Comments (7)
dimus
commented on May 27, 2024
adding parameter with_vernaculars=true will add common names information to the output
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jhpoelen
commented on May 27, 2024
Thanks for adding the vernacular names @dimus . Some observations:
- for frogs (Anura), GBIF seems to include many languages but not English.
- WoRMS doesn't seems to have any vernaculars
- NCBI has vernaculars, but doesn't set the language (seems to be English by default).
- ITIS has some vernaculars, and they seem to be Spanish only. The language code that is used doesn't seem to be the two letter code that I am used to (e.g. "es"), instead it looks like bagre boca chica @spanish.
You can find some specific example in globalbioticinteractions/globalbioticinteractions@5d6ab97 .
Are these results expected?
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jhpoelen
commented on May 27, 2024
After running a couple of batches in production with globalbioticinteractions, I noticed that the name resolving against globalnames is causing internal server errors and gateway timeouts after the introduction of the vernacular names. I've disabled the feature for now, and hoping to re-enabled when we understand how to fix it.
here's an example from the logs:
2015-08-20 12:31:51,812 [main] ERROR org.eol.globi.tool.LinkerGlobalNames - batch #1117 problem matching terms: [4475460
|Zilora ferruginea|4474176|Xerocomus communis|4474947|Xylota segnis|4475203|Zaraea fasciata|4474447|Xylaria filiformis|4
475477|Zodion|4474960|Xylota sylvarum|4475216|Zaraea lonicerae|4474973|Xylota tarda|4475480|Iberis|4475225|Zelleromyces
stephensii|4475238|Zenillia libatrix|4474978|Xylota xanthocnema|4475490|Zodion cinereum|4474479|Xylaria guepinii|4475503
|Zoellneria eucalypti|4474473|Xylaria friesii|4475241|Archiearis notha|4474987|Xylotachina diluta|4474484|Xylaria hypoxy
lon|4474992|Xyphosia miliaria|4475512|Zoellneria rosarum|4475142|Carabus (Megodontus) violaceus|4475654|Zygorhizidium me
losirae|4474369|Xyela julii|4475139|Zaira cinerea|4475651|Aulacoseira italica subsp. subarctica|4475662|Kirchneriella ob
esa|4475147|Carabus (Morphocarabus) monilis|4475659|Zygorhizidium parvum|4475157|Pterostichus (Platysma) niger|4474641|X
yleborus dryographus|4474386|Xyela longula|4475667|Kirchneriella|4475164|Zalerion arboricola|4474911|Xylohypha ortmansia
e|4474395|Xylaplothrips fuliginosus|4475430|Galerucella|4474658|Xylechinus pilosus|4475181|Zalerion maritima|4474671|Xyl
etinus longitarsis|4474920|Xylohypha pinicola|4474420|Xylaria carpophila|4475445|Zignoëlla morthieri|4474934|Xylophaga p
raestans|4475703|Zygospermella striata|4474929|Xylophaga dorsalis|4475698|Zygospermella insignis|4475455|Zignoëlla slapt
onensis|4474681|Xylobolus frustulatus|4474426|Xylaria|4475194|Zaraea aenea|4475450|Zignoëlla rhytidodes|4475078|Zabrus t
enebrioides|4475585|Zwackhiomyces dispersus|4474307|Xerula radicata|4474829|Xylohypha ferruginosa|4474824|Xylocoris (Xyl
ocoris) formicetorum|4475350|Zeugophora turneri|4475095|Zacladus exiguus|4475607|Zwackhiomyces sphinctrinoides|4474320|X
estobium rufovillosum|4475602|Zwackhiomyces lacustris|4475100|Zacladus geranii|4474334|Xestophanes potentillae|4474591|X
yleborinus saxesenii|4475610|Leptogium turgidum|1632955|Xylota|4475111|Phillyrea latifolia|4475619|Clauzadea metzleri|44
74604|Xyleborus dispar|4474351|Xiphydria prolongata|4474858|Xylohypha nigrescens|4475114|Zaghouania phillyreae|4475371|Z
euzera pyrina|4475639|Zygogloea gemellipara|9397|Halictus|4475634|Zygiobia carpini|4474364|Xyela curva|4475644|Zygophial
a jamaicensis|4475269|Zeugophora flavicollis|4475264|Zenobiana prismatica|4475521|Zoopage thamnospira|4475535|Zoophthora
anglica|4475530|Zoophagus insidians|816095|Phillyrea latifolia|4475544|Zoophthora radicans|4474790|Xylocleptes bispinus
|4475558|Zoothamnion arbuscula|4474273|Xerula caussei|4475043|Pisum sativum var. sativum|4474798|Cryptolestes ferrugineu
s|4474795|Xylocoris (Proxylocoris) galactinus|4475563|Zopfia rhizophila|4475572|Zopfiella erostrata|4474806|Xylocoris (X
ylocoris) cursitans|4474545|Xylaria oxyacanthae|4474803|Bitoma crenata|4474809|Rhizophagus|4474298|Xerula pudens]
org.eol.globi.service.PropertyEnricherException: Failed to query
at org.eol.globi.service.GlobalNamesService.findTermsForNames(GlobalNamesService.java:74)
at org.eol.globi.tool.LinkerGlobalNames.handleBatch(LinkerGlobalNames.java:66)
at org.eol.globi.tool.LinkerGlobalNames.link(LinkerGlobalNames.java:45)
at org.eol.globi.tool.Normalizer.linkTaxa(Normalizer.java:127)
at org.eol.globi.tool.Normalizer.run(Normalizer.java:98)
at org.eol.globi.tool.Normalizer.main(Normalizer.java:57)
Caused by: org.apache.http.client.HttpResponseException: Internal Server Error
at org.apache.http.impl.client.BasicResponseHandler.handleResponse(BasicResponseHandler.java:67)
at org.apache.http.impl.client.BasicResponseHandler.handleResponse(BasicResponseHandler.java:52)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:218)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:160)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:136)
at org.eol.globi.service.GlobalNamesService.queryForNames(GlobalNamesService.java:99)
at org.eol.globi.service.GlobalNamesService.findTermsForNames(GlobalNamesService.java:71)
... 5 more
another one:
2015-08-20 12:30:51,543 [main] ERROR org.eol.globi.tool.LinkerGlobalNames - batch #1115 problem matching terms: [4471364
|Valsella amphoraria|4471621|Velutina plicatilis|4472135|Verticillium|4472128|Lecanora albescens|4471618|Hydrozoa|447238
6|Vibrissea guernisacii|4472140|Verticillium albo-atrum|4471373|Valsella clypeata|4471624|Styela coriacea|4471627|Veluti
na velutina|4471382|Valsella polyspora|4471632|Venturia carpophila|4471888|Venturia maculiformis|347923|Scilla|4472154|V
erticillium catenulatum|4471387|Valsella salicis|4471396|Vankya ornithogali|4470375|Bellevalia|4472167|Verticillium dahl
iae|4471905|Venturia minuta|4470127|Ustilago maydis|4471919|Venturia populina|4471914|Venturia palustris|4471147|Valsa i
ntermedia|4471156|Valsa laurocerasi|1052452|Salix matsudana|4471422|Vararia gallica|4472185|Verticillium insectorum|4470
534|Valsa ambiens|4472070|Veronaea botryosa|4470529|Valsa abrupta|4471555|Velutarina rufo-olivacea|4472079|Veronaea cari
cis|4472084|Veronaea carlinae|4472089|Veronaea parvispora|4471322|Valsaria insitiva|4470305|Ustilago tritici|4471086|Val
sa cypri|4471855|Venturia macularis|4472111|Verpa conica|4471081|Valsa ceuthospora|4472116|Verrucaria conturmatula|44703
20|Scilla sardensis|4470323|Ustilago vaillantii|4472371|Vespula (Vespula) austriaca|4472381|Vibrissea flavovirens|447212
1|Verrucaria latericola|4470330|Muscari botryoides|4272191|Valsa|4471355|Valsella adhaerens|4470470|Valdensia heterodoxa
|4472007|Venturia saliciperda|4472263|Physarum compressum|4472268|Physarum leucopus|4470217|Elytrigia juncea|4472277|Ste
monitis axifera|4471260|Valsaria anserina|4471516|Vasates pedicularis|4470493|Gaultheria|4471519|Acer saccharinum|447229
3|Vesiculomyces citrinus|4471527|Vasates retiolatus|4472288|Verticillium|4471265|Valsaria cincta|4471522|Vasates quadrip
edes|4471779|Venturia crataegi|4470504|Valsa abietis|4471784|Venturia ditricha|4471540|Vasates rigidus|4471793|Venturia
fraxini|4472061|Venturiocistella ulicicola|4471550|Velutarina juniperi|4471806|Venturia geranii|4472056|Venturiocistella
heterotricha|4471545|Vascellum pratense|4471941|Venturia pyrina|4471936|Venturia potentillae|4470414|Ustilentyloma bref
eldii|4470927|Valsa auerswaldii|4472200|Verticillium nubilum|4472213|Verticillium psalliotae|4471190|Valsa sordida|44711
85|Valsa pini|4471441|Climbing plants|4470431|Animalia|4470424|Ustilentyloma fluitans|4470936|Valsa ceratosperma|4471448
|Vararia ochroleuca|4471705|Venturia cerasi|4472218|Verticillium rexianum|4470438|Utricularia australis|4471974|Venturia
rumicis|4472230|Ceratiomyxa fruticulosa|4472225|Arcyria nutans|4470441|Crustacea|4471209|Populus balsamifera|4470448|Ut
ricularia minor|4470194|Ustilago serpens|4471738|Venturia chlorospora|4470459|Diaptomus]
org.eol.globi.service.PropertyEnricherException: Failed to query
at org.eol.globi.service.GlobalNamesService.findTermsForNames(GlobalNamesService.java:74)
at org.eol.globi.tool.LinkerGlobalNames.handleBatch(LinkerGlobalNames.java:66)
at org.eol.globi.tool.LinkerGlobalNames.link(LinkerGlobalNames.java:45)
at org.eol.globi.tool.Normalizer.linkTaxa(Normalizer.java:127)
at org.eol.globi.tool.Normalizer.run(Normalizer.java:98)
at org.eol.globi.tool.Normalizer.main(Normalizer.java:57)
Caused by: org.apache.http.client.HttpResponseException: Gateway Time-out
at org.apache.http.impl.client.BasicResponseHandler.handleResponse(BasicResponseHandler.java:67)
at org.apache.http.impl.client.BasicResponseHandler.handleResponse(BasicResponseHandler.java:52)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:218)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:160)
at org.apache.http.impl.client.CloseableHttpClient.execute(CloseableHttpClient.java:136)
at org.eol.globi.service.GlobalNamesService.queryForNames(GlobalNamesService.java:99)
at org.eol.globi.service.GlobalNamesService.findTermsForNames(GlobalNamesService.java:71)
... 5 more
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jhpoelen
commented on May 27, 2024
@dimus suggest to re-open this issue given the reported behaviors above.
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dimus
commented on May 27, 2024
@jhpoelen -- do these examples consistently break resolver?
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jhpoelen
commented on May 27, 2024
yep.
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jhpoelen
commented on May 27, 2024
@dimus I was able to reproduce and fix the issue on my end. It turned out to be a character encoding issue in the http post request that GloBI sends to the resolver. Thanks again for adding the vernacular names to the resolver results.
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Related Issues (20)
- Provide GNI data sources for BioGUID Identifier Domains
- Fuzzy matching on genus name
- exact canonical match of resolver includes NCBI subspecies/strains HOT 10
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- import ITIS
- Add human readable match status
- Add date when matched result was imported to resolver
- add wikidata to the source list HOT 1
- Hyperlinks from name search results page to particular taxonomies
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- Add OTOL reference taxonomy to the index
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- suspicious mapping: C. fluminea resolves to C.
- resolver used to point Arius felis to Ariopsis felis when using Open Tree of Life
- Current Taxonomy
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- World flora online - Invalid accepted name reported
- Update datasource POWO (WCVP)
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