0.14.1

Features

• support stream processing of rdf/quads towards #52 and globalbioticinteractions/globalbioticinteractions#1030
• introduce elton tee to copy resources described in rdf/n-quads stream into preston compatible, content addressed data dir.
• introduce --prov-mode to let elton commands (e.g., elton prov, elton interactions. elton names, elton review, elton stream, elton nanopubs, and elton ls --online) details the processing methods and their inputs/outputs in machine readable rdf/nquads stream.

Example 1 - Append tracked interaction dataset and their dependencies to a preston archive.

elton track --prov-mode globalbioticinteractions/template-dataset\
 | elton tee\
 | preston append\
 | tail -1

yielding

<urn:uuid:76ae2794-b9a2-4a27-b235-927377d77370> <http://www.w3.org/ns/prov#endedAtTime> "2025-01-07T23:53:04.402Z"^^<http://www.w3.org/2001/XMLSchema#dateTime> <urn:uuid:76ae2794-b9a2-4a27-b235-927377d77370> .

Example 2 - generate interaction table from lastest version of a preston archive generated via Example 1.

preston head\
 | preston cat\
 | elton stream --record-type interaction --data-dir data\
 | mlr --itsvlite --oxtab cat\
 | tail

yielding

localityName                           
referenceDoi                           10.1007/s13127-011-0039-1
referenceUrl                           https://doi.org/10.1007/s13127-011-0039-1
referenceCitation                      Gittenberger, A., Gittenberger, E. (2011). Cryptic, adaptive radiation of endoparasitic snails: sibling species of Leptoconchus (Gastropoda: Coralliophilidae) in corals. Org Divers Evol, 11(1), 21–41. doi:10.1007/s13127-011-0039-1
namespace                              globalbioticinteractions/template-dataset
citation                               Jorrit H. Poelen. 2014. Species associations manually extracted from literature.
archiveURI                             hash://sha256/5b4ee64e7384bdf3d75b1d6617edd5d82124567b4ec52b47920ea332837ff060
lastSeenAt                             2025-01-07T23:55:26.792Z
contentHash                            
eltonVersion                           0.14.0-SNAPSHOT

Example 3 - generate a review report of a tracked dataset, append their inputs (datasets)/outputs (review table) to a preston archive, then save the review report in to a file review.tsv.

elton track --prov-mode globalbioticinteractions/template-dataset\
 | elton tee\
 | preston append\
 | elton stream --record-type review --data-dir data
 > review.tsv

Improvements

• upgrade to globi-lib v0.27.0 to help improve elton <> preston integration
• upgrade to preston v0.10.2
• allow for separate configuration of work-dir, prov-dir and data-dir.
• reduce repeated cache updates; use hash uris to avoid leaking local p…

…aths in prov logs; related to globalbioticinteractions/globalbioticinteractions#1030 #52

Bugs

• avoid splitting arguments; see bio-guoda/preston@d226274