No longer being indexed?

[seltmann]

@jhpoelen This repo is no longer indexed by GloBI and I cannot find the error. Help?

[jhpoelen]

@seltmann having a look.

Some notes:

1. According to a recent review at https://travis-ci.org/github/Extended-Bee-Network/bee-interaction-database/builds/738436408 , there's 3068 interaction in the datasets.
2. your data was last updated on GloBI's index server at 2020-12-08T23:54:05.408Z
3. elton was able to extract interaction from the server's most recent versioned copy

   $ elton interactions Extended-Bee-Network/bee-interaction-database | head -n1
   argumentTypeId  sourceOccurrenceId  sourceCatalogNumber sourceCollectionCode    sourceCollectionId  sourceInstitutionCode   sourceTaxonId   sourceTaxonName sourceTaxonRank sourceTaxonPathIds  sourceTaxonPath sourceTaxonPathNames    sourceBodyPartId    sourceBodyPartName  sourceLifeStageId   sourceLifeStageName sourceSexId sourceSexName   interactionTypeId   interactionTypeName targetOccurrenceId  targetCatalogNumber targetCollectionCode    targetCollectionId  targetInstitutionCode   targetTaxonId   targetTaxonName targetTaxonRank targetTaxonPathIds  targetTaxonPath targetTaxonPathNames    targetBodyPartId    targetBodyPartName  targetLifeStageId   targetLifeStageName targetSexId targetSexName   basisOfRecordId basisOfRecordName   http://rs.tdwg.org/dwc/terms/eventDate  decimalLatitude decimalLongitude    localityId  localityName    referenceDoi    referenceUrl    referenceCitation   namespace   citation    archiveURI  lastSeenAt  contentHash eltonVersion
   listing interactions [Extended-Bee-Network/bee-interaction-database]... https://en.wiktionary.org/wiki/support              https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=699376   Melissodes pullatella               Female  http://purl.obolibrary.org/obo/RO_0002622   visitsFlowersOf                     https://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=535920   Grindelia integrifolia x Grindelia nana             44.60417    -123.2389           10.1007/s10531-010-9897-7   https://doi.org/10.1007/s10531-010-9897-7   Severns, P. M. & Moldenke, A. R. (2010) Management tradeoffs between focal species and biodiversity: Endemic plant) conservation and solitary bee extinction. Biodivers. Conserv. 19, 3605-3609.    Extended-Bee-Network/bee-interaction-database   Seltmann, K., Van Wagner, J., Behm, R., Brown, Z., Tan, E., & Liu, K. (2020). BID: A project to share biotic interaction and ecological trait data about bees (Hymenoptera: Anthophila). UC Santa Barbara: Cheadle Center for Biodiversity and Ecological Restoration. Retrieved from https://escholarship.org/uc/item/1g21k7bf https://github.com/Extended-Bee-Network/bee-interaction-database/archive/3360aeafab9b30b34ddb45ddfd170eda69536904.zip   2020-12-08T23:54:05.611Z    0b9e47a7178db8a49416e4f4a6e5e1c21b27aae1687756886af9b46a57ecc0f0    0.10.4

4. no errors are apparent in the most recent indexing logs
5. however, on https://globalbioticinteractions.org/datasets page, the dataset Extended-Bee-Network/bee-interaction-database does not appear.

continuing to investigate, more later.

[jhpoelen]

After updating the GloBI index to a more recent version, the Extended-Bee-Network/bee-interaction-database reappeared, see attached screenshot.

The older index (generated 1 Dec 2020, over a week ago), did not have the interaction database. Still looking into root cause.

[jhpoelen]

@seltmann I noticed that you've been actively working on the dataset in the recent past. However, travis-ci.org is not showing automated reviews after each commit. If you enable automated reviews, you can see whether there's unexpected notes, like "no interactions found". Having automated travis reviews would have helped to pin point the root cause of the non-indexing by inspecting the build log (aka review log). Can you please enable this?

[jhpoelen]

@seltmann I've identified the most likely cause of the Extended-Bee-Network/bee-interaction-database not being indexed, and you fixed this some days ago via:

https://github.com/Extended-Bee-Network/bee-interaction-database/commit/9779f5682efe9268b3725b2c38b680d44c819e4f

Currently, a malformed globi.json will prevent GloBI from understanding and indexing your datasets.

In summary - you found an unexpected result because the GloBI index wasn't updated (due to maintenance work) for about a week, and that older index did not include an older version of the bee-interaction-database because of syntax issues on globi.json .

[seltmann]

@jhpoelen perfect, thanks!