@smile-digital-health/crl 0.7.0

package/dist/transformer/fsh-to-crl/mapping/activityDefinition.js

@@ -0,0 +1,229 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.ACTIVITY_DEFINITION_URLS = void 0;
+exports.getActivityPerformClause = getActivityPerformClause;
+exports.getNextActivityId = getNextActivityId;
+exports.emitActivityBlock = emitActivityBlock;
+const fshPathFunctions_1 = require("../utils/fshPathFunctions");
+exports.ACTIVITY_DEFINITION_URLS = [
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-communicationactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-collectinformationactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-enrollmentactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-generatereportactivityn",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-medicationrequestactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-dispensemedicationactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-administermedicationactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-documentmedicationactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-immunizationactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-servicerequestactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-proposediagnosisactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-recorddetectedissueactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-recordinferenceactivity",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-reportflagactivity",
+];
+function formatActivityValue(value) {
+    if (!value) {
+        return "";
+    }
+    return value.length > 80 ? `\n    of ${value}` : ` of ${value}`;
+}
+function getActivityPerformClause(activityDef) {
+    let kind = undefined;
+    let doNotPerform = false;
+    if (activityDef && Array.isArray(activityDef.rules)) {
+        const kindRule = activityDef.rules.find((r) => r.path === "kind");
+        if (kindRule) {
+            if (typeof kindRule.value === "string") {
+                kind = "CPG" + kindRule.value.replace(/#/g, "");
+            }
+            else if (kindRule.value && typeof kindRule.value === "object" && "code" in kindRule.value) {
+                kind = "CPG" + String(kindRule.value.code).replace(/#/g, "");
+            }
+        }
+        const doNotPerformRule = activityDef.rules.find((r) => r.path === "doNotPerform");
+        if (doNotPerformRule && doNotPerformRule.value === true) {
+            doNotPerform = true;
+        }
+        if (!kindRule) {
+        }
+    }
+    let activityValue = undefined;
+    let value = undefined;
+    let terminology = undefined;
+    if (activityDef && Array.isArray(activityDef.rules)) {
+        const pccRule = activityDef.rules.find((r) => r.path === "medicationCodeableConcept");
+        if (pccRule) {
+            if (typeof pccRule.value === "object" &&
+                pccRule.value !== null &&
+                "display" in pccRule.value &&
+                typeof pccRule.value.display === "string") {
+                activityValue = `"${pccRule.value.display}"`;
+                value = pccRule.value.display;
+                const system = "system" in pccRule.value && typeof pccRule.value.system === "string"
+                    ? pccRule.value.system
+                    : "";
+                const code = "code" in pccRule.value && typeof pccRule.value.code === "string"
+                    ? pccRule.value.code
+                    : "";
+                const displayStr = pccRule.value.display;
+                if (displayStr && code && system) {
+                    terminology = { identifier: displayStr, code, system };
+                }
+            }
+            else if (typeof pccRule.value === "object" &&
+                pccRule.value !== null &&
+                "code" in pccRule.value &&
+                typeof pccRule.value.code === "string") {
+                activityValue = `"${pccRule.value.code}"`;
+                value = pccRule.value.code;
+            }
+            else if (typeof pccRule.value === "string") {
+                const match = /^.*?"(.*?)"$/.exec(pccRule.value);
+                if (match) {
+                    activityValue = `"${match[1]}"`;
+                    value = match[1];
+                }
+            }
+        }
+        if (!activityValue) {
+            const dvRules = activityDef.rules.filter((r) => r.path.startsWith("dynamicValue"));
+            for (const rule of dvRules) {
+                if (rule.path.endsWith(".path") && rule.value === "code.coding") {
+                    const prefix = rule.path.replace(/\.path$/, "");
+                    const descRule = activityDef.rules.find((r) => r.path === `${prefix}.expression.description`);
+                    const exprRule = activityDef.rules.find((r) => r.path === `${prefix}.expression.expression`);
+                    if (descRule && typeof descRule.value === "string") {
+                        activityValue = `"${descRule.value}"`;
+                        value = descRule.value;
+                    }
+                    if (exprRule && typeof exprRule.value === "string") {
+                        const codeStr = (0, fshPathFunctions_1.extractCodeExpression)(exprRule.value);
+                        let system = "", code = "";
+                        const sysMatch = /system "([^"]+)"/.exec(codeStr);
+                        const codeMatch = /code "([^"]+)"/.exec(codeStr);
+                        if (sysMatch)
+                            system = sysMatch[1];
+                        if (codeMatch)
+                            code = codeMatch[1];
+                        if (descRule && typeof descRule.value === "string" && code) {
+                            terminology = { identifier: descRule.value, code, system };
+                        }
+                    }
+                }
+            }
+        }
+    }
+    if (!kind && !activityValue) {
+        return { clauseString: "", value };
+    }
+    const clauseString = `\n    ${doNotPerform ? "do not perform" : "perform"} ${kind}${formatActivityValue(activityValue)}`;
+    return { clauseString, value, terminology };
+}
+let activityIdCounter = 0;
+function getNextActivityId() {
+    return `activity_${++activityIdCounter}`;
+}
+function emitActivityBlock(node, canonicalValueStr, allInstances, activities, indent, hasPlanDef, doReferences) {
+    const referenced = allInstances.find((inst) => inst.name === canonicalValueStr);
+    const doIdentifier = node.title ? (0, fshPathFunctions_1.toIdentifier)(node.title) : "UnnamedActivity";
+    let activityDescription = node.description ? node.description : undefined;
+    if (referenced?.rules) {
+        const descRule = referenced.rules.find((r) => r.path === "Description");
+        activityDescription = descRule ? descRule.value : undefined;
+    }
+    let hasActivityDef = false;
+    let activityDefInstance = null;
+    let useIdentifier = "";
+    if (canonicalValueStr) {
+        if (referenced && exports.ACTIVITY_DEFINITION_URLS.includes(referenced.instanceOf ?? "")) {
+            hasActivityDef = true;
+            activityDefInstance = referenced;
+        }
+        if (hasPlanDef && referenced?.title) {
+            useIdentifier = (0, fshPathFunctions_1.toIdentifier)(referenced.title);
+        }
+        else if (hasPlanDef && canonicalValueStr) {
+            useIdentifier = (0, fshPathFunctions_1.toIdentifier)(canonicalValueStr);
+        }
+    }
+    let rationale = undefined;
+    if (Array.isArray(node.extension)) {
+        const rationaleExt = node.extension.find((ext) => ext.url === "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-rationale" &&
+            typeof ext.valueMarkdown === "string" &&
+            ext.valueMarkdown.trim() !== "");
+        if (rationaleExt) {
+            rationale = `\n    because \`${rationaleExt.valueMarkdown.replace(/`/g, "`")}\``;
+        }
+    }
+    let output = "";
+    if (hasPlanDef && hasActivityDef) {
+        output += `:\n`;
+        output += `${indent}    use ${useIdentifier}.\n`;
+        const activityId = getNextActivityId();
+        const placeholder = `<<ACTIVITY_REF:${activityId}>>`;
+        output += `${indent}    do ${placeholder}.\n`;
+        output += `${indent}done\n`;
+        if (activityDefInstance) {
+            const { clauseString, value, terminology } = getActivityPerformClause(activityDefInstance);
+            activities.push({
+                id: activityId,
+                name: doIdentifier,
+                value,
+                original: `activity ${doIdentifier}${clauseString}${rationale ?? ""}.\n\n`,
+                ...(terminology ? { terminology } : {}),
+            });
+            doReferences.push({ id: activityId, placeholder });
+        }
+        else {
+            activities.push({
+                id: activityId,
+                name: doIdentifier,
+                value: undefined,
+                original: `activity ${doIdentifier} // TODO: activity details${rationale ?? ""}.\n\n`,
+            });
+            doReferences.push({ id: activityId, placeholder });
+        }
+    }
+    else if (hasPlanDef) {
+        output += ` use ${useIdentifier}.\n`;
+    }
+    else if (hasActivityDef) {
+        const activityId = getNextActivityId();
+        const placeholder = `<<ACTIVITY_REF:${activityId}>>`;
+        output += ` do ${placeholder}.\n`;
+        if (activityDefInstance) {
+            const { clauseString, value, terminology } = getActivityPerformClause(activityDefInstance);
+            activities.push({
+                id: activityId,
+                name: doIdentifier,
+                value,
+                original: `activity ${doIdentifier}${clauseString}${rationale ?? ""}.\n\n`,
+                ...(terminology ? { terminology } : {}),
+            });
+            doReferences.push({ id: activityId, placeholder });
+        }
+        else {
+            activities.push({
+                id: activityId,
+                name: doIdentifier,
+                value: undefined,
+                original: `activity ${doIdentifier} // TODO: activity details${rationale ?? ""}.\n\n`,
+            });
+            doReferences.push({ id: activityId, placeholder });
+        }
+    }
+    else {
+        const activityId = getNextActivityId();
+        const placeholder = `<<ACTIVITY_REF:${activityId}>>`;
+        output += ` do ${placeholder}.\n`;
+        activities.push({
+            id: activityId,
+            name: doIdentifier,
+            value: activityDescription,
+            original: `activity ${doIdentifier}\n    perform CPGCommunicationRequest${formatActivityValue("`" + (activityDescription ?? "TODO: fill in message.") + "`")}${rationale ?? ""}.\n\n`,
+        });
+        doReferences.push({ id: activityId, placeholder });
+    }
+    return output;
+}
+//# sourceMappingURL=activityDefinition.js.map

package/dist/transformer/fsh-to-crl/mapping/activityDefinition.js.map

@@ -0,0 +1 @@
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package/dist/transformer/fsh-to-crl/mapping/concept.d.ts

@@ -0,0 +1 @@
+export declare function mapConcept(identifiers: string[]): string;

package/dist/transformer/fsh-to-crl/mapping/concept.js

@@ -0,0 +1,14 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.mapConcept = mapConcept;
+const fshPathFunctions_1 = require("../utils/fshPathFunctions");
+function mapConcept(identifiers) {
+    return identifiers
+        .map((id) => `concept ${(0, fshPathFunctions_1.toIdentifier)(id)}:
+    has type Observation.
+    has valuetype boolean.
+    coded by ${(0, fshPathFunctions_1.toIdentifier)(id)}.
+done\n`)
+        .join("\n");
+}
+//# sourceMappingURL=concept.js.map

package/dist/transformer/fsh-to-crl/mapping/concept.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"concept.js","sourceRoot":"","sources":["../../../../src/transformer/fsh-to-crl/mapping/concept.ts"],"names":[],"mappings":";;AAMA,gCAWC;AAjBD,gEAAyD;AAMzD,SAAgB,UAAU,CAAC,WAAqB;IAC9C,OAAO,WAAW;SACf,GAAG,CACF,CAAC,EAAE,EAAE,EAAE,CACL,WAAW,IAAA,+BAAY,EAAC,EAAE,CAAC;;;eAGpB,IAAA,+BAAY,EAAC,EAAE,CAAC;OACxB,CACF;SACA,IAAI,CAAC,IAAI,CAAC,CAAC;AAChB,CAAC"}

package/dist/transformer/fsh-to-crl/mapping/planDefinition.d.ts

@@ -0,0 +1,14 @@
+import { ActivityDef } from "./activityDefinition";
+export declare function mapPlanDefinitionToDecision(instance: unknown, allInstances: ActivityDef[]): {
+    decision: string;
+    activities: {
+        id: string;
+        name: string;
+        value: string | undefined;
+        original: string;
+    }[];
+    doReferences: {
+        id: string;
+        placeholder: string;
+    }[];
+};

package/dist/transformer/fsh-to-crl/mapping/planDefinition.js

@@ -0,0 +1,235 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.mapPlanDefinitionToDecision = mapPlanDefinitionToDecision;
+const PLAN_DEFINITION_URLS = [
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-strategydefinition",
+    "http://hl7.org/fhir/uv/cpg/StructureDefinition/cpg-recommendationdefinition",
+];
+const fshPathFunctions_1 = require("../utils/fshPathFunctions");
+const activityDefinition_1 = require("./activityDefinition");
+function emitWhenBlocksRecursive(nodes, activities, allInstances, instance, indent = "    ", doReferences) {
+    let output = "";
+    const groups = {};
+    for (const node of nodes) {
+        const cond = node.conditionExpression ?? "";
+        if (!groups[cond])
+            groups[cond] = [];
+        groups[cond].push(node);
+    }
+    for (const cond in groups) {
+        const group = groups[cond];
+        if (cond === "") {
+            for (const node of group) {
+                if (node.title) {
+                    output += `${indent}// ${node.title}\n`;
+                }
+            }
+        }
+        if (group.length === 1 && group[0].children.length > 0) {
+            const node = group[0];
+            output += `${indent}when "${cond}" then:\n`;
+            output += emitWhenBlocksRecursive(node.children, activities, allInstances, instance, indent + "    ", doReferences);
+            output += `${indent}done\n`;
+            continue;
+        }
+        if (group.length > 1) {
+            output += `${indent}when "${cond}" then:\n`;
+            for (const node of group) {
+                let canonicalValueStr = undefined;
+                if (node.definitionCanonical) {
+                    if (typeof node.definitionCanonical === "string") {
+                        if (node.definitionCanonical.startsWith("Canonical(")) {
+                            canonicalValueStr = node.definitionCanonical.replace(/^Canonical\((.*)\)$/, "$1");
+                        }
+                        else {
+                            canonicalValueStr = node.definitionCanonical;
+                        }
+                    }
+                    else if (typeof node.definitionCanonical === "object" &&
+                        "entityName" in node.definitionCanonical) {
+                        canonicalValueStr = node.definitionCanonical.entityName;
+                    }
+                }
+                let hasPlanDef = false;
+                if (canonicalValueStr) {
+                    const referenced = allInstances.find((inst) => typeof inst === "object" &&
+                        inst !== null &&
+                        "name" in inst &&
+                        typeof inst.name === "string" &&
+                        inst.name === canonicalValueStr &&
+                        "instanceOf" in inst &&
+                        typeof inst.instanceOf === "string");
+                    if (referenced &&
+                        typeof referenced === "object" &&
+                        referenced !== null &&
+                        "instanceOf" in referenced &&
+                        PLAN_DEFINITION_URLS.includes(referenced.instanceOf)) {
+                        hasPlanDef = true;
+                    }
+                }
+                const actionLine = (0, activityDefinition_1.emitActivityBlock)(node, canonicalValueStr, allInstances, activities, indent + "    ", hasPlanDef, doReferences).trim();
+                if (actionLine.length > 0) {
+                    output += `${indent}    ${actionLine}\n`;
+                }
+            }
+            output += `${indent}done\n`;
+        }
+        else if (group.length === 1 && group[0].children.length === 0) {
+            const node = group[0];
+            let canonicalValueStr = undefined;
+            if (node.definitionCanonical) {
+                if (typeof node.definitionCanonical === "string") {
+                    if (node.definitionCanonical.startsWith("Canonical(")) {
+                        canonicalValueStr = node.definitionCanonical.replace(/^Canonical\((.*)\)$/, "$1");
+                    }
+                    else {
+                        canonicalValueStr = node.definitionCanonical;
+                    }
+                }
+                else if (typeof node.definitionCanonical === "object" &&
+                    "entityName" in node.definitionCanonical) {
+                    canonicalValueStr = node.definitionCanonical.entityName;
+                }
+            }
+            let hasPlanDef = false;
+            if (canonicalValueStr) {
+                const referenced = allInstances.find((inst) => typeof inst === "object" &&
+                    inst !== null &&
+                    "name" in inst &&
+                    typeof inst.name === "string" &&
+                    inst.name === canonicalValueStr &&
+                    "instanceOf" in inst &&
+                    typeof inst.instanceOf === "string");
+                if (referenced &&
+                    typeof referenced === "object" &&
+                    referenced !== null &&
+                    "instanceOf" in referenced &&
+                    PLAN_DEFINITION_URLS.includes(referenced.instanceOf)) {
+                    hasPlanDef = true;
+                }
+            }
+            output += `${indent}when "${cond}" then`;
+            let actionLine = (0, activityDefinition_1.emitActivityBlock)(node, canonicalValueStr, allInstances, activities, "", hasPlanDef, doReferences).trim();
+            if (actionLine.startsWith(":"))
+                actionLine = actionLine.slice(1).trim();
+            output += ` ${actionLine}\n`;
+        }
+    }
+    return output;
+}
+function parseActions(rules, basePath = "action") {
+    const nodes = [];
+    let currentNode = null;
+    let currentExtensions = [];
+    let currentExtension = null;
+    for (let i = 0; i < rules.length; i++) {
+        const rule = rules[i];
+        if (rule.path === `${basePath}[+]`) {
+            if (currentNode) {
+                if (currentExtensions.length > 0)
+                    currentNode.extension = currentExtensions.filter((ext) => ext.url !== undefined && ext.url !== null && ext.url !== "");
+                nodes.push(currentNode);
+            }
+            currentNode = { children: [] };
+            currentExtensions = [];
+            currentExtension = null;
+        }
+        else if (typeof rule.path === "string" && rule.path.startsWith(`${basePath}[=]`)) {
+            if (!currentNode)
+                continue;
+            const subPath = rule.path.slice(`${basePath}[=]`.length);
+            if (subPath.startsWith(".action[+]")) {
+                const childBase = `${basePath}[=].action`;
+                const childRules = [];
+                let j = i;
+                while (j < rules.length &&
+                    typeof rules[j].path === "string" &&
+                    rules[j].path.startsWith(childBase)) {
+                    childRules.push(rules[j]);
+                    j++;
+                }
+                currentNode.children = parseActions(childRules, childBase);
+                i = j - 1;
+            }
+            else if (subPath.startsWith(".action[=]")) {
+                continue;
+            }
+            else if (subPath === ".extension[+]") {
+                currentExtension = { url: "" };
+                currentExtensions.push(currentExtension);
+            }
+            else if (subPath.startsWith(".extension[=]")) {
+                if (!currentExtension) {
+                    currentExtension = { url: "" };
+                    currentExtensions.push(currentExtension);
+                }
+                if (subPath.endsWith(".url"))
+                    currentExtension.url = rule.value;
+                if (subPath.endsWith(".valueMarkdown"))
+                    currentExtension.valueMarkdown = rule.value;
+            }
+            else {
+                if (subPath === ".title")
+                    currentNode.title = rule.value;
+                if (subPath === ".description")
+                    currentNode.description = rule.value;
+                if (subPath.endsWith(".condition[=].expression.expression"))
+                    currentNode.conditionExpression = rule.value;
+                if (subPath === ".definitionCanonical")
+                    currentNode.definitionCanonical = rule.value;
+            }
+        }
+    }
+    if (currentNode) {
+        if (currentExtensions.length > 0) {
+            currentNode.extension = currentExtensions.filter((ext) => ext.url !== undefined && ext.url !== null && ext.url !== "");
+        }
+        nodes.push(currentNode);
+    }
+    return nodes;
+}
+function mapPlanDefinitionToDecision(instance, allInstances) {
+    if (typeof instance !== "object" ||
+        instance === null ||
+        !("instanceOf" in instance) ||
+        !PLAN_DEFINITION_URLS.includes(instance.instanceOf)) {
+        return { decision: "", activities: [], doReferences: [] };
+    }
+    let description = instance.description;
+    const rules = instance.rules || [];
+    if (!description) {
+        const descriptionRule = rules.find((r) => r.path === "Description");
+        description = descriptionRule ? descriptionRule.value : undefined;
+    }
+    const title = instance.title ??
+        rules.find((r) => r.path === "Title")?.value;
+    const plandefTitle = title ? (0, fshPathFunctions_1.toIdentifier)(title) : "[UnnamedPlanDefinition]";
+    const plandefDescription = description ? (0, fshPathFunctions_1.toString)(description) : "";
+    const citationRule = rules.find((r) => r.path === "relatedArtifact[=].citation");
+    let citation = citationRule ? (0, fshPathFunctions_1.toString)(citationRule.value) : "";
+    if (citation.startsWith('"') && citation.endsWith('"')) {
+        citation = citation.slice(1, -1);
+    }
+    let output = "";
+    if (instance.name) {
+        output += `// Instance: ${instance.name}\n`;
+    }
+    if (plandefDescription) {
+        let desc = plandefDescription;
+        if (desc.startsWith('"') && desc.endsWith('"')) {
+            desc = desc.slice(1, -1);
+        }
+        output += `// Description: ${desc}\n`;
+    }
+    if (citation) {
+        output += `// Provenance: ${citation}\n`;
+    }
+    output += `decision ${plandefTitle}:\n`;
+    const actionTree = parseActions(rules);
+    const activities = [];
+    const doReferences = [];
+    output += emitWhenBlocksRecursive(actionTree, activities, allInstances, instance, "    ", doReferences);
+    output += "done\n\n";
+    return { decision: output, activities, doReferences };
+}
+//# sourceMappingURL=planDefinition.js.map

package/dist/transformer/fsh-to-crl/mapping/planDefinition.js.map

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package/dist/transformer/fsh-to-crl/mapping/terminology.d.ts

@@ -0,0 +1 @@
+export declare function mapTerminology(identifiers: string[]): string;

package/dist/transformer/fsh-to-crl/mapping/terminology.js

@@ -0,0 +1,10 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.mapTerminology = mapTerminology;
+const fshPathFunctions_1 = require("../utils/fshPathFunctions");
+function mapTerminology(identifiers) {
+    return identifiers
+        .map((id) => `terminology ${(0, fshPathFunctions_1.toIdentifier)(id)} system \`http://sdh.com/cqis/kalm\` code ${(0, fshPathFunctions_1.toCode)(id)}.`)
+        .join("\n");
+}
+//# sourceMappingURL=terminology.js.map

package/dist/transformer/fsh-to-crl/mapping/terminology.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"terminology.js","sourceRoot":"","sources":["../../../../src/transformer/fsh-to-crl/mapping/terminology.ts"],"names":[],"mappings":";;AAMA,wCAOC;AAbD,gEAAiE;AAMjE,SAAgB,cAAc,CAAC,WAAqB;IAClD,OAAO,WAAW;SACf,GAAG,CACF,CAAC,EAAE,EAAE,EAAE,CACL,eAAe,IAAA,+BAAY,EAAC,EAAE,CAAC,6CAA6C,IAAA,yBAAM,EAAC,EAAE,CAAC,GAAG,CAC5F;SACA,IAAI,CAAC,IAAI,CAAC,CAAC;AAChB,CAAC"}

package/dist/transformer/fsh-to-crl/transformer.d.ts

@@ -0,0 +1 @@
+export declare function transformFSHToCRL(fshProjectDir: string): string;