fhirsmith 0.12.0 → 0.13.0

package/tx/workers/translate.js

@@ -10,7 +10,7 @@
 const { TerminologyWorker } = require('./worker');
 const { TxParameters } = require('../params');
 const { Parameters } = require('../library/parameters');
-const { Issue, OperationOutcome } = require('../library/operation-outcome');
+const { Issue, OperationOutcome, buildOperationOutcome, outcomeFromError } = require('../library/operation-outcome');
 const {ConceptMap} = require("../library/conceptmap");
 const {Extensions} = require("../library/extensions");
 const {VersionUtilities} = require("../../library/version-utilities");
@@ -62,8 +62,7 @@ class TranslateWorker extends TerminologyWorker {
         oo.addIssue(error);
         return res.status(error.statusCode || 500).json(oo.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));
       }
     }
   }
@@ -85,8 +84,7 @@ class TranslateWorker extends TerminologyWorker {
         oo.addIssue(error);
         return res.status(error.statusCode || 500).json(oo.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));
       }
     }
   }
@@ -1013,21 +1011,17 @@ class TranslateWorker extends TerminologyWorker {
     }
   }
   /**
-   * Build an OperationOutcome
+   * Build an OperationOutcome. Delegates to the shared builder so that every outcome this
+   * server emits has details.text and a tx-issue-type coding: diagnostics is stripped by
+   * the test harness, so nothing a caller needs may live there.
    * @param {string} severity - error, warning, information
-   * @param {string} code - Issue code
-   * @param {string} message - Diagnostic message
+   * @param {string} code - FHIR issue type
+   * @param {string} message - the human readable account of the problem
+   * @param {string} [txIssueType] - tx-issue-type; defaulted from code when not given
    * @returns {Object} OperationOutcome resource
    */
-  operationOutcome(severity, code, message) {
-    return {
-      resourceType: 'OperationOutcome',
-      issue: [{
-        severity,
-        code,
-        diagnostics: message
-      }]
-    };
+  operationOutcome(severity, code, message, txIssueType = null) {
+    return buildOperationOutcome(severity, code, message, txIssueType);
   }
 
   /**

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");
@@ -953,7 +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);
@@ -1051,6 +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;
@@ -1082,6 +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;
@@ -1249,6 +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;
@@ -1290,6 +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
@@ -1323,7 +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) {
@@ -1335,9 +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);
@@ -1535,7 +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);
@@ -1569,7 +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'));
@@ -1745,6 +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;
         }
@@ -1875,56 +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) {
@@ -1990,8 +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));
       }
 
     }
@@ -2099,8 +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));
     }
   }
 
@@ -2125,8 +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));
       }
     }
   }
@@ -2200,8 +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));
     }
   }
 
@@ -2541,18 +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

@@ -1062,8 +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
 };