Current instance failing intermittantly

[jvwong]

Sending a request:

POST https://semanticsearch.baderlab.org/

{"query":"32353859","documents":["32408336","32645325","32366720","32457038","32883368","32467561","32843534","32693122","32405156","32604797","32473310","32374074","32807895","32533062","32786284","32447571","32747425","32563698","32707573","32913009","32532085","32644275","32387014","32559285","32360182","32817221","32624257","32661214","33103435","32564623","32344177","32890913","32993136","32859008","32738360","32687696","32444382","32891497","32820005","33059719","32828312","32320852","33082259","32591346","32679055","32357553","32754161","32532094","32753646","32511329","33060197","32416070","32733001","32680882","32979938","32413319","33080218","32661059","32529952","33097660","33147445","32726355","32726803","32443810","32444466","32376634","32438371","33116300","32906143","32908316","32526206","32838362","32544429","32492406","32589897","32522207","32728199","32697968","32788292","32358203","33024307","32665542","32839770","32995787","32972995","32555321","32464097","33147444","32935098","32699849","32811513","33037393","32526208","34389034","34387838","34386522","34386498","34385425","34384361","34381970","34381116","34373855","34372515","34367059","34366621","34358117","34357135","34356777","34356077","34349364","34349236","34346317","34345597","34345219","34344552","34344455","34340747","34339864","34339582","34337272","34336145","34335977","34335604","34335504","34333072","34332351","34324563","34321669","34320442","34320401","34313439","34312622","34311528","34311260","34306570","34305949","34305655","34303107","34297909","34297570","34294141","34292740","34291385","32253226","32160149","32142651","32109012","32060427","32031583","32015508","31987001","31986257","31978945","31969702","31924756","31805977","31691834","31273098","31240472","30833725","30778233","30777892","30550790","30357367","30357350","30291362","30118682","30082464","30068649","29324744","29258862","29258238","28784718","27924013","27920254","27899562","27712623","27306108","27012512","26789921","26651998","26479676","26186194","25883141","25754993","25736566","25720466","25487801","25314029","25075342","24942700","24927547","24727771","32631826","32510142","32711111","32710969","32450198","32811406","33055231","33132205","32598985","32402186","32317408","32125140","32723801","32563814","32574699","32661235","33548227"]}

Results in an 500 Internal Server Error.

However, splitting this into two equal size batches is successful when sent serially:

{"query":"32353859","documents":["32408336","32645325","32366720","32457038","32883368","32467561","32843534","32693122","32405156","32604797","32473310","32374074","32807895","32533062","32786284","32447571","32747425","32563698","32707573","32913009","32532085","32644275","32387014","32559285","32360182","32817221","32624257","32661214","33103435","32564623","32344177","32890913","32993136","32859008","32738360","32687696","32444382","32891497","32820005","33059719","32828312","32320852","33082259","32591346","32679055","32357553","32754161","32532094","32753646","32511329","33060197","32416070","32733001","32680882","32979938","32413319","33080218","32661059","32529952","33097660","33147445","32726355","32726803","32443810","32444466","32376634","32438371","33116300","32906143","32908316","32526206","32838362","32544429","32492406","32589897","32522207","32728199","32697968","32788292","32358203","33024307","32665542","32839770","32995787","32972995","32555321","32464097","33147444","32935098","32699849","32811513","33037393","32526208","34389034","34387838","34386522","34386498"]}

{"query":"32353859","documents":["34385425","34384361","34381970","34381116","34373855","34372515","34367059","34366621","34358117","34357135","34356777","34356077","34349364","34349236","34346317","34345597","34345219","34344552","34344455","34340747","34339864","34339582","34337272","34336145","34335977","34335604","34335504","34333072","34332351","34324563","34321669","34320442","34320401","34313439","34312622","34311528","34311260","34306570","34305949","34305655","34303107","34297909","34297570","34294141","34292740","34291385","32253226","32160149","32142651","32109012","32060427","32031583","32015508","31987001","31986257","31978945","31969702","31924756","31805977","31691834","31273098","31240472","30833725","30778233","30777892","30550790","30357367","30357350","30291362","30118682","30082464","30068649","29324744","29258862","29258238","28784718","27924013","27920254","27899562","27712623","27306108","27012512","26789921","26651998","26479676","26186194","25883141","25754993","25736566","25720466","25487801","25314029","25075342","24942700","24927547","24727771","32631826","32510142","32711111","32710969","32450198","32811406","33055231","33132205","32598985","32402186","32317408","32125140","32723801","32563814","32574699","32661235","33548227"]}

This relates to the current instance (may possibly be out of date as we haven't updated Factoid PathwayCommons/factoid#990)

[jvwong]

Failing case on 1 PMID for https://biofactoid.org/document/a2d4d2da-132e-4207-a8dd-1d534d893495:

POST https://semanticsearch.baderlab.org/

{
  "query":"32432943",
  "documents":[   
    "32816848"
  ]
}

Returns 500 HTTP status

Here is the raw response from NCBI PubMed:

GET https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=32816848

id: 32816848 Error occurred: The following PMID is not available: 32816848

POST /entrez/eutils/efetch.fcgi HTTP/2
Host: eutils.ncbi.nlm.nih.gov
user-agent: insomnia/2021.5.2
cookie: ncbi_sid=333AA6EB4A752843_9D5CSID
content-type: application/x-www-form-urlencoded
accept: /
content-length: 85
| id=32816848%20&db=pubmed&api_key=...&retmode=xml&=&=

<?xml version="1.0" ?>
<!DOCTYPE PubmedArticleSet PUBLIC "-//NLM//DTD PubMedArticle, 1st January 2019//EN" "https://dtd.nlm.nih.gov/ncbi/pubmed/out/pubmed_190101.dtd">
<PubmedArticleSet></PubmedArticleSet>

[jvwong]

I am seeing more failures of the service (HTTP 500) on a basis that is difficult to predict.

Example failing case:

POST https://semanticsearch.baderlab.org/

{
  "query": "33264621",
  "documents": [
    "27053424",
    "24313847",
    "16887800",
    "31956021",
    "18499676",
    "26888284"
  ]
}

The above fails, but when I remove the last entry "26888284" it passes, but trying the last entry alone passes?

POST https://semanticsearch.baderlab.org/

{
  "query": "33264621",
  "documents": [
    "26888284"
  ]
}

Now I try the first failed case a few minutes later and it passes?

Thius is related to the document with id 3af11b24-c292-4d7a-af94-d0a9b7699081

[jvwong]

Note: The instance at https://semanticsearch.baderlab.org/ is pretty ancient (Oct 2020) so all these issues might just go away with an update (June 2021). Will test this.