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About:Pharmacopedia.ext

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Revision as of 08:16, 22 May 2026 by MDElliottMD (talk | contribs) (Document HYD-PCP, the thirteenth assessment (the wellbeing check-in shipped in v0.9.8.0))

Pharmacopedia extension specification

Version: 0.9.8.0 · Requires: MediaWiki >= 1.46.0 · PHP >= 8.5 Author: MDElliottMD · License: GPL-2.0-or-later Source: /var/www/mediawiki/extensions/Pharmacopedia/

The Pharmacopedia extension turns a MediaWiki install into a structured, community-edited medicine reference with rich user-profile, assessment, life-story, and visibility-sharing infrastructure. It adds parser tags, special pages, API modules, two dark skins, a chip-picker / autosave UI framework, a vis-timeline-based visual life timeline, a granular per-record sharing subsystem, an observer-perspective subsystem, a token-gated subsystem for administering assessments to people outside the wiki, a two-origin diptych front-of-house, and a database schema that together support:

  • Structured medicine pages via the {{MedTemplate}} template
  • Per-user rating on effects, problems, titration strategies, anecdotes, and drug-drug interactions (continuous 0–100 sliders, ±100 valence; no 0–5 likert anywhere)
  • Binary AND choice/multi voting on arbitrary content (type="single" / type="multi" with 2-5 options, results-visibility policy per element)
  • Two-perspective data capture (personal vs. provider) wherever clinically meaningful
  • User profile with dimensional personality / autism assessments (CATI, CAT-Q, MBTI, Enneagram, PID-5-BF, OCEAN/BFI-10) and rich auto-generated reports
  • Further self-report instruments (BPNS, NFCS, OCI-PCP, WHOQOL-BREF) and the HYD-PCP wellbeing check-in, on the same auto-scored, report-bearing pattern
  • ADHD screening (ASRS and AMAAS-SR) plus a Formal testing log of standardized-test scores, every score field carrying its own visibility
  • Diagnosis autocomplete backed by ~41,500 ICD-10-CM, ICD-11, and DSM-5 codes
  • Life-story timeline: visual swimlanes (vis-timeline 7.7.3, vendored Apache-2.0) plus a synchronized trait-trajectory overlay (vis.Graph2d); card-list view alongside; quick-add free-text observation parser; range-date episode form with severity slider
  • Per-record sharing subsystem: rule types include public, private, users, cohort, link_token, reciprocal; time-bounded; audit log of who-viewed-what; bulk free-text → structured ref upgrader; privacy mode that disables legacy fallback
  • Observer perspectives: token-gated, no-account second-party input on something a user owns, under a two-gate consent model
  • Administer to others: send any registered assessment scale to people outside the wiki by one-time link, collect their results, and follow them over time, under per-owner public-key encryption with an optional zero-knowledge passphrase mode
  • Two-origin diptych: the Main Page and Category index render as chromeless full-viewport splashes giving the pharmaceutical and plant origins equal face
  • Chip-picker / autosave / slider-precise-input UI framework shared across editor surfaces
  • Date + time + range kit: PCPDatePicker (point/range/possibility), PCPTimePicker (fuzzy time-only: "4p", "noon", "quarter past 6")
  • Verified-provider role with document-based verification
  • Fail-closed ClamAV scan on every image / file upload (hard project rule)
  • Per-user research_id (stable 10-char hex, opaque, never reassigned) for de-identified research participation

Precision doctrine

A standing design rule (memorialised 2026-05-17) that shapes every storage / UI decision in the extension:

  • No bucketing where a number or free-text will do. Income is numeric + currency, not a 5-band dropdown. Education keeps the bucketed dropdown and adds numeric years of schooling + free-text field of study.
  • No single-select where multi-select reflects reality. Languages, gender identities, ethnicities, pronouns, religion, marital status, stop-reasons, all use chip-pickers (with optional severity per chip where relevant).
  • No forced category where a continuous score works. All assessments (Enneagram 9 type sliders, MBTI 4 dichotomy sliders, OCEAN 5 trait sliders, CATI/CAT-Q/PID-5-BF items) use continuous 0–100 sliders, never radio buttons or button rows. Valence is ±100, not ±3.
  • Storage in canonical form, UI converts at display. Heights stored cm regardless of user's preferred unit (cm or ft+in); ICD codes stored as ISO; date capture as range / possibility-mix JSON.
  • Browser auto-fill as suggestion only. Country chip pre-fills from navigator.language; languages from navigator.languages; time zone from Intl.DateTimeFormat().resolvedOptions().timeZone. User can always edit or remove.
  • Always allow custom free-text where the curated list might miss someone. Chip-pickers accept Enter-to-add custom chips for all picklists except ISO-coded ones (country, language).

High-level architecture

  • Backend (PHP): includes/, one class per parser tag, store, special page, or API module. Auto-loaded under MediaWiki\Extension\Pharmacopedia\. Assessment classes under includes/Assessments/. API modules under includes/Api/.
  • Frontend (JS / CSS): multiple ResourceModules per surface area:
    • ext.pharmacopedia: main IIFE (chip-picker, dx autocomplete, BFI-10 compute, vote logic for both binary and choice/multi)
    • ext.pharmacopedia.styles: base extension stylesheet (self-hosted Geist / Newsreader / Source Serif fonts, core component styling)
    • ext.pharmacopedia.blocksave: debounced autosave per block (race-safe)
    • ext.pharmacopedia.bounceback: preserves the reader's scroll position across POST-then-reload actions via sessionStorage
    • ext.pharmacopedia.confirmdelete: styled red warning prompt replacing window.confirm() on destructive actions
    • ext.pharmacopedia.datepicker + .datepicker.styles: range / possibility-mix date widget
    • ext.pharmacopedia.timepicker + .timepicker.styles: time-only widget (fuzzy parsing, extracted from DatePicker)
    • ext.pharmacopedia.share: per-record share dialog (People / Link / Cohorts tabs)
    • ext.pharmacopedia.perspective: observer-perspective form enhancement (slider readout, progress, consent/delete confirm)
    • ext.pharmacopedia.administer: the administer-to-others surfaces (take-flow slider readout + "Not sure" toggling, owner-hub styling)
    • ext.pharmacopedia.observation: quick-add observation textarea + live preview
    • ext.pharmacopedia.refupgrade: bulk linker for free-text → structured refs
    • ext.pharmacopedia.vis-timeline-vendor: vis-timeline 7.7.3 (vendored)
    • ext.pharmacopedia.lifetimeline: visual life-story timeline + swimlanes + toolbar
    • ext.pharmacopedia.lifegraph: trait-trajectory overlay (vis.Graph2d) synced to timeline
    • ext.pharmacopedia.kitsync: glue that propagates kit-widget changes into legacy hidden inputs + drives privacy-mode toggle
    • ext.pharmacopedia.frontpage / ext.pharmacopedia.categoryindex: the two diptych splash modules, each self-contained so it renders with no skin loaded
    • ext.pharmacopedia.appearance: the collapsible Appearance rail (reader text-size control)
    • ext.pharmacopedia.skin.plants / ext.pharmacopedia.skin.fungi: the earth-toned plants-skin overlay and the fungi sub-skin override layer
  • Schema: sql/, roughly three dozen core tables plus migration patches. Picked up via the LoadExtensionSchemaUpdates hook.

Skins, layout, and the Appearance rail

Two skins. Every page renders in one of two dark skins. The default pharmaceutical skin is the violet-on-near-black clinical identity. The plants skin is an earth-toned treatment (ext.pharmacopedia.skin.plants) applied to plant-origin medicine pages. Both skins are dark; there is no light mode. The fungi sub-skin (ext.pharmacopedia.skin.fungi) is a specialization of the plants skin for fungal medicine pages: a fungus page carries both the pcp-skin-plants and pcp-skin-fungi body classes, loading the plants base plus a fungi override layer (a damp cool-dark palette, a spore-dust grain, the mushroom mark, fungi section-marker hues); everything else inherits from the plants skin.

Hooks::resolvePcpSkin picks the skin. A content (medicine) page is read by its OWN DIRECT origin category: a direct Category:Fungi tag gives the fungi sub-skin (checked first), a direct Category:Plants tag gives the plants skin, anything else pharma. There is no recursive category walk, so a page sitting inside a dual-parented class category (Category:Psychedelics parents under both origins) is skinned by its own origin tag, not by its class. A category page has no single direct origin, so it is resolved by walking its category chain (plants only when the chain is purely plant).

Full-width layout. The content frame runs edge to edge rather than in a fixed-width column; prose is held to a readable measure by its own constraint, and the layout gutters are set by layout tokens.

The Appearance rail. A collapsible rail (ext.pharmacopedia.appearance) gives the reader appearance controls, currently a text-size control. The chromeless diptych splashes suppress the rail.

Front-of-house: the diptych

The Main Page and the Category index are built as a two-origin diptych: a pharmaceutical column and a plant column side by side, the two origins of the materia medica given equal face. Both render as chromeless full-viewport splashes. A body.pcp-diptych-page class, added by the BeforePageDisplay hook on those two pages, hides all Vector chrome, and the module supplies its own topbar and footer. A full-height two-origin split gradient runs the page edge to edge, the pharma dark on the left half and the plant dark on the right, a 1px seam down the middle, so the diptych reads top to bottom with no separate bands.

Two parser tags generate the diptych from live wiki data:

  • <frontpage> (FrontPageTag), the Main Page: a featured medicine and featured plant medicine, class / Pharmako-volume browse lists, recently-updated lists, portal links, a status strip.
  • <categoryindex> (CategoryIndexTag), the Category index: the pharmacological classes and the plant lineages as two side-by-side trees.

DiptychChrome supplies the shared topbar and footer for both. The modules are ext.pharmacopedia.frontpage and ext.pharmacopedia.categoryindex; each carries its own palette tokens so the splash renders correctly with no skin stylesheet loaded.

Parser tags

Registered via Hooks::onParserFirstCallInit:

Tag Purpose Class
<vote> after-vote\|hidden" for tally-visibility policy. VoteTag
<effect> Therapeutic or adverse effect; patient + provider perspectives; provider freq slider 0–100; shared valence slider ±100 EffectTag
<discuss> Threaded comment widget CommentTag
<effectsummary> Roll-up aggregate header EffectSummaryTag
<titration> Titration strategy card with up/down vote TitrationTag
<anecdote> Personal or provider story with up/down vote AnecdoteTag
<problem> A problem the medicine addresses; 0–100 efficacy likert slider + "don't know" toggle ProblemTag
<pharmaInteractions/> Self-closing; renders the Interactions section for the current page InteractionTag
<pharmaExperience/> Self-closing; renders the Experience report form (efficacy, burden, dose, route, schedule, stop-reasons) ExperienceTag
<pharmaLiterature/> Self-closing; per-medicine "Relevant literature" section: approved pcp_literature entries plus a collapsed submission form LiteratureTag
<classGrid/> A grid of medicine-class categories (those tagged Category:MedCategory); count + exclude attributes; 5-minute cache ClassGridTag
<classTree/> The MedCategory classes as a hierarchy with member counts; exclude attribute; 5-minute cache ClassTreeTag
<frontpage/> The two-origin diptych Main Page (see Front-of-house) FrontPageTag
<categoryindex/> The two-origin diptych Category index CategoryIndexTag

All non-self-closing rating tags take a slug argument and (where relevant) a title, label, author, ref, or perspective.

Tag wikitext examples

<problem slug="depression" title="Major depressive disorder"
  author="MDElliottMD">First-line for moderate to severe MDD.</problem>

<effect slug="nausea" label="Nausea"/>

<effect ref="hyperkalemia"/>   <!-- ref to global effect library -->

<titration slug="slow-start-elderly" title="Slow start (elderly)"
  author="MDElliottMD">Begin at 10 mg q AM; titrate by 10 mg every 14 days.</titration>

<anecdote slug="qi8sg2" perspective="provider"
  author="MDElliottMD">One patient developed serotonin syndrome at week 3...</anecdote>

<pharmaInteractions/>
<pharmaExperience/>

<vote slug="fav-color" type="single" options="Red; Blue; Green">
What's your favorite color?</vote>

<vote slug="side-effects" type="multi" results="after-vote"
  options="Dry mouth; Insomnia; Anxiety; Headache; None">
Which side effects did you experience?</vote>

Voting / rating semantics

Element Scale Perspectives Storage
Vote tag (binary) +1 / −1 binary single pcp_votes.v_value
Vote tag (single-choice) one of 2-5 options single pcp_votes.v_choices (CSV index)
Vote tag (multi-choice) any subset of 2-5 options single pcp_votes.v_choices (CSV indices)
Titration +1 / −1 binary single pcp_votes
Anecdote +1 / −1 binary single (perspective is metadata) pcp_votes
Problem (efficacy likert) 0–100 continuous slider, optional "Don't know" (-1) single pcp_likert_reports
Effect (patient) experienced ∈ {yes, no, unsure} + valence ±100 slider patient pcp_effect_reports (perspective=1)
Effect (provider) frequency 0–100 continuous slider + "Don't know" (-1) + valence ±100 slider provider pcp_effect_reports (perspective=2)
Interaction experience 1–5 + valence ±100 slider + optional note user + provider, separate aggregates pcp_interaction_reports

Choice / multi vote elements expose per-option tallies via tallyChoices() on demand. Per-option bars render inline in the picker. The results attribute gates tally visibility:

  • live (default), tally always visible
  • after-vote, tally hidden until viewer has voted
  • hidden, tally never shown (only options + "thanks" on submit)

Server-side options-hash (ve_options_h) detects post-vote option-list edits; the API rejects new votes whose submitted hash doesn't match the live one. Voter identities are stored as HMAC-SHA256 (v_voter_hash) so admins reading the DB cannot map votes to user accounts without the HMAC secret.

Server-side aggregates: n, mean of the rating field, and (for interactions) severe = (vmean ≤ −83.0) (rescaled from the original ±3-scale −2.5). Aggregates are recomputed and returned by every report-submit API call so the row re-renders in place without a page reload.

Effect bucketing

When a wiki <ul> contains only <effect> cards, JavaScript groups them into buckets by the provider frequency mean (data-fmean):

Bucket fmean band Default state
Common > 20 expanded, always visible
Uncommon > 5 and ≤ 20 collapsed
Rare ≤ 5, provider vmean > −83 collapsed
Rare but Severe ≤ 5 and vmean ≤ −83 expanded by default, red highlight
Not yet rated no provider data (n=0) collapsed, only renders if non-empty

The vmean ≤ −83 threshold is also the trip-wire for the "severe" red treatment on interaction rows.

User profile

Special:MyProfile is the user-facing editor for everything personal. Every block on it autosaves on a 800 ms debounce (see Autosave infrastructure).

Visible at top: a Privacy-mode panel toggling whether legacy public fallback applies (privacy-mode ON = only explicit share rules grant access; OFF = the field-level pf_visibility enum applies).

🔗 Share chips appear in each fieldset legend (Demographics, Diagnoses, Medicines) so the owner can scope a share-rule to that namespace via the modal Share dialog.

Block list

  • Identity (display alias, default attribution, experience-report visibility, read-only Research ID badge)
  • Demographics (full chip-picker rebuild, see below)
  • Personality (Big Five OCEAN sliders + collapsible assessments)
  • Enneagram (9 type sliders + 45-item screening test)
  • MBTI (4 dichotomy sliders + 32-item OEJTS test)
  • Self-report assessments (PID-5-BF, CATI, CAT-Q, BPNS, NFCS, OCI-PCP, WHOQOL-BREF, HYD-PCP, each a collapsible inline test)
  • ADHD screening (ASRS adult-ADHD screener and AMAAS-SR attention self-report, each a collapsible inline test)
  • Formal testing (a log of standardized-test scores; raw score, percentile and pass/fail each carry their own privacy setting)
  • Diagnoses (multi-row with ICD-10-CM + ICD-11 autocomplete, severity slider 0–100, disability slider 0–100, status, origin, dates, notes)
  • Medicines I have tried (multi-row with med-name autocomplete, dose, route 16-option dropdown, schedule with datalist suggestions, efficacy + burden sliders 0–100, periods via date-picker)

Demographics (chip-picker / structured-widget rebuild)

All categorical demographics use the chip-picker widget (single or multi, with optional primary marker, optional custom free-text). All quantitative demographics use numeric inputs or structured composite widgets.

  • Birthday DatePicker (single / range / possibility-mix). Setting (or changing) the birthday auto-syncs a TYPE_STORY life event tagged auto-birth titled 'Born!' on the life-story timeline. Subsequent birthday edits move ONLY the event's date; user edits to title, body, tags, images are preserved.
  • Sex assigned at birth single-select (clinical category)
  • Gender identity multi-select chip-picker, 27 common terms + custom
  • Pronouns multi-select chip-picker, 17 common sets + custom
  • Ethnicity / race multi-select chip-picker, 23 broad categories + custom
  • Country of residence chip-picker single-value, ISO 3166 list (~100 entries), auto-suggested from navigator.language
  • Languages chip-picker multi-select with ★ primary marker, ISO 639-1 list (~70 entries with endonyms), auto-suggested from navigator.languages
  • Height / weight unit toggle (Metric cm/kg or US ft+in/lb); stored canonically as cm/kg regardless
  • Handedness single-select (3 options)
  • Smoking structured widget: status + cigs/day + years smoked + quit date (PCPDatePicker); auto-computes pack-years
  • Alcohol structured widget: drinks/week + typical drink type + max one occasion
  • Education bucketed highest-level + numeric years + free-text field of study
  • Employment bucketed status + free-text occupation + numeric hours/week
  • Income numeric amount + currency selector (20 options) + individual/household scope
  • Marital / relationship status chip-picker single + custom
  • Religion / spirituality chip-picker single + custom, 36 traditions + secular stances
  • Housing chip-picker single + custom
  • Number of children numeric
  • Time zone free text, auto-detects IANA TZ on first load if empty
  • Chronotype / sleep schedule two PCPTimePicker widgets (typical bedtime, typical wake; fuzzy parsing accepts "10p", "bedtime", "quarter past 6")
  • Political orientation two-axis compass sliders (economic ±100, social ±100)

Diagnosis subsystem

Diagnoses are stored in pcp_profile_diagnoses with autocomplete backed by pcp_diagnosis_abbreviations (~41,500 rows):

System Rows Notes
ICD-10-CM 25,542 CMS FY2026 valid-codes file, chapters A B C D E F G H I J K L M N O P Q R U + 553 friendly-alias rows (mdd, adhd, stroke, htn, etc.)
ICD-11 15,823 WHO MMS Apr 2026 linearization, chapters 01–24 except billing (22) / external causes (23) / extension modifiers (X) / functioning assessment (V) + 361 friendly-alias rows
DSM-5 32 Legacy hand-seed for codes without ICD equivalents
Other 34 somatic, unofficial, ICD-10 (WHO), instrument

Skipped intentionally: ICD-10-CM S/T (injury body) ~41k codes, V/W/X/Y (external causes) ~7.5k codes; ICD-11 chapter 22 (injury), 23 (external causes), 25 (special purposes), V (functioning scales), X (17.7k extension modifiers). These are billing scaffolding, not diagnoses.

Autocomplete via action=pharmacopediadxsearch, multi-token AND search (e.g. "ADHD inattentive" matches the F90.0 row that contains both substrings); ORDER BY FIELD(da_system, 'ICD-10-CM', 'ICD-11', 'DSM-5', ...) so ICD-10-CM leads, then ICD-11, then everything else.

Self-report assessments

The six dimensional assessments all have continuous-slider items, a "Not sure" toggle per item, auto-computed subscale + total scores, and a rich auto-generated report at Special:MyAssessment/{key}:

Assessment Items Score range Cutoffs / threshold Report
CATI 42 (6 subscales) 1–5 per item, sum per subscale 148 / 139 / 141 / 156 (English 2025 gender-specific) gender-specific scoring against English 2025 normative tables (12,253-row CatiNorms.php from OSF supplementary)
CAT-Q 25 (3 subscales) 1–7 per item, sum per subscale Total ≥ 110 + per-subscale cutoffs (NeurodivUrgent recalibration) subscale narratives, top-item analysis
PID-5-BF 25 (5 domains) 0–3 per item, mean per domain mean ≥ 2.0 per domain domain narratives, cross-system mapping (DSM-5 AMPD ↔ ICD-11 PD ↔ Big Five)
MBTI 32 OEJTS items + 4 direct dichotomy sliders ±2 per axis none (dimensional treatment, no forced categorisation) 4-axis Position column with letter + strength + bar, cognitive function stack, Big Five mapping, top-item analysis
Enneagram 45 (5 per type × 9 types) 0–100 per type none (no clinical cutoffs for typology) hero banner (primary + wing + tritype), 9-bar profile, primary deep-dive, wing analysis, centers, Hornevian + Harmonic groups, stress / growth lines, cross-system map (Big Five, MBTI)
OCEAN (Big Five) 5 direct sliders + optional BFI-10 (10 items) 0–100 per trait none (personality, not pathology) trait deep-dives (high / mid / low at your score), BFI-10 item table, cross-system mapping (MBTI ↔ Enneagram ↔ PID-5-BF) pulling live data from the profile

Five further self-report instruments are available on the same collapsible-inline-test, auto-scored, report-bearing pattern:

Instrument Items Structure Measures
BPNS-PCP 21 3 subscales (Autonomy, Competence, Relatedness), 7-point Likert basic psychological need satisfaction, per Self-Determination Theory
NFCS-PCP 15 5 facets (Order, Predictability, Decisiveness, Ambiguity intolerance, Closed-mindedness), 6-point Likert need for cognitive closure (brief 15-item Roets & Van Hiel form)
OCI-PCP 18 6 subscales (Washing, Obsessing, Hoarding, Ordering, Checking, Neutralizing), 0–4 per item; screening cutoff total ≥ 21 obsessive-compulsive symptoms, adapted from the OCI-R
WHOQOL-BREF-PCP 26 4 domains (Physical, Psychological, Social, Environment) + 2 overall items, 5-point Likert quality of life
HYD-PCP 8 8 single-item domains, each one bipolar slider (−100 really poorly to +100 really well); no subscales, no cutoffs everyday wellbeing, re-taken and watched over time; a locally authored check-in, not validated

All assessment items submit raw responses to pcp_profile_fields under namespace {key}_raw (e.g. cati_raw); the computed scores live under namespace {key} with keys like subscale_SOC, total, plus a taken_at timestamp. Re-scoring happens automatically on every save (autosave fires scoreResponses() on the full raw set, skipping "unsure" rows). Each completed assessment also auto-upserts a Life-story keyframe row (see Life-story timeline) so trajectories plot over time.

All thirteen assessments (the six dimensional, these five, and the two ADHD screeners below) are registered in AssessmentRegistry and so can also be administered to outside respondents (see Administer assessments to others).

ADHD screening

Two attention / ADHD instruments sit alongside the dimensional assessments, each a collapsible inline test on Special:MyProfile and a card render on the public profile:

  • ASRS (Adult ADHD Self-Report Scale, Part A): a 6-item binary screener. The card counts how many of the 6 cardinal items fall in the screening range; 4 or more is a positive screen. The public profile renders it as a verdict card, a screen-positive or screen-negative result word with a 6-cell cardinal-item strip and a screening-result detail line.
  • AMAAS-SR (a 30-item experimental attention self-report): three symptom subscales, inattention, hyperactivity and impulsivity, each scored as a percentage of the subscale maximum. The public profile renders it as a featured radar card, a 3-axis radar carrying a deliberately arbitrary 66.66% threshold triangle that is labelled experimental and not a validated cutoff. AMAAS has no validated norms; the card discloses this in plain sight rather than presenting a clinical cutoff.

Both instruments store responses in pcp_profile_fields under the asrs and amaas namespaces, the same pattern as the dimensional assessments.

Formal testing

The Formal testing block on Special:MyProfile is a log of standardized tests the user has taken (entrance exams, AP exams, IQ tests, and the like; retakes are welcome, and the year disambiguates them). Each entry resolves against a catalog (pcp_formal_tests) or is a custom free-text test, and records up to three score fields, raw score, percentile and pass/fail, each with an optional estimate flag.

Every score field has its own per-field visibility. Raw score, percentile and pass/fail each carry a separate privacy setting (uts_vis_raw, uts_vis_pct, uts_vis_passfail), so a user can publish a percentile while keeping the raw score private. The Special:MyProfile editor shows three privacy toggles per entry; the public Special:UserProfile gates each score line independently by its own field visibility. Scores are stored in pcp_user_test_scores, managed through the pharmacopediaformaltest API.

Life-story timeline

Special:MyLifeStory is the owner-facing editor + viewer for everything time-anchored about the user. Backed by pcp_life_events with extension columns for episode / observation / keyframe metadata.

Event types

le_type Meaning Notes
0 (TYPE_STORY) Plain timeline entry title, body, optional image
1 (TYPE_IMAGE) Image-primary entry same shape, image is the main payload
2 (TYPE_KEYFRAME) Auto-created assessment snapshot populated by upsertAssessmentKeyframe on every assessment save
3 (TYPE_OBSERVATION) Plain-text observation created via the quick-add textarea; parser extracts date, polarity, refs
4 (TYPE_EPISODE) Time-bounded period start + end (PCPDatePicker range mode); type / subtype / severity 0-100

Quick-add observation

A textarea at the top of Special:MyLifeStory (and a 📝 modal trigger on Special:MyProfile) accepts plain text like: 

anxiety from bupropion in jan 2020
did not experience anxiety from bupropion in feb 2018
panic attack 2 months ago
depressed as a freshman
i had a manic episode sep 1 2020 till nov 15 2020
no insomnia while on melatonin in summer 2023
felt great on christmas 2020
happiest on my 30th birthday

ObservationParser::parse() extracts:

  • Date (point or range): ISO, MM/DD/YYYY, "Month D YYYY", "Month YYYY", "Season YYYY", "early/mid/late YYYY", bare year, decades ("2010s"); date RANGES via "X to Y", "X till Y", "from X to Y", "X - Y"; relative-to-now ("yesterday", "last week/month/year", "N months ago", "a few weeks ago"); holidays (christmas, halloween, new year's, valentine's, july 4th, thanksgiving with computed 4th-Thursday-of-Nov, MLK / Memorial / Labor day); age-relative ("7y8mo", "51.2yo", "at age 14", "ages 2-10"); life stages ("in childhood", "as a teen", "as a freshman", "junior year"); Nth birthday ("my 30th birthday")
  • Polarity (negation detection): "not", "didn't", "did not experience", "never", "without", "denied" → polarity=0 (negative); else 1 (positive)
  • Leading verbs stripped: "I was diagnosed with", "I took", "started taking", "tried", "was on", "experienced", "felt", so the subject is the noun, not the verb
  • Adverbs stripped: "briefly", "occasionally", "frequently", "sometimes", "always", so the subject is the noun, not the modifier
  • Role splitting: "from / caused by / due to / while on" → role='cause'; "with / during / while" → role='context'
  • Ref resolution, in priority order:
    1. User's meds (pcp_user_meds)
    2. Wiki pages in Category:Medicines
    3. Effects catalog (pcp_effects)
    4. Problems catalog (pcp_problem + pcp_problem_alias)
    5. User's diagnoses (pcp_profile_diagnoses)
    6. Global ICD diagnosis abbreviations (pcp_diagnosis_abbreviations)
    7. Free-text fallback (stored as type='free' for later upgrade)
  • Auto-promote unrecognized subjects to custom-trait keyframes: when the subject doesn't match an existing entity but the input has BOTH a numeric value AND a date (e.g. my neuroticism was 5 at 10yo), the subject is treated as a NEW custom trait (namespace='custom', key derived from subject text). Creates a TYPE_KEYFRAME event with the value + a trajectory point. Future inputs with the same subject auto-append to that series.
  • Flexible range separators: X to Y, X through Y, X thru Y, X until Y, X till Y, em-dash, en-dash, flexible-whitespace hyphens (digit-aware so 2026-05-31 ISO dates aren't split), .. / ... ellipsis.
  • Age-range phrases without literal "ages": when I was 11-13, from 11 to 13, between ages 5 and 12, aged 10 to 14. Negative lookahead prevents false matches on dosages (10-20 mg), durations (5-10 years ago), measurements (cm/mm/ft/lb/etc).
  • Episode-shape detection: "manic episode" → type=mood, subtype=manic; "psychotic break", "panic attack", "anxiety attack", "trauma response" all route to addEpisode instead of addObservation. A date RANGE alone is enough to force is_episode=true.

Live preview chips appear under the textarea as you type. Submit routes to pharmacopediaobservation API which writes the row + refs via setEventRefs().

Episode form

Click the "🌀 Episode" button (or the quick-add detects an episode shape) for the structured form:

  • Type selector: mood / psychotic / anxiety / panic / trauma response / dissociative / substance use / eating / sleep disturbance / pain flare / migraine / medication adjustment / hospitalization / creative surge / spiritual / transcendent / relationship crisis / grief / somatic / other
  • Subtype (text + datalist), for mood: depressive / manic / hypomanic / mixed / dysphoric / euthymic
  • Severity slider 0-100 (per precision doctrine)
  • Date range via PCPDatePicker locked to range mode
  • Title, body, single virus-scanned image, visibility (4-state)

Visual timeline

Top of Special:MyLifeStory has a tabbed view: Visual timeline (default) / Card list.

The visual timeline uses vis-timeline 7.7.3 (vendored Apache-2.0 at resources/vendor/vis-timeline/) with these features:

  • Swimlanes (toggleable chips): Episodes (range bars), Events, Observations, Keyframes (off by default), Derived
  • Trait-trajectory overlay: a synchronized vis.Graph2d draws smooth (centripetal Catmull-Rom interpolated) lines for every keyframe trait series (CATI subscales, PID-5-BF domains, CAT-Q, custom traits like "shyness") DIRECTLY on top of the timeline plot area. Same X-axis; the graph's data + time axes are CSS-hidden so only the lines + points show. Values are normalized to 0-100% within each series so different scales coexist.
  • Toolbar: Visual/Card tabs, group toggle chips, magnifier + zoom +/- buttons, Fit visible / Fit everything
  • Plain wheel = vertical scroll inside the timeline (520px fixed height); Ctrl+wheel = zoom; Shift+wheel = horizontal pan
  • Click empty timeline area: prefills the quick-add textarea with "on YYYY-MM-DD" at that date + scrolls + triggers live preview
  • Click an item: routes to its edit form (event / episode / observation, each has its own route)
  • Collapsible "Trait series (N)" legend with chip toggles to show/hide individual series

Edit / delete / duplicate flows

Each event type has its own edit route under Special:MyLifeStory:

  • Special:MyLifeStory/edit-observation/<id>, re-parses raw text on save; supports polarity override + date override
  • Special:MyLifeStory/edit-episode/<id>, full episode form
  • Special:MyLifeStory?edit_event=<id>, existing event / image / keyframe form

All three forms have side-by-side "Delete X" + "Duplicate X" buttons. Duplicate copies fields + refs + keyframe traits (NOT images) and redirects to the new row's edit form.

When the parser stored a free-text ref (because the entity wasn't in the user's data at the time), Special:MyRefLinks finds all such refs and offers one-click "link to {match}" buttons. Matches come from the same catalogs the parser checks at write time. A banner on Special:MyLifeStory ("📎 N free-text references could be linked → Review & link") appears when unmatched refs exist.

Per-record sharing subsystem

A granular per-record sharing system layered on top of the legacy pf_visibility enum without removing it. Resolved by VisibilityResolver; the new model is additive (legacy fallback preserved unless Privacy mode is on).

Rule types (vr_rule_type)

  • private, explicit deny (only owner)
  • public, explicit allow (anyone)
  • users, payload {user_ids: [...]}; allow if viewer in list
  • cohort, payload {cohort_id: N}; allow if viewer in pcp_cohort_members for that cohort
  • link_token, payload {token: '...', uses_remaining: null|N}; allow if URL ?pcpshare=TOKEN matches
  • reciprocal, allow if viewer has a matching users rule sharing the same shape back to owner

Rules scope at three levels: (profile, namespace, key), (profile, namespace, NULL), or (profile, '*', NULL). Most-specific-first matching. Rules can have vr_expires (time-bounded) and vr_revoked (preserves audit trail).

Privacy mode

When Privacy mode is ON for a profile, a *-wide private rule is created. VisibilityResolver::canView() short-circuits to false instead of falling through to the legacy pf_visibility check, so only explicit share rules grant access. Default: OFF (back-compat).

Share dialog

Triggered by 🔗 chips on assessment reports, profile sections, life-story timeline. Modal with three tabs:

  • People: username autocomplete (↓/↑/Enter/Esc keyboard nav), per-shared-user pill with × to remove just that user, optional expires DatePicker, "Auto-share back" reciprocal toggle
  • Link: "Generate link" creates a link_token rule; copies the URL to clipboard with toast; optional max-uses + expires
  • Cohorts: dropdown of the owner's cohorts (managed at Special:MyCohorts); optional expires

Audit log

Every permitted view through a rule (not legacy) writes a row to pcp_visibility_view_log. Special:MyShareLog shows the last 200 views with timestamp, viewer (or anonymous IP masked to /24), namespace, key, rule id.

Observer perspectives

A structured way to collect second-party (observer) input on something a user owns, without the observer needing an account. The v1 use case is an observer-rated attention report: a registered user invites someone who knows them well to rate them. A two-gate consent model governs the whole flow.

  • Gate 1, contribution. An owner-issued, token-bearing invite link is the only way to submit a perspective. The invitee URL carries only an opaque random token (VisibilityResolver::generateLinkToken()); the owner's identity is never in the URL. The invitee sees only the owner's chosen display name.
  • Gate 2, publication. Every submission is born psp_consent = 0, private to the owner. Only the owner, re-checked for ownership, can flip it to published. A perspective is never publicly visible while unconsented.

Flow: the owner opens Special:MyPerspectives, picks a display name, mints an invite link, and sends it. The invitee opens Special:Perspective/<token>, reads a generic intro and a non-anonymity notice, optionally states their relationship to the owner, fills the type-specific slider form (with per-item "not sure" markers), clears a Turnstile challenge, and submits. The perspective lands in the owner's consent inbox, where the owner can publish it, return it to private, or delete it.

Special:Perspective is unlisted and unauthenticated; its POST path is defended by pingLimiter, a per-token APCu velocity cap, and fail-closed Turnstile. pcp_perspective_invite holds the token-bearing invitations (pvi_max_uses NULL means an unlimited reusable link); pcp_perspective holds the submissions, each with a psp_validity response-quality flag and the psp_consent gate. The client module ext.pharmacopedia.perspective adds the slider readout and progress bar on the invitee form and the confirm steps on the owner inbox.

Administer assessments to others

A registered user (the owner) can send any of the thirteen registered assessment scales to people outside the wiki (the respondents), collect their results, and follow them over time. Respondents need no account; a one-time invite link is their only credential. The subsystem is built so that, by default, a respondent's results are readable only by the owner, and the owner can additionally choose a zero-knowledge mode in which not even a site administrator can read them.

Assessment registry

AssessmentRegistry (includes/Assessments/AssessmentRegistry.php) is the single source of truth: an assessment registered there once autopopulates the owner's scale-picker, the respondent take-flow, and the dashboards. Each entry names a scorer class and a response model:

  • radio, discrete labelled radio buttons (CATI, CAT-Q, PID-5-BF, NFCS, BPNS, OCI-PCP, WHOQOL-BREF, ASRS)
  • slider, one continuous slider per item with uniform end anchors (OCEAN, Enneagram, AMAAS, HYD-PCP)
  • bipolar, one slider per item with the item's own two opposing phrases as the anchors (MBTI)

Every take-flow item also carries a "Not sure" control that disables the item.

The four surfaces

  • Entry point, a control that opens the feature.
  • Owner hub (Special:AdministerAssessments): the owner manages respondents (a named contact list), composes a send (a respondent plus one or more scales), generates a one-time link, and reviews each respondent's results over time. The owner can delete an invite.
  • Respondent take-flow (Special:RespondToAssessment/<token>), reached only by the invite link: a consent screen, then the model-aware item forms; once every scale is done the same URL becomes a revisitable results dashboard. Either party can delete.
  • Key setup, where the owner chooses how their results are protected (see below).

Cryptography

Each owner has an X25519 keypair. The public key is stored in the clear; the secret key is wrapped at rest. A respondent submits while the owner is absent, so the result is sealed to the owner's public key with crypto_box_seal, which needs only the public key; only the owner's secret key can open it. Two protection modes:

  • Managed (default, seamless): the secret key is wrapped with a server master key held in a file outside the web root, never in the database. No passphrase to remember, and a forgotten site password never costs the owner their data. A site administrator could technically read results.
  • Passphrase (opt-in, zero-knowledge): the secret key is wrapped with an Argon2id-derived key from a passphrase only the owner knows. Not even the site can read the results. The passphrase cannot be recovered or reset; losing it makes every collected result permanently unreadable.

AES-256-GCM is used for key wrapping in both modes. AdminCrypto (includes/Assessments/AdminCrypto.php) is the helper: setupOwnerKey, verifyPassphrase, unlockSecretKey, encryptForOwner / decryptForOwner, encryptForRespondent / decryptForRespondent, mintInviteToken / hashInviteToken. Invite tokens are 256-bit; only their SHA-256 hash is stored, so a stolen database yields no usable tokens. The respondent's own copy of each result is sealed to a key derived from the raw invite token, so the link doubles as the respondent's read credential. A scheme-version column on the key and result rows lets the cipher or KDF be revised over time; the Mode A passphrase KDF currently runs at scheme v2 (Argon2id at MODERATE limits), and an owner created under an earlier scheme is transparently re-wrapped on their next unlock.

De-identified research pool

Each submission also writes one row to pcp_administer_research, decoupled from the result write, with no foreign key to the invite, respondent, or owner. res_id is a random 128-bit value (not sequential) and the only time field is res_month ('YYYY-MM', no day), so a research row cannot be time-correlated or rank-correlated back to the owner-side tables. The payload is the plaintext item responses plus the computed score. Deleting an invite removes the owner-sealed and respondent-sealed result copies but intentionally leaves the de-identified research row, as the consent screen states.

Tables

  • pcp_administer_respondents, an owner's named contacts (the label is sealed to the owner's public key, so the roster is readable only by the owner)
  • pcp_administer_invites, one token-bearing link per send (stores only the SHA-256 of the token)
  • pcp_administer_assessments, the scale(s) inside an invite, each with the owner-sealed (aa_payload_enc) and respondent-sealed (aa_respondent_enc) result copies
  • pcp_administer_userkey, per-owner key material (public key, wrapped secret key, Mode-A salt and verifier)
  • pcp_administer_research, the de-identified research pool

The 13-instrument submission handler reuses the existing assessment scorers in includes/Assessments/ rather than reimplementing scoring.

Choice / multi voting

The <vote> tag's binary up/down mode is unchanged. With type="single" or type="multi" + options="A; B; C" (2-5 entries, semicolon separator), it renders a compact chart-icon chip that expands inline to a radio (single) or checkbox (multi) picker with per-option count bars.

Server-side storage:

  • pcp_votable_elements.ve_options (JSON array of labels)
  • pcp_votable_elements.ve_options_h (first 8 hex of sha256; drift hash)
  • pcp_votable_elements.ve_results_policy (live / after-vote / hidden)
  • pcp_votes.v_choices (CSV indices)
  • pcp_votes.v_options_h (drift hash at vote time)

API route: same pharmacopediavote endpoint; presence of choices or options_h params routes to castChoice(). Response includes tally + user_choices (null for binary). Tally hidden per results policy.

Drift behavior: if the page editor changes the options list after votes exist, ve_options_h updates and new votes' v_options_h reflects the new value. Existing votes stay but their hash no longer matches (marked stale). New votes whose submitted hash mismatches the live one are rejected, protects against browser cache races. Tallies still aggregate by raw index, so RENAMING an option in place silently turns old votes into new-label votes; reordering is the dangerous case. Appending new options is safe.

Research ID

Every user profile carries a research_id: a 10-character hex string (bin2hex(random_bytes(5)) = 40 bits), generated once at profile create, stored UNIQUE in pcp_user_profiles.prof_research_id, and never reassigned.

Purpose: provides a stable opaque identifier for de-identified research participation. It does not reveal the user's wiki username, user_id, or HMAC voter_hash; it survives username changes; and it stays constant across the user's lifetime on the wiki. Users can find theirs in the Public identity fieldset on Special:MyProfile (single-click to select-and-copy).

Backfilled retroactively for all pre-existing profiles on 2026-05-18 (v0.9.4).

ClamAV scan rule (project standard)

Hard rule, set 2026-05-17: every server-accepted file upload (image, PDF, document, anything) MUST go through VirusScanner::scanFile($path) (includes/VirusScanner.php) BEFORE being moved to permanent storage. Fail-closed: if /usr/bin/clamdscan is unavailable or returns error, the upload is rejected.

Wired into:

  • LifeStoryStore::addImage(), life events / episodes / observations
  • LiteratureStore::storeUploadedPdf(), literature PDFs
  • ProviderAppStore::saveUploadedFile(), provider verification documents

AttachmentScanner (used by feature-request attachments) is left alone, its status-return model is intentional for the queued-moderation flow there. AntivirusHelper (the old silent-no-op variant) was deleted; all callers consolidated onto VirusScanner.

Autosave infrastructure

Every block on Special:MyProfile is wrapped in <div data-pcp-save-block="block-name">. The blocksave.js library:

  1. Listens for input and change events on every input inside any save-block
  2. 800 ms after the last event, POSTs the block's serialized form data to Special:SaveProfileBlock with block=block-name
  3. Shows a transient chip (top-right and bottom of the block): pending… → saving… → ✓ saved (fades after 1.2 s) or ✗ error (sticks, clickable to retry)
  4. Race-safe: if user keeps typing during an in-flight save, the in-flight save records what it sent; newer changes mark the block dirty again and schedule another save when the response returns
  5. Diagnosis + medicines "Add a row" slots are exempted from autosave (would create duplicates); they require an explicit + Add button
  6. Programmatic widgets (chip-pickers, units, smoking, alcohol, chronotype) fire change events on their hidden fields so the listener notices

Slider numbers are also clickable: a single delegated handler on every <output> next to a range slider swaps it for a number input on click, accepts a precise typed value (clamps to the slider's min/max), commits with Enter, cancels with Escape.

Scroll position is preserved across the rare reloads (delete operations on diagnoses / medicines / experience reports, and the auto-reload after a new diagnosis or medicine is added) via sessionStorage (the ext.pharmacopedia.bounceback module).

Special pages

Page Purpose
Special:MyProfile Edit your full profile (identity, demographics, personality, dx, meds). Autosave throughout. Privacy mode toggle + share chips per fieldset.
Special:UserProfile/<name> Public profile view (filtered by per-field visibility + rule-based access). 🔗 Share chip in subtitle for self-view.
Special:MyAssessment Index of rich assessment reports
Special:MyAssessment/cati, /catq, /pid5bf, /mbti, /enneagram, /ocean Rich report per assessment; 🔗 Share chip in subtitle for owner
Special:TakeAssessment/<key> Generic paginated self-assessment runner; stores raw items and computes scores
Special:MyLifeStory Owner editor + visual timeline + card list. Quick-add observation textarea + Event/Episode buttons. 🔗 Share chip in subtitle. Privacy-mode + free-text-refs banners.
Special:MyLifeStory/add-episode, /edit-episode/<id> Episode form (create / edit)
Special:MyLifeStory/edit-observation/<id> Observation edit form (re-parses raw text)
Special:LifeStory/<name> Public life-story view (read-only, visibility-filtered)
Special:LifeImage Visibility-gated image streamer for life-story event images
Special:MyCohorts Owner-managed groups for share-with-cohort flows; create / rename / delete / add+remove members
Special:MyShareLog Who has viewed your shared content (timestamp, viewer, namespace, rule id; anonymous IPs masked)
Special:MyRefLinks Bulk linker: find free-text refs in observations that now match a structured entity; one-click upgrade or dismiss
Special:MyPerspectives Owner: mint observer-perspective invite links and review the consent inbox
Special:Perspective/<token> Public, token-gated observer-perspective form (no account; unlisted, anti-abuse defended)
Special:AdministerAssessments Owner hub: send assessment scales to outside respondents and follow their results
Special:RespondToAssessment/<token> Token-gated respondent take-flow and revisitable results dashboard
Special:SaveProfileBlock AJAX endpoint for autosave (POST-only, JSON response)
Special:Problems Browse the problems repository (165+ entries, 18 categories)
Special:Problem/<slug> Individual problem page
Special:SuggestProblem User-facing form to suggest a new problem (page-tied or standalone)
Special:SuggestAnecdote Logged-in users propose an anecdote for a medicine page
Special:SuggestEffect Logged-in users propose an effect for a medicine page
Special:SuggestTitration Logged-in users propose a titration schedule for a medicine page
Special:ManageProblems Sysop tool for problem-repository moderation
Special:ManageEffects Sysop CRUD for the global effects vocabulary
Special:ManageInteractions Sysop bulk-edit interaction reports
Special:ReviewExperience Sysop queue for pending experience reports
Special:DeletePharmaElement Sysop delete tool for any votable element
Special:VerifyProvider User-facing form to apply for provider verification and check status
Special:ProviderApplications Sysop queue to approve / reject provider-verification applications
Special:VerificationDoc Permission-gated streamer for provider-verification document files
Special:FeatureRequests User-facing feature-request board (submit and browse)
Special:RequestReview Sysop feature-request review console (status counters, prioritized queue, triage)
Special:LiteratureDoc Download proxy for approved literature PDFs (reviewers may preview pending)
Special:LiteratureQueue Sysop literature review queue (approve / reject / delete)
Special:PharmacopediaActivity Recent-activity feed: last 30 votes, effect reports, comments, literature submissions
Special:NewUsers The 20 most recently registered accounts
Special:ProfileAnalysis Sysop dashboard of cross-table profile aggregates; per-section CSV export
Special:ProfileFilter Sysop cross-filter UI over user profiles (demographics, OCEAN ranges, dx, med); CSV export
Special:PCPCtrls Sysop controls hub (gated by $wgSpecialPageLockdown)
Special:AdminCtrls Admin-controls landing page (renders sysop-editable MediaWiki:Adminctrls-body)
Special:DatePickerTest Developer sandbox exercising the date-input widget (point / range / possibility)

API modules

Action Purpose
pharmacopediavote Binary OR choice/multi vote (routes by presence of choices param). Returns tally + user_choices for choice modes; gated by results-policy.
pharmacopedialikert Submit problem-efficacy likert (0–100 + −1 DK)
pharmacopediaeffect Submit effect report (patient or provider perspective)
pharmacopediainteractionreport Submit interaction report
pharmacopediainteractionadd Create a new interaction edge
pharmacopediacomment Threaded discussion ops (add / edit / delete / reply)
pharmacopediaexperiencesubmit Submit experience report (multi-field form)
pharmacopediaexperiencereview Sysop approve / reject experience report
pharmacopediadxsearch Diagnosis autocomplete against the 41k-row abbreviation table
pharmacopediaproblemsearch Problem-repository autocomplete
pharmacopediaeffectslookup Picker used by the experience-submit form
pharmacopedialiteratureadd, literaturedelete Literature attachment ops
pharmacopediaobservation op=preview / op=submit for plain-text observations (routes to addObservation OR addEpisode)
pharmacopediavisrules Visibility rule CRUD (list / create / update / revoke / newtoken)
pharmacopediausersearch Username autocomplete for share-with-people picker
pharmacopediacohorts Cohort CRUD + membership
pharmacopediarefupgrade Free-text ref linker (op=candidates / apply / dismiss)
pharmacopediaformaltest Formal-testing score operations (list / add / update / delete), with per-field visibility

Interactions feature

The Interactions section is rendered by placing <pharmaInteractions/> anywhere in the wikitext of a med article (NS_MAIN) or a Category page (NS_CATEGORY).

Entity model

An interaction is an undirected edge between two endpoints. Each endpoint has a type (med or category) and a slug (DB-key form of the page title). Pairs are stored in canonical order: smaller (type, slug) tuple on the left.

Rendering rules

  • On a med page M, list:
    • Direct edges: rows where M is one side.
    • Transitive edges: rows where one side is a category C that M is itself a member of (via MW's categorylinks).
  • Direct wins: if the same counterparty is reachable both directly and transitively, drop the transitive duplicate.
  • On a Category page, list direct edges only (no transitive walk).
  • Sort: pooled valence_mean ascending (most negative on top). Nulls sink. Tiebreakers: n desc, then alphabetic.
  • Severe (any of pooled / user / provider vmean ≤ −83.0): red 4 px left border + red-tinted background + "severe" pill + counterparty title in red.

Add-interaction modal

Triggered by the + Add interaction button at the bottom of the section. Two-stage UX: search → click Use → confirm with Add interaction → POST to pharmacopediainteractionadd. Categories appear in the modal only if tagged with the marker category (default Category:MedCategory, configurable via $wgPharmacopediaInteractionCategoryMarker).

Experience reports

User-submitted reports of personal or clinical experience with a medicine, via <pharmaExperience/> on a med page. Stored pending in pcp_experience_reports; visible publicly only after sysop approval through Special:ReviewExperience.

Captured fields:

  • Perspective (personal / clinical)
  • Currently taking it (yes / no, stopped)
  • Duration (value + unit)
  • Dose (mg, decimal-precise)
  • Route (16-option dropdown: PO, IV, IM, SC, SL, buccal, inhaled, intranasal, topical, transdermal, PR, ophthalmic, otic, vaginal, insufflated, other)
  • Schedule (free text with datalist of QD / BID / TID / QID / q4h / q6h / q8h / q12h / qHS / qAM / qPM / PRN)
  • Patient count (clinical only): min + optional max for ranges
  • Efficacy (0–100 slider)
  • Side-effect burden (0–100 slider)
  • Stop reasons (personal + stopped only): JSON multi-select with optional severity slider per reason, codes: side_effects / ineffective / cost / no_longer_needed / clinician_advised / other
  • Free-text anecdote
  • Problems addressed (multi-pick with per-problem efficacy)
  • Effects experienced (multi-pick with per-effect valence + frequency)

Storage tables (selected)

Table Purpose
pcp_votable_elements Stable per-(page, slug) handle reused by votes / likert / comments. Also ve_options + ve_options_h + ve_results_policy for choice votes.
pcp_votes Binary +1/−1 votes (v_value) AND choice/multi votes (v_choices CSV + v_options_h drift hash)
pcp_likert_reports Problem efficacy (0–100 + −1 DK), TINYINT signed
pcp_effect_reports Effect ratings: experienced / frequency / valence (±100); perspective 1/2
pcp_interaction_reports Interaction ratings: experience 1–5 / valence ±100 / note; perspective 1/2
pcp_interactions Interaction edges (canonical-ordered pair)
pcp_comments Threaded <discuss>-tag discussions (soft-delete, optional display name)
pcp_user_profiles Per-user profile meta (alias, attribution, voter hash, prof_research_id)
pcp_profile_fields Generic key-value field store: (namespace, key, num, text, visibility)
pcp_profile_diagnoses Per-user diagnoses (system, code, description, status, origin, severity 0–100, disability 0–100, dates, notes, visibility)
pcp_user_meds Per-user medicines (name, page_id, efficacy 0–100, burden 0–100, dose_mg, route, schedule, duration, periods JSON, current, notes, visibility)
pcp_diagnosis_abbreviations ICD-10-CM + ICD-11 + DSM-5 + aliases (~41,500 rows, VARCHAR/utf8mb4 for native case-insensitive search)
pcp_problem, pcp_problem_alias Problems repository + alias lookup
pcp_experience_reports Experience reports (pending → approved); efficacy + burden 0–100; route + schedule; stop-reasons JSON; patient-count min + max
pcp_life_events Timeline events. Columns: le_type (0=story, 1=image, 2=keyframe, 3=observation, 4=episode), le_polarity, le_raw_text (parser input), le_episode_type, le_episode_subtype, le_severity, le_date_struct (PCPDatePicker JSON; supports range)
pcp_life_event_refs Join table linking events to entities (med / effect / problem / diagnosis / med_page / diagnosis_code / free); role (subject / cause / context / symptom / trigger / treatment)
pcp_life_traits Keyframe trait values (assessment subscale snapshots → trajectory graph)
pcp_life_images Image attachments (ClamAV-scanned)
pcp_visibility_rules Per-(profile, namespace, key) sharing rules. Types: public / private / users / cohort / link_token / reciprocal. Optional vr_expires, vr_revoked, vr_attribution, vr_label.
pcp_cohorts, pcp_cohort_members Owner-managed user groups for share-with-cohort flows
pcp_visibility_view_log Audit trail of rule-permitted views (Special:MyShareLog)
pcp_perspective_invite Token-bearing observer-perspective invitations (display name, object, type, max-uses)
pcp_perspective Submitted observer perspectives (payload JSON, validity flag, consent gate)
pcp_administer_respondents An owner's named contacts; the label is sealed to the owner's public key
pcp_administer_invites One token-bearing administer link per send; stores only SHA-256 of the token
pcp_administer_assessments The scale(s) in an invite; owner-sealed and respondent-sealed result copies
pcp_administer_userkey Per-owner key material (X25519 public key, wrapped secret key, Mode-A salt + verifier)
pcp_administer_research De-identified research pool: random id, coarsened month, no link back to the owner
pcp_provider_apps Provider-verification applications (profession, specialty, jurisdiction, license, status, doc paths)
pcp_literature Per-page literature submissions (citation metadata, optional PDF, status, reviewer)
pcp_feature_request, pcp_feature_request_attachment, pcp_feature_request_comment Feature-request board: requests, ClamAV-scanned attachments, threaded comments
pcp_formal_tests Catalog of standardized tests (abbrev, full name, category, score format)
pcp_user_test_scores Per-user formal-test scores; raw score / percentile / pass-fail, each with its own visibility (uts_vis_raw / uts_vis_pct / uts_vis_passfail) and an estimate flag

Notable lessons learned

  • Synthetic Event needs bubbles:true to trigger delegated listeners. new Event('input') defaults to bubbles:false, so listeners on parent wrappers never see programmatic dispatches. Native input/change events bubble by default; only JS-fired ones don't. Pass { bubbles: true } explicitly. Bit DatePicker calendar-cell clicks 2026-05-18, typing in the text field autosaved fine, but picking a date from the calendar didn't, because blocksave's wrapper listener never received the event.
  • MediaWiki form-field names collide with reserved URL params. A form <input name="title"> or name="action"> with user-controlled value silently HIJACKS MW's dispatch when POSTed (body param overrides URL param). Symptom: form submits but lands on a wiki article named whatever the user typed, with URL bar still showing the special page. Bit the episode form 2026-05-18 (user typed 'Fake one' as title → got a 404 'create article: Fake one' page). Fix: prefix ALL custom form inputs with pcp_ (both the input name="..." AND the matching $request->getVal('...', ...) read). Self-referential hidden inputs (name="title" value="<getPageTitle()>") are safe.
  • Cargo string fields cap at ~300 chars. structure and mechanism on MedTemplate are short VARCHARs; long prose goes in MEDIUMBLOB sections. Overruns silently lose Cargo data (MySQL Error 1406).
  • VARBINARY + LOWER() is a no-op. MariaDB's LOWER() returns binary types unchanged. pcp_diagnosis_abbreviations was migrated VARBINARY → VARCHAR/utf8mb4 so case-insensitive LIKE works natively without CONVERT() wrappers.
  • FlaggedRevs locks template inclusions by default. Config fix: $wgFlaggedRevsHandleIncludes=0 + remove NS_TEMPLATE from $wgFlaggedRevsNamespaces via an extension-function callback.
  • CSP must allow Cloudflare Turnstile and any other 3rd-party widget script source. Audit script-src / frame-src / connect-src / style-src whenever adding any 3rd-party JS widget.
  • Sidebar cache must be purged after CLI maintenance/edit.php writes to MediaWiki:Sidebar or other chrome pages.
  • CLI E_USER_DEPRECATED suppressed in LocalSettings.php (EmbedVideo / FlaggedRevs spam on MW 1.46). Web behavior unaffected.
  • MW ApiResult drops keys starting with _. Any field whose key starts with underscore in an ApiResult payload is treated as internal metadata and stripped. Rename to plain identifier. Bit Phase 2-4 of visibility-rules subsystem.
  • MW API serializes int-keyed assoc arrays unreliably. [23 => 'Alice'] may arrive as {"23": "Alice"} or worse. Always use list-of-objects ([{"id": 23, "name": "Alice"}]) for id-to-value maps across the API boundary.
  • PHP single-quoted strings don't interpret \xNN byte escapes. '\xF0\x9F\x94\x97' is 16 literal chars, NOT the 4-byte UTF-8 for 🔗. Use literal Unicode char or double-quoted \u{1F517}. Bit three times in one session.
  • PHP "0" is FALSY. !"0" evaluates to TRUE. So if ( !$x ) silently treats "0" (string zero) as missing. Bit choice-vote tallying when voter picked option index 0; vote was IN the DB but invisible to readers. Use === null || === for "missing or blank" intent. empty() has the same problem.
  • <span> can't contain <p>. MediaWiki auto-wraps tag content in <p> when there are newlines; browsers auto-close any <span> before the <p>, scattering child elements into wrong DOM positions. Use <div> for parser-tag wrappers whose content can span paragraphs (choice votes, life-story cards).
  • vis.Graph2d group style belongs at TOP LEVEL not nested in options. Nesting silently fails (no error, just invisible lines). Bit the trait-trajectory graph on first build.
  • A symmetric data-key cannot serve an asynchronous flow. The administer-to-others result must be encryptable while the owner is absent. A purely symmetric per-owner key has no holder at submission time; the model must be an asymmetric keypair, with the public key stored openly so a sealed box can always be written and only the owner's wrapped secret key can open it.
  • A de-identified row must carry no order and no link. An auto-increment id rank-correlates with the source table and an insert timestamp time-correlates with it. The research pool uses a random 128-bit id and a month-only date so a row genuinely cannot be traced back.

Hooks

  • ParserFirstCallInit: register all parser tags
  • LoadExtensionSchemaUpdates: install / migrate schema (the sql/ directory + patches)
  • BeforePageDisplay: inject the ext.pharmacopedia.* ResourceLoader modules; resolve and apply the page skin (the pcp-skin-* body class) and, on the Main Page / Category index, the pcp-diptych-page chromeless class
  • UserGetRights + UserEffectiveGroups: verified-provider role wiring
  • Various special-page registrations via SpecialPage_initList

Configuration globals

  • $wgPharmacopediaInteractionCategoryMarker (default Category:MedCategory): only categories tagged with this marker appear in the add-interaction modal
  • $wgPharmacopediaVoteHashSecret (required): HMAC secret for v_voter_hash so vote rows can't be mapped back to user accounts by anyone reading the DB without the secret
  • $wgPharmacopediaAdminKeyDir: filesystem directory, outside the web root, holding the administer-to-others server master key (managed mode); never in the database, never in the DB backup set
  • (Various permission-grant arrays via standard MW $wgGroupPermissions)

Source layout

 extensions/Pharmacopedia/
  |-- extension.json
  |-- includes/
  |   |-- Hooks.php
  |   |-- *Tag.php                  (parser tags: VoteTag, EffectTag, ProblemTag,
  |   |                              ClassGridTag, ClassTreeTag, LiteratureTag,
  |   |                              FrontPageTag, CategoryIndexTag, ...)
  |   |-- DiptychChrome.php          (shared topbar + footer for the diptych splashes)
  |   |-- *Store.php                (data access: EffectStore, ProblemStore, ElementStore, LifeStoryStore, ...)
  |   |-- UserProfileStore.php      (the big one; profile / dx / meds / abbreviations)
  |   |-- VisibilityResolver.php    (per-record sharing decision engine)
  |   |-- VirusScanner.php          (ClamAV gate; fail-closed)
  |   |-- ObservationParser.php     (plain-text -> structured observation)
  |   |-- SpecialMyProfile.php      (the user profile editor; large)
  |   |-- SpecialMyAssessment.php   (rich reports for the dimensional assessments; large)
  |   |-- SpecialMyLifeStory.php    (life-story editor + visual timeline; large)
  |   |-- SpecialMyPerspectives.php / SpecialPerspective.php (observer perspectives)
  |   |-- SpecialAdministerAssessments.php / SpecialRespondToAssessment.php (administer to others)
  |   |-- SpecialPCPCtrls.php       (sysop controls hub)
  |   |-- Special*.php              (other special pages)
  |   |-- ProfileDatasets.php       (countries, languages, genders, religions, etc.)
  |   |-- DatePicker.php            (range / possibility-mix date widget backend + injectBirthdayContextOnce)
  |   |-- Assessments/
  |   |   |-- AssessmentRegistry.php (single source of truth for the 13 instruments)
  |   |   |-- AdminCrypto.php        (X25519 / Argon2id / AES-256-GCM helper)
  |   |   |-- Cati.php, CatiNorms.php
  |   |   |-- Catq.php, CatqNorms.php
  |   |   |-- Pid5bf.php, Pid5bfNorms.php
  |   |   |-- Mbti.php
  |   |   |-- Enneagram.php
  |   |   |-- Ocean.php, OceanNorms.php
  |   |   |-- Asrs.php, Amaas.php
  |   |   |-- Bpns.php, BpnsNorms.php
  |   |   |-- Nfcs.php, NfcsNorms.php
  |   |   |-- Ocipcp.php
  |   |   |-- WhoqolBref.php, WhoqolBrefNorms.php
  |   |   `-- Raadsr.php            (deprecated 2026-05-17 in favor of CATI, kept for archival reads)
  |   `-- Api/
  |       |-- VoteApi.php, EffectApi.php, ...
  |       |-- ObservationApi.php
  |       |-- VisibilityRulesApi.php, UserSearchApi.php, CohortsApi.php
  |       `-- RefUpgradeApi.php
  |-- resources/
  |   |-- ext.pharmacopedia.js              (single IIFE: chip-picker, dx autocomplete, vote logic, ...)
  |   |-- ext.pharmacopedia.styles.css      (base stylesheet, self-hosted fonts)
  |   |-- ext.pharmacopedia.blocksave.js    (debounced autosave per block)
  |   |-- ext.pharmacopedia.bounceback.js   (scroll-position preservation)
  |   |-- ext.pharmacopedia.confirmdelete.* (styled destructive-action prompt)
  |   |-- ext.pharmacopedia.datepicker.js + .datepicker.styles.css
  |   |-- ext.pharmacopedia.timepicker.js + .timepicker.styles.css
  |   |-- ext.pharmacopedia.share.js + .css
  |   |-- ext.pharmacopedia.perspective.* (observer-perspective form enhancement)
  |   |-- ext.pharmacopedia.administer.* (administer-to-others surfaces)
  |   |-- ext.pharmacopedia.observation.js + .css
  |   |-- ext.pharmacopedia.refupgrade.js + .css
  |   |-- ext.pharmacopedia.lifetimeline.js + .css
  |   |-- ext.pharmacopedia.lifegraph.js + .css
  |   |-- ext.pharmacopedia.kitsync.js
  |   |-- ext.pharmacopedia.frontpage.* / ext.pharmacopedia.categoryindex.* (diptych splashes)
  |   |-- ext.pharmacopedia.appearance.* (the Appearance rail)
  |   |-- ext.pharmacopedia.skin.plants.css (plants-skin overlay)
  |   `-- vendor/vis-timeline/              (vis-timeline 7.7.3, Apache-2.0 + MIT)
  |       |-- vis-timeline-graph2d.min.js
  |       |-- vis-timeline-graph2d.min.css
  |       `-- LICENSE
  |-- sql/
  |   |-- (one .sql per table; patches as patch-*.sql)
  `-- i18n/
      `-- en.json
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