Releases · bio-guoda/preston

10 Jul 12:40

jhpoelen

0.10.14

61953df

0.10.14 Latest

Latest

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

28 May 21:59

jhpoelen

0.10.9

38a3e61

0.10.9

Features

n/a

Improvements

Bugs

support counting bytes in large files when preparing for Zenodo uploa……d; related to #337

Contributors

myrmoteras and alexlancaster

Assets 5

15 May 07:26

jhpoelen

0.10.8

a621a4f

0.10.8

Features

n/a

Improvements

n/a

Bugs

fixes related to newly introduced rpm package #332 big thanks to @alexlancaster for review comments and suggestions

Contributors

alexlancaster

Assets 5

14 May 11:56

jhpoelen

0.10.7

d4baf7a

0.10.7

Features

n/a

Improvements

populate journal issue as discussed in #327 suggested by Plazi's @myrmoteras
remove trailing comma for RIS author string; related to #326 suggested by Plazi's @myrmoteras
add biodiversity keyword for bhl related RIS entries; related to #328 suggested by Plazi's @myrmoteras
use constant for Zenodo relation types; related to #331
upgrade of jetty following GHSA-q4rv-gq96-w7c5 .
add integration for zenodo license mapping; related to #325 as needed for Plazi's @mymoteras BHL license normalization
introduce [preston zenodo --explicit-license-only]; related to #325
towards supporting preston rpm install #332 @alexlancaster

Example using explicit license and license mapping for Zenodo deposits -

export ZENODO_ENDPOINT=https://sandbox.zenodo.org
export ZENODO_TOKEN=[secret]

git clone https://github.com/jhpoelen/bhl-corpus-tracker
cd bhl-corpus-tracker

# generate test set up to 50 deposits
./sample.sh 50 

# generate the license map
cd target/[sample uuid]

cat zenodo-sample.json\
 | preston track

LICENSE_MAP_VERSION=$(../../ls-part-licenses.sh| preston track | grep hasVersion | tail -n1 | grep -oE "hash://sha256/[a-f0-9]{64}")

preston ls\
 | preston zenodo --explicit-license-only --license ${LICENSE_MAP_VERSION}

Bugs

n/a

Contributors

myrmoteras and alexlancaster

Assets 5

17 Apr 19:22

jhpoelen

0.10.6

7f4dd25

0.10.6

Features

n/a

Improvements

Bugs

n/a

Contributors

jhammock and KatjaSchulz

Assets 4

15 Jan 23:52

jhpoelen

0.10.5

a1d6641

0.10.5

Features

n/a

Improvements

implement workaround for un-escaped characters Zenodo file content url #317

instead of url offered by Zenodo API

https://zenodo.org/api/records/13505983/files/Thuiller%20et%20al.%20-%202006%20-%20INTERACTIONS%20BETWEEN%20ENVIRONMENT,%20SPECIES%20TRAITS,%20.]/content

the following url is constructed (note the escaped , and ]

https://zenodo.org/api/records/13505983/files/Thuiller%20et%20al.%20-%202006%20-%20INTERACTIONS%20BETWEEN%20ENVIRONMENT%2C%20SPECIES%20TRAITS%2C%20.%5D/content

Bugs

n/a

Assets 4

Releases: bio-guoda/preston

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!

0.10.9

Features

Improvements

Bugs

Contributors

Uh oh!

0.10.8

Features

Improvements

Bugs

Contributors

Uh oh!

0.10.7

Features

Improvements

Bugs

Contributors

Uh oh!

0.10.6

Features

Improvements

Bugs

Contributors

Uh oh!

0.10.5

Features

Improvements

Bugs

Uh oh!