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    ==Process==
    ==Process==
    * Initial seed:
    === Data collection and indexing ===
    ** Build pageset
    ; PubPeer Data (index_pubpeer.py)
    *** Pull usages of identifiers from Wikimedia Cloud DB Replicas
    * '''Initial Seed:'''
    *** Create database table (wikipedia):
    ** Starts from 2000-01-01
    **** id (incrementing key)
    ** Uses an initial large date window (2000-01-01 to 2014-12-31) followed by 30-day increments
    **** language_code
    ** API query handles pagination (per_page: 300) and automatically reduces the time window if the result set hits the 10,000-record limit to ensure no data is missed
    **** mw_page_id
    * '''Subsequent Builds:'''
    **** mw_page_title (probably should have a process to refresh this before the full process runs)
    ** Triggered via <code>python index_pubpeer.py --update</code>
    ** API query: <code>2006-01-01..2025-12-31</code>
    ** Identifies the latest_comment_date from the local database and starts fetching from that date to the present
    *** To prevent overloading the script, I'll probably end up going one month at a time, 2006-01-01..2006-01-31
    * '''Database Updates:'''
    ** Iterate through as many pages as needed to get to the end
    ** Updates the pubpeer_articles table
    ** Build internal database (pubpeer_articles table):
    ** Fields: id_pubpeer (URL), id_doi, id_pubmed, id_arxiv, title (truncated to 250 chars), and time_last_comment
    *** id_pubpeer (key)
    ; Wikipedia Citations (index_citations.py)
    *** id_doi (update on conflict)
    * '''Process:'''
    *** id_pubmed (update on conflict)
    ** Pulls current external links from Wikimedia Cloud DB Replicas for DOI (org.doi.), PubMed (gov.nih.nlm.ncbi.pubmed.), and arXiv (org.arxiv.)
    *** id_arxiv (update on conflict)
    ** Restricted to Main (0) and Draft (118) namespaces
    **Build minimal citations database (citations table):
    ** Matches these links against the local pubpeer_articles table
    ***id_pubpeer (key to pubpeer_articles table)
    * '''Database Updates:'''
    ***id_wiki_page (key to wikipedia table)
    ** '''wikipedia table:''' Stores language_code, mw_page_id, mw_page_title, and mw_talk_page_id. Page titles are refreshed during each run
    ***cited_id_type (integer)
    ** '''citations table:''' Maps id_pubpeer to id_wiki_page
    ****0 = unknown/other
    ** '''Stale Data:''' Automatically removes citations from the local database if the link has been removed from Wikipedia
    ****1 = doi
     
    ****2 = pubmed
    === Reporting and wiki updates ===
    ****3 = arxiv
    * '''Wiki Maintenance:'''
    ****Why not use enum? It's easier to add a new value Python-side than it is to carry out a database schema migration
    ** Automatically handles page moves and deletions via sync_wikipedia_titles.py before updating reports
    ***cited_id_value (string)
    * '''Report Generation (report.py):'''
    ***time_last_updated_table (<code>null</code> when created)
    ** '''Alerts Report:''' Lists new citations (time_last_updated_table IS NULL) or existing citations with new comments (time_last_comment > time_last_updated_table)
    ***time_last_talk_page_post (<code>null</code> when created)
    ** '''Most Affected Report:''' Lists Wikipedia articles with the highest number of unique PubPeer-commented citations
    *** time_most_recent_comment (on conflict, update if submitted > stored)
    ** '''Article List Reports:''' Large table and alphabetical subpages (/By article/A, etc.) listing all matched citations
    **Post initial report to wiki as a table
    ** '''Frequency Report:''' Aggregates by PubPeer article to show which research is most cited across Wikipedia
    **Post initial notification that the report is posted
    * '''User Interactions (Dismissals):''' (pending working implementation)
    * Subsequent builds:
    ** The bot reads the current wiki report and compares it to its previous version
    ** Get most recent <code>time_most_recent_comment</code> from database
    ** If an editor removes a row from a wiki table, the bot marks that citation as dismissed = TRUE in the database and stops reporting it
    ** API query: <code>that date...present day</code>
     
    ** Iterate through as many result pages as needed (probably only one page)
    === Database Schema (schema.sql) ===
    ** Submit into database, which should transparently handle conflicts
    * '''wikipedia:''' id, language_code, mw_page_id, mw_page_title, mw_talk_page_id, librarybase_id
    ** Build new wiki table based on citations database table
    * '''pubpeer_articles:''' id_pubpeer, id_doi, id_pubmed, id_arxiv, title, time_last_comment
    *** Check database for
    * '''citations:'''
    ****null time_last_updated_table
    ** Links articles to wiki pages
    ****time_most_recent_comment > time_last_updated_table
    ** cited_id_type: 1 (DOI), 2 (PubMed), 3 (arXiv)
    ** Come up with alerts describing changes to table.
    *** 0 is reserved for "other"
    *** Retire old notifications to a subpage
    ** time_last_updated_table: Tracks when the wiki report last included this citation
    *If/when talk page notifications are approved:
    ** time_last_talk_page_post: (Reserved for future talk page notifications)
    **Check database for
    ** dismissed: Boolean flag for editor-driven dismissals
    ***null time_last_talk_page_post
     
    ***time_most_recent_comment > time_last_talk_page_post
    === Post-Implementation Status ===
    **Queue up talk pages to notify
    * '''Talk Page Notifications:''' Code includes fields for tracking (time_last_talk_page_post), but the active workflow currently focuses on centralized reports (Wikipedia:PubPeer/*) rather than automated talk page posting
    **Check presence for message already on talk page.
    * '''Frequency of Runs:''' Designed to be run periodically (e.g., via cron) using the --update flag for index_pubpeer.py
    ***No message comment: add post to talk page
    * '''Dismissals Not Recognized:''' The logic to recognize user removals of report entries does not work yet and has been disabled.
    ***Presence of message comment: skip over talk page

    Revision as of 23:37, 13 January 2026

    API

    https://dashboards.pubpeer.com/docs/api#/operations/partner

    Relevant parameters:

    • page: start with 1 then iterate based on whether there are more results
    • per_page: set at maximum value 300
    • sort:
    • published_at: concerns when the document was published; I only care about comments

    Resources

    • Wikimedia Cloud Services
      • Toolforge: project "pubpeer"
        • Don't think it's being used for anything
      • Cloud VPS: project "wikicite"
        • VM wikicite-refsdb-proc-1.wikicite.eqiad1.wikimedia.cloud
        • Trove DB: ouqdvgrbzf3.svc.trove.eqiad1.wikimedia.cloud

    Process

    Data collection and indexing

    PubPeer Data (index_pubpeer.py)
    • Initial Seed:
      • Starts from 2000-01-01
      • Uses an initial large date window (2000-01-01 to 2014-12-31) followed by 30-day increments
      • API query handles pagination (per_page: 300) and automatically reduces the time window if the result set hits the 10,000-record limit to ensure no data is missed
    • Subsequent Builds:
      • Triggered via python index_pubpeer.py --update
      • Identifies the latest_comment_date from the local database and starts fetching from that date to the present
    • Database Updates:
      • Updates the pubpeer_articles table
      • Fields: id_pubpeer (URL), id_doi, id_pubmed, id_arxiv, title (truncated to 250 chars), and time_last_comment
    Wikipedia Citations (index_citations.py)
    • Process:
      • Pulls current external links from Wikimedia Cloud DB Replicas for DOI (org.doi.), PubMed (gov.nih.nlm.ncbi.pubmed.), and arXiv (org.arxiv.)
      • Restricted to Main (0) and Draft (118) namespaces
      • Matches these links against the local pubpeer_articles table
    • Database Updates:
      • wikipedia table: Stores language_code, mw_page_id, mw_page_title, and mw_talk_page_id. Page titles are refreshed during each run
      • citations table: Maps id_pubpeer to id_wiki_page
      • Stale Data: Automatically removes citations from the local database if the link has been removed from Wikipedia

    Reporting and wiki updates

    • Wiki Maintenance:
      • Automatically handles page moves and deletions via sync_wikipedia_titles.py before updating reports
    • Report Generation (report.py):
      • Alerts Report: Lists new citations (time_last_updated_table IS NULL) or existing citations with new comments (time_last_comment > time_last_updated_table)
      • Most Affected Report: Lists Wikipedia articles with the highest number of unique PubPeer-commented citations
      • Article List Reports: Large table and alphabetical subpages (/By article/A, etc.) listing all matched citations
      • Frequency Report: Aggregates by PubPeer article to show which research is most cited across Wikipedia
    • User Interactions (Dismissals): (pending working implementation)
      • The bot reads the current wiki report and compares it to its previous version
      • If an editor removes a row from a wiki table, the bot marks that citation as dismissed = TRUE in the database and stops reporting it

    Database Schema (schema.sql)

    • wikipedia: id, language_code, mw_page_id, mw_page_title, mw_talk_page_id, librarybase_id
    • pubpeer_articles: id_pubpeer, id_doi, id_pubmed, id_arxiv, title, time_last_comment
    • citations:
      • Links articles to wiki pages
      • cited_id_type: 1 (DOI), 2 (PubMed), 3 (arXiv)
        • 0 is reserved for "other"
      • time_last_updated_table: Tracks when the wiki report last included this citation
      • time_last_talk_page_post: (Reserved for future talk page notifications)
      • dismissed: Boolean flag for editor-driven dismissals

    Post-Implementation Status

    • Talk Page Notifications: Code includes fields for tracking (time_last_talk_page_post), but the active workflow currently focuses on centralized reports (Wikipedia:PubPeer/*) rather than automated talk page posting
    • Frequency of Runs: Designed to be run periodically (e.g., via cron) using the --update flag for index_pubpeer.py
    • Dismissals Not Recognized: The logic to recognize user removals of report entries does not work yet and has been disabled.
    Retrieved from "https://librarybase.org/w/index.php?title=Project:Analytics/PubPeer&oldid=247980"