(log file starts at Sat Feb  7 03:25:02 UTC 2026)

[harvester info] --> Processing pagexml-tools (https://github.com/knaw-huc/pagexml) [Sat Feb  7 03:25:02 UTC 2026]

[harvester info] Git updating cached clone of https://github.com/knaw-huc/pagexml...

[harvester info] Found release v0.7.1

[harvester info] Using 'v0.7.1'

[harvester info] Git reference: v0.7.1

[harvester info] Scanning directory /tmp/codemeta-harvester.cache/pagexml-tools for harvestable resources...

[harvester info] found CITATION.cff for pagexml-tools, converting to codemeta

[harvester info] found python setup for pagexml-tools, converting to codemeta

[harvester info] Looking for license....

[harvester info] Found license MIT

[harvester info] Getting contributors from git...

[harvester info] Getting top contributor from git...

[harvester info] Git top contributor Bram Buitendijk <bram.buitendijk@di.huc.knaw.nl> will be assigned as author (and maintainer) if none are found in the metadata

[harvester info] Extracting last and first commit date from git log....

[harvester info] Date created: 2021-05-07T23:31:51Z+0200, date modified: 2025-05-26T11:30:18Z+0200

[harvester info] Querying Github/GitLab API (https://github.com/knaw-huc/pagexml)

[harvester info] Adding URL for found README: README.md

[harvester info] Found releaseNotes

[harvester info] Querying Zenodo API for DOI (access token provided)...

[harvester info] Looking for TRL information in README.md...

[harvester info] Looking for repostatus information in README.md...

[harvester info] Found repostatus https://www.repostatus.org/#active

[harvester info] Looking for continuous integration information in README.md...

[harvester info] Looking for documentation links in README.md...

[harvester info] Scraping title from https://pagexml.readthedocs.io/en/latest/

[harvester info] Found documentation at https://pagexml.readthedocs.io/en/latest/ : "name": "pagexml-tools — pagexml-tools 0.3.2 documentation",

[harvester info] Scraping title from https://pagexml.readthedocs.io/en/latest/?badge=latest

[harvester info] Found documentation at https://pagexml.readthedocs.io/en/latest/?badge=latest : "name": "pagexml-tools — pagexml-tools 0.3.2 documentation",

[harvester info] Falling back to git tag (v0.7.1) if no version number is specified...

[harvester info] Inferring repostatus information from git activity (used only as a fallback if not explicitly provided)...

[harvester info] Inferred repostatus https://www.repostatus.org/#active

[harvester info] Looking for repostatus information in README.md in master branch...

[harvester info] Found repostatus (master branch) https://www.repostatus.org/#active

[harvester info] Reconciliating: codemetapy  --baseuri https://tools.clariah.nl --baseuri https://tools.clariah.nl --includecontext --addcontext https://w3id.org/nwo-research-fields --addcontext https://w3id.org/research-technology-readiness-levels --addcontextgraph https://vocabs.dariah.eu/rest/v1/tadirah/data?format=text/turtle --trl --identifier "pagexml-tools" --codeRepository "https://github.com/knaw-huc/pagexml" --validate /etc/software.ttl --released --enrich --textv "Please consult the CLARIAH Software Metadata Requirements at https://github.com/CLARIAH/clariah-plus/blob/main/requirements/software-metadata-requirements.md for an in-depth explanation of any found problems" -O /tmp/out/pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/99-version.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/99-repostatus.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/90-authors.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/50-documentation.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/43-releasenotes.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/41-readme.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/40-gitapi.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/39-gitdate.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/32-contributors.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/29-license.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/20-python.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/12-citationcff.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/11-repostatus.pagexml-tools.codemeta.json /tmp/codemeta-harvester.cache//tmp/05-repostatus.pagexml-tools.codemeta.json 

-- begin log --

/usr/lib/python3.12/site-packages/pyshacl/extras/__init__.py:6: UserWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.

  import pkg_resources

Passed 14 files/sources but specified 0 input types! Automatically guessing types...

Detected input types: [('/tmp/codemeta-harvester.cache//tmp/99-version.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/99-repostatus.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/90-authors.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/50-documentation.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/43-releasenotes.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/41-readme.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/40-gitapi.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/39-gitdate.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/32-contributors.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/29-license.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/20-python.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/12-citationcff.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/11-repostatus.pagexml-tools.codemeta.json', 'json'), ('/tmp/codemeta-harvester.cache//tmp/05-repostatus.pagexml-tools.codemeta.json', 'json')]

Adding to contextgraph: /tmp/turtle

Initial URI automatically generated, may be overriden later: https://tools.clariah.nl/pagexml-tools

Processing source #1 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/99-version.pagexml-tools.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 1 new triples, total is now 2

Processing source #2 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/99-repostatus.pagexml-tools.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 1 new triples, total is now 3

Processing source #3 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/90-authors.pagexml-tools.codemeta.json

    Found main resource with URI https://tools.clariah.nl/pagexml-tools.topcontributor/snapshot

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 8 new triples, total is now 10

Processing source #4 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/50-documentation.pagexml-tools.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 8 new triples, total is now 18

Processing source #5 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/43-releasenotes.pagexml-tools.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 2 new triples, total is now 20

Processing source #6 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/41-readme.pagexml-tools.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 1 new triples, total is now 21

Processing source #7 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/40-gitapi.pagexml-tools.codemeta.json

    Found main resource with URI https://tools.clariah.nl/pagexml/snapshot

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 12 new triples, total is now 32

Processing source #8 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/39-gitdate.pagexml-tools.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] overriding old http://schema.org/dateCreated (2021-05-07T21:11:32Z -> 2021-05-07T23:31:51Z+0200)

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] overriding old http://schema.org/dateModified (2026-01-16T13:22:58Z -> 2025-05-26T11:30:18Z+0200)

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 2 new triples, total is now 32

Processing source #9 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/32-contributors.pagexml-tools.codemeta.json

    Found main resource with URI https://tools.clariah.nl/pagexml-tools.contributors/snapshot

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 32 new triples, total is now 59

Processing source #10 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/29-license.pagexml-tools.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] overriding old http://schema.org/license (http://spdx.org/licenses/MIT -> MIT)

[CODEMETA CORRECTION (https://tools.clariah.nl/pagexml-tools)] automatically converting license to spdx URI

[CODEMETA COMPOSITION (https://tools.clariah.nl/pagexml-tools)] processed 1 new triples, total is now 59

Processing source #11 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/20-python.pagexml-tools.codemeta.json

    Found main resource with URI https://tools.clariah.nl/pagexml-tools/0.7.1

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (pagexml-tools)] overriding old http://schema.org/author (https://tools.clariah.nl/stub/H-69742f0d19df8087 -> https://tools.clariah.nl/stub/H-3ceda685cc926360)

[CODEMETA COMPOSITION (pagexml-tools)] overriding old https://codemeta.github.io/terms/developmentStatus (https://www.repostatus.org/#active -> https://www.repostatus.org/#wip)

[CODEMETA COMPOSITION (pagexml-tools)] overriding old http://schema.org/name (pagexml -> pagexml-tools)

[CODEMETA COMPOSITION (pagexml-tools)] overriding old http://schema.org/version (v0.7.1 -> 0.7.1)

[CODEMETA COMPOSITION (pagexml-tools)] processed 116 new triples, total is now 159

Processing source #12 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/12-citationcff.pagexml-tools.codemeta.json

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (pagexml-tools)] overriding old http://schema.org/author (https://tools.clariah.nl/stub/H-3ceda685cc926360 -> https://tools.clariah.nl/stub/H6c8a2826f2547b54)

[CODEMETA COMPOSITION (pagexml-tools)] processed 15 new triples, total is now 170

Processing source #13 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/11-repostatus.pagexml-tools.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (pagexml-tools)] overriding old https://codemeta.github.io/terms/developmentStatus (https://www.repostatus.org/#wip -> https://www.repostatus.org/#active)

[CODEMETA COMPOSITION (pagexml-tools)] processed 1 new triples, total is now 170

Processing source #14 of 14

Parsing json-ld file from /tmp/codemeta-harvester.cache//tmp/05-repostatus.pagexml-tools.codemeta.json

    NOTE: Not a valid JSON-LD document, @context missing! Attempting to inject automatically...

    Injected (possibly temporary) URI https://tools.clariah.nl/pagexml-tools

[CODEMETA COMPOSITION (pagexml-tools)] processed 1 new triples, total is now 170

Remapping URI to (possibly) new identifier and version component: https://tools.clariah.nl/pagexml-tools -> https://tools.clariah.nl/pagexml-tools/0.7.1

[CODEMETA VALIDATION (pagexml-tools)] done

[CODEMETA ENRICHMENT (pagexml-tools)] automatically adding programmingLanguage Python derived from runtimePlatform Python

[CODEMETA ENRICHMENT (pagexml-tools)] considering first author as maintainer

VALIDATION https://tools.clariah.nl/pagexml-tools/0.7.1 #1: Info: Software source code *SHOULD* link to a continuous integration service that builds the software and runs the software's tests (This is missing in the metadata)

VALIDATION https://tools.clariah.nl/pagexml-tools/0.7.1 #2: Info: Reference publications *SHOULD* be expressed, if any (This is missing in the metadata)

VALIDATION https://tools.clariah.nl/pagexml-tools/0.7.1 #3: Info: The funder *SHOULD* be acknowledged (This is missing in the metadata)

VALIDATION https://tools.clariah.nl/pagexml-tools/0.7.1 #4: Info: A research domain *SHOULD* be expressed as a category using the NWO Research Fields vocabulary, if applicable (This is missing in the metadata)

VALIDATION https://tools.clariah.nl/pagexml-tools/0.7.1 #5: Info: A research activity *SHOULD* be expressed as a category using the TaDiRaH vocabulary (This is missing in the metadata)

-- end log --

[harvester info] Output written to /tmp/out/pagexml-tools.codemeta.json

[harvester info] <-- Finished processing pagexml-tools (https://github.com/knaw-huc/pagexml) [Sat Feb  7 03:25:24 UTC 2026]