fhirsmith 0.11.2 → 0.13.0

package/tx/workers/validate.js

@@ -11,12 +11,12 @@
 // POST /ValueSet/{id}/$validate-code
 //
 
-const { TerminologyWorker } = require('./worker');
+const { TerminologyWorker, Unknown_Code_in_VersionSCT, SCTVersion } = require('./worker');
 const {Languages, Language} = require("../../library/languages");
 const {Extensions} = require("../library/extensions");
 const {validateParameter, isAbsoluteUrl, validateOptionalParameter, getValuePrimitive} = require("../../library/utilities");
 const {TxParameters} = require("../params");
-const {OperationOutcome, Issue} = require("../library/operation-outcome");
+const { OperationOutcome, Issue, buildOperationOutcome, outcomeFromError } = require('../library/operation-outcome');
 const {Parameters} = require("../library/parameters");
 const {Designations, DisplayCheckingStyle, DisplayDifference, SearchFilterText} = require("../library/designations");
 const ValueSet = require("../library/valueset");
@@ -293,6 +293,8 @@ class ValueSetChecker {
         }
       }
     }
+    // R6's ValueSet.compose.property
+    this.params.seeCompose(this.valueSet.jsonObj.compose);
     if (!this.params.HTTPLanguages && this.valueSet.jsonObj.language) {
       this.params.HTTPLanguages = Languages.fromAcceptLanguage(this.valueSet.jsonObj.language, this.worker.languages, false);
     }
@@ -951,7 +953,7 @@ class ValueSetChecker {
         let msg = this.worker.i18n.translate('INACTIVE_CONCEPT_FOUND', this.params.HTTPLanguages, [vstatus.value, coding.code]);
         messages.push(msg);
         op.addIssue(new Issue('warning', 'business-rule', path, 'INACTIVE_CONCEPT_FOUND', msg, 'code-comment'));
-      } else if (vstatus.value.toLowerCase() === 'deprecated') {
+      } else if (vstatus.value && vstatus.value.toLowerCase() === 'deprecated') {
         result.addParamCode('status', vstatus.value);
         let msg = this.worker.i18n.translate('DEPRECATED_CONCEPT_FOUND', this.params.HTTPLanguages, [vstatus.value, coding.code]);
         messages.push(msg);
@@ -1049,6 +1051,7 @@ class ValueSetChecker {
     this.checkCanonicalStatus(issuePath, op, this.valueSet.jsonObj, this.valueSet.jsonObj);
     let list = new Designations(this.worker.languages);
     let ok = false;
+    let matchedCodings = new Set();
     let codelist = '';
     mt = [];
     let i = 0;
@@ -1080,6 +1083,9 @@ class ValueSetChecker {
       if (v === false) {
         cause.value = 'code-invalid';
       }
+      if (v === true) {
+        matchedCodings.add(i);
+      }
       let ws;
       if (impliedSystem.value) {
         ws = impliedSystem.value;
@@ -1247,6 +1253,17 @@ class ValueSetChecker {
               c.version = prov.version();
             }
             await this.worker.listDisplaysFromCodeSystem(list, prov, ctxt.context);
+            // the code resolved in the code system, so its status is known whether or not it
+            // turns out to be in the value set. check() only picks the status up on the paths
+            // where the code was found in the value set, so pick it up here for the rest
+            if (!this.params.membershipOnly && !inactive.value && await prov.isInactive(ctxt.context)) {
+              inactive.value = true;
+              inactive.path = path;
+              const st = await prov.getStatus(ctxt.context);
+              if (st) {
+                vstatus.value = st;
+              }
+            }
             let pd = list.preferredDisplay(this.params.workingLanguages());
             if (pd) {
               pdisp = pd;
@@ -1288,6 +1305,36 @@ class ValueSetChecker {
       }
       i++;
     }
+
+    // A required binding on a CodeableConcept is satisfied when ANY coding is in the value set, so
+    // a coding whose code system could not be resolved must not veto a membership that another
+    // coding has confirmed. It is still reported, but as a warning, and with a message that does
+    // not read as though nothing could be validated (hapifhir/org.hl7.fhir.core#2272).
+    if (issuePath === 'CodeableConcept' && matchedCodings.size > 0) {
+      const notChecked = ['UNKNOWN_CODESYSTEM', 'UNKNOWN_CODESYSTEM_VERSION', 'UNKNOWN_CODESYSTEM_VERSION_NONE'];
+      let j = 0;
+      for (let c of code.coding || []) {
+        if (!matchedCodings.has(j)) {
+          let sysPath = issuePath + '.coding[' + j + '].system';
+          for (let iss of op.jsonObj.issue || []) {
+            let mid = (iss.extension || []).find(e => e.url === 'http://hl7.org/fhir/StructureDefinition/operationoutcome-message-id');
+            if (iss.severity === 'error' && mid && notChecked.includes(mid.valueString) && (iss.expression || []).includes(sysPath)) {
+              let was = iss.details.text;
+              let now = this.worker.i18n.translate('UNKNOWN_CODESYSTEM_CODING_NOT_CHECKED', this.params.HTTPLanguages,
+                [c.version ? c.system + '|' + c.version : c.system]);
+              iss.severity = 'warning';
+              iss.details.text = now;
+              mid.valueString = 'UNKNOWN_CODESYSTEM_CODING_NOT_CHECKED';
+              // the summary message is built from mt, so it has to say the same thing
+              mt = mt.filter(t => t !== was);
+              msg(now);
+            }
+          }
+        }
+        j++;
+      }
+    }
+
     // for an internally defined value set (CodeSystem validation), the code-system-level
     // message is preferred - but if nothing produced an error, this is the only
     // explanation there will be, so it can't be suppressed
@@ -1321,7 +1368,10 @@ class ValueSetChecker {
       }
     }
 
-    result.addParamBool('result', ok === true && !op.hasErrors());
+    // the answer, which is not the same as ok: a coding can be in the value set and still carry an
+    // error of its own (an unknown version, say), and then the CodeableConcept is not valid
+    let valid = ok === true && !op.hasErrors();
+    result.addParamBool('result', valid);
     if (psys) {
       result.addParamUri('system', psys);
     } else if (ok === true && impliedSystem.value) {
@@ -1333,9 +1383,10 @@ class ValueSetChecker {
     for (let us of unknownSystems) {
       if (ok === false) {
         result.addParamCanonical('x-unknown-system', us);
-      } else {
+      } else if (!valid) {
         result.addParamCanonical('x-caused-by-unknown-system', us);
       }
+      // if the CodeableConcept is valid, the unknown system caused nothing: neither parameter applies
     }
     if (normalForm.value) {
       result.addParamCode('normalized-code', normalForm.value);
@@ -1478,7 +1529,11 @@ class ValueSetChecker {
           list.allowedDisplays(ts2, null, defLang.value);
           let mid = 'INACTIVE_DISPLAY_FOUND';
           let m = this.worker.i18n.translatePlural(ts2.length, mid, this.params.HTTPLanguages, [c.display, c.code, ts2.join(','), list.status(c.display)]);
-          op.addIssue(new Issue('warning', 'invalid', addToPath(path, 'display'), mid, m, 'display-comment'));
+          // The display IS a designation of this concept, just not a current one,
+          // so lenient-display-validation decides whether that fails the code:
+          // a warning (and result true) when lenient, an error when not - the
+          // same rule the other display checks use.
+          op.addIssue(new Issue(this.dispWarning(), 'invalid', addToPath(path, 'display'), mid, m, 'display-comment'));
         }
       }
     }
@@ -1529,7 +1584,7 @@ class ValueSetChecker {
         let msg = this.worker.i18n.translate('INACTIVE_CONCEPT_FOUND', this.params.HTTPLanguages, [vstatus.value, code]);
         messages.push(msg);
         op.addIssue(new Issue('warning', 'business-rule', 'code', 'INACTIVE_CONCEPT_FOUND', msg, 'code-comment'));
-      } else if (vstatus.value.toLowerCase() === 'deprecated') {
+      } else if (vstatus.value && vstatus.value.toLowerCase() === 'deprecated') {
         result.addParamCode('status', vstatus.value);
         let msg = this.worker.i18n.translate('DEPRECATED_CONCEPT_FOUND', this.params.HTTPLanguages, [vstatus.value, code]);
         messages.push(msg);
@@ -1563,7 +1618,7 @@ class ValueSetChecker {
       let loc = await cs.locate(code);
       result = false;
       if (loc.context == null) {
-        this.worker.opContext.addNote(this.valueSet, 'Code "' + code + '" not found in ' + this.worker.renderer.displayCoded(cs)+": "+loc.mesage, this.indentCount);
+        this.worker.opContext.addNote(this.valueSet, 'Code "' + code + '" not found in ' + this.worker.renderer.displayCoded(cs)+": "+loc.message, this.indentCount);
         if (!this.params.membershipOnly && role !== 'not in') {
           if (cs.contentMode() !== 'complete') {
             op.addIssue(new Issue('warning', 'code-invalid', addToPath(path, 'code'), 'UNKNOWN_CODE_IN_FRAGMENT', this.worker.i18n.translate('UNKNOWN_CODE_IN_FRAGMENT', this.params.HTTPLanguages, [code, cs.system(), cs.version()]), 'invalid-code'));
@@ -1739,6 +1794,19 @@ class ValueSetChecker {
             if (!vcc.coding) { vcc.coding = []}
             vcc.coding.push( { system : cs.system(), version: cs.version(), code: await cs.code(loc), display: displays.preferredDisplay(this.params.workingLanguages())});
           }
+          if (role !== 'not in' && !inactive.value) {
+            if (await cs.isInactive(loc)) {
+              inactive.value = true;
+              inactive.path = path;
+              // only replace a status we already have with a real one - a filter context
+              // doesn't always carry the status (SNOMED, LOINC), and the assembly reads
+              // vstatus for the message wording as well as for the status parameter
+              const st = await cs.getStatus(loc);
+              if (st) {
+                vstatus.value = st;
+              }
+            }
+          }
           result = true;
           return result;
         }
@@ -1869,56 +1937,6 @@ function addToPath(path, name) {
 }
 
 
-function Unknown_Code_in_VersionSCT(url, version) {
-  if (url === 'http://snomed.info/sct') {
-    return 'Unknown_Code_in_Version_SCT';
-  } else if (version) {
-    return 'Unknown_Code_in_Version';
-  } else {
-    return 'Unknown_Code_in';
-  }
-}
-
-function SCTVersion(url, ver) {
-  if (url !== 'http://snomed.info/sct' || !ver) {
-    return '';
-  } else {
-    let result = 'unknown';
-    let s = ver.split('/');
-    if (s.length >= 5) {
-      if (s[4] === '900000000000207008') result = 'International Edition';
-      else if (s[4] === '449081005') result = 'International Spanish Edition';
-      else if (s[4] === '11000221109') result = 'Argentinian Edition';
-      else if (s[4] === '32506021000036107') result = 'Australian Edition (with drug extension)';
-      else if (s[4] === '11000234105') result = 'Austrian Edition';
-      else if (s[4] === '11000172109') result = 'Belgian Edition';
-      else if (s[4] === '20621000087109') result = 'Canadian English Edition';
-      else if (s[4] === '20611000087101') result = 'Canadian Canadian French Edition';
-      else if (s[4] === '11000279109') result = 'Czech Edition';
-      else if (s[4] === '554471000005108') result = 'Danish Edition';
-      else if (s[4] === '11000181102') result = 'Estonian Edition';
-      else if (s[4] === '11000229106') result = 'Finnish Edition';
-      else if (s[4] === '11000274103') result = 'German Edition';
-      else if (s[4] === '1121000189102') result = 'Indian Edition';
-      else if (s[4] === '827022005') result = 'IPS Terminology';
-      else if (s[4] === '11000220105') result = 'Irish Edition';
-      else if (s[4] === '11000146104') result = 'Netherlands Edition';
-      else if (s[4] === '21000210109') result = 'New Zealand Edition';
-      else if (s[4] === '51000202101') result = 'Norwegian Edition';
-      else if (s[4] === '11000267109') result = 'Republic of Korea Edition (South Korea)';
-      else if (s[4] === '900000001000122104') result = 'Spanish National Edition';
-      else if (s[4] === '45991000052106') result = 'Swedish Edition';
-      else if (s[4] === '2011000195101') result = 'Swiss Edition';
-      else if (s[4] === '83821000000107') result = 'UK Edition';
-      else if (s[4] === '999000021000000109') result = 'UK Clinical Edition';
-      else if (s[4] === '5631000179106') result = 'Uruguay Edition';
-      else if (s[4] === '21000325107') result = 'Chilean Edition';
-      else if (s[4] === '731000124108') result = 'US Edition';
-      else if (s[4] === '5991000124107') result = 'US Edition (with ICD-10-CM maps)';
-    }
-    return result;
-  }
-}
 
 
 function toText(st, sep) {
@@ -1984,8 +2002,7 @@ class ValidateWorker extends TerminologyWorker {
           // this is actually handled in the inner method
         }
       } else {
-        return res.status(error.statusCode || 500).json(this.operationOutcome(
-          'error', error.issueCode || 'exception', error.message));
+        return res.status(error.statusCode || 500).json(outcomeFromError(error));
       }
 
     }
@@ -2093,8 +2110,7 @@ class ValidateWorker extends TerminologyWorker {
     } catch (error) {
       this.log.error(error);
       debugLog(error);
-      return res.status(error.statusCode || 500).json(this.operationOutcome(
-        'error', error.issueCode || 'exception', error.message));
+      return res.status(error.statusCode || 500).json(outcomeFromError(error));
     }
   }
 
@@ -2119,8 +2135,7 @@ class ValidateWorker extends TerminologyWorker {
         op.addIssue(error);
         return res.status(error.statusCode || 500).json(op.jsonObj);
       } else {
-        return res.status(error.statusCode || 500).json(this.operationOutcome(
-          'error', error.issueCode || 'exception', error.message));
+        return res.status(error.statusCode || 500).json(outcomeFromError(error));
       }
     }
   }
@@ -2194,8 +2209,7 @@ class ValidateWorker extends TerminologyWorker {
     } catch (error) {
       this.log.error(error);
       debugLog(error);
-      return res.status(error.statusCode || 500).json(this.operationOutcome(
-        'error', error.issueCode || 'exception', error.message));
+      return res.status(error.statusCode || 500).json(outcomeFromError(error));
     }
   }
 
@@ -2535,18 +2549,9 @@ class ValidateWorker extends TerminologyWorker {
   /**
    * Build an OperationOutcome
    */
-  operationOutcome(severity, code, message) {
-    return {
-      resourceType: 'OperationOutcome',
-      issue: [{
-        severity,
-        code,
-        details: {
-          text: message
-        },
-        diagnostics: message
-      }]
-    };
+  operationOutcome(severity, code, message, txIssueType = null) {
+    // the shared builder, so that every outcome has details.text and a tx-issue-type coding
+    return buildOperationOutcome(severity, code, message, txIssueType);
   }
 
 

package/tx/workers/worker.js

@@ -137,9 +137,10 @@ class TerminologyWorker {
         }
       }
       const found = matches[latest];
-      if (this.additionalResourcesCacheId && this.log) {
-        this.log.info(`cache-id '${this.additionalResourcesCacheId}': using cached ${found.resourceType} ${found.url}${found.version ? '|' + found.version : ''} for lookup of ${url}${version ? '|' + version : ''}`);
-      }
+      // enable for logging
+      // if (this.additionalResourcesCacheId && this.log) {
+      //   this.log.info(`cache-id '${this.additionalResourcesCacheId}': using cached ${found.resourceType} ${found.url}${found.version ? '|' + found.version : ''} for lookup of ${url}${version ? '|' + version : ''}`);
+      // }
       return found;
     }
   }
@@ -462,7 +463,9 @@ class TerminologyWorker {
   /**
    * Process a ValueSet, recording context and extracting embedded expansion parameters
    * @param {Object} vs - ValueSet resource (raw JSON)
-   * @param {Object} params - Parameters resource to add extracted params to
+   * @param {TxParameters} params - the parameters to add what the ValueSet declares to.
+   *   Note: this is the caller's parameters, not this.params - the worker's own
+   *   params is null when expanding an imported ValueSet
    */
   seeValueSet(vs, params) {
     // Build canonical URL from url and version
@@ -482,12 +485,14 @@ class TerminologyWorker {
           if (nameExt && valueExt) {
             const name = nameExt.valueString || nameExt.valueCode;
             if (name) {
-              this.params.seeParameter(name, valueExt, false);
+              params.seeParameter(name, valueExt, false);
             }
           }
         }
       }
     }
+    // R6's ValueSet.compose.property
+    params.seeCompose(vs.jsonObj.compose);
     if (!params.FHTTPLanguages && vs.jsonObj.language) {
       params.HTTPLanguages = Languages.fromAcceptLanguage(vs.jsonObj.language, this.languages, !this.isValidating());
     }
@@ -666,9 +671,12 @@ class TerminologyWorker {
       // The cache must already exist: caches are created explicitly via
       // $cache-control?mode=start, which is the only thing that mints a cache-id.
       // A cache-id the server doesn't know is an unambiguous, server-authoritative
-      // error condition (never created, or expired / released) - report it with a
-      // specific coded issue rather than silently auto-creating a fresh cache and
-      // then failing obscurely later when a by-reference resource can't be found.
+      // error condition - report it with a specific coded issue rather than silently
+      // auto-creating a fresh cache and then failing obscurely later when a
+      // by-reference resource can't be found. The cache keeps a tombstone for every
+      // id it has retired, so describeMissing() names which fate this id met
+      // (never issued here / closed by the client / idle-expired) instead of
+      // offering the client a list of possibilities to guess between.
       if (!this.opContext.resourceCache.has(cacheId)) {
         // A comma in the cache-id means the request carried multiple X-Cache-Id
         // headers (Node joins duplicate headers with ", "): server-minted ids are
@@ -684,8 +692,12 @@ class TerminologyWorker {
             'started a second cache on a connection that already had one, without removing the first header.',
             'cache-id-duplicate', 400);
         }
-        throw new Issue('error', 'not-found', null, 'CACHE_ID_UNKNOWN',
-          this.i18n.translate('CACHE_ID_UNKNOWN', this.opContext.langs, [cacheId]),
+        // The issue *code* stays cache-id-unknown for every fate: clients switch on
+        // the coding, and all three mean the same thing to them (this cache is gone,
+        // don't retry). Only the human-readable diagnostics differ.
+        const { messageId, params } = this.opContext.resourceCache.describeMissing(cacheId);
+        throw new Issue('error', 'not-found', null, messageId,
+          this.i18n.translate(messageId, this.opContext.langs, params),
           'cache-id-unknown', 404);
       }
 
@@ -1050,8 +1062,77 @@ class TerminologyWorker {
   }
 }
 
+
+/**
+ * Choose the message id to use when reporting an unknown code, based on the
+ * code system and whether a version is known. SNOMED CT gets its own message
+ * because the edition is named in the message (see SCTVersion below)
+ * @param {string} url - code system url
+ * @param {string} version - code system version (may be null)
+ * @returns {string} message id
+ */
+function Unknown_Code_in_VersionSCT(url, version) {
+  if (url === 'http://snomed.info/sct') {
+    return 'Unknown_Code_in_Version_SCT';
+  } else if (version) {
+    return 'Unknown_Code_in_Version';
+  } else {
+    return 'Unknown_Code_in';
+  }
+}
+
+/**
+ * Human readable name for the SNOMED CT edition in a SNOMED CT version URI.
+ * Returns '' for anything that isn't a versioned SNOMED CT reference
+ * @param {string} url - code system url
+ * @param {string} ver - code system version
+ * @returns {string} edition name, or ''
+ */
+function SCTVersion(url, ver) {
+  if (url !== 'http://snomed.info/sct' || !ver) {
+    return '';
+  } else {
+    let result = 'unknown';
+    let s = ver.split('/');
+    if (s.length >= 5) {
+      if (s[4] === '900000000000207008') result = 'International Edition';
+      else if (s[4] === '449081005') result = 'International Spanish Edition';
+      else if (s[4] === '11000221109') result = 'Argentinian Edition';
+      else if (s[4] === '32506021000036107') result = 'Australian Edition (with drug extension)';
+      else if (s[4] === '11000234105') result = 'Austrian Edition';
+      else if (s[4] === '11000172109') result = 'Belgian Edition';
+      else if (s[4] === '20621000087109') result = 'Canadian English Edition';
+      else if (s[4] === '20611000087101') result = 'Canadian Canadian French Edition';
+      else if (s[4] === '11000279109') result = 'Czech Edition';
+      else if (s[4] === '554471000005108') result = 'Danish Edition';
+      else if (s[4] === '11000181102') result = 'Estonian Edition';
+      else if (s[4] === '11000229106') result = 'Finnish Edition';
+      else if (s[4] === '11000274103') result = 'German Edition';
+      else if (s[4] === '1121000189102') result = 'Indian Edition';
+      else if (s[4] === '827022005') result = 'IPS Terminology';
+      else if (s[4] === '11000220105') result = 'Irish Edition';
+      else if (s[4] === '11000146104') result = 'Netherlands Edition';
+      else if (s[4] === '21000210109') result = 'New Zealand Edition';
+      else if (s[4] === '51000202101') result = 'Norwegian Edition';
+      else if (s[4] === '11000267109') result = 'Republic of Korea Edition (South Korea)';
+      else if (s[4] === '900000001000122104') result = 'Spanish National Edition';
+      else if (s[4] === '45991000052106') result = 'Swedish Edition';
+      else if (s[4] === '2011000195101') result = 'Swiss Edition';
+      else if (s[4] === '83821000000107') result = 'UK Edition';
+      else if (s[4] === '999000021000000109') result = 'UK Clinical Edition';
+      else if (s[4] === '5631000179106') result = 'Uruguay Edition';
+      else if (s[4] === '21000325107') result = 'Chilean Edition';
+      else if (s[4] === '731000124108') result = 'US Edition';
+      else if (s[4] === '5991000124107') result = 'US Edition (with ICD-10-CM maps)';
+    }
+    return result;
+  }
+}
+
 module.exports = {
   TerminologyWorker,
   TerminologySetupError,
-  CACHE_ID_HEADER
+  CACHE_ID_HEADER,
+  Unknown_Code_in_VersionSCT,
+  SCTVersion
 };