lforms 29.3.1 → 33.3.0

package/app/scripts/fhir/R4/sdc-export.js

@@ -1,455 +0,0 @@
-/**
- * A package to handle FHIR Questionnaire and SDC (STU2) Questionnaire and QuestionnaireResponse for LForms
- *
- * FHIR Questionnaire:
- * https://www.hl7.org/fhir/questionnaire.html
- *
- * R4 Ballot (3.5) for comment:
- * http://hl7.org/fhir/uv/sdc/2018Sep/sdc-questionnaire.html
- * http://hl7.org/fhir/uv/sdc/2018Sep/sdc-questionnaireresponse.html
- *
- * It provides the following functions:
- * convertLFormsToQuestionnaire()
- * -- Convert existing LOINC panels/forms data in LForms format into FHIR (standard or SDC) Questionnaire data
- * convertLFormsToQuestionnaireResponse()
- * -- Generate FHIR (standard or SDC) QuestionnaireResponse data from captured data in LForms
- */
-var sdcVersion = '2.7';
-var fhirVersionNum = '4.0';
-
-var self = {
-
-  SDCVersion: sdcVersion,
-  QProfile: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaire|'+sdcVersion,
-  QRProfile: 'http://hl7.org/fhir/uv/sdc/StructureDefinition/sdc-questionnaireresponse|'+sdcVersion,
-  stdQProfile: 'http://hl7.org/fhir/'+fhirVersionNum+'/StructureDefinition/Questionnaire',
-  stdQRProfile: 'http://hl7.org/fhir/'+fhirVersionNum+'/StructureDefinition/QuestionnaireResponse',
-
-  /**
-   *  Convert LForms captured data to a bundle consisting of a FHIR SDC
-   *  QuestionnaireResponse and any extractable resources. (Currently this means
-   *  any Observations that can be extracted via the observationLinkPeriod
-   *  extension).
-   *
-   * @param lfData a LForms form object
-   * @param noExtensions a flag that a standard FHIR Questionnaire is to be created without any extensions.
-   *  The default is false.
-   * @param subject A local FHIR resource that is the subject of the output resource.
-   *  If provided, a reference to this resource will be added to the output FHIR
-   *  resource when applicable.
-   * @returns an array of QuestionnaireResponse and Observations.  Observations
-   *  will have derivedFrom set to a temporary reference created for the returned
-   *  QuestionnaireResponse (the first element of the array). The caller may
-   *  wish to put all of the returned resources into a transaction Bundle for
-   *  creating them on a FHIR server.
-   */
-  convertLFormsToFHIRData: function(lfData, noExtensions, subject) {
-    var qr = this.convertLFormsToQuestionnaireResponse(lfData, noExtensions, subject);
-    if (!qr.id) {
-      qr.id = this._commonExport._getUniqueId(
-        qr.identifier && qr.identifier.value || 'QR')
-    }
-
-    var qrRef = 'QuestionnaireResponse/'+qr.id;
-    var rtn = [qr];
-    for (var i=0, len=lfData.itemList.length; i<len; ++i) {
-      var item = lfData.itemList[i];
-      if (self._getExtractValue(item) && item.value) {
-        var obs = this._commonExport._createObservation(item);
-        for (var j=0, jLen=obs.length; j<jLen; j++) {
-          // Following
-          // http://hl7.org/fhir/uv/sdc/2019May/extraction.html#observation-based-extraction
-          if (qr.basedOn)
-            obs[j].basedOn = qr.basedOn;
-          if (qr.partOf)
-            obs[j].partOf = qr.partOf;
-          if (qr.subject)
-            obs[j].subject = qr.subject;
-          if (qr.encounter)
-            obs[j].encounter = qr.encounter;
-          if (qr.authored) {
-            obs[j].effectiveDateTime = qr.authored;
-            obs[j].issued = qr.authored;
-          }
-          if (qr.author)
-            obs[j].performer = qr.author;
-          obs[j].derivedFrom = [{reference: qrRef}];
-
-          rtn.push(obs[j]);
-
-        }
-      }
-    }
-    return rtn;
-  },
-
-
-  /**
-   *  Proceses the LForms questionCardinality into FHIR.
-   * @param targetItem an item in Questionnaire
-   * @param item a LForms item
-   */
-  _processQuestionCardinality: function(targetItem, item) {
-    if (item.questionCardinality) {
-      if (item.questionCardinality.max === "*") {
-        targetItem.repeats = true;
-      }
-      else if (parseInt(item.questionCardinality.max) > 1) {
-        targetItem.repeats = true;
-        targetItem.extension.push({
-          "url": "http://hl7.org/fhir/StructureDefinition/questionnaire-maxOccurs",
-          "valueInteger": parseInt(item.questionCardinality.max)
-        });
-      }
-    }
-    else {
-      // No default in R4
-      // targetItem.repeats = false;
-    }
-  },
-
-
-  /**
-   * Handle special requirements for 'display' items
-   * @param targetItem an item in Questionnaire
-   * @param item a LForms item
-   * @private
-   */
-  _handleSpecialConstraints: function(targetItem, item) {
-    //Display items cannot have a "code" asserted
-    //Required and repeat aren't permitted for display items
-    //Read-only can't be specified for "display" items
-    if (targetItem && item.dataType === "TITLE") {
-      delete targetItem.code;
-      delete targetItem.required;
-      delete targetItem.repeats;
-      delete targetItem.readOnly;
-    }
-  },
-
-
-  /**
-   * Process various restriction settings
-   * @param targetItem an item in FHIR SDC Questionnaire object
-   * @param item an item in LForms form object
-   * @private
-   */
-  _handleRestrictions: function(targetItem, item) {
-    // http://hl7.org/fhir/StructureDefinition/minLength
-    // http://hl7.org/fhir/StructureDefinition/regex
-    // http://hl7.org/fhir/StructureDefinition/minValue
-    // http://hl7.org/fhir/StructureDefinition/maxValue
-    // http://hl7.org/fhir/StructureDefinition/maxDecimalPlaces, not supported yet
-    // http://hl7.org/fhir/StructureDefinition/maxSize, for attachment, not supported yet
-    // maxLength
-    if (item.restrictions) {
-      for (var key in item.restrictions) {
-        var value = item.restrictions[key];
-        var extValue = null;
-        var dataType = this._getAssumedDataTypeForExport(item);
-        var valueKey = this._getValueKeyByDataType("value", item);
-
-        switch (key) {
-          // http://hl7.org/fhir/StructureDefinition/minValue
-          // { // Must be >= this value
-          //   // from Element: extension
-          //   "url" : "http://hl7.org/fhir/StructureDefinition/minValue", // R!
-          //   // value[x]: Value of extension. One of these 6:
-          //   "valueDate" : "<date>" // R! Value of extension
-          //   "valueDateTime" : "<dateTime>", // R! Value of extension
-          //   "valueTime" : "<time>", // R! Value of extension
-          //   "valueInstant" : "<instant>", // R! Value of extension
-          //   "valueDecimal" : <decimal>, // R! Value of extension
-          //   "valueInteger" : <integer>, // R! Value of extension
-          // }
-          case "minExclusive":
-          case "minInclusive":
-          // http://hl7.org/fhir/StructureDefinition/maxValue
-          case "maxExclusive":
-          case "maxInclusive":
-            extValue = this._exportMinMax(dataType, value, valueKey, key);
-            break;
-          // http://hl7.org/fhir/StructureDefinition/minLength
-          case "minLength":
-            if (dataType === "ST" || dataType === "TX" || dataType === "URL" ||
-                dataType === "QTY") {
-              extValue = {
-                "url":"http://hl7.org/fhir/StructureDefinition/minLength",
-                "valueInteger": parseInt(value)
-              };
-            }
-            break;
-          // maxLength, not an extension, directly on item
-          case "maxLength":
-            if (dataType === "ST" || dataType === "TX" || dataType === "URL" ||
-                dataType === "QTY") {
-              targetItem.maxLength = parseInt(value);
-            }
-            break;
-          // http://hl7.org/fhir/StructureDefinition/regex
-          case "pattern":
-            if (dataType === "ST" || dataType === "TX" ) {
-              extValue = {
-                "url":"http://hl7.org/fhir/StructureDefinition/regex",
-                "valueString": value
-              };
-            }
-            break
-        }
-        if (extValue) {
-          targetItem.extension.push(extValue);
-        }
-      }
-    }
-  },
-
-
-  /**
-   *  Processes settings for a list field with choices.
-   * @param targetItem an item in FHIR SDC Questionnaire object
-   * @param item an item in the LForms form object
-   * @param noExtensions a flag that a standard FHIR Questionnaire is to be created without any extensions.
-   *        The default is false.
-   */
-  _handleChoiceField: function(targetItem, item, noExtensions) {
-    // an extension for the search url of the auto-complete field.
-    if(item.externallyDefined) {
-      this._handleExternallyDefined(targetItem, item);
-    }
-    // option, for answer list
-    else if (item.answers && !item.answerValueSet) {
-      // Make sure the answers did not come from answerExpression.
-      if (!item._fhirExt || !item._fhirExt[this.fhirExtAnswerExp])
-        targetItem.answerOption = this._handleAnswers(item, noExtensions);
-    }
-    else if (item.answerValueSet)
-      targetItem.answerValueSet = item.answerValueSet;
-  },
-
-
-  /**
-   * Process an item's answer list
-   * @param item an item in the LForms form object
-   * @param noExtensions a flag that a standard FHIR Questionnaire is to be created without any extensions.
-   *        The default is false.
-   * @returns {Array}
-   * @private
-   */
-  _handleAnswers: function(item, noExtensions) {
-    var optionArray = [];
-    for (var i=0, iLen=item.answers.length; i<iLen; i++) {
-      var answer = item.answers[i];
-      var option = {};
-
-      // needs an extension for label
-      if (!noExtensions) {
-        var ext = [];
-        if(answer.label) {
-          ext.push({
-            "url" : "http://hl7.org/fhir/StructureDefinition/questionnaire-optionPrefix",
-            "valueString" : answer.label
-          });
-        }
-
-        if (answer.score !== null && answer.score !== undefined) {
-          ext.push({
-            "url" : "http://hl7.org/fhir/StructureDefinition/ordinalValue",
-            "valueDecimal" : parseFloat(answer.score)
-          });
-        }
-        if(ext.length > 0) {
-          option.extension = ext;
-        }
-      }
-      // option's value supports integer, date, time, string and Coding
-      // for LForms, all answers are Coding
-      option.valueCoding = {};
-      if (answer.code) option.valueCoding.code = answer.code;
-      if (answer.text) option.valueCoding.display = answer.text;
-
-      if (answer.system) {
-        option.valueCoding.system = LForms.Util.getCodeSystem(answer.system);
-      }
-
-      optionArray.push(option);
-    }
-    return optionArray;
-  },
-
-
-  /**
-   * Process default values
-   * @param targetItem an item in FHIR SDC Questionnaire object
-   * @param item an item in LForms form object
-   * @private
-   */
-  _handleInitialValues: function(targetItem, item) {
-    if(item.defaultAnswer === null || item.defaultAnswer === undefined || item.defaultAnswer === '') {
-      return;
-    }
-    // item.defaultAnswer could be an array of multiple default values or a single value
-    var defaultAnswers = (this._answerRepeats(item) && Array.isArray(item.defaultAnswer)) ?
-      item.defaultAnswer : [item.defaultAnswer];
-
-    var dataType = this._getAssumedDataTypeForExport(item);
-    var valueKey = this._getValueKeyByDataType("value", item);
-    var answer = null;
-    targetItem.initial = [];
-
-    // go through each default value and handle it based on the data type.
-    for(var i=0, iLen=defaultAnswers.length; i<iLen; i++ ) {
-      // dataType:
-      // boolean, decimal, integer, date, dateTime, instant, time, string, uri,
-      // Attachment, Coding, Quantity, Reference(Resource)
-
-      // for Coding
-      if (dataType === 'CWE' || dataType === 'CNE' ) {
-        // could be a code object or a string
-        if (typeof defaultAnswers[i] === 'object') {
-          var coding = {"code": defaultAnswers[i].code};
-          if(defaultAnswers[i].text !== undefined) {
-            coding.display = defaultAnswers[i].text;
-          }
-          // code system
-          var codeSystem = defaultAnswers[i].system || item.answerCodeSystem;
-          if (codeSystem) {
-            coding.system = LForms.Util.getCodeSystem(codeSystem);
-          }
-
-          answer = {};
-          answer[valueKey] = coding;
-          targetItem.initial.push(answer);
-        }
-        // user typed answer that is not on the answer list.
-        else if (typeof defaultAnswers[i] === 'string') {
-          targetItem.initial.push({
-            "valueString": defaultAnswers[i]
-          })
-        }
-      }
-      // for Quantity,
-      // [{
-      //   // from Element: extension
-      //   "value" : <decimal>, // Numerical value (with implicit precision)
-      //   "comparator" : "<code>", // < | <= | >= | > - how to understand the value
-      //   "unit" : "<string>", // Unit representation
-      //   "system" : "<uri>", // Code System that defines coded unit form
-      //   "code" : "<code>" // Coded form of the unit
-      // }]
-      else if (dataType === 'QTY') {  // for now, handling only simple quantities without the comparators.
-        answer = {};
-        answer[valueKey] = this._makeQuantity(defaultAnswers[i], item.units);
-        targetItem.initial.push(answer);
-      }
-      // for boolean, decimal, integer, date, dateTime, instant, time, string, uri
-      else if (dataType === "INT" || dataType === "REAL" || dataType === "BL" ||
-        dataType === "TM" || dataType === "ST" || dataType === "TX" || dataType === "URL") {
-        answer = {};
-        answer[valueKey] = defaultAnswers[i];
-        targetItem.initial.push(answer);
-      }
-      else if (dataType === "DT" || dataType === "DTM") { // transform to FHIR date/datetime format.
-        var dateValue = LForms.Util.stringToDate(defaultAnswers[i]);
-        if(dateValue) {
-          dateValue = dataType === "DTM"?
-            LForms.Util.dateToDTMString(dateValue): LForms.Util.dateToDTStringISO(dateValue);
-          targetItem.initial.push({[valueKey]: dateValue});
-        }
-        else { // LForms.Util.stringToDate returns null on invalid string
-          // TODO: should save the errors or emitting events.
-          console.error(defaultAnswers[i] + ': Invalid date/datetime string as defaultAnswer for ' + item.questionCode);
-        }
-      }
-      // no support for reference
-    }
-  },
-
-
-  /**
-   * Process units list
-   * @param targetItem an item in FHIR SDC Questionnaire object
-   * @param item an item in LForms form object
-   * @private
-   */
-  _handleLFormsUnits: function(targetItem, item) {
-
-    if (item.units && item.units.length > 0) {
-      var dataType = this._getAssumedDataTypeForExport(item);
-      if(dataType === "REAL" || dataType === "INT") {
-
-        targetItem.extension.push({
-          "url": this.fhirExtUrlUnit,
-          // Datatype with multiple units is quantity. There is only one unit here.
-          "valueCoding" : this._createFhirUnitCoding(item.units[0])
-        });
-      }
-      else if(dataType === 'QTY') {
-        var defUnit = this._getDefaultUnit(item.units);
-        // Skip if units are already set in default answer conversion.
-        if ((defUnit && defUnit.default) && !(targetItem.initial && targetItem.initial.length > 0)) {
-          // Use initial[].valueQuantity.unit to export the default unit.
-          if (!targetItem.initial) {
-            targetItem.initial = [];
-          }
-          var qty = {};
-          self._setUnitAttributesToFhirQuantity(qty, defUnit);
-          targetItem.initial.push({valueQuantity: qty});
-        }
-        for (var i=0, iLen=item.units.length; i<iLen; i++) {
-          var unit = item.units[i];
-          var fhirUnitExt = {
-            "url": this.fhirExtUrlUnitOption,
-            "valueCoding": self._createFhirUnitCoding(unit)
-          };
-          targetItem.extension.push(fhirUnitExt);
-        }
-      }
-    }
-  },
-
-
-  /**
-   * Process skip logic
-   * @param targetItem an item in FHIR SDC Questionnaire object
-   * @param item an item in LForms form object
-   * @param source a LForms form object
-   * @private
-   */
-  _handleSkipLogic: function(targetItem, item, source) {
-    if (item.skipLogic) {
-      var enableWhen = [];
-      var rangeFound = false;
-
-      // ignore "ANY", "ALL" on item.skipLogic.logic
-      // ignore "show" on item.skipLogic.action
-
-      for (var i=0, iLen=item.skipLogic.conditions.length; i<iLen; i++) {
-        var condition = item.skipLogic.conditions[i];
-        var sourceItem = source._getSkipLogicSourceItem(item,condition.source);
-        let enableWhenRules = self._createEnableWhenRulesForSkipLogicCondition(condition, sourceItem);
-
-        if(enableWhenRules.length > 1) {
-          rangeFound = true;
-        }
-        enableWhen = enableWhen.concat(enableWhenRules);
-      }
-
-      if(rangeFound && item.skipLogic.conditions.length > 1) {
-        // TODO: Multiple skip logic conditons included with range specification is not supported with core FHIR.
-        // Use SDC extensions with fhirpath expressions, but not all fhirpath functionality is
-        // available yet. Revisit after implementation of variables, %resource etc. in fhirpath.
-        throw new Error('Multiple skip logic conditons included with range specification is not supported yet.');
-      }
-
-      targetItem.enableWhen = enableWhen;
-      if(item.skipLogic.logic === 'ALL' || rangeFound) {
-        targetItem.enableBehavior = 'all';
-      }
-      else if(enableWhen.length > 1) {
-        targetItem.enableBehavior = 'any';
-      }
-    }
-  }
-};
-
-export default self;