Releases · bio-guoda/preston

17 Dec 19:43

jhpoelen

0.11.4

4e49001

0.11.4 Latest

Latest

Features

support discovery of data archives for anchored preston datasets published in Zenodo #356 .

Example usage:

preston ls \
 --remote https://zenodo.org \
 --anchor hash://md5/58de50154e330c331993fe5d0852ad84 \
 --algo md5 \
 | grep .zip \
 | grep hasVersion \
 | grep DwC \
 | head -1 \
 | preston dwc-stream \
 --remote https://zenodo.org \
 --anchor hash://md5/58de50154e330c331993fe5d0852ad84 \
 --algo md5 \
 | head -1 \
 | jq .

to discover first dwc records encountered in

Elton, Nomer, & Preston. (2025). Versioned Archive and Review of Biotic Interactions and Taxon Names Found within globalbioticinteractions/scan hash://md5/58de50154e330c331993fe5d0852ad84. Zenodo. https://doi.org/10.5281/zenodo.16894884

as seen below.

To disable archive discovery and retrieve the entire archive to scan for requested content, use --disable-archive-discovery option.

{
  "http://www.w3.org/ns/prov#wasDerivedFrom": "line:zip:hash://md5/f0116c11643a3465d94ec7511621c232!/occurrences.csv!/L2",
  "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "http://rs.tdwg.org/dwc/terms/Occurrence",
  "http://rs.tdwg.org/dwc/text/id": "29693343",
  "http://rs.tdwg.org/dwc/terms/basisOfRecord": "Pinned Specimen",
  "http://rs.tdwg.org/dwc/terms/verbatimEventDate": null,
  "http://rs.tdwg.org/dwc/terms/catalogNumber": "ARTHARCH00034603",
  "http://rs.tdwg.org/dwc/terms/dynamicProperties": null,
  "http://rs.tdwg.org/dwc/terms/scientificNameAuthorship": "Emery, 1884",
  "http://rs.tdwg.org/dwc/terms/eventDate": "2004-06-29",
  "http://rs.tdwg.org/dwc/terms/taxonID": "234621",
  "http://rs.tdwg.org/dwc/terms/georeferencedBy": null,
  "http://rs.tdwg.org/dwc/terms/fieldNumber": null,
  "http://rs.tdwg.org/dwc/terms/sex": null,
  "http://rs.tdwg.org/dwc/terms/maximumDepthInMeters": null,
  "http://rs.tdwg.org/dwc/terms/decimalLatitude": "26.122",
  "http://rs.tdwg.org/dwc/terms/infraspecificEpithet": null,
  "http://rs.tdwg.org/dwc/terms/stateProvince": "Florida",
  "http://rs.tdwg.org/dwc/terms/georeferenceProtocol": null,
  "http://purl.org/dc/elements/1.1/rights": "http://creativecommons.org/licenses/by-nc/4.0/",
  "http://purl.org/dc/terms/accessRights": null,
  "http://rs.tdwg.org/dwc/terms/lifeStage": null,
  "http://rs.tdwg.org/dwc/terms/identificationRemarks": null,
  "http://rs.tdwg.org/dwc/terms/recordedBy": "Mark Deyrup",
  "http://rs.tdwg.org/dwc/terms/coordinateUncertaintyInMeters": null,
  "http://rs.tdwg.org/dwc/terms/taxonRank": null,
  "http://rs.tdwg.org/dwc/terms/class": "Insecta",
  "http://rs.tdwg.org/dwc/terms/informationWithheld": null,
  "http://purl.org/dc/terms/rightsHolder": "Archbold Biological Station",
  "http://purl.org/dc/terms/language": null,
  "http://rs.tdwg.org/dwc/terms/associatedTaxa": null,
  "http://rs.tdwg.org/dwc/terms/collectionCode": "ARTHARCH",
  "http://rs.tdwg.org/dwc/terms/individualCount": null,
  "http://rs.tdwg.org/dwc/terms/verbatimElevation": null,
  "http://rs.tdwg.org/dwc/terms/disposition": null,
  "http://rs.tdwg.org/dwc/terms/otherCatalogNumbers": null,
  "http://rs.tdwg.org/dwc/terms/typeStatus": null,
  "http://rs.tdwg.org/dwc/terms/country": "United States",
  "http://rs.tdwg.org/dwc/terms/verbatimDepth": null,
  "http://rs.tdwg.org/dwc/terms/family": "Formicidae",
  "http://rs.tdwg.org/dwc/terms/phylum": "Arthropoda",
  "http://rs.tdwg.org/dwc/terms/samplingEffort": null,
  "http://rs.tdwg.org/dwc/terms/geodeticDatum": null,
  "http://rs.tdwg.org/dwc/terms/identifiedBy": null,
  "http://symbiota.org/terms/recordEnteredBy": null,
  "http://rs.tdwg.org/dwc/terms/reproductiveCondition": null,
  "http://purl.org/dc/terms/references": "https://scan-bugs.org:443/portal/collections/individual/index.php?occid=29693343",
  "http://rs.tdwg.org/dwc/terms/collectionID": "f52df103-0126-47fd-8836-934641444fcd",
  "http://rs.tdwg.org/dwc/terms/occurrenceRemarks": "2 specimens on pin; Specimen voucher for Ants of Florida CRC Press 2016; Images of this species available at https://www.antweb.org",
  "http://rs.tdwg.org/dwc/terms/endDayOfYear": null,
  "http://rs.tdwg.org/dwc/terms/habitat": null,
  "http://portal.idigbio.org/terms/recordId": "urn:uuid:85dc3937-5e0b-438c-8401-f93af4d0a38f",
  "http://purl.org/dc/terms/modified": "2019-06-24 12:45:21",
  "http://rs.tdwg.org/dwc/terms/decimalLongitude": "-80.144",
  "http://rs.tdwg.org/dwc/terms/order": "Hymenoptera",
  "http://rs.tdwg.org/dwc/terms/georeferenceVerificationStatus": null,
  "http://rs.tdwg.org/dwc/terms/day": "29",
  "http://rs.tdwg.org/dwc/terms/minimumElevationInMeters": null,
  "http://rs.tdwg.org/dwc/terms/municipality": null,
  "http://rs.tdwg.org/dwc/terms/georeferenceRemarks": null,
  "http://rs.tdwg.org/dwc/terms/locality": "Fort Lauderdale: Bonnet House, disturbed mesic area",
  "http://rs.tdwg.org/dwc/terms/georeferenceSources": null,
  "http://rs.tdwg.org/dwc/terms/occurrenceID": "85dc3937-5e0b-438c-8401-f93af4d0a38f",
  "http://rs.tdwg.org/dwc/terms/specificEpithet": "mayri",
  "http://rs.tdwg.org/dwc/terms/genus": "Anochetus",
  "http://rs.tdwg.org/dwc/terms/associatedOccurrences": null,
  "http://rs.tdwg.org/dwc/terms/ownerInstitutionCode": null,
  "http://rs.tdwg.org/dwc/terms/month": "6",
  "http://rs.tdwg.org/dwc/terms/locationRemarks": null,
  "http://rs.tdwg.org/dwc/terms/samplingProtocol": null,
  "http://rs.tdwg.org/dwc/terms/dateIdentified": null,
  "http://rs.tdwg.org/dwc/terms/taxonRemarks": null,
  "http://rs.tdwg.org/dwc/terms/county": "Broward County",
  "http://rs.tdwg.org/dwc/terms/kingdom": "Animalia",
  "http://rs.tdwg.org/dwc/terms/verbatimCoordinates": null,
  "http://rs.tdwg.org/dwc/terms/recordNumber": null,
  "http://rs.tdwg.org/dwc/terms/identificationReferences": null,
  "http://rs.tdwg.org/dwc/terms/year": "2004",
  "http://rs.tdwg.org/dwc/terms/establishmentMeans": null,
  "http://rs.tdwg.org/dwc/terms/maximumElevationInMeters": null,
  "http://rs.tdwg.org/dwc/terms/identificationQualifier": null,
  "http://rs.tdwg.org/dwc/terms/preparations": null,
  "http://rs.tdwg.org/dwc/terms/institutionCode": "ABS",
  "http://rs.tdwg.org/dwc/terms/startDayOfYear": "181",
  "http://rs.tdwg.org/dwc/terms/minimumDepthInMeters": null,
  "http://rs.tdwg.org/dwc/terms/scientificName": "Anochetus mayri",
  "http://rs.tdwg.org/dwc/terms/dataGeneralizations": null
}

Improvements

override default stderr logging by xerces xml parser
add support for zotero record items without explicit attachments; in … …addition support implicitly linked attachments also

Bugs

replace file movement with copy/delete in an attempt to make process … …more resilient when dealing with mapped network drives.

Assets 7

12 Dec 00:39

jhpoelen

0.11.3

f6b5329

0.11.3

Features

n/a

Improvements

log unhandled Zenodo metadata; #361
reduce log verbosity when handling non-Zenodo data in preston zenodo deposit workflow. #361

Bugs

address out of bounds exception on empty common name in plazi treatment likely causing premature ending of plazi record stream via preston plazi-stream . Possibly related to jhpoelen/hmw#14 (comment) .

Assets 7

05 Nov 19:43

jhpoelen

0.11.2

03e8e1b

0.11.2

Features

allow for Zotero records to be streamed into RIS records bat-literature/bat-literature.github.io#117
allow for GOOGLE_TOKEN to access non-public google docs #360

Improvements

n/a

Bugs

handle "name" elements in Zotero metadata bat-literature/bat-literature.github.io#113 thanks to @arw36

Contributors

arw36

Assets 5

17 Oct 15:15

jhpoelen

0.11.1

f7283a7

0.11.1

Features

introduce /history endpoint to list provenance/history of doi / dataset uuid or dwc-a urls related to #357 @Jegelewicz

Improvements

add alias preston snapshot for preston track fyi @ajacsherman
add alias preston publish for preston zenodo
working towards discovering data.zip in Zenodo deposits see #356


## Bugs
n/a

Contributors

Jegelewicz and ajacsherman

Assets 5

15 Jul 09:25

jhpoelen

0.11.0

d833b9a

0.11.0

Features

n/a

Improvements

revert support for SciELO DOI inference #344 due to inconsistent doi naming: SciELO DOIs cannot be consistently be inferred from their article pid
add zip/tar.gz binary distributions to work towards #348


## Bugs
n/a

Assets 7

10 Jul 12:40

jhpoelen

0.10.14

61953df

0.10.14

Features

n/a

Improvements

support SciELO DOI inference #344 using

domain	doi prefix	example url	example doi
http://www.scielo.br	10.1590	http://www.scielo.br/scielo.php?script=sci_arttext&pid=S2236-89062014000200010	https://doi.org/10.1590/s2236-89062014000200010
http://www.scielo.org.mx	NA	NA	NA
http://www.scielo.cl	10.4067	https://www.scielo.cl/scielo.php?script=sci_pdf&pid=S0717-65382015000100003	https://doi.org/10.4067/s0717-65382015000100003
http://www.scielo.org.co	NA	NA	NA
http://www.scielo.org.ar	NA	NA	NA

update man preston-ris-stream documentation:

PRESTON-RIS-STREAM(1)           Preston Manual           PRESTON-RIS-STREAM(1)

NAME
       preston-ris-stream - translates bibliographic citations from RIS format
       into Zenodo metadata in JSON lines format

SYNOPSIS
       preston ris-stream [--no-cache] [--no-progress] [--reuse-doi]
       [-a=<hashType>] [-d=<depth>] [--data-dir=<dataDir>] [-l=<logMode>]
       [-r=<provenanceAnchor>] [--tmp-dir=<tmpDir>]
       [--community=<communities>[,<communities>...]]...
       [--repos=<remotes>[,<remotes>...]]...

DESCRIPTION
       Stream RIS records into line-json with Zenodo metadata

OPTIONS
       -a, --algo, --hash-algorithm=<hashType>
           Hash algorithm used to generate primary content identifiers.
           Supported values: sha256, md5, sha1.

       --community, --communities=<communities>[,<communities>...]
           select which Zenodo communities to submit to. If community is known
           (e.g., batlit, taxodros), default metadata is included.

       -d, --depth=<depth>
           folder depth of data dir

       --data-dir=<dataDir>
           Location of local content cache

       -l, --log=<logMode>
           Log format. Supported values: tsv, nquads.

       --no-cache, --disable-cache
           Disable local content cache

       --no-progress
           Disable progress monitor

       -r, --anchor, --provenance-root, --provenance-anchor=<provenanceAnchor>
           specify the provenance root/anchor of the command. By default, any
           available data graph will be traversed up to it’s most recent
           additions. If the provenance root is set, only specified provenance
           signature and their origins are included in the scope.

       --repos, --remote, --remotes, --include,
       --repositories=<remotes>[,<remotes>...]
           Included repository dependencies (e.g.,
           https://linker.bio/,https://softwareheritage.org,https://wikimedia.org,https://dataone.org,https://zenodo.org)

       --reuse-doi
           use existing DOI in Zenodo deposit if available

       --tmp-dir=<tmpDir>
           Location of local tmp dir

EXAMPLES
       1.
       First, append the associated bhl pdf via:

           preston track https://www.biodiversitylibrary.org/partpdf/326364

       Following, generate a RIS record, record.ris:

           cat > record.ris <<__EOL__
           TY  - BOOK
           TI  - Faber, Helen R May 5, 1913
           T2  - Walter Deane correspondence
           UR  - https://www.biodiversitylibrary.org/part/326364
           PY  - 1913-05-05
           AU  - Faber, Helen R.,
           ER  -
           __EOL__

       Then, track record.ris using Preston into Zenodo metadata using:

           cat record.ris\
            | preston track

       Finally, generate Zenodo metadata record.json using:

           preston head\
            | preston cat\
            | preston ris-stream\
            > record.json

       where record.json:

           {
             "metadata": {
               "description": "(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.",
               "communities": [],
               "http://www.w3.org/ns/prov#wasDerivedFrom": "https://linker.bio/line:hash://sha256/5fd5944b52b22efc56f901d96ff53a64c42e1f2264763e2f1074ac2c589e47cf!/L1-L7",
               "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "application/x-research-info-systems",
               "title": "Faber, Helen R May 5, 1913",
               "upload_type": "publication",
               "publication_type": "other",
               "journal_title": "Walter Deane correspondence",
               "publication_date": "1913-05-05",
               "referenceId": "https://www.biodiversitylibrary.org/part/326364",
               "filename": "bhlpart326364.pdf",
               "keywords": [
                 "Biodiversity",
                 "BHL-Corpus",
                 "Source: Biodiversity Heritage Library",
                 "Source: https://biodiversitylibrary.org",
                 "Source: BHL"
               ],
               "creators": [
                 {
                   "name": "Faber, Helen R."
                 }
               ],
               "related_identifiers": [
                 {
                   "relation": "isDerivedFrom",
                   "identifier": "https://linker.bio/line:hash://sha256/5fd5944b52b22efc56f901d96ff53a64c42e1f2264763e2f1074ac2c589e47cf!/L1-L7"
                 },
                 {
                   "relation": "isDerivedFrom",
                   "identifier": "https://www.biodiversitylibrary.org/part/326364"
                 },
                 {
                   "relation": "isAlternateIdentifier",
                   "identifier": "urn:lsid:biodiversitylibrary.org:part:326364"
                 },
                 {
                   "relation": "isPartOf",
                   "identifier": "hash://sha256/3983c9abbba981838de5d47a5dadf94c4afcea7df63486effb71d780e592ebe8"
                 },
                 {
                   "relation": "hasVersion",
                   "identifier": "hash://md5/7fddbf186c6bbddb0b49919fc340bb61"
                 },
                 {
                   "relation": "hasVersion",
                   "identifier": "hash://sha256/9b30af8f432b78e0d739b0457376dac998057a5b4b5fccd52b81560ec1f4f146"
                 }
               ]
             }
           }

                                  2025-07-09             PRESTON-RIS-STREAM(1)

Bugs

n/a

Assets 5

02 Jul 22:06

jhpoelen

0.10.13

eca2753

0.10.13

Features

n/a

Improvements

include man pages for sub-commands #343 ; add example sections for man preston-track and man preston-cat
follow multi-layer redirect A -> B -> C via alternateOf/seeAlso #336
allow for tracing gbif dataset DOIs to their reported dwc endpoint
add markdown export for google docs; remove epub and rtf

Example from man preston-track

preston track\
            https://doi.org/10.15468/w6hvhv\
            | preston dwc-stream\
            | head -1\
            | jq .\
            > specimen.json

Bugs

n/a

Assets 5

25 Jun 18:20

jhpoelen

0.10.12

5bdb961

0.10.12

Features

n/a

Improvements

n/a

Bugs

make sure that post-content tracking actions are executed using preston track [something], as well as when using the -f tracking option: preston track -f <(cat [something]) . related to #342 .

Assets 5

25 Jun 16:55

jhpoelen

0.10.11

3b93899

0.10.11

Features

n/a

Improvements

bhl pdf endpoints cannot be inferred from bhl item part id for extern… …ally hosted pdfs; related to #339
when encountering a sciELO resource with pdf request; check for javas… …cript-redirects and register associated content; #336 fyi @myrmoteras
favor alternate/seeAlso contentIds associated over content associated…… with original locations; related to #336
support copy-paste tracking of GBIF dataset via their landing page ht…
…tps://www.gbif.org/dataset/e4d3fc77-1d94-495b-96ff-3fe8b8f7a3bd fyi @seltmann

Example:

preston track https://www.gbif.org/dataset/e4d3fc77-1d94-495b-96ff-3fe8b8f7a3bd\
 | preston dwc-stream\
 | head -1\
 | jq .

yields

{
  "http://www.w3.org/ns/prov#wasDerivedFrom": "line:zip:hash://sha256/c2e545a14943beb12878b57e02f0718d3e784151b692ffdb51ebf08ffbb73dfe!/occurrence.txt!/L2",
  "http://www.w3.org/1999/02/22-rdf-syntax-ns#type": "http://rs.tdwg.org/dwc/terms/Occurrence",
  "http://rs.tdwg.org/dwc/text/id": "861c9d4e-d8e1-11e2-99a2-0026552be7ea",
  "http://rs.tdwg.org/dwc/terms/country": "MEXICO",
  "http://rs.tdwg.org/dwc/terms/minimumDepthInMeters": null,
  "http://rs.tdwg.org/dwc/terms/verbatimLongitude": "098 47 00 W",
  "http://rs.tdwg.org/dwc/terms/datasetName": "AMNH Hymenoptera",
  "http://rs.tdwg.org/dwc/terms/individualCount": "1",
  "http://rs.tdwg.org/dwc/terms/associatedOrganisms": null,
  "http://rs.tdwg.org/dwc/terms/stateProvince": "Tamaulipas",
  "http://rs.tdwg.org/dwc/terms/basisOfRecord": "PreservedSpecimen",
  "http://rs.tdwg.org/dwc/terms/infraspecificEpithet": null,
  "http://rs.tdwg.org/dwc/terms/occurrenceID": "861c9d4e-d8e1-11e2-99a2-0026552be7ea",
  "http://rs.tdwg.org/dwc/terms/municipality": null,
  "http://rs.tdwg.org/dwc/terms/locality": "Padilla",
  "http://rs.tdwg.org/dwc/terms/specificEpithet": "completa",
  "http://rs.tdwg.org/dwc/terms/island": null,
  "http://rs.tdwg.org/dwc/terms/family": "Apidae",
  "http://rs.tdwg.org/dwc/terms/verbatimEventDate": "5/17/1952",
  "http://rs.tdwg.org/dwc/terms/locationID": "0004be86-935b-4850-84fe-78ef6cbc2954",
  "http://rs.tdwg.org/dwc/terms/minimumElevationInMeters": null,
  "http://rs.tdwg.org/dwc/terms/phylum": "Arthropoda",
  "http://rs.tdwg.org/dwc/terms/typeStatus": null,
  "http://rs.tdwg.org/dwc/terms/class": "Insecta",
  "http://purl.org/dc/terms/license": "Attribution 4.0 International https://creativecommons.org/licenses/by/4.0/",
  "http://rs.tdwg.org/dwc/terms/preparations": "Pinned",
  "http://rs.tdwg.org/dwc/terms/county": null,
  "http://rs.tdwg.org/dwc/terms/associatedOccurrences": null,
  "http://rs.tdwg.org/dwc/terms/taxonID": "562d1f89-9d1b-4f4b-83a5-29f12f9e99f0",
  "http://rs.tdwg.org/dwc/terms/order": "Hymenoptera",
  "http://rs.tdwg.org/dwc/terms/genus": "Anthophorula",
  "http://rs.tdwg.org/dwc/terms/catalogNumber": "AMNH_BEE 00198554",
  "http://rs.tdwg.org/dwc/terms/institutionCode": "AMNH",
  "http://rs.tdwg.org/dwc/terms/kingdom": "Animalia",
  "http://rs.tdwg.org/dwc/terms/scientificName": "Anthophorula (Anthophorula) completa Cockerell, 1935",
  "http://rs.tdwg.org/dwc/terms/recordedBy": "M. A. Cazier, W. J. Gertsch & R. Schrammel",
  "http://rs.tdwg.org/dwc/terms/samplingProtocol": "Netting",
  "http://rs.tdwg.org/dwc/terms/verbatimLatitude": "24 01 00 N",
  "http://rs.tdwg.org/dwc/terms/subgenus": "Anthophorula",
  "http://rs.tdwg.org/dwc/terms/waterBody": null,
  "http://purl.org/dc/terms/rightsHolder": "American Museum of Natural History",
  "http://rs.tdwg.org/dwc/terms/sex": "Male",
  "http://rs.tdwg.org/dwc/terms/otherCatalogNumbers": null
}

Bugs

add default bhl keywords even when custom RIS keywords are present; r… …elated to #340; and #325 (comment)

Contributors

seltmann and myrmoteras

Assets 5

28 May 23:00

jhpoelen

0.10.10

5c7fce9

0.10.10

Features

n/a

Improvements

n/a

Bugs

make Zenodo existing record match by alternate identifier exact; #338

Assets 5

Releases: bio-guoda/preston

0.11.4

Features

Improvements

Bugs

Uh oh!

0.11.3

Features

Improvements

Bugs

Uh oh!

0.11.2

Features

Improvements

Bugs

Contributors

Uh oh!

0.11.1

Features

Improvements

Contributors

Uh oh!

0.11.0

Features

Improvements

Uh oh!

0.10.14

Features

Improvements

Bugs

Uh oh!

0.10.13

Features

Improvements

Bugs

Uh oh!

0.10.12

Features

Improvements

Bugs

Uh oh!

0.10.11

Features

Improvements

Bugs

Contributors

Uh oh!

0.10.10

Features

Improvements

Bugs

Uh oh!