lforms 29.3.0 → 33.2.0

package/app/scripts/fhir/diagnostic-report.js

@@ -1,707 +0,0 @@
-/**
- * A package to handle FHIR DiagnosticReport for LForms
- * https://www.hl7.org/fhir/diagnosticreport.html
- *
- * Note that this was written for DSTU2 and has not been updated.
- *
- * It provides the following functions:
- * createDiagnosticReport()
- * -- Convert existing LOINC panels/forms data in LForms format into FHIR DiagnosticReport data
- * mergeDiagnosticReportToLForms()
- * -- Merge FHIR SDC DiagnosticReport data into corresponding LForms data
- */
-
-var LForms = require('../lforms-index');
-
-var dr = {
-
-  // a prefix for references to Observation resources
-  _OBX_REF_PREFIX: "Observation/",
-
-
-  /**
-   * Functions for creating a DiagnosticReport instance from an LFormsData object
-   */
-
-  /** Get date in a standard string format
-   * @param dateObj, a date object
-   * @returns {string} a formatted date string
-   * @private
-   */
-  _getFormattedDate : function (dateObj) {
-    //"2013-01-27T11:45:33+11:00",
-    return dateObj ? LForms.Util.dateToDTMString(dateObj) : "";
-  },
-
-
-  /**
-   * Get the additional data in a form's formHeaderItems
-   * Note: For DiagnosticReport only the effectiveDateTime is needed
-   * @param formData an LFormsData object
-   * @returns {{}} the extra data captured in the "OBR" fields of an LForms form
-   * @private
-   */
-  _getExtensionData : function(formData) {
-    var extension = {};
-    if (formData.templateOptions.formHeaderItems &&
-        formData.templateOptions.formHeaderItems.length>0) {
-      for(var i=0, iLen= formData.templateOptions.formHeaderItems.length; i<iLen; i++) {
-        var obrItem = formData.templateOptions.formHeaderItems[i];
-        if (obrItem.questionCode === 'date_done' && obrItem.value) {
-          extension["lforms_dateDone"] = obrItem.value;
-        }
-
-        if (obrItem.questionCode === 'where_done' && obrItem.value) {
-          extension["lforms_whereDone"] = {
-            display: obrItem.value.text
-          }
-        }
-        if (obrItem.questionCode === 'time_done' && obrItem.value) {
-          extension["lforms_timeDone"] = obrItem.value;
-        }
-        if (obrItem.questionCode === 'comment' && obrItem.value) {
-          extension["lforms_comments"] = obrItem.value;
-        }
-
-      }
-    }
-    return extension;
-  },
-
-
-  /**
-   * A recursive function that generates the DiagnosticReport content by
-   * going through the LForms form data structure
-   * @param item an LForms item
-   * @param contained the "contained" field in a DiagnosticReport where all the Observation instances are kept.
-   * @returns {{result: Array, resultObj: Array}} the content part of a Diagnostic Report instance
-   * @private
-   */
-  _createDiagnosticReportContent : function (item, contained) {
-    // return the content of "result" and "contained"
-    var content = {
-      result: [],
-      resultObj: []
-    };
-
-    for(var i=0, iLen=item.items.length; i<iLen; i++) {
-      var subItem = item.items[i];
-      if (subItem) {
-        var obx = this._commonExport._createObservation(subItem, true);
-        if (subItem.items && subItem.items.length>0) {
-          // single obx returned if it is a header item
-          obx[0].related = [];
-          var ret = this._createDiagnosticReportContent(subItem, contained);
-          for(var j=0, jLen=ret.result.length; j<jLen; j++) {
-            var subObxRef = ret.result[j];
-            obx[0].related.push({
-              type: "has-member",
-              target: {
-                reference: subObxRef.reference
-              }
-            });
-          }
-        }
-        for (var l=0, lLen=obx.length; l<lLen; l++) {
-          contained.push(obx[l]);
-          content.result.push({
-            reference: "#" + obx[l].id
-          });
-          content.resultObj.push(obx[l]);
-        }
-      }
-    }
-    return content;
-  },
-
-
-  /**
-   * Convert a DiagnosticReport resource with contained Observation resources to
-   * a FHIR Bundle resource that includes a DiagnosticReport resource and associated Observation resources
-   * @param dr a DiagnosticReport resource with contained Observation resources
-   * @param bundleType the FHIR Bundle type. Only "transaction" and "collection" types are allowed.
-   * @returns {{}} a Bundle resource that includes a DiagnosticReport resource and associated Observation resources
-   */
-  _convertFromContainedToBundle: function (dr, bundleType) {
-    var bundleDr = {};
-
-    // default bundleType
-    if (!bundleType) {
-      bundleType = "transaction";
-    }
-    if (dr) {
-      switch(bundleType) {
-        case "transaction":
-          bundleDr = this._convertContainedToTransactionBundle(dr);
-          break;
-        case "collection":
-          bundleDr = this._convertContainedToCollectionBundle(dr);
-          break;
-        default:
-          console.log("Bundle type not supported: " + bundleType);
-      }
-    }
-    return bundleDr;
-  },
-
-
-  /**
-   * Convert a DiagnosticReport resource with contained Observation resources to
-   * a FHIR "transaction" typed Bundle resource that includes a DiagnosticReport resource
-   * and associated Observation resources
-   * @param dr a DiagnosticReport resource with contained Observation resources
-   * @returns {{}} a Bundle resource that includes a DiagnosticReport resource and associated Observation resources
-   * @private
-   */
-  _convertContainedToTransactionBundle: function(dr) {
-
-    var bundleDr = {
-      resourceType:"Bundle",
-      type: "transaction",
-      entry: []
-    };
-
-    var contained = dr.contained;
-    delete dr.contained;
-
-    // update reference to Observation resources
-    for (var i=0, iLen=dr.result.length; i<iLen; i++) {
-      var ref = dr.result[i];
-      ref.reference = this._OBX_REF_PREFIX + ref.reference.slice(1);
-    }
-    // add DiagnosticReport resource into Bundle entry
-    bundleDr.entry.push({
-      resource: dr,
-      request: {
-        method: "POST",
-        url: "DiagnosticReport"
-      }
-    });
-
-    // add Observation resources into Bundle entry
-    for (var j=0, jLen=contained.length; j<jLen; j++) {
-      var res = contained[j];
-
-      // if it has related Observation resources (as it is a section in LForms)
-      // update values of the references to the related Observation resources
-      if (res.related) {
-        for (var k=0, kLen=res.related.length; k<kLen; k++) {
-          var targetObservation = res.related[k];
-          targetObservation.target.reference = this._OBX_REF_PREFIX + targetObservation.target.reference.slice(1);
-        }
-      }
-
-      // add to the Bundle entry
-      bundleDr.entry.push({
-        resource: res,
-        request: {
-          method: "POST",
-          url: "Observation"
-        }
-      });
-    }
-
-    return bundleDr;
-  },
-
-
-  /**
-   * Convert a DiagnosticReport resource with contained Observation resources to
-   * a FHIR "collection" typed Bundle resource that includes a DiagnosticReport resource
-   * and associated Observation resources
-   * @param dr a DiagnosticReport resource with contained Observation resources
-   * @returns {{}} a Bundle resource that includes a DiagnosticReport resource and associated Observation resources
-   * @private
-   */
-  _convertContainedToCollectionBundle: function(dr) {
-    var bundleDr = {
-      resourceType:"Bundle",
-      type: "collection",
-      entry: []
-    };
-
-    var contained = dr.contained;
-    delete dr.contained;
-
-    // add DiagnosticReport resource into Bundle entry
-    bundleDr.entry.push({
-      resource: dr
-    });
-
-    // add Observation resources into Bundle entry
-    for (var j=0, jLen=contained.length; j<jLen; j++) {
-      var res = contained[j];
-      // add to the Bundle entry
-      bundleDr.entry.push({
-        resource: res
-      });
-    }
-
-    return bundleDr;
-  },
-
-
-  /**
-   * Generate FHIR DiagnosticReport data from an LForms form data
-   * @param formData an LFormsData object
-   * @param subject optional, A local FHIR resource that is the subject for this
-   *  DiagnoticReport.
-   * @param inBundle optional, a flag that a DiagnosticReport resources and associated Observation resources
-   *        should be placed into a FHIR Bundle. The default is false.
-   * @param bundleType, optional, the FHIR Bundle type if inBundle is true.
-   *        Only "transaction" and "collection" types are allowed.
-   * @returns {{}} a Diagnostic Report instance
-   */
-  createDiagnosticReport : function(formData, subject, inBundle, bundleType) {
-    var dr = null, contained =[];
-    if (formData) {
-
-      var formAndUserData = formData.getFormData(true,true,true);
-
-      var drContent = this._createDiagnosticReportContent(formAndUserData, contained);
-
-      dr = {
-        resourceType: "DiagnosticReport",
-        id: this._commonExport._getUniqueId(formAndUserData.code),
-        status: "final",
-        code: {
-          "coding": [
-            {
-              "system": "http://loinc.org",
-              "code": formAndUserData.code,
-              "display": formAndUserData.name
-            }
-          ],
-          "text": formAndUserData.name
-        },
-        result: drContent.result,
-        contained: contained
-      };
-      this._commonExport._addVersionTag(dr);
-
-      if (subject)
-        dr.subject = LForms.Util.createLocalFHIRReference(subject);
-
-      // obr data
-      var extension = this._getExtensionData(formAndUserData);
-      if (extension["lforms_dateDone"]) {
-        dr["effectiveDateTime"] = extension["lforms_dateDone"];
-      }
-      // issued
-      dr["issued"] = this._getFormattedDate(new Date());
-    }
-
-    var ret = inBundle ? this._convertFromContainedToBundle(dr, bundleType) : dr;
-    LForms.Util.pruneNulls(ret);
-    return ret;
-  },
-
-
-  /**
-   * Functions for merging a DiagnosticReport instance into an LFormsData object
-   */
-
-  /**
-   * Find an observation from the "contained" list by an observation id
-   * @param refId an observation instance's id
-   * @param contained the "contained" field in a DiagnosticReport instance
-   * @returns {{}} an observation instance
-   * @private
-   */
-  _findObxById : function(refId, contained) {
-    var obx = null;
-    if (refId) {
-      var id = refId[0] === "#" ? refId.slice(1) : refId;
-      for(var i=0, iLen=contained.length; i<iLen; i++) {
-        if (contained[i].id === id) {
-          obx = contained[i];
-          break;
-        }
-      }
-    }
-    return obx;
-  },
-
-
-  /**
-   * Merge an Observation instance into an item object
-   * @param obx an observation instance
-   * @param item an item in an LForms object
-   * @private
-   */
-  _setupItemValueAndUnit : function(obx, item) {
-    if (item && obx.code.coding[0].code === item.questionCode) {
-      var dataType = item.dataType;
-      // any one has a unit must be a numerical type, let use REAL for now.
-      // dataType conversion should be handled when panel data are added to lforms-service.
-      if ((!dataType || dataType==="ST") && item.units && item.units.length>0 ) {
-        dataType = "REAL";
-      }
-
-      switch (dataType) {
-        case "INT":
-          if (obx.valueInteger) {
-            item.value = obx.valueInteger;
-            break;
-          }
-          // else handle as Quantity
-        case "REAL": // handle as Quantity
-        case "QTY":
-          let qty = obx.valueQuantity;
-          item.value = qty.value;
-          let unitName = qty.unit || qty.code;
-          if (unitName || qty.code || qty.system) {
-            item.unit = {};
-            if (unitName)
-              item.unit.name = unitName;
-            if (qty.code)
-              item.unit.code = qty.code;
-            if (qty.system)
-              item.unit.system = qty.system;
-          }
-          break;
-        case "DT":
-          item.value = LForms.Util.stringToDTDateISO(obx.valueDate);
-          break;
-        case "DTM":
-          item.value = LForms.Util.stringToDate(obx.valueDateTime);
-          break;
-        case "CNE":
-        case "CWE":
-          // get the value from Observation resource.
-          // for multiple-selected answers/values in LForms, each selected answer is exported as
-          // a separated Observation resource
-          var itemValue;
-          if (obx.valueCodeableConcept) {
-            itemValue = {
-              "code": obx.valueCodeableConcept.coding[0].code,
-              "text": obx.valueCodeableConcept.coding[0].display,
-              "codeSystem": obx.valueCodeableConcept.coding[0].system
-            };
-          }
-          else if (obx.valueString) {
-            itemValue = obx.valueString;
-          }
-
-          if (item.answerCardinality &&
-              (item.answerCardinality.max === "*" || parseInt(item.answerCardinality.max) > 1)) {
-            if (!item.value) {
-              item.value = [];
-            }
-            item.value.push(itemValue)
-          }
-          else {
-            item.value = itemValue;
-          }
-          break;
-        case "SECTION":
-        case "TITLE":
-        case "":
-          // do nothing
-          break;
-        default:
-          item.value = obx.valueString;
-      }
-    }
-  },
-
-
-  /**
-   * Find the number of the repeating items that have the same code
-   * in the "contained" field of a DiagnosticReport instance
-   * @param refIdList a list Observation instance IDs to be checked
-   * @param code an item code
-   * @param contained a list of Observation instances (in the "contained")
-   * @returns a structural info object for a repeating item
-   * of the repeating items
-   * @private
-   */
-  _findTotalRepeatingNum : function(refIdList, code, contained) {
-
-    var total = 0;
-    var refIds = [];
-    for (var i=0, iLen=refIdList.length; i<iLen; i++) {
-      var obx = this._findObxById(refIdList[i], contained);
-      if (obx.code.coding[0].code === code) {
-        refIds.push(refIdList[i]);
-        total += 1;
-      }
-    }
-
-    return {
-      total: total,
-      refIds: refIds
-    }
-  },
-
-
-  /**
-   * Get structural info of a DiagnosticReport by going though each level of observations
-   * @param parentObxInfo the structural info of a parent Observation
-   * @param parentRefId the instance ID of a parent Observation
-   * @param diagnosticReport a DiagnosticReport instance
-   * @private
-   */
-  _checkRepeatingItems : function(parentObxInfo, parentRefId, diagnosticReport) {
-
-    var obxInfoList = [];
-    var repeatingItemInfo = {};
-    var obxIdList = [];
-
-    // the report level
-    if (!parentRefId && diagnosticReport.result) {
-      for (var i=0, iLen=diagnosticReport.result.length; i<iLen; i++) {
-        obxIdList.push(diagnosticReport.result[i].reference);
-      }
-    }
-    // obx level
-    else {
-      var parentObx = this._findObxById(parentRefId, diagnosticReport.contained);
-      if (parentObx && parentObx.related) {
-        for (var i=0, iLen=parentObx.related.length; i<iLen; i++) {
-          obxIdList.push(parentObx.related[i].target.reference);
-        }
-      }
-    }
-
-    // go through each observation instance
-    for (var i=0, iLen=obxIdList.length; i<iLen; i++) {
-      var refId = obxIdList[i];
-      var obx = this._findObxById(refId, diagnosticReport.contained);
-      var itemCode =  obx.code.coding[0].code;
-      // first obx that has the same item code, either repeating or non-repeating
-      if (!repeatingItemInfo[itemCode]) {
-        var repeatingInfo = this._findTotalRepeatingNum(obxIdList, itemCode, diagnosticReport.contained);
-        repeatingItemInfo[itemCode] = {
-          total: repeatingInfo.total,
-          refIds: repeatingInfo.refIds
-        };
-      }
-      // create structure info for the obx
-      var repeatingRefIds = repeatingItemInfo[itemCode].refIds;
-      for (var j=0, jLen=repeatingRefIds.length; j<jLen; j++) {
-        if (refId === repeatingRefIds[j]) {
-          var obxInfo = {
-            code: itemCode,
-            refId: refId,
-            index: j,
-            total: repeatingItemInfo[itemCode].total
-          };
-          // check observation instances in the sub level
-          this._checkRepeatingItems(obxInfo, refId, diagnosticReport);
-          obxInfoList.push(obxInfo);
-        }
-      }
-    }
-    parentObxInfo.obxInfoList = obxInfoList;
-  },
-
-
-  /**
-   * Get structure information of a DiagnosticReport instance
-   * @param diagnosticReport a DiagnosticReport instance
-   * @returns {{}} a Diagnostic Report data structure object
-   * @private
-   */
-  _getReportStructure : function(diagnosticReport) {
-    var reportStructure = {
-      obxInfoList: []
-    };
-
-    if (diagnosticReport) {
-      this._checkRepeatingItems(reportStructure, null, diagnosticReport);
-    }
-    return reportStructure;
-  },
-
-
-  /**
-   * Find a matching repeating item
-   * @param parentItem a parent item
-   * @param itemCode code of a repeating (or non-repeating) item
-   * @param index index of the item in the sub item array of the parent item
-   * @returns {{}} a matching item
-   * @private
-   */
-  _findTheMatchingItemByCodeAndIndex : function(parentItem, itemCode, index) {
-    var item = null;
-    var idx = 0;
-    if (parentItem.items) {
-      for(var i=0, iLen=parentItem.items.length; i<iLen; i++) {
-        var subItem = parentItem.items[i];
-        if (itemCode === subItem.questionCode) {
-          if ((subItem.dataType === "CNE" || subItem.dataType === "CWE") &&
-              subItem.answerCardinality && (subItem.answerCardinality.max ==="*" || parseInt(subItem.answerCardinality.max)>1) ) {
-            item = subItem;
-            break;
-
-          }
-          else if (idx === index) {
-            item = subItem;
-            break;
-          }
-          else {
-            idx += 1;
-          }
-        }
-      }
-    }
-    return item;
-  },
-
-
-  /**
-   * Add repeating items
-   * @param parentItem a parent item
-   * @param itemCode code of a repeating item
-   * @param total total number of the repeating item with the same code
-   * @private
-   */
-  _addRepeatingItems : function(parentItem, itemCode, total) {
-    // find the first (and the only one) item
-    var item = null;
-    if (parentItem.items) {
-      for(var i=0, iLen=parentItem.items.length; i<iLen; i++) {
-        if (itemCode === parentItem.items[i].questionCode) {
-          item = parentItem.items[i];
-          break;
-        }
-      }
-      // insert new items unless it is a CNE/CWE and has multiple answers.
-      if (item && !((item.dataType === "CNE" || item.dataType ==="CWE") &&
-          item.answerCardinality &&
-          (item.answerCardinality.max === "*" || parseInt(item.answerCardinality.max) > 1))) {
-        while(total > 1) {
-          var newItem = LForms.Util.deepCopy(item);
-          parentItem.items.splice(i, 0, newItem);
-          total -= 1;
-        }
-      }
-    }
-  },
-
-
-  /**
-   * Merge Observation instances into items on the same level
-   * @param parentObxInfo structural information of a parent item
-   * @param parentItem a parent item
-   * @param diagnosticReport a DiagnosticReport instance
-   * @private
-   */
-  _processObxAndItem : function(parentObxInfo, parentItem, diagnosticReport) {
-    for(var i=0, iLen=parentObxInfo.obxInfoList.length; i<iLen; i++) {
-
-      var obxInfo = parentObxInfo.obxInfoList[i];
-      var obx = this._findObxById(obxInfo.refId, diagnosticReport.contained);
-      if (obx) {
-        // first repeating obx
-        if (obxInfo.total > 1 && obxInfo.index === 0) {
-          // add repeating items in form data
-          this._addRepeatingItems(parentItem, obxInfo.code, obxInfo.total);
-        }
-
-        var item = this._findTheMatchingItemByCodeAndIndex(parentItem, obxInfo.code, obxInfo.index);
-        this._setupItemValueAndUnit(obx, item);
-
-        // process items on sub level
-        if (obxInfo.obxInfoList && obxInfo.obxInfoList.length>0) {
-          this._processObxAndItem(obxInfo, item, diagnosticReport);
-        }
-      }
-    }
-  },
-
-  /**
-   * Convert a FHIR Bundle resource that includes a DiagnosticReport resource and associated Observation resources
-   * to a DiagnosticReport resource with contained Observation resources
-   * @param bundleDr a Bundle that includes a DiagnosticReport resource and associated Observation resources.
-   *        Only "searchset" type is allowed.
-   * @returns {{}} a DiagnosticReport resource with contained Observation resources
-   */
-  _convertFromBundleToContained: function (bundleDr) {
-
-    var containedDr;
-    // "searchset" is the only supported type at this point.
-    if (bundleDr && bundleDr.type === "searchset") {
-      var entry = bundleDr.entry;
-      // find the DiagnosticReport in the bundle
-      for (var i=0, iLen=entry.length; i<iLen; i++) {
-        if (entry[i].resource.resourceType === "DiagnosticReport") {
-          containedDr = entry[i].resource;
-          // change reference ids in result
-          for (var j=0, jLen=containedDr.result.length; j<jLen; j++) {
-            var ref = containedDr.result[j];
-            if (ref.reference && ref.reference.match(new RegExp(this._OBX_REF_PREFIX))) {
-              ref.reference = ref.reference.slice(this._OBX_REF_PREFIX.length);
-            }
-          }
-          containedDr.contained =[];
-          break;
-        }
-      }
-      // if DiagnosticReport is found
-      if (containedDr) {
-        // Move all Observation resource into "contained" field of the DiagnosticReport resource
-        for (var i=0, iLen=entry.length; i<iLen; i++) {
-          if (entry[i].resource.resourceType === "Observation") {
-            var obx = entry[i].resource;
-            // change reference ids in related
-            if (obx.related) {
-              for (var j=0, jLen=obx.related.length; j<jLen; j++) {
-                var related = obx.related[j];
-                if (related.target && related.target.reference &&
-                    related.target.reference.match(new RegExp(this._OBX_REF_PREFIX))) {
-                  related.target.reference = related.target.reference.slice(this._OBX_REF_PREFIX.length);
-                }
-              }
-            }
-            containedDr.contained.push(obx)
-          }
-        }
-      }
-    }
-
-    return containedDr;
-  },
-
-
-  /**
-   * Merge a DiagnosticReport instance into an LForms form definition or LFormsData object
-   * @param formData an LForms form definition or LFormsData object.
-   * @param diagnosticReport a DiagnosticReport resource with contained Observation resources,
-   * or a Bundle that includes a DiagnosticReport resource and associated Observation resources
-   * @param bundleType, optional, the FHIR Bundle type if inBundle is true.
-   * @returns {{}} an updated LForms form definition, with answer data
-   */
-  mergeDiagnosticReportToLForms : function(formData, diagnosticReport) {
-
-    if (!(formData instanceof LForms.LFormsData)) {
-      // get the default settings in case they are missing in the form data
-      // not to set item values by default values for saved forms with user data
-      formData.hasSavedData = true;
-      formData = (new LForms.LFormsData(formData)).getFormData();
-    }
-
-    var inBundle = diagnosticReport && diagnosticReport.resourceType === "Bundle";
-
-    // move Observation resources in Bundle to be in "contained" in DiagnosticReport resource
-    // as a base data structure for converting
-    var dr = inBundle ? this._convertFromBundleToContained(diagnosticReport) : diagnosticReport;
-
-    var reportStructure = this._getReportStructure(dr);
-
-    this._processObxAndItem(reportStructure, formData, dr);
-
-    // date
-    if (dr.effectiveDateTime && formData.templateOptions.formHeaderItems) {
-      var whenDone = new LForms.Util.dateToString(dr.effectiveDateTime);
-      if (whenDone) {
-        formData.templateOptions.formHeaderItems[0].value = whenDone;
-      }
-    }
-    return formData;
-  }
-
-};
-
-export default dr;