0.14.3

Features

n/a

Improvements

• upgrade to globi-lib v0.27.6; include default interaction types mappi… …ngs in provenance graph; preparation to #61
• support config override for [preston stream]; related to #61 and Big-Bee-Network/bif#11 to allow for setting custom, re-usable, interaction type mappings when stream processing (possible large, GBIF large) collections of datasets and extract species interaction claims.

with this, you can do -

preston track "https://api.gbif.org/v1/dataset/d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0"\
 | elton stream\
 --data-dir data\
 --config hash://sha256/02682fdd62a3e985dc06236662299f00ec5453c4e6f707d02efa93628f927649\
 --remote https://softwareheritage.org\
 | head -2\
 | mlr --itsvlite --oxtab cat

producing

argumentTypeId                         https://en.wiktionary.org/wiki/support
sourceOccurrenceId                     4a98a813-85bc-41fc-bca4-0c9937ba6966
sourceCatalogNumber                    UCSB-IZC 00000304
sourceCollectionCode                   IZC
sourceCollectionId                     b03a3f0c-bfa5-4e02-b5d3-56ff38626302
sourceInstitutionCode                  UCSB
sourceTaxonId                          82680
sourceTaxonName                        Hemiptera
sourceTaxonRank                        
sourceTaxonPathIds                     
sourceTaxonPath                        Animalia | Arthropoda | Insecta
sourceTaxonPathNames                   kingdom | phylum | class
sourceBodyPartId                       
sourceBodyPartName                     
sourceLifeStageId                      
sourceLifeStageName                    
sourceSexId                            
sourceSexName                          
interactionTypeId                      http://purl.obolibrary.org/obo/RO_0002437
interactionTypeName                    interactsWith
targetOccurrenceId                     
targetCatalogNumber                    
targetCollectionCode                   
targetCollectionId                     
targetInstitutionCode                  
targetTaxonId                          
targetTaxonName                        Calandrinia menziesii
targetTaxonRank                        
targetTaxonPathIds                     
targetTaxonPath                        
targetTaxonPathNames                   
targetBodyPartId                       
targetBodyPartName                     
targetLifeStageId                      
targetLifeStageName                    
targetSexId                            
targetSexName                          
basisOfRecordId                        
basisOfRecordName                      PreservedSpecimen
http://rs.tdwg.org/dwc/terms/eventDate 2017-03-17T00:00:00Z
decimalLatitude                        34.4095
decimalLongitude                       -119.8491
localityId                             
localityName                           UCSB Campus Lagoon Island
referenceDoi                           
referenceUrl                           https://ecdysis.org/collections/individual/index.php?occid=826935
referenceCitation                      UCSB-IZC 00000304 https://ecdysis.org/collections/individual/index.php?occid=826935
namespace                              local
citation                               University of California Santa Barbara Invertebrate Zoology Collection. 2025-02-03. Ecdysis Portal - 00efd88c-9458-4860-acfd-eaa043f77b7c.
archiveURI                             hash://sha256/14289a70968588a29f8e566053c4509e0784bded38b6ab7172569ac7ceb7cae7
lastSeenAt                             2025-02-07T00:54:18.471Z
contentHash                            
eltonVersion                           0.14.3-SNAPSHOT

Where

• preston track "https://api.gbif.org/v1/dataset/d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0" tracks the DwC-A associated with UCSB-IZC GBIF registration at https://www.gbif.org/dataset/d6097f75-f99e-4c2a-b8a5-b0fc213ecbd0
• elton stream --data-dir data --config hash://sha256/02682fdd62a3e985dc06236662299f00ec5453c4e6f707d02efa93628f927649 --remote https://softwareheritage.org takes the provenance logs (or manifests) that describe UCSB-IZC and attempt to extract interaction data from them. --config points to a specific configuration (i.e., globi.json), identified by a hash://sha256/026... of which copies exist in https://github.com/jhpoelen/ucsb-izc-config and archive in the https://softwareheritage.org . In this case, if the referenced configuration is not available locally (in the data/ folder) it'll be downloaded retrieved from https://softwareheritage.org archives.
• head -2 | mlr --itsvlite --oxtab cat takes the first two rows (the header and one line of data), and presents them in the vertically oriented XTAB format using the mlr tool.

Bugs

n/a