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phylotastic / phylotastic-portal

Web tool (ruby on rails) providing access to phylotastic services for acquiring species trees.
https://github.com/phylotastic/phylotastic/wiki
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name dropped from uploaded list #113

Closed arlin closed 8 years ago

arlin commented 8 years ago

I uploaded the list of 5 species below, but the portal only shows me 4. Even if a name is not found in OpenTree's taxonomy, we should present the name in its own row. This is the feature that users want-- the taxon report should show the result for every input name, even if the there is no match

Bos taurus Ovis aries Hippopotamus amphibius Balaenoptera acutorostrata Megaptera novaeangliae

ducvan0212 commented 8 years ago

@arlin I checked. Hippo didnot represent in response from finding names service. The service did fail to detect Hippopotamus amphibius. Can @abusalehmdtayeen verify this issue?

abusalehmdtayeen commented 8 years ago

@ducvan0212 : I tried the tnrs service (http://phylo.cs.nmsu.edu:5004/phylotastic_ws/tnrs/ot/resolve?names=Bos%20taurus|Ovis%20aries|Hippopotamus%20amphibius|Balaenoptera%20acutorostrata|Megaptera%20novaeangliae) with all 5 species and it returned me match for all of them. It seems that the problem is not within the web service. Would you please check your end carefully?

When I checked with GNRD, I found that it can not detect the Hippopotamus amphibius. @ducvan0212 : As I understand, when a user uploads a list of species, you don't need to send the list to GNRD to find names. The scientific names are already there. In this case, your work-flow should start from taxonomic name resolver service. This will solve the problem with this issue.

ducvan0212 commented 8 years ago

You should use extracting names from files service because Arlin put 5 these names into a file. I remember I called service 2 to extract names.

ducvan0212 commented 8 years ago

It is fine, I will refactor my endpoint.

ducvan0212 commented 8 years ago

I finished upgrade portal. Now, you can upload a one-name-per-line list and if there is any names that can not be resolved, portal will display these names and allow you to edit them.

arlin commented 8 years ago

OK. The first issue (no hippo from OT) seems to have disappeared. The second issue was not providing a line item for un-matched names. This has now been fixed. which I can verify with the list below, which includes 5 real and 5 imaginary species (unicorn, selki, kraken, chimaera, dragon).

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