wdk : sending nosense columns to store as preferences

[aurreco-uga]

These errors keep happening.. just FYI

The attached step is new. We do store the wrong column name in preferences.. this time in the preferences table.

I know the client will ignore next time it reads it..

It must be a client error..? Though the backend should not store this wrong value?

[dmfalke]

It must be a client error..? Though the backend should not store this wrong value?

I think it must be a client error, too. Maybe we can dig up a service request to see what the referring url is, when this preference update happens.

[aurreco-uga]

the error above: Referred from: https://plasmodb.org/plasmo/app/workspace/strategies/327837883/433042823

[dmfalke]

I did a little more digging. This is a guest user, so it's unlikely this attribute has been in their user preferences for a while. That means that something on that day caused that url to be added as an attribute value.

I also found the requests related to updating the user preference and step details:

[02/Apr/2024|05:49:39] sid:EF2CA rid: 462643       1ms   130.92.82.100 - INFO  - org.gusdb.wdk.service.filter.RequestLoggingFilter:85 - HTTP PATCH /users/current/preferences/project
Request Body: {
  "action": "UPDATE",
  "updates": {"GeneQuestions.GenesByMotifSearch_summary": "https://plasmodb.org/plasmo/app/record/gene/PBANKA_0207900,primary_key,transcript_link,organism,gene_location_text,gene_product,Locations,MatchCount,Sequence"}
}
[02/Apr/2024|05:49:39] sid:EF2CA rid: 462644       1ms   130.92.82.100 - INFO  - org.gusdb.wdk.service.filter.RequestLoggingFilter:85 - HTTP PATCH /users/current/steps/433042753
Request Body: {"displayPreferences": {
  "columnSelection": [
    "https://plasmodb.org/plasmo/app/record/gene/PBANKA_0207900",
    "primary_key",
    "transcript_link",
    "organism",
    "gene_location_text",
    "gene_product",
    "Locations",
    "MatchCount",
    "Sequence"
  ],
  "sortColumns": [
    {
      "name": "organism",
      "direction": "ASC"
    },
    {
      "name": "MatchCount",
      "direction": "DESC"
    },
    {
      "name": "gene_location_text",
      "direction": "ASC"
    }
  ]
}}

I also analyzed the apache logs, and the user was looking at jbrowse tracks related to PbANKA_10_v3. Seems like it could somehow be related.

[dmfalke]

Hmm... actually, that url is for the record page of the first gene in the result, so that might be even more related

[dmfalke]

All that being said... should we start removing unrecognized attributes?

[aurreco-uga]

you mean the backend?

today, 2 logged in users, we seem to be storing the wrong pref in user preferences

Date: 2024-04-10T05:03:40.521 Request URI: https://plasmodb.org/plasmo Remote Host: 134.176.158.140 Referred from: https://plasmodb.org/plasmo/app/workspace/strategies/327875523/433122993 wdk_user = User #104 - przyborski@me.com

"message": "The following unknown attributes were encountered from either user preferences or step details.\n\nSearch name: GeneByLocusTag\nStep ID: 433122993\nUnknown attributes: signalp_scores" }

checked in userdb: select * from userlogins5.preferences where user_id = 104 and project_id = 'PlasmoDB' order by project_id,preference_name

104 PlasmoDB GeneQuestions.GeneByLocusTag_summary primary_key,transcript_link,gene_name,gene_product,transcript_product,tm_count,s ignalp_peptide,signalp_scores,molecular_weight,isoelectric_point,cds_length,prot ein_length

---

Date: 2024-04-09T21:08:53.446 Request URI: https://fungidb.org/fungidb Remote Host: 98.179.129.12 Referred from: https://fungidb.org/fungidb/app/workspace/strategies/327079253/431550793

wdk_user = User #257115283 - hlb82@nau.edu

"message": "The following unknown attributes were encountered from either user preferences or step details.\n\nSearch name: boolean_question_TranscriptRecordClasses_TranscriptRecordClass\nStep ID: 431550793\nUnknown attributes: cimmRS_Taylor_SaprobicParasitic_rnaSeq_RSRC_expr_graph"

[dmfalke]

I mean, on the client, when we find these nonsense attributes, we can also remove them from user prefs

[aurreco-uga]

would be better to fix it but i guess cleaning up the database when possible will help