viewer bug

[arlin]

This bug happens due to extra parentheses in the Newick string. You can replicate it in the web viewer as follows. Here is the tree with extra: http://128.123.177.13/Phylotastic_DisplayTree_Project/display_tree.html?uri=&tree_data=(((((((Limacina%20helicina,Atlanta%20peroni),(Bolitaena,Architeuthis%20dux))),Lumbriculus%20variegatus),Phronima%20sedentaria),(((Orycteropus%20afer),Pomacanthus%20imperator))),(Diploria%20labyrinthiformis));&format=newick_text

Without extra:

http://128.123.177.13/Phylotastic_DisplayTree_Project/display_tree.html?uri=&tree_data=((((((Limacina%20helicina,Atlanta%20peroni),(Bolitaena,Architeuthis%20dux)),Lumbriculus%20variegatus),Phronima%20sedentaria),(Orycteropus%20afer,Pomacanthus%20imperator)),Diploria%20labyrinthiformis);&format=newick_text

I suspect that OpenTree is giving us these trees as an artefact when there are intermediate nodes with only one daughter in the induced subtree. This is probably a bug in OpenTree v3 services that should be reported to them. I seem to recall something like this being discussed previously. Maybe it was fixed in v2.

[thanhnh-infinity]

So, Dr @arlin , do you want me to remove extra parentheses OR wait for fixing from Open Tree ?

[arlin]

@thanhnh-infinity, if you can verify that this is coming from OpenTree, then the next step is to notify them of the problem. Before posting an issue, I would mention this in their chat room (https://gitter.im/OpenTreeOfLife/public), because I'm pretty sure that this bug has happened before.

[thanhnh-infinity]

Dr @arlin , Could you please send to me the species list that you built above tree?

I tried to copy/paste scientific names in above link and make request to OpenTree but it returned to me a different tree, therefore I cannot check the extra parenthesis.

http://phylo.cs.nmsu.edu:5004/phylotastic_ws/gt/ot/get_tree?taxa=Limacina%20helicina|Atlanta%20peroni|Bolitaena|Architeuthis%20dux|Lumbriculus%20variegatus|Phronima%20sedentaria|Orycteropus%20afer|Pomacanthus%20imperator|Diploria%20labyrinthiformis

The result is :

{"message": "Success", "newick": "((((((Bolitaena_ott2868325,Architeuthis_dux_ott251385)Neocoleoidea_ott329546,(Limacina_helicina_ott386772,Atlanta_peroni_ott2889292)),Lumbriculus_variegatus_ott180477),Phronima_sedentaria_ott2987222)Protostomia_ott189832,(Pomacanthus_imperator_ott133821,Orycteropus_afer_ott561087)Euteleostomi_ott114654),Diploria_labyrinthiformis_ott706970);"}

[arlin]

@thanhnh-infinity , I'm sorry for letting this slip. First of all, there are 2 issues here. One of them is that our tree viewer should be able to handle non-branching internal nodes (i.e., internal nodes with a single child ) without messing it up. So, we should fix our viewer so that either (1) it strips out such nodes or (2) it displays them properly. The second issue is that OT might be returning trees with non-branching nodes.

With regard to the second issue, this is the list of species: Pomacanthus imperator Phronima sedentaria Orycteropus afer Neocirrhites armatus Lumbriculus variegatus Limacina helicina Diploria labyrinthiformis Bolitaena pygmaea Atlanta peroni Architeuthis dux

[thanhnh-infinity]

Thank you Dr @arlin , I will figure it out this issue

[thanhnh-infinity]

Hi Dr @arlin , Could you update and install our newest Mobile app ? I tried to check your text that you mentioned above and get the tree : (((((Architeuthis dux,(Limacina helicina,Atlanta peroni)),Lumbriculus variegatus),Phronima sedentaria),(Orycteropus afer,(Neocirrhites armatus,Pomacanthus imperator))),Diploria labyrinthiformis);

And we can see this tree :

[arlin]

Try this tree:

http://128.123.177.13/Phylotastic_DisplayTree_Project/display_tree.html?uri=&tree_data=((A,B),((C,D)));&format=newick_text

Then this tree:

http://128.123.177.13/Phylotastic_DisplayTree_Project/display_tree.html?uri=&tree_data=((A,B),(C,D));&format=newick_text

Do you see the difference?

[thanhnh-infinity]

@arlin , But the links you showed me above, they are a Web page, that is not mobile application. In mobile application, bug is not procedured

[arlin]

@thanhnh-infinity, this is a photo of a list that will produce the bug. If you can get this photo into your phone's photo library, the mobile app will be able to scrape out the names and you can reproduce the bug. If you don't know how to get a photo from your computer into the phone's photo library, I can explain how I do it.

[arlin]

moving this into backlog until we decide to start working on the mobile app again.