@tekkare/romulus 0.1.253 → 0.1.255

package/layer/app/oip-patients/vaccineLabels.ts

@@ -0,0 +1,180 @@
+/**
+ * Libelles des vocabulaires de l'index des cas apres vaccination.
+ *
+ * Les listes fermees viennent du pipeline (ai-pipelines, backend/app/vaccine.py) :
+ * gravite, evolution, avis des auteurs, dose suivante, type de cas, delai. Les
+ * cles de produit et d'agent sont derivees du nom ecrit dans l'article ; une
+ * cle que ce module ne connait pas s'affiche mise en forme, jamais vide.
+ */
+import type { PatientLang } from "./labels";
+
+type Labels = Record<string, { fr: string; en: string }>;
+
+/** `sars_cov_2` → « Sars cov 2 » : le dernier recours, pour une cle inconnue. */
+function prettify(value: string): string {
+  return value.replace(/_/g, " ").replace(/^\w/, (c) => c.toUpperCase());
+}
+
+/** Le libelle d'une valeur, ou la valeur mise en forme quand le vocabulaire ne la connait pas. */
+export function vaccineLabelOf(labels: Labels, value: string | number | null | undefined, lang: PatientLang): string {
+  if (value === null || value === undefined || value === "") return "";
+  const key = String(value);
+  return labels[key]?.[lang] ?? prettify(key);
+}
+
+export const SERIOUSNESS_LABELS: Labels = {
+  death: { fr: "Décès", en: "Died" },
+  life_threatening: { fr: "Pronostic vital engagé", en: "Life-threatening" },
+  hospitalisation: { fr: "Hospitalisation", en: "Admitted to hospital" },
+  disability: { fr: "Séquelle invalidante", en: "Lasting disability" },
+  medically_important: { fr: "Soins médicaux nécessaires", en: "Needed medical care" },
+  not_serious: { fr: "Non grave", en: "Not serious" },
+};
+
+/** Les gravites qui font un cas « grave » au sens de la pharmacovigilance. */
+export const SERIOUS_KEYS = ["death", "life_threatening", "hospitalisation", "disability"];
+
+export const EVENT_OUTCOME_LABELS: Labels = {
+  recovered: { fr: "Guéri", en: "Recovered" },
+  recovering: { fr: "En voie de guérison", en: "Recovering" },
+  sequelae: { fr: "Guéri avec séquelles", en: "Recovered with after-effects" },
+  not_recovered: { fr: "Non guéri", en: "Not recovered" },
+  fatal: { fr: "Décès", en: "Died" },
+  unknown: { fr: "Non précisé", en: "Not reported" },
+};
+
+export const CAUSALITY_LABELS: Labels = {
+  certain: { fr: "Lien certain", en: "Certain link" },
+  probable: { fr: "Lien probable", en: "Probable link" },
+  possible: { fr: "Lien possible", en: "Possible link" },
+  unlikely: { fr: "Lien peu probable", en: "Unlikely link" },
+  temporal_only: { fr: "Chronologie seule, sans conclusion", en: "Timing only, no causal claim" },
+  not_assessed: { fr: "Non discuté", en: "Not discussed" },
+};
+
+export const RECHALLENGE_LABELS: Labels = {
+  re_vaccinated_no_event: { fr: "Dose suivante reçue, sans récidive", en: "Next dose given, no problem" },
+  re_vaccinated_recurrence: { fr: "Dose suivante reçue, récidive", en: "Next dose given, it happened again" },
+  not_re_vaccinated: { fr: "Pas de dose suivante", en: "No further dose" },
+  advised_against: { fr: "Doses suivantes déconseillées", en: "Further doses advised against" },
+  unknown: { fr: "Non précisé", en: "Not reported" },
+};
+
+export const EVENT_CATEGORY_LABELS: Labels = {
+  adverse_event: { fr: "Événement après vaccination", en: "Event after vaccination" },
+  breakthrough_infection: { fr: "Infection malgré la vaccination", en: "Infection despite vaccination" },
+  vaccine_failure: { fr: "Échec de protection", en: "Vaccine did not protect" },
+  vaccination_in_special_population: { fr: "Vaccination en situation particulière", en: "Vaccination in a special situation" },
+  not_vaccine_related: { fr: "Sans lien avec un vaccin", en: "Not about a vaccine" },
+};
+
+/** Dans l'ordre du temps : la facette les range ainsi, pas par effectif. */
+export const ONSET_BAND_LABELS: Labels = {
+  same_day: { fr: "Le jour même", en: "Same day" },
+  within_week: { fr: "Dans la semaine", en: "Within a week" },
+  within_month: { fr: "1 à 4 semaines", en: "1 to 4 weeks" },
+  within_3_months: { fr: "1 à 3 mois", en: "1 to 3 months" },
+  later: { fr: "Plus de 3 mois", en: "More than 3 months" },
+  unknown: { fr: "Non précisé", en: "Not stated" },
+};
+export const ONSET_BAND_ORDER = Object.keys(ONSET_BAND_LABELS);
+
+export const PLATFORM_LABELS: Labels = {
+  mrna: { fr: "ARN messager", en: "mRNA" },
+  "viral vector": { fr: "Vecteur viral", en: "Viral vector" },
+  inactivated: { fr: "Inactivé", en: "Inactivated" },
+  "live attenuated": { fr: "Vivant atténué", en: "Live attenuated" },
+  subunit: { fr: "Sous-unitaire", en: "Subunit" },
+  toxoid: { fr: "Anatoxine", en: "Toxoid" },
+  conjugate: { fr: "Conjugué", en: "Conjugate" },
+  polysaccharide: { fr: "Polysaccharidique", en: "Polysaccharide" },
+};
+
+export const PATHOGEN_LABELS: Labels = {
+  sars_cov_2: { fr: "Covid-19 (SARS-CoV-2)", en: "Covid-19 (SARS-CoV-2)" },
+  varicella_zoster: { fr: "Varicelle, zona", en: "Chickenpox, shingles" },
+  hpv: { fr: "Papillomavirus (HPV)", en: "Papillomavirus (HPV)" },
+  tuberculosis: { fr: "Tuberculose", en: "Tuberculosis" },
+  measles: { fr: "Rougeole", en: "Measles" },
+  yellow_fever: { fr: "Fièvre jaune", en: "Yellow fever" },
+  rabies: { fr: "Rage", en: "Rabies" },
+  influenza: { fr: "Grippe", en: "Influenza" },
+  pneumococcus: { fr: "Pneumocoque", en: "Pneumococcus" },
+  meningococcus: { fr: "Méningocoque", en: "Meningococcus" },
+  hepatitis_b: { fr: "Hépatite B", en: "Hepatitis B" },
+  hepatitis_a: { fr: "Hépatite A", en: "Hepatitis A" },
+  tetanus: { fr: "Tétanos, diphtérie, coqueluche", en: "Tetanus, diphtheria, pertussis" },
+  rotavirus: { fr: "Rotavirus", en: "Rotavirus" },
+  rsv: { fr: "Virus respiratoire syncytial (VRS)", en: "Respiratory syncytial virus (RSV)" },
+  dengue: { fr: "Dengue", en: "Dengue" },
+  japanese_encephalitis: { fr: "Encéphalite japonaise", en: "Japanese encephalitis" },
+  typhoid: { fr: "Typhoïde", en: "Typhoid" },
+  polio: { fr: "Poliomyélite", en: "Polio" },
+  mpox: { fr: "Mpox, variole", en: "Mpox, smallpox" },
+  ebola: { fr: "Ebola", en: "Ebola" },
+  tick_borne_encephalitis: { fr: "Encéphalite à tiques", en: "Tick-borne encephalitis" },
+  rubella: { fr: "Rubéole", en: "Rubella" },
+  mumps: { fr: "Oreillons", en: "Mumps" },
+  cholera: { fr: "Choléra", en: "Cholera" },
+};
+
+export const PRODUCT_LABELS: Labels = {
+  comirnaty: { fr: "Comirnaty (Pfizer-BioNTech)", en: "Comirnaty (Pfizer-BioNTech)" },
+  spikevax: { fr: "Spikevax (Moderna)", en: "Spikevax (Moderna)" },
+  vaxzevria: { fr: "Vaxzevria (AstraZeneca)", en: "Vaxzevria (AstraZeneca)" },
+  jcovden: { fr: "Jcovden (Janssen)", en: "Jcovden (Janssen)" },
+  nuvaxovid: { fr: "Nuvaxovid (Novavax)", en: "Nuvaxovid (Novavax)" },
+  coronavac: { fr: "CoronaVac (Sinovac)", en: "CoronaVac (Sinovac)" },
+  bbibp_corv: { fr: "BBIBP-CorV (Sinopharm)", en: "BBIBP-CorV (Sinopharm)" },
+  covaxin: { fr: "Covaxin", en: "Covaxin" },
+  convidecia: { fr: "Convidecia (CanSino)", en: "Convidecia (CanSino)" },
+  sputnik_v: { fr: "Spoutnik V", en: "Sputnik V" },
+  other_covid: { fr: "Autre vaccin Covid-19", en: "Other Covid-19 vaccine" },
+  unspecified_covid: { fr: "Vaccin Covid-19 non précisé", en: "Unspecified Covid-19 vaccine" },
+  shingrix: { fr: "Shingrix", en: "Shingrix" },
+  zostavax: { fr: "Zostavax", en: "Zostavax" },
+  varicella: { fr: "Varicelle", en: "Varicella" },
+  hpv: { fr: "HPV", en: "HPV" },
+  bcg: { fr: "BCG", en: "BCG" },
+  mmr: { fr: "ROR", en: "MMR" },
+  measles: { fr: "Rougeole", en: "Measles" },
+  yellow_fever: { fr: "Fièvre jaune", en: "Yellow fever" },
+  rabies: { fr: "Rage", en: "Rabies" },
+  influenza: { fr: "Grippe", en: "Influenza" },
+  pneumococcal: { fr: "Pneumocoque", en: "Pneumococcal" },
+  meningococcal: { fr: "Méningocoque", en: "Meningococcal" },
+  hepatitis_b: { fr: "Hépatite B", en: "Hepatitis B" },
+  hepatitis_a: { fr: "Hépatite A", en: "Hepatitis A" },
+  dtp: { fr: "Diphtérie, tétanos, coqueluche", en: "Diphtheria, tetanus, pertussis" },
+  rotavirus: { fr: "Rotavirus", en: "Rotavirus" },
+  rsv: { fr: "VRS", en: "RSV" },
+  dengue: { fr: "Dengue", en: "Dengue" },
+  japanese_encephalitis: { fr: "Encéphalite japonaise", en: "Japanese encephalitis" },
+  typhoid: { fr: "Typhoïde", en: "Typhoid" },
+  polio: { fr: "Poliomyélite", en: "Polio" },
+  mpox_smallpox: { fr: "Mpox, variole", en: "Mpox, smallpox" },
+  ebola: { fr: "Ebola", en: "Ebola" },
+  tbe: { fr: "Encéphalite à tiques", en: "Tick-borne encephalitis" },
+  rubella: { fr: "Rubéole", en: "Rubella" },
+  mumps: { fr: "Oreillons", en: "Mumps" },
+  cholera: { fr: "Choléra", en: "Cholera" },
+};
+
+/** Ce qui retient une fiche d'etre comptee sans relecture, en clair. */
+export const VACCINE_FLAG_LABELS: Labels = {
+  exposure_missing: { fr: "L'article ne nomme aucun vaccin pour cette personne", en: "The paper names no vaccine for this person" },
+  exposure_unsupported: { fr: "Le vaccin indiqué ne figure pas dans le texte de l'article", en: "The vaccine named was not found in the paper's own text" },
+  event_missing: { fr: "Aucun événement clair n'a été trouvé", en: "No clear event was found" },
+  onset_before_vaccination: { fr: "Les troubles ont commencé avant la dose", en: "The problem started before the dose" },
+  not_vaccine_related: { fr: "Le cas ne concerne pas un vaccin", en: "The report is not about a vaccine" },
+  block_failed: { fr: "Les informations sur le vaccin n'ont pas pu être lues", en: "The vaccine details could not be read" },
+  delay_not_from_dose: { fr: "Le délai est compté depuis un traitement ou un événement, pas depuis la dose", en: "The delay is counted from a treatment or event, not from the dose" },
+  delay_implausible: { fr: "Le délai dépasse dix ans : probablement un âge plutôt qu'un délai", en: "The delay is over ten years, more likely an age than a delay" },
+  reported_elsewhere: { fr: "Cas déjà publié ailleurs : la personne peut être comptée deux fois", en: "Case published elsewhere, so the person may be counted twice" },
+};
+
+export const CHECK_LABELS: Labels = {
+  all: { fr: "Toutes les fiches", en: "All records" },
+  clean: { fr: "Sans contrôle ouvert", en: "No open check" },
+  flagged: { fr: "À vérifier", en: "Needing a check" },
+};

package/layer/app/utils/oipResources.ts

@@ -16,6 +16,8 @@
 import type { RmProjectKind, RmProjectLang } from "@tekkare/romulus/utils/projects";
 import scienceIndexConfig from "../oip-science/indexConfig.json";
 import { DRUG_PROJECT_KINDS } from "../oip-drugs/kinds";
+import { OIP_PATIENT_INDEXES } from "../oip-patients/indexes";
+import { PATIENT_KIND, VACCINE_KIND } from "../oip-patients/kinds";
 
 /** Les apps qui ont des fiches a montrer, et ou les ouvrir. */
 export const OIP_RESOURCE_APPS = {
@@ -27,6 +29,10 @@ export const OIP_RESOURCE_APPS = {
     name: "France Drugs",
     url: "https://france-drugs.app.tekkare.com",
   },
+  ww_oip_patients: {
+    name: "OIP Case Atlas",
+    url: "https://global-case-atlas.app.tekkare.com",
+  },
 } as const;
 
 export type OipResourceApp = keyof typeof OIP_RESOURCE_APPS;
@@ -121,6 +127,28 @@ function drugsSpec(kind: RmProjectKind, view: string): OipResourceSpec {
   };
 }
 
+/**
+ * Une fiche d'OIP Case Atlas (cas de maladie rare, cas apres vaccination),
+ * lue sur le cluster `science` et montree d'un seul tenant, ses onglets
+ * compris. Elle s'adresse par son `record_id`, que le document donne.
+ */
+function patientsSpec(kind: RmProjectKind, view: string): OipResourceSpec {
+  return {
+    type: kind.type,
+    app: "ww_oip_patients",
+    cluster: "science",
+    kind,
+    routeId: (id) => id,
+    base: () => "",
+    tabs: [],
+    view,
+    detailPath: (id, tab, doc) => {
+      const path = kind.path!(doc ?? {}, id);
+      return tab && tab !== "summary" ? `${path}?tab=${encodeURIComponent(tab)}` : path;
+    },
+  };
+}
+
 /** La vue de chaque famille de fr_drugs_app (cf. useOipResourceViews). */
 const DRUG_VIEWS: Record<string, string> = {
   FrHasBrand: "drugs-brand",
@@ -338,6 +366,8 @@ export const OIP_RESOURCE_SPECS: OipResourceSpec[] = [
     tabs: [T.trials, T.publications],
   }),
   ...DRUG_PROJECT_KINDS.map((kind) => drugsSpec(kind, DRUG_VIEWS[kind.type]!)),
+  patientsSpec(PATIENT_KIND, "patients-patient"),
+  patientsSpec(VACCINE_KIND, "patients-vaccine"),
 ];
 
 export function oipResourceSpec(type: string): OipResourceSpec | undefined {
@@ -370,7 +400,9 @@ export const OIP_SCIENCE_INDEXES: string[] = Object.values(scienceIndexConfig as
 /** Les index que le proxy du layer accepte de lire, par cluster. */
 export function oipResourceIndexes(cluster: OipEsCluster): string[] {
   const declared = OIP_RESOURCE_SPECS.filter((spec) => spec.cluster === cluster).map((spec) => spec.kind.index);
-  return cluster === "science" ? [...new Set([...declared, ...OIP_SCIENCE_INDEXES])] : declared;
+  return cluster === "science"
+    ? [...new Set([...declared, ...OIP_SCIENCE_INDEXES, ...Object.values(OIP_PATIENT_INDEXES)])]
+    : declared;
 }
 
 /**

package/layer/nuxt.config.ts

@@ -22,12 +22,14 @@ export default defineNuxtConfig({
     compatibilityVersion: 4,
   },
   // Regles du cadre communes aux apps (bandeau de page, barre de filtres), et
-  // classes des fiches de France Augmented Science, limitees a `.oip-science`
-  // (cf. app/oip-science/science.css).
+  // classes des fiches de France Augmented Science, de fr_drugs_app et d'OIP
+  // Case Atlas, limitees a leur conteneur (`.oip-science`, `.oip-drugs`,
+  // `.oip-patients`).
   css: [
     fileURLToPath(new URL("./app/assets/oip-frame.css", import.meta.url)),
     fileURLToPath(new URL("./app/oip-science/science.css", import.meta.url)),
     fileURLToPath(new URL("./app/oip-drugs/drugs.css", import.meta.url)),
+    fileURLToPath(new URL("./app/oip-patients/patients.css", import.meta.url)),
   ],
   // Reglages serveur propres au layer. Les cles Directus (directus*Url,
   // directus*Token) restent declarees par l'app, qui les avait deja.
@@ -57,12 +59,14 @@ export default defineNuxtConfig({
     /**
      * Clusters Elasticsearch des vues de ressources (/api/oip/es) : domaine et
      * cle ApiKey. `science` porte les index de France Augmented Science
-     * (PubMed, essais), `hcp` l'annuaire, `drugs` ceux de fr_drugs_app. Une
+     * (PubMed, essais) et ceux d'OIP Case Atlas (patients), `hcp` l'annuaire, `drugs` ceux de fr_drugs_app. Une
      * app les remplit depuis ses propres variables, ou par
      * NUXT_OIP_ES_SCIENCE_DOMAIN / NUXT_OIP_ES_SCIENCE_AUTH, etc.
      */
     oipEs: {
-      science: { domain: "", auth: "" },
+      // Cas apres vaccination d'OIP Case Atlas : une autre cle sur le meme
+      // domaine. Vide : la cle principale.
+      science: { domain: "", auth: "", authVaccines: "" },
       hcp: { domain: "", auth: "" },
       // Associations et registres d'autorisation etrangers : une autre cle sur
       // le meme domaine, comme dans fr_drugs_app. Vides : la cle principale.

package/layer/server/api/oip/es.post.ts

@@ -3,6 +3,7 @@ import { requireOipSession } from "../../utils/oipAuth";
 import { findOipEsIndex, resolveOipEsIndex } from "../../utils/oipEsIndices";
 import { oipResourceIndexes, type OipEsCluster } from "../../../app/utils/oipResources";
 import { ES_INDEX } from "../../../app/oip-drugs/esIndices";
+import { OIP_PATIENT_INDEXES } from "../../../app/oip-patients/indexes";
 
 /**
  * POST /api/oip/es?cluster=&index=, servi par le layer OIP.
@@ -18,9 +19,13 @@ import { ES_INDEX } from "../../../app/oip-drugs/esIndices";
  * dans fr_drugs_app. Ses associations et ses registres d'autorisation
  * etrangers demandent une autre cle sur le meme domaine (`authAssociations`,
  * `authApprovals`) ; a defaut, la cle principale.
+ *
+ * Cluster `science` : les cas apres vaccination d'OIP Case Atlas ne se lisent
+ * pas avec la cle PubMed, mais avec une autre sur le meme domaine
+ * (`authVaccines`) ; a defaut, la cle principale.
  */
 
-type DrugsKeyGroup = "auth" | "authAssociations" | "authApprovals";
+type KeyGroup = "auth" | "authAssociations" | "authApprovals" | "authVaccines";
 
 const DRUG_IDS = new Set<string>(Object.values(ES_INDEX) as string[]);
 const ASSOCIATION_IDS = new Set<string>(
@@ -45,7 +50,7 @@ async function drugsKeyOf(ref: string): Promise<string> {
   return id && DRUG_IDS.has(id) ? id : "";
 }
 
-function drugsKeyGroup(id: string): DrugsKeyGroup {
+function drugsKeyGroup(id: string): KeyGroup {
   if (ASSOCIATION_IDS.has(id)) return "authAssociations";
   if (APPROVAL_IDS.has(id)) return "authApprovals";
   return "auth";
@@ -71,7 +76,7 @@ export default defineEventHandler(async (event) => {
   if (!index || !/^[A-Za-z0-9_.,-]+$/.test(index)) throw createError({ status: 400, message: "Invalid index" });
 
   const refs = index.split(",");
-  let authKey: DrugsKeyGroup = "auth";
+  let authKey: KeyGroup = "auth";
   if (cluster === "drugs") {
     // Une requete multi-index part avec une seule cle : ses index en relevent tous.
     const ids = await Promise.all(refs.map(drugsKeyOf));
@@ -82,6 +87,11 @@ export default defineEventHandler(async (event) => {
   } else {
     const allowed = oipResourceIndexes(cluster as OipEsCluster);
     if (refs.some((ref) => !allowed.includes(ref))) throw createError({ status: 403, message: "Index not allowed" });
+    if (cluster === "science") {
+      const groups = new Set(refs.map((ref) => (ref === OIP_PATIENT_INDEXES.VACCINE_PATIENTS ? "authVaccines" : "auth")));
+      if (groups.size > 1) throw createError({ status: 400, message: "Indexes require different credentials" });
+      authKey = [...groups][0]!;
+    }
   }
 
   const auth = target[authKey] || target.auth;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@tekkare/romulus",
-  "version": "0.1.253",
+  "version": "0.1.255",
   "description": "Romulus Design System - Nuxt module by Tekkare",
   "license": "MIT",
   "type": "module",
@@ -19,7 +19,8 @@
     },
     "./layer": "./layer/nuxt.config.ts",
     "./layer-utils/*": "./layer/app/utils/*.ts",
-    "./layer-composables/*": "./layer/app/composables/*.ts"
+    "./layer-composables/*": "./layer/app/composables/*.ts",
+    "./layer-patients/*": "./layer/app/oip-patients/*.ts"
   },
   "main": "./dist/module.cjs",
   "module": "./dist/module.mjs",
@@ -48,6 +49,8 @@
     "@tiptap/starter-kit": "^3.31.4",
     "@tiptap/suggestion": "^3.31.4",
     "@tiptap/vue-3": "^3.31.4",
+    "cytoscape": "^3.33.1",
+    "cytoscape-fcose": "^2.2.0",
     "echarts": "^5.6.0",
     "html2canvas-pro": "^1.6.7",
     "jspdf": "^4.2.0",