Closed seltmann closed 3 years ago
@seltmann having a look.
Some notes:
$ 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
continuing to investigate, more later.
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.
@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?
@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:
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 .
@jhpoelen perfect, thanks!
@jhpoelen This repo is no longer indexed by GloBI and I cannot find the error. Help?