up

Author: Adafede

_extensions/cito/_extension.yml

@@ -0,0 +1,6 @@
+title: cito
+author: Albert Krewinkel
+version: 0.0.1
+contributes:
+  filters:
+    - cito.lua

_extensions/cito/cito.lua

@@ -0,0 +1,233 @@
+-- Copyright © 2017–2022 Albert Krewinkel, Robert Winkler,
+--+          © 2023-2024 Albert Krewinkel, Egon Willighagen
+--
+-- This library is free software; you can redistribute it and/or modify it
+-- under the terms of the MIT license. See LICENSE for details.
+
+local _version = '1.1.0'
+local properties_and_aliases = {
+  agreesWith = {
+    'agreeWith',
+    'agree_with',
+    'agrees_with',
+  },
+  citation = {
+  },
+  cites = {
+  },
+  citesAsAuthority = {
+    'asAuthority',
+    'cites_as_authority',
+    'as_authority',
+    'authority'
+  },
+  citesAsDataSource = {
+    "asDataSource",
+    "dataSource",
+    'cites_as_data_source',
+    "as_data_source",
+    "data_source"
+  },
+  citesAsEvidence = {
+    'asEvidence',
+    'cites_as_evidence',
+    'as_evidence',
+    'evidence'
+  },
+  citesAsMetadataDocument = {
+    'asMetadataDocument',
+    'metadataDocument',
+    'cites_as_metadata_document',
+    'as_metadata_document',
+    'metadata_document',
+    'metadata'
+  },
+  citesAsPotentialSolution = {
+    'cites_as_potential_solution',
+    'potentialSolution',
+    'potential_solution',
+    'solution'
+  },
+  citesAsRecommendedReading = {
+    'asRecommendedReading',
+    'recommendedReading',
+    'cites_as_recommended_reading',
+    'as_recommended_reading',
+    'recommended_reading'
+  },
+  citesAsRelated = {
+    'cites_as_related',
+    'related',
+  },
+  citesAsSourceDocument = {
+    'cites_as_source_document',
+    'sourceDocument',
+    'source_document'
+  },
+  citesForInformation = {
+    'cites_for_information',
+    'information',
+  },
+  compiles = {
+  },
+  confirms = {
+  },
+  containsAssertionFrom = {
+  },
+  corrects = {
+  },
+  credits = {
+  },
+  critiques = {
+  },
+  derides = {
+  },
+  describes = {
+  },
+  disagreesWith = {
+    'disagrees_with',
+    'disagree',
+    'disagrees'
+  },
+  discusses = {
+  },
+  disputes = {
+  },
+  documents = {
+  },
+  extends = {
+  },
+  includesExcerptFrom = {
+    'excerptFrom',
+    'excerpt',
+    'excerpt_from',
+    'includes_excerpt_from',
+  },
+  includesQuotationFrom = {
+    'quotationFrom',
+    'includes_quotation_from',
+    'quotation',
+    'quotation_from'
+  },
+  linksTo = {
+    'links_to',
+    'link'
+  },
+  obtainsBackgroundFrom = {
+    'backgroundFrom',
+    'obtains_background_from',
+    'background',
+    'background_from'
+  },
+  providesDataFor = {
+  },
+  obtainsSupportFrom = {
+  },
+  qualifies = {
+  },
+  parodies = {
+  },
+  refutes = {
+  },
+  repliesTo = {
+    'replies_to',
+  },
+  retracts = {
+  },
+  reviews = {
+  },
+  ridicules = {
+  },
+  speculatesOn = {
+  },
+  supports = {
+  },
+  updates = {
+  },
+  usesConclusionsFrom = {
+    'uses_conclusions_from'
+  },
+  usesDataFrom = {
+    'dataFrom',
+    'uses_data_from',
+    'data',
+    'data_from'
+  },
+  usesMethodIn = {
+    'methodIn',
+    'uses_method_in',
+    'method',
+    'method_in'
+  },
+}
+
+local default_cito_property = 'citation'
+
+--- Map from cito aliases to the actual cito property.
+local properties_by_alias = {}
+for property, aliases in pairs(properties_and_aliases) do
+  -- every property is an alias for itself
+  properties_by_alias[property] = property
+  for _, alias in pairs(aliases) do
+    properties_by_alias[alias] = property
+  end
+end
+
+--- Split citation ID into cito property and the actual citation ID. If
+--- the ID does not seem to contain a CiTO property, the
+--- `default_cito_property` will be returned, together with the
+--- unchanged input ID.
+local function split_cito_from_id (citation_id)
+  local pattern = '^([^:]+):(.+)$'
+  local prop_alias, split_citation_id = citation_id:match(pattern)
+
+  if properties_by_alias[prop_alias] then
+    return properties_by_alias[prop_alias], split_citation_id
+  end
+
+  return default_cito_property, citation_id
+end
+
+--- Citations by CiTO properties.
+local function store_cito (cito_cites, prop, cite_id)
+  if not prop then
+    return
+  end
+  if not cito_cites[prop] then
+    cito_cites[prop] = {}
+  end
+  table.insert(cito_cites[prop], cite_id)
+end
+
+--- Returns a Cite filter function which extracts CiTO information and
+--- add it to the given collection table.
+local function extract_cito (cito_cites)
+  return function (cite)
+    local placeholder = cite.content
+    for _, citation in pairs(cite.citations) do
+      local cito_prop, cite_id = split_cito_from_id(citation.id)
+      store_cito(cito_cites, cito_prop, cite_id)
+      cite.content = cite.content:walk {
+        -- replace in placeholder
+        Str = function (str)
+          return str.text:gsub(citation.id, cite_id)
+        end
+      }
+      citation.id = cite_id
+    end
+
+    return cite
+  end
+end
+
+return {
+  {
+    Pandoc = function (doc)
+      --- Lists of citation IDs, indexed by CiTO properties.
+      local citations_by_property = {}
+      doc = doc:walk{Cite = extract_cito(citations_by_property)}
+      doc.meta.cito_cites = citations_by_property
+      return doc
+    end
+  }
+}

_quarto.yml

@@ -1,6 +1,8 @@
 ---
 project:
   type: website
+  pre-render:
+    - scripts/prerender.py
   render:
     - 404.qmd
     - index.qmd
@@ -10,6 +12,7 @@ project:
     - articles/first/*.qmd
     - articles/shared/*.qmd
     - articles/thesis.qmd
+    - posts/*.qmd
     - talks.qmd
     - talks/*.qmd
     - teaching.qmd

posts/2025-08-04_rogue-scholar.qmd

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+---
+author:
+  - name:
+      given: Adriano
+      family: Rutz
+    orcid: 0000-0003-0443-9902
+    number: 1
+    affiliations:
+      - ref: imsb
+affiliations:
+  - id: imsb
+    number: 1
+    name: ETH Zürich
+    department: Institute for Molecular Systems Biology
+    group: Zamboni
+    address: Otto-Stern-Weg, 3
+    city: Zürich
+    country: Switzerland
+    postal-code: 8093
+    ror: https://ror.org/03j5gm982
+categories:
+- Open Science
+citation: true
+# description: TODO
+filters:
+  - cito
+format: html
+google-scholar: true
+license: CC BY-SA
+title: "Open Science Upgrade: Now Adding DOIs through Rogue Scholar"
+bibliography: references.bib
+---
+
+I have finally set up **Rogue Scholar** on my Quarto-based website!
+Every post should now automatically get a DOI.
+
+This is something I have wanted to do for a long time, largely inspired by the tireless and consistent example set by [Egon Willighagen](https://scholia.toolforge.org/author/Q20895241) [@cites:willighagen2024; @cites:willighagen2024a; @cites:willighagen2025].
+
+It was today's post of [@cites_as_related:fenner2025] that finally motivated me to look into it again.
+That led me down a productive rabbit hole: first landing on [@obtains_background_from:voncsefalvay2023]'s excellent guide, and then [@uses_method_in:fruehwald2025]’s clear write-up, both of which made the process of integrating Rogue Scholar into a Quarto-based site surprisingly smooth.
+
+All the changes are documented in the following commit:
+
+<!-- INSERT LINK -->
+
+If you're using Quarto and care about attribution, long-term archiving, and DOIs and metadata, I highly recommend looking into [Rogue Scholar](https://rogue-scholar.org/).

posts/_metadata.yml

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+date: '2025-08-04'
+doi: 10.59350/38tz1-47k08

posts/references.bib

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+
+@misc{willighagen2025,
+	title = {Blog updates},
+	author = {Willighagen, Egon},
+	year = {2025},
+	month = {01},
+	date = {2025-01-19},
+	url = {http://dx.doi.org/10.59350/cf885-kee54}
+}
+
+@misc{willighagen2024a,
+	title = {FAIR blog-to-blog citations},
+	author = {Willighagen, Egon},
+	year = {2024},
+	month = {12},
+	date = {2024-12-30},
+	url = {http://dx.doi.org/10.59350/er1mn-m5q69}
+}
+
+@misc{willighagen2024,
+	title = {GoatCounter, Rogue Scholar and more new things},
+	author = {Willighagen, Egon},
+	year = {2024},
+	month = {07},
+	date = {2024-07-21},
+	url = {http://dx.doi.org/10.59350/8x2f1-h6d21}
+}
+
+@misc{fruehwald2025,
+	title = {Setting Up Rogue Scholar},
+	author = {Fruehwald, Josef},
+	year = {2025},
+	month = {07},
+	date = {2025-07-31},
+	url = {http://dx.doi.org/10.59350/3fp6d-e6z90}
+}
+
+@misc{voncsefalvay2023,
+	title = {Auto-DOI for Quarto posts via Rogue Scholar},
+	author = {von Csefalvay, Chris},
+	year = {2023},
+	month = {11},
+	date = {2023-11-13},
+	url = {http://dx.doi.org/10.59350/5hxdg-fz574}
+}
+
+@misc{fenner2025,
+	title = {Rogue Scholar citation tracking launches to production},
+	author = {Fenner, Martin},
+	year = {2025},
+	month = {08},
+	date = {2025-08-04},
+	url = {http://dx.doi.org/10.53731/zyg15-qv911}
+}