bio-guoda/preston: 0.10.14

Features

n/a

Improvements

• support SciELO DOI inference https://github.com/bio-guoda/preston/issues/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