DOI publication lookup leaves out latin binomials?

[cjconroy]

Issue Documentation is http://handbook.arctosdb.org/how_to/How-to-Use-Issues-in-Arctos.html

Describe the bug A couple of us (CJC and CLS) at MVZ have noticed randomly that pubs gotten through the DOI lookup lack the latin words.

To Reproduce Pull a publication with a DOI. Unfortunately, I rechecked the one I saw yesterday, and it works fine. Has anyone else seen this behavior?

The pub I saw yesterday looked like this. It is 2019, so it was loaded fairly recently. Silvia E Pavan. 2019. A revision of the group (Didelphidae: Marmosini), with a description of a new species from Roraima, Brazil. Journal of Mammalogy 100(1):103-117. But should have been Silvia E Pavan. 2019. A revision of the Monodelphis glirina group (Didelphidae: Marmosini), with a description of a new species from Roraima, Brazil. Journal of Mammalogy 100(1):103-117.

Expected behavior That all words in a publication come along.

Desktop (please complete the following information):

• Mac
• Chrome
• Latest version

Additional context This is supposed to be a tool to save time, but if we have to lookup every DOI and title word by word, then it is not.

Priority Medium

[dustymc]

I think I'll need an example to figure this out. It's not inconceivable that the pull is dropping something, but I suspect whatever you're seeing is what's coming out of crossref.

FWIW given the DOI I can look up lots of things whenever I want, and variations in the title in Arctos, at the publisher, in a reprint, in crossref, etc. - all of which are incredibly common - won't get in my way. One-click publication creation is pretty cool, but that's a small part of the whole picture.

[campmlc]

I'm assuming that the Latin name would be italicized or underlined . . . is that causing display problems?

On Wed, Jun 10, 2020 at 10:08 AM dustymc notifications@github.com wrote:

• [EXTERNAL]*

I think I'll need an example to figure this out. It's not inconceivable that the pull is dropping something, but I suspect whatever you're seeing is what's coming out of crossref.

FWIW given the DOI I can look up lots of things whenever I want, and variations in the title in Arctos, at the publisher, in a reprint, in crossref, etc. - all of which are incredibly common - won't get in my way. One-click publication creation is pretty cool, but that's a small part of the whole picture.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/2763#issuecomment-642108972, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADQ7JBBPV37NZOC5IX2VNKLRV6VYXANCNFSM4N2QMYIQ .

[dustymc]

italicized or underlined

See http://handbook.arctosdb.org/documentation/encoding.html - there are lots of ways to do that, it's not impossible that some of them don't display correctly in some contexts. I still need an example to say anything definitive.

[atrox10]

For me it's just usually dropping the latin name if it's italicized in the pub title, also it won't save for me. I have to edit it, as there are a lot of extra spaces where the latin name was, so you have to erase all those before it will save. I will try to find a pub that does this and send as example.

On Wed, Jun 10, 2020 at 9:53 AM Mariel Campbell notifications@github.com wrote:

I'm assuming that the Latin name would be italicized or underlined . . . is that causing display problems?

On Wed, Jun 10, 2020 at 10:08 AM dustymc notifications@github.com wrote:

• [EXTERNAL]*

I think I'll need an example to figure this out. It's not inconceivable that the pull is dropping something, but I suspect whatever you're seeing is what's coming out of crossref.

FWIW given the DOI I can look up lots of things whenever I want, and variations in the title in Arctos, at the publisher, in a reprint, in crossref, etc. - all of which are incredibly common - won't get in my way. One-click publication creation is pretty cool, but that's a small part of the whole picture.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/2763#issuecomment-642108972, or unsubscribe < https://github.com/notifications/unsubscribe-auth/ADQ7JBBPV37NZOC5IX2VNKLRV6VYXANCNFSM4N2QMYIQ

.

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-- Carol L. Spencer, Ph.D. Staff Curator of Herpetology & Researcher Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California, Berkeley, CA, USA 94720-3160

atrox10@gmail.com atrox@berkeley.edu TEL: 510-643-5778 /FAX: 510-643-8238

http://mvz.berkeley.edu/Herp_Collection.html http://www.vertnet.org

[atrox10]

Here's an example for a DOI 10.3099/MCZ42.1

It's this pub that's already in Arctos:Bingham, R. E., T. J. Papenfuss, L. Lindstrand III and D. B. Wake. 2018. Phylogeography and species boundaries in the Hydromantes shastae complex, with description of two new species (Amphibia; Caudata; Plethodontidae). Bulletin of the Museum of Comparative Zoology, 161(10):403-427. http://arctos.database.museum/publication/10008280

When you go here to add the DOI: http://arctos.database.museum/Publication.cfm?action=newPub the italicized Hydromantes shasta is left out of the title that is made by the DOI. Something in Arctos is getting rid of the italicized text and leaving a bunch of spaces.

It was doing this before we switched to PG.

On Wed, Jun 10, 2020 at 1:40 PM dustymc notifications@github.com wrote:

italicized or underlined

See http://handbook.arctosdb.org/documentation/encoding.html - there are lots of ways to do that, it's not impossible that some of them don't display correctly in some contexts. I still need an example to say anything definitive.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/ArctosDB/arctos/issues/2763#issuecomment-642245970, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABCJF4MS3V6CGAHOYZZXJTLRV7VVLANCNFSM4N2QMYIQ .

-- Carol L. Spencer, Ph.D. Staff Curator of Herpetology & Researcher Museum of Vertebrate Zoology 3101 Valley Life Sciences Building University of California, Berkeley, CA, USA 94720-3160

atrox10@gmail.com atrox@berkeley.edu TEL: 510-643-5778 /FAX: 510-643-8238

http://mvz.berkeley.edu/Herp_Collection.html http://www.vertnet.org

[dustymc]

Excellent, thanks! Looks like an "interesting" combination of crossref's antique XML service and Arctos trying to interpret maybe-not-so-valid XML. I'll see if I can swap us to their JSON service.

The linebreaks and tabs are in the crossref data (at least the XML data) - I'll see if I can strip some of that if it's in the JSON as well.

[dustymc]

I rebuilt the function to use crossref's JSON services, which are much nicer. Crossref also has a formatter option now, which is amazing. I've just got a couple options hard-coded in a dropdown on create publication, at some point we might pull some or all of http://api.crossref.org/styles into a code table. (Probably "some" - surely nobody wants to scroll through 921 cryptic values?)

Let me know if you want something else from the list and I'll add it.

The formatted publication for 10.3099/MCZ42.1 is still a bit of a mess, I'm stripping linebreaks and returns now but it's coming from Crossref in every format as ...Boundaries In theHydromantes shastaeComplex,..., which I can't do much about.

Basic functionality should be in the next release, suggest we add a 'refresh as {format}' option to edit publication for dealing with old and funky full citations.

[Jegelewicz]

Nice.