Real users: Article metadata retrieval failures

jvwong commented 4 years ago

Just logging some failures I noticed with real user input

1. Error: Unable to retrieve a PubmedArticle / Error filling doc article
  - Date: 2020-09-29T14:39:24.221050250Z
  - Author input: Human insulin growth factor 2 mRNA binding protein 2 increases miR-33a/b inhibition of liver ABCA1 expression and alters low-density apolipoprotein levels in mice
  - Possible reason: Title in PubMed is ...Increases MicroRNA 33a/b...
1. Error: getRelPprsForDoc: Bad Request (400)
  - Date: Tue Sep 29 2020 13:47:15 GMT+00:00
  - Author input: Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits [https://pubmed.ncbi.nlm.nih.gov/32610139/]
  - Possible reason: Something in semanti-search ("value is not a valid dict")
1. Error: HTTPStatusError: Bad Request (400) / Error filling doc article
  - Date: 2020-09-29T17:11:02.430147444Z
  - Author input: 'Critical roles of phosphoinositides and NF2 in Hippo pathway regulation'
  - Possible reason: I refreshed the data and it worked???
1. Problem: System kept giving me an 'Author correction: ..' entry
  - Date: 2020-09-29
  - Author input: ROCK-mediated selective activation of PERK signalling causes fibroblast reprogramming and tumour progression through a CRELD2-dependent mechanism [https://pubmed.ncbi.nlm.nih.gov/32451439/]
  - Problem: Exact input to title match isn't prioritised, only 'contains'
1. Error: Unable to retrieve a PubmedArticle
  - Date: 2020-10-02T11:02:50.823177975Z
  - Author put in Coordinated conformational processing of p53 by the Hsp70 and Hsp90 chaperones machineries for Coordinated Conformational Processing of the Tumor Suppressor Protein p53 by the Hsp70 and Hsp90 Chaperone Machineries [https://pubmed.ncbi.nlm.nih.gov/31027879/]
  - Possible reason: They're playing fast and lose as if it's a search engine?
1. Unable to retrieve a PubmedArticle
  - Date: 1602119209.78
  - Author entered NRBP1-containing CRL2/CRL4A regulates amyloid beta production by targeting BRI2 and BRI3 for degradation. but actual was NRBP1-Containing CRL2/CRL4A Regulates Amyloid β Production by Targeting BRI2 and BRI3 for Degradation
  - Problem: β vs beta
  - Also a whole bunch of errors on submit (below).

Comments: User for vi and the other user (i) seem to know that the system didn't find their article, so they repeatedly enter the same text over and over again in the CTA

jvwong commented 4 years ago

* 1. Error: `getRelPprsForDoc: Bad Request (400)`

  * Date:  Tue Sep 29 2020 13:47:15 GMT+00:00
  * Author input: `Atrx Deletion in Neurons Leads to Sexually Dimorphic Dysregulation of miR-137 and Spatial Learning and Memory Deficits` [https://pubmed.ncbi.nlm.nih.gov/32610139/]
  * Possible reason: Something in semanti-search (`"value is not a valid dict"`)

https://github.com/PathwayCommons/factoid/blob/4bf3fdc23bec447b487cae7d2193898b4014563a/src/server/routes/api/document/index.js#L1561

Reproduce with parameter:
- query: 32610139
- pmid: ```js ["31713968","28093507","30992372","29459374","28978667","32580781","28173139","30209204","29793972","20865721","25395668","23742761","19088125","26612516","26773099","29915867","26888934","28970783","23175442","32264905","19020049","28624414","24742619","24934177","26758828","30670054","27171262","28687800","23218253","30728170","19649270","31671722","25452430","31263066","22367974","31249508","29279308","27029610","25740514","28851397","15668733","28720484","29712785","21289602","27535911","29874582","26612208","29617377","25808129","17172010","31502810","31301273","30104731","29976930","29927554","29785027","29665782","29650040","29635364","29196732","29180823","29155950","29133437","28902423","28898627","28683304","27468717","27335314","27286292","27240256","27130160","26925227","26423861","26350204","26095359","26056561","26005852","25963561","25755632","25690850","25687692","25516281","25404090","25264773","25206554","24581740","24157548","24151012","24030948","23689500","23592037","23563309","23252729","23201973","22743772","22537595"]

See https://github.com/PathwayCommons/semantic-search/pull/21

jvwong commented 4 years ago

Failure retrieving network-related papers:

Doc: https://biofactoid.org/document/e3ad1fe0-7cc9-4075-b9a7-32626ce0c2ff
Error log

weebapp_container | 2020-10-02T11:28:41.379903284Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=11998%40HGNC
webapp_container | 2020-10-02T11:28:41.380235613Z error:   504: Gateway Timeout
webapp_container | 2020-10-02T11:28:41.380400899Z info:    Retrying, attempt 1
webapp_container | 2020-10-02T11:28:41.382618637Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=5258%40HGNC&agent1=11998%40HGNC
webapp_container | 2020-10-02T11:28:41.382925393Z error:   504: Gateway Timeout
webapp_container | 2020-10-02T11:28:41.383091726Z info:    Retrying, attempt 1
webapp_container | 2020-10-02T11:28:41.384061682Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=5232%40HGNC&agent1=11998%40HGNC
webapp_container | 2020-10-02T11:28:41.384237935Z error:   504: Gateway Timeout
webapp_container | 2020-10-02T11:28:41.384395806Z info:    Retrying, attempt 1
webapp_container | 2020-10-02T11:29:01.865262624Z info:    Related papers table is updated for document e3ad1fe0-7cc9-4075-b9a7-32626ce0c2ff

Couldn't get any network- related papers on local instance either...

Unfortunately, this author also typed in a modified variant of their title (see v in issue) and so had no PubMed ID/ doc-level related papers but we got their data nonetheless.

Superseded by #851

jvwong commented 4 years ago

probably should have something in the admin for related papers issues as I had to manually inspect each new doc then dive around the logs to figure out what happened

Superseded by #852

jvwong commented 4 years ago

I'm reopening because this exact string matching approach is causing problems (see case vi)

Also on user submit - a bunch of errors from INDRA but it retried successfully!

webapp_container | 2020-10-08T01:28:26.188493310Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=21696%40HGNC
webapp_container | 2020-10-08T01:28:26.189156964Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.189422363Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.190860954Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=2554%40HGNC
webapp_container | 2020-10-08T01:28:26.191225205Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.191509834Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.192543085Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=2717%40HGNC
webapp_container | 2020-10-08T01:28:26.192852640Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.193114833Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.194072221Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=NRBP1-ubiquitin%20ligase%20(E3)%40TEXT
webapp_container | 2020-10-08T01:28:26.194345017Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.194640278Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.195658885Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=7993%40HGNC&agent1=6175%40HGNC
webapp_container | 2020-10-08T01:28:26.195926188Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.196185768Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.197239043Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=7993%40HGNC&agent1=2552%40HGNC
webapp_container | 2020-10-08T01:28:26.197523246Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.197780992Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.200323490Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=7993%40HGNC&agent1=6174%40HGNC
webapp_container | 2020-10-08T01:28:26.200592149Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.200902858Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.201870885Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=2552%40HGNC
webapp_container | 2020-10-08T01:28:26.202182995Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.202397381Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.203364489Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=7993%40HGNC&agent1=7993%40HGNC
webapp_container | 2020-10-08T01:28:26.203631471Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.203889354Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.226682781Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=11617%40HGNC
webapp_container | 2020-10-08T01:28:26.226934167Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.227103173Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.232779574Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=6175%40HGNC
webapp_container | 2020-10-08T01:28:26.233153000Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.233317700Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.236197983Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=3051%40HGNC
webapp_container | 2020-10-08T01:28:26.236467478Z error:   504: Gateway Timeout
webapp_container | 2020-10-08T01:28:26.236647622Z info:    Retrying, attempt 1
webapp_container | 2020-10-08T01:28:26.237650471Z error:   Error for https://db.indra.bio/latest/statements/from_agents?format=json-js&agent0=6174%40HGNC
webapp_container | 2020-10-08T01:28:26.237839378Z error:   504: Gateway Timeout

jvwong commented 4 years ago

Also for above blank image for https://biofactoid.org/document/7d452a55-234e-47a7-aed2-33646f2a2e9d

PathwayCommons / factoid

Real users: Article metadata retrieval failures #845