ottids that are not forwarded?
and it does look like that taxon got a different ottid at some point anyways... https://tree.opentreeoflife.org/taxonomy/browse?id=3707055
@kcranston any ideas?
Karen Cranston
@kcranston
I am trying to remember if we ever had a process for going through the list of deprecated ids (in the forwards.tsv file of OTT) and updating / flagging phylesystem tips mapped to that id
although maybe that's not what is happening here? (is the issue that the id was not forwarded?)
Mark T. Holder
@mtholder
folks, I'm sorry for a couple of things: 1. I meant to deploy to tree, but still have not. I'll try in the morning.
  1. I have another call that conflicts with our call tomorrow. I could meet earlier or later. (at 2:00 CDT or at 4:00CDT).
I knew about my conflicting meeting, but I thought that it had been cancelled. However, the convener decided to move to a video conference, so it is back on.
Benjamin Redelings
@bredelings
Either works for me.
Jonathan A Rees
@jar398
@kcranston Downstream consumers of phylesystem are advised to respect the forwards list, and I'm pretty sure everything inside of open tree does. I guess you're trying to make life easier for outside consumers?
I think it is inevitable that stale ids will be stored in persistent storage, just as e.g. NCBI ids are (they have exactly the same problem).
Jim Allman
@jimallman
Either time is OK for me
Mark T. Holder
@mtholder
we're going to move the call to one hour earlier (2:00 CDT)
Mark T. Holder
@mtholder
we are in maintenance mode
we are back out of maintenance mode
Mark T. Holder
@mtholder
(with master of opentree deployed to tree)
TonyRees
@TonyRees
Just letting you know, there is a new IRMNG release now available (Mar 2020 version) via the IRMNG downloads page, plus an accompanying summary in this publication: https://www.mapress.com/j/mt/article/view/megataxa.1.2.3/39250 . Just to genus level, we do not maintain the species component any more, at this time anyway...
Karen Cranston
@kcranston
thanks, @TonyRees ! we need to do some re-tooling for the dwc import, so it might be a bit before we get this incorporated
Jonathan A Rees
@jar398
@kcranston I've been increasing my familiarity with dwca if you have any questions. E.g. I wrote a converter that transforms NCBI's taxonomy format to dwca (although I haven't done the meta.xml yet). I think a good architecture for open tree at this point might be to take all source taxonomies in dwc form, and writer converters as needed. In that case you'd need something like the NCBI converter.
Karen Cranston
@kcranston
thanks, @jar398 I agree with that architecture. Working on some deployment stuff now, but I'll ping you when I go back to taxonomy work
For anyone using nexttree, I am going to be using that server for some ansible testing, so be not surprised if / when it breaks
Jonathan A Rees
@jar398
[I think it was clear but just in case, "writer converters as needed" should be "write converters from native form to dwca as needed"]
Karen Cranston
@kcranston
yup!
Jonathan A Rees
@jar398
(Putting OTT into dwca would require some thought. Definitely the sources list ought to be put in a separate file, with one row per taxonid - source - id in source. And if you do that you want a separate sources table, so that sources have unique ids, tied to particular versions, with their properties spelled out in that table - name, URL(s), date(s), etc. So this is not really a small job. The question is whether it's a pain point yet.)
Jim Allman
@jimallman
@kcranston @mtholder @snacktavish Anybody got a few minutes to help me with a blocker? It looks like y'all are the owners of our GitHub organization. To move forward with github registered apps, i think we need to install my test apps on dev "data" repos (phylesystem-0, collections-0, amendments-0, feedback). Hopefully I can retain ownership of the apps for now, but we'll want to transfer those eventually.
Benjamin Redelings
@bredelings
The script-managed-trees field in the nexson looks like this:
        "otusById": {
            "otus1": {
                "otuById": {}
            }
        }, 
        "externalTree": {
            "path": "gtdb/RefSeq78/mapped_gtdb_rs78.tre"
        },
        "treesById": {
            "trees1": {
                "@otus": "otus1", 
                "^ot:treeElementOrder": [], 
                "treeById": {}
            }
        }
Just the externalTree part matters -- the rest is just for context.
Karen Cranston
@kcranston
@jimallman - sorry, missed this yesterday. I can help. What do you need me to do?
Jim Allman
@jimallman
No worries @kcranston . Mark has given me admin role, at least temporarily. No longer blocked!
Karen Cranston
@kcranston
excellent