Fix broken links from issue #714

content/clusters/cluster5.md

@@ -156,7 +156,7 @@ There are 6 sub-clusters which aim to further parse the learning and teaching pr
 
 * COS: [10 Tips for Making a Great Preregistration](https://cos.io/blog/10-preregistration-tips/)
 
-* COS: [8 Answers About Registered Reports and Research Preregistration](https://www.wiley.com/network/researchers/being-a-peer-reviewer/8-answers-about-registered-reports-research-preregistration-and-why-both-are-important)
+* COS: [8 Answers About Registered Reports and Research Preregistration](https://www.wiley.com/network/researchers/being-a-peer-reviewer/registered-reports-good-for-both-science-and-authors)
 
 <br>
 </div>

content/glossary/_create_glossaries.py

@@ -85,6 +85,26 @@ def process_references(references_text, apa_lookup, missing_refs_log=None):
 
     return list(dict.fromkeys(formatted_refs))
 
+def fix_bare_urls_in_parens(text):
+    """Convert bare URLs inside parentheses to markdown links.
+
+    Hugo's auto-linker treats (https://url.com) as a link to https://url.com)
+    — including the closing paren — which generates a broken %29 URL.
+    Wrapping the URL as [url](url) makes Hugo recognise it as a markdown
+    link so the ) is treated as closing punctuation, not part of the URL.
+
+    Skips URLs that are already inside a markdown link ([text](url)).
+    """
+    # Match ( optional-prefix https://url ) but only when ( is NOT preceded by ]
+    # (which would mean it's already the URL part of [text](url))
+    def _replace(m):
+        prefix = m.group(1) or ''
+        url = m.group(2)
+        return f'({prefix}[{url}]({url}))'
+
+    return re.sub(r'(?<!\])\(([^()]*?)(https?://[^\s)]+)\)', _replace, text)
+
+
 def safe_get(row, column, default=""):
     """Safely get a value from a pandas Series row"""
     try:
@@ -171,6 +191,7 @@ def clean_filename(title, max_length=200):
         definition = safe_get(row, f"{language_code}_definition" if language_code == "EN" else f"{language_code}_def")
         if not definition:
             continue
+        definition = fix_bare_urls_in_parens(definition)
 
         entry = {
             "type": "glossary",

content/glossary/_index.md

@@ -132,7 +132,7 @@ There are two outputs for this project. First, the entire glossary will appear o
 
 5. Contributions and Authorship
 
-In this project we will use the CREDIT taxonomy ([https://casrai.org/credit/](https://casrai.org/credit/)) in this prepared [contributors spreadsheet](https://docs.google.com/spreadsheets/d/1zvgAHWfTq6cbj3wMAr46zFU0w5JdV6796sM8FsO13y0). Please add your details (including ORCID) and contributions as you make them. This will facilitate the development of this project, allow us to easily communicate with all contributors, and ensure that all contributions are recognized. 
+In this project we will use the CREDIT taxonomy ([https://credit.niso.org/](https://credit.niso.org/)) in this prepared [contributors spreadsheet](https://docs.google.com/spreadsheets/d/1zvgAHWfTq6cbj3wMAr46zFU0w5JdV6796sM8FsO13y0). Please add your details (including ORCID) and contributions as you make them. This will facilitate the development of this project, allow us to easily communicate with all contributors, and ensure that all contributions are recognized. 
 
 Every few days, one of the team will review this document to finalize definitions that have had sufficient input. 
 
@@ -164,11 +164,11 @@ We invite several specific contributions: _original draft preparation_, and _rev
 
 **Term: CRediT**
 
-**Definition:**  The Contributor Roles Taxonomy (CRediT; https://casrai.org/credit/) is a high-level taxonomy, including 14 roles, that can be used to indicate the roles typically adopted by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output. They can be assigned multiple times to different authors and one author can also be assigned multiple roles. CRediT includes the following roles: Conceptualization, Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing. A description of the different roles can be found in the work of Brand et al., (2015).  
+**Definition:**  The Contributor Roles Taxonomy (CRediT; https://credit.niso.org/) is a high-level taxonomy, including 14 roles, that can be used to indicate the roles typically adopted by contributors to scientific scholarly output. The roles describe each contributor’s specific contribution to the scholarly output. They can be assigned multiple times to different authors and one author can also be assigned multiple roles. CRediT includes the following roles: Conceptualization, Data curation, Formal Analysis, Funding acquisition, Investigation, Methodology, Project administration, Resources, Software, Supervision, Validation, Visualization, Writing – original draft, Writing – review & editing. A description of the different roles can be found in the work of Brand et al., (2015).  
 **Related terms:** Authorship  
 **Alternative definition:** (if applicable)  
 **Related terms to alternative definition:** (if applicable)  
-**Reference(s):** Brand et al. (2015); Holcombe (2019); https://casrai.org/credit/  
+**Reference(s):** Brand et al. (2015); Holcombe (2019); https://credit.niso.org/  
 **Drafted by:** Sam Parsons  
 **Reviewed (or Edited) by:** Myriam A. Baum; Matt Jaquiery; Connor Keating; Yuki Yamada
 

content/glossary/apa_lookup.json

@@ -1,6 +1,6 @@
 {
   "CESSDA_DataManagement": "CESSDA. (n.d.). Data Management Expert Guide—CESSDA TRAINING. https://www.cessda.eu/Training/Training-Resources/Library/Data-Management-Expert-Guide",
-  "Stanford_DataManagementPlans": "Stanford Libraries. (n.d.). Data Management Plans | Stanford Libraries. https://library.stanford.edu/research/data-management-services/data-management-plans",
+  "Stanford_DataManagementPlans": "Stanford Libraries. (n.d.). Data Management Plans | Stanford Libraries. https://guides.library.stanford.edu/dmps",
   "EU_DataProtection": "European Commission. (n.d.). Data Protection. https://ec.europa.eu/info/law/law-topic/data-protection_en",
   "DataCite_MetadataSchema": "DataCite Schema. (n.d.). Datacite Metadata Schema. https://schema.datacite.org/",
   "cook1979quasi": "Cook, T. D., & Campbell, D. T. (1979). Quasi-Experimentation. Rand McNally.",
@@ -15,7 +15,7 @@
   "AlbayrakOkoroji2019": "Albayrak, N., & Okoroji, C. (2019). Facing the challenges of postgraduate study as a minority student. A Guide for Psychology Postgraduates, 63.",
   "AlbayrakAydemir2020": "Albayrak-Aydemir, N. (2020). The hidden costs of being a scholar from the global south. Retrieved from https://blogs.lse.ac.uk/highereducation/2020/02/20/the-hidden-costs-of-being-a-scholar-from-the-global-south/",
   "ALLEA2017": "Academies, A. A. E. (2017). The European Code of Conduct for Research Integrity. Revised Edition. Retrieved from https://allea.org/code-of-conduct/",
-  "AllenMcGonagleOConnellND": "Allen, L., & McGonagle-O’Connell, A. (n.d.). CRediT – Contributor Roles Taxonomy. Retrieved from https://casrai.org/credit/",
+  "AllenMcGonagleOConnellND": "Allen, L., & McGonagle-O’Connell, A. (n.d.). CRediT – Contributor Roles Taxonomy. Retrieved from https://credit.niso.org/",
   "Ali2021": "Ali, M. J. (2021). Understanding the Altmetrics. Seminars in Ophthalmology. https://doi.org/10.1080/08820538.2021.1930806",
   "APA2007": "American Psychological Association, Task Force on Socioeconomic Status. (2007). Report of the APA Task Force on Socioeconomic Status. American Psychological Association.",
   "Anderson2010": "Anderson, M. S., Ronning, E. A., Devries, R., & Martinson, B. C. (2010). Extending the Mertonian norms: Scientists’ subscription to norms of research. Journal of Higher Education, 81(3), 366–393. https://doi.org/10.1353/jhe.0.0095",
@@ -33,11 +33,11 @@
   "AnonFOSTERND": "Anon. (n.d.). Open Source in Open Science | FOSTER. Retrieved from https://www.fosteropenscience.eu/foster-taxonomy/open-source-open-science",
   "AnonDOIHandbook2019": "Anon. (2019). The DOI Handbook.",
   "AnonSherpaRomeoND": "Anon. (n.d.). Welcome to Sherpa Romeo - v2.sherpa. Retrieved from https://v2.sherpa.ac.uk/romeo/",
-  "AnonCodebookND": "Anon. (n.d.). What is a codebook?. Retrieved from https://www.icpsr.umich.edu/icpsrweb/content/shared/ICPSR/faqs/what-is-a-codebook.html",
+  "AnonCodebookND": "Anon. (n.d.). What is a codebook?. Retrieved from https://www.icpsr.umich.edu/sites/icpsr/posts/shared/what-is-a-codebook",
   "icpsr_codebook": "Inter-university Consortium for Political and Social Research. (2025). What is a Codebook? https://www.icpsr.umich.edu/web/ICPSR/cms/1983",
   "AnonDOIAPA2009_2020": "Anon. (n.d.). What is a digital object identifier, or DOI?. Retrieved from https://apastyle.apa.org/learn/faqs/what-is-doi",
   "AnonReportingGuidelineND": "Anon. (n.d.). What is a reporting guideline?. Retrieved from https://www.equator-network.org/about-us/what-is-a-reporting-guideline/",
-  "AnonImpact2021": "Anon. (2021). What is impact?. Retrieved from https://esrc.ukri.org/research/impact-toolkit/what-is-impact/",
+  "AnonImpact2021": "Anon. (2021). What is impact?. Retrieved from https://www.ukri.org/councils/esrc/impact-toolkit-for-economic-and-social-sciences/defining-impact/",
   "AnonOpenEducationND": "Anon. (n.d.). What is open education?. Retrieved from https://opensource.com/resources/what-open-education",
   "AnonPlagiarismND": "Anon. (n.d.). What is plagiarism?. Retrieved from https://www.scribbr.co.uk/category/preventing-plagiarism/",
   "AnonDataAvailabilityND": "Anon. (n.d.). Data availability statements. Retrieved from https://www.springernature.com/gp/authors/research-data-policy/data-availability-statements",
@@ -69,7 +69,7 @@
   "BenjaminiBraun2002": "Benjamini, Y., & Braun, H. (2002). John W. Tukey’s contributions to multiple comparisons. The Annals of Statistics, 30(6), 1576–1594. https://doi.org/10.1214/aos/1043351247",
   "BenoitEtAl2016": "Benoit, K., Conway, D., Lauderdale, B. E., Laver, M., & Mikhaylov, S. (2016). Crowd-sourced text analysis: Reproducible and agile production of political data. American Political Science Review, 110(2), 278–295. https://doi.org/10.1017/S0003055416000058",
   "BhopalEtAl1997": "Bhopal, R., Rankin, J., McColl, E., Thomas, L., Kaner, E., Stacy, R., Pearson, P., Vernon, B., & Rodgers, H. (1997). The vexed question of authorship: views of researchers in a British medical faculty. BMJ, 314, 1009–1012. https://doi.org/10.1136/bmj.314.7086.1009",
-  "LexicoBias": "BIAS | Definition of BIAS by Oxford Dictionary on Lexico.com also meaning of BIAS. (n.d.). Lexico Dictionaries | English. https://www.lexico.com/definition/bias",
+  "LexicoBias": "BIAS | Definition of BIAS by Oxford Dictionary on Lexico.com also meaning of BIAS. (n.d.). Lexico Dictionaries | English. https://www.oxfordlearnersdictionaries.com/definition/english/bias_1",
   "BIDSModalityND": "BIDS. (n.d.). Modality agnostic files. Retrieved from https://bids-specification.readthedocs.io/en/stable/03-modality-agnostic-files.html",
   "BIDSAbout2020": "BIDS. (2020). About BIDS. Retrieved from https://bids.neuroimaging.io",
   "BikEtAl2016": "Bik, E. M., Casadevall, A., & Fang, F. C. (2016). The prevalence of inappropriate image duplication in biomedical research publications. MBio, 7(3), e00809-16.",
@@ -156,7 +156,7 @@
   "Nature2006": "Correction or retraction? (2006). Nature, 444(7116), 123–124. https://doi.org/10.1038/444123b",
   "Corti2019": "Corti, L., Van den Eynden, V., Bishop, L., & Woollard, M. (2019). Managing and sharing research data: a guide to good practice. Sage.",
   "Cowan2020": "Cowan, N., Belletier, C., Doherty, J. M., Jaroslawska, A. J., Rhodes, S., Forsberg, A., & Logie, R. H. (2020). How do scientific views change? Notes from an extended adversarial collaboration. Perspectives on Psychological Science, 15(4), 1011–1025. https://doi.org/10.1177/1745691620906415",
-  "CRediT": "CRediT - Contributor Roles Taxonomy. (n.d.). Casrai. https://casrai.org/credit/",
+  "CRediT": "CRediT - Contributor Roles Taxonomy. (n.d.). Casrai. https://credit.niso.org/",
   "Crenshaw1989": "Crenshaw, K. W. (1989). Demarginalizing the Intersection of Race and Sex: A Black Feminist Critique of Antidiscrimination Doctrine. University of Chicago Legal Forum, 1989(8), 139–168.",
   "Cronbach1955": "Cronbach, L. J., & Meehl, P. E. (1955). Construct validity in psychological tests. Psychological Bulletin, 52(4), 281–302. https://doi.org/10.1037/h0040957",
   "Cronin2001": "Cronin, B. (2001). Hyperauthorship: A postmodern perversion or evidence of a structural shift in scholarly communication practices? Journal of the American Society for Information Science and Technology, 52(7), 558–569. https://doi.org/10.1002/asi.1097",
@@ -499,7 +499,7 @@
   "Ottmann2011": "Ottmann, G., Laragy, C., Allen, J., & Feldman, P. (2011). Coproduction in practice: Participatory action research to develop a model of community aged care. Systemic Practice and Action Research, 24, 413–427. https://doi.org/10.1007/s11213-011-9192-x",
   "Oxford_Dictionaries2017": "Bias—definition of bias in English. (2017). https://en.oxforddictionaries.com/definition/bias",
   "Oxford_Reference2017": "Reflexivity. (2017). http://www.oxfordreference.com/view/10.1093/acref/9780199599868.001.0001/acref-9780199599868-e-1530",
-  "CoProductionCollective": "Co-Production Collective. (n.d.). Our Approach. Co-Production Collective. https://www.coproductioncollective.co.uk/what-is-co-production/our-approach",
+  "CoProductionCollective": "Co-Production Collective. (n.d.). Our Approach. Co-Production Collective. https://www.coproductioncollective.co.uk/championing-co-production/what-does-co-production-mean-to-us",
   "Padilla1994": "Padilla, A. M. (1994). Research news and comment: Ethnic minority scholars; research, and mentoring: Current and future issues. Educational Researcher, 23(4), 24–27. https://doi.org/10.3102/0013189X023004024",
   "Page2021": "Page, M. J., Moher, D., Bossuyt, P. M., Boutron, I., Hoffmann, T. C., Mulrow, C. D., & McKenzie, J. E. (2021). PRISMA 2020 explanation and elaboration: updated guidance and exemplars for reporting systematic reviews. British Medical Journal, 372. https://doi.org/10.1136/bmj.n160",
   "Patience2019": "Patience, G. S., Galli, F., Patience, P. A., & Boffito, D. C. (2019). Intellectual contributions meriting authorship: Survey results from the top cited authors across all science categories. PLoS One, 14(1), e0198117. https://doi.org/10.1371/journal.pone.0198117",
@@ -539,7 +539,7 @@
   "Rakow2014": "Rakow, T., Thompson, V., Ball, L., & Markovits, H. (2014). Rationale and guidelines for empirical adversarial collaboration: A Thinking & Reasoning initiative. Thinking & Reasoning, 21(2), 167–175. https://doi.org/10.1080/13546783.2015.975405",
   "Ramagopalan2014": "Ramagopalan, S. V., Skingsley, A. P., Handunnetthi, L., Klingel, M., Magnus, D., Pakpoor, J., & Goldacre, B. (2014). Prevalence of primary outcome changes in clinical trials registered on ClinicalTrials.gov: A cross-sectional study. F1000Research, 3, 77. https://doi.org/10.12688/f1000research.3784.1",
   "RecommendedDataRepositories": "Scientific Data. (n.d.). Recommended Data Repositories. Scientific Data. https://www.nature.com/sdata/policies/repositories",
-  "ReplicationMarkets": "Replication Markets. (n.d.). Replication Markets – Reliable research replicates…you can bet on it. Replication Markets. https://www.replicationmarkets.com/",
+  "ReplicationMarkets": "Replication Markets. (n.d.). Replication Markets – Reliable research replicates…you can bet on it. Replication Markets. https://replicationmarkets.org/",
   "RepliCATS_project2020": "project, R. (2020). Collaborative Assessment for Trustworthy Science. The University of Melbourne. https://replicats.research.unimelb.edu.au/",
   "ReproducibiliTea_n_d": "ReproducibiliTea. (n.d.). https://reproducibilitea.org/",
   "Research_Data_Alliance2020": "Alliance, R. D. (2020). Data management plan (DMP) common standard. https://github.com/RDA-DMP-Common/RDA-DMP-Common-Standard",
@@ -677,11 +677,11 @@
   "Wasserstein2016": "Wasserstein, R. L., & Lazar, N. A. (2016). The ASA Statement on p-Values: Context, Process, and Purpose. The American Statistician, 70, 129–133. https://doi.org/10.1080/00031305.2016.1154108",
   "Webster2020": "Webster, M. M., & Rutz, C. (2020). How STRANGE are your study animals? Nature, 582, 337–340. https://doi.org/10.1038/d41586-020-01751-5",
   "Wendl2007": "Wendl, M. C. (2007). H-index: however ranked, citations need context. Nature, 449(7161), 403–403. https://doi.org/10.1038/449403b",
-  "ICPSR2021": "ICPSR. (n.d.). What is a Codebook? Retrieved 9 July 2021. https://www.icpsr.umich.edu/icpsrweb/content/shared/ICPSR/faqs/what-is-a-codebook.html",
+  "ICPSR2021": "ICPSR. (n.d.). What is a Codebook? Retrieved 9 July 2021. https://www.icpsr.umich.edu/sites/icpsr/posts/shared/what-is-a-codebook",
   "EQUATOR2021": "Network, T. E. (n.d.). What is a reporting guideline? Retrieved 10 July 2021. https://www.equator-network.org/about-us/what-is-a-reporting-guideline/",
   "CrowdsourcingWeek2021": "Week, C. (2021). What is Crowdsourcing? https://crowdsourcingweek.com/what-is-crowdsourcing/",
-  "EUDatasharing2021": "for Data Sharing, S. C. (n.d.). What is data sharing? Retrieved 11 July 2021. https://eudatasharing.eu/what-data-sharing",
-  "ESRC2021": "Economic, & Council, S. R. (n.d.). What is impact? Retrieved 8 July 2021. https://esrc.ukri.org/research/impact-toolkit/what-is-impact/",
+  "EUDatasharing2021": "for Data Sharing, S. C. (n.d.). What is data sharing? Retrieved 11 July 2021. https://futurium.ec.europa.eu/en/support-centre-data-sharing/pages/about",
+  "ESRC2021": "Economic, & Council, S. R. (n.d.). What is impact? Retrieved 8 July 2021. https://www.ukri.org/councils/esrc/impact-toolkit-for-economic-and-social-sciences/defining-impact/",
   "OpenDataHandbook2021": "Handbook, O. D. (n.d.). What is Open Data? Retrieved 9 July 2021. https://opendatahandbook.org/guide/en/what-is-open-data/",
   "OpensourceCom2021": "Opensource.Com. (n.d.). What is open education? Retrieved 9 July 2021. https://opensource.com/resources/what-open-education",
   "Whitaker2020": "Whitaker, K., & Guest, O. (2020).  #bropenscience is broken science. The Psychologist, 33, 34–37.",