blue-button-fhir - npm Package Compare versions

Comparing version 1.4.0 to 1.4.1

lib/fhir.js

 "use strict";
 
-var engine = require('./engine');
+var bbu = require('blue-button-util');
+
+var json2Json = require('./json2Json');
 var rootLogger = require('./logger');
-var resourceStore = require('./resourceStore');
+var templates = require('./templates');
 
-var condition = require('./resource/condition');
-var allergyIntolerance = require('./resource/allergyIntolerance');
-var observation_vital = require('./resource/observation-vital');
-var observation_result = require('./resource/observation-result');
-var observation_result_single = require('./resource/observation-result-single');
-var medicationAdministration = require('./resource/medicationAdministration');
-var medicationPrescription = require('./resource/medicationPrescription');
+var bbuobject = bbu.object;
 
@@ -19,4 +15,16 @@ var logger = rootLogger.child({
 
-var resourceToModel = exports.resourceToModel = function (store, resourceModel, resource) {
-    var resourceDict = Object.create(store.index);
+var toResourceDictionary = exports.toResourceDictionary = function (bundleEntries) {
+    var result = {};
+    if (bundleEntries) {
+        bundleEntries.forEach(function (bundleEntry) {
+            var resource = bundleEntry.content;
+            var id = bundleEntry.id;
+            result[id] = resource;
+        });
+    }
+    return result;
+};
+
+var resourceToModel = exports.resourceToModel = function (resourceDictionary, template, resource) {
+    var localResourceDictionary = Object.create(resourceDictionary);
     var contained = resource.contained;
@@ -26,13 +34,13 @@ if (contained) {
             var id = e.id;
-            resourceDict['#' + id] = e;
+            localResourceDictionary['#' + id] = e;
         });
     }
-    var runner = engine(resourceDict);
-    var result = runner.run(resource, resourceModel.template);
+    var j2j = json2Json.instance(localResourceDictionary);
+    var result = j2j.run(template, resource);
     return result;
 };
 
-var entryResources = exports.entryResources = (function () {
-    var pullRelatedOutOfContention = function (body, r, indexDictionary, doNotAddDictionary) {
-        body.related.forEach(function (component) {
+var topBundleEntryInfos = exports.topBundleEntryInfos = (function () {
+    var pullRelatedOutOfContention = function (content, r, indexDictionary, doNotAddDictionary) {
+        content.related.forEach(function (component) {
             var id = component.target.reference;
@@ -54,19 +62,18 @@ doNotAddDictionary[id] = true;
         },
-        Observation: function (resource, r, indexDictionary, doNotAddDictionary) {
-            var body = resource.body;
-            var isVital = body && body.extension && body.extension[0].valueCoding && (body.extension[0].valueCoding.code === '8716-3');
-            if (isVital) {
-                if (body.related) {
+        Observation: function (bundleEntry, r, indexDictionary, doNotAddDictionary) {
+            var content = bundleEntry.content;
+            var extensionCode = bbuobject.deepValue(content, 'extension.0.valueCoding.code');
+            if (extensionCode === '8716-3') {
+                if (content.related) {
                     return null;
                 } else {
-                    return 'observation_vital';
+                    return 'observation-vital';
                 }
             }
-            var isResult = body && body.extension && body.extension[0].valueCoding && (body.extension[0].valueCoding.code === '11502-2');
-            if (isResult) {
-                if (body.related) {
-                    pullRelatedOutOfContention(body, r, indexDictionary, doNotAddDictionary);
-                    return 'observation_result';
+            if (extensionCode === '11502-2') {
+                if (content.related) {
+                    pullRelatedOutOfContention(content, r, indexDictionary, doNotAddDictionary);
+                    return 'observation-result';
                 } else {
-                    return 'observation_result_single';
+                    return 'observation-result-single';
                 }
@@ -78,4 +85,4 @@ }
         },
-        MedicationAdministration: function (resource, r, indexDictionary, doNotAddDictionary) {
-            var id = resource.body.prescription.reference;
+        MedicationAdministration: function (bundleEntry, r, indexDictionary, doNotAddDictionary) {
+            var id = bundleEntry.content.prescription.reference;
             doNotAddDictionary[id] = true;
@@ -90,16 +97,16 @@ var existingIndex = indexDictionary[id];
 
-    return function (resources) {
+    return function (bundleEntries) {
         var indexDictionary = {};
         var doNotAddDictionary = {};
-        var preliminaryResult = resources.reduce(function (r, resource) {
-            var type = resource.type;
+        var preliminaryResult = bundleEntries.reduce(function (r, bundleEntry) {
+            var type = bundleEntry.content.resourceType;
             var fn = resourceToHandlerKey[type];
             if (fn) {
-                var id = type + '/' + resource.id;
+                var id = bundleEntry.id;
                 if (!doNotAddDictionary[id]) {
-                    var hk = fn(resource, r, indexDictionary, doNotAddDictionary);
+                    var hk = fn(bundleEntry, r, indexDictionary, doNotAddDictionary);
                     if (hk) {
                         r.push({
-                            resource: resource,
-                            handlerKey: hk
+                            bundleEntry: bundleEntry,
+                            templateKey: hk
                         });
@@ -135,39 +142,35 @@ indexDictionary[id] = r.length - 1;
 
-    var modellers = {
-        condition: condition,
-        allergyIntolerance: allergyIntolerance,
-        observation_vital: observation_vital,
-        observation_result: observation_result,
-        observation_result_single: observation_result_single,
-        medicationAdministration: medicationAdministration,
-        medicationPrescription: medicationPrescription
-    };
-
-    return function (input) {
-        var resources = input;
-        if (input.resourceType === 'Bundle') {
-            var bundle = input;
-            resources = [];
-            var entries = bundle && bundle.entry;
-            entries.forEach(function (entry) {
-                var pieces = entry.id.split('/');
-                var resource = {
-                    type: pieces[0],
-                    id: pieces[1],
-                    body: entry.content
+    var backwardCompatibility = function (bundle) {
+        if (Array.isArray(bundle)) {
+            var resources = bundle;
+            bundle = {
+                resourceType: 'Bundle',
+                entry: []
+            };
+            resources.forEach(function (resource) {
+                var bundleEntry = {
+                    id: resource.type + '/' + resource.id,
+                    content: resource.body
                 };
-                resources.push(resource);
+                bundle.entry.push(bundleEntry);
             });
+            return bundle;
+        } else {
+            return bundle;
         }
+    };
 
+    return function (bundle) {
         logger.trace('started toModel');
+        bundle = backwardCompatibility(bundle); // remove in 1.5
 
-        var store = resourceStore.create(resources);
+        var bundleEntries = bundle && bundle.entry;
+        var resourceDictionary = toResourceDictionary(bundleEntries);
 
-        var fn = function (entryResource) {
-            var handlerKey = entryResource.handlerKey;
-            var modeller = modellers[handlerKey];
-            var value = resourceToModel(store, modeller, entryResource.resource.body);
+        var fn = function (topBundleEntryInfo) {
+            var templateKey = topBundleEntryInfo.templateKey;
+            var template = templates[templateKey];
+            var value = resourceToModel(resourceDictionary, template, topBundleEntryInfo.bundleEntry.content);
             return {
-                type: modeller.type,
+                type: template.type,
                 value: value
@@ -177,3 +180,3 @@ };
 
-        var ers = entryResources(resources);
+        var ers = topBundleEntryInfos(bundleEntries);
         var results = ers.map(fn);
@@ -180,0 +183,0 @@ var model = {

package.json

 {
     "name": "blue-button-fhir",
-    "version": "1.4.0",
+    "version": "1.4.1",
     "description": "Blue Button FHIR to Model Translator",
@@ -27,3 +27,4 @@ "main": "./index.js",
         "blue-button-meta": "~1.3.0",
-        "blue-button-util": "~1.4.0",
+        "blue-button-util": "~1.4.1",
+        "blue-button-json2json": "~1.4.0",
         "bunyan": "~1.2.3",
@@ -30,0 +31,0 @@ "lodash": "~2.4.1"

README.md

@@ -49,1 +49,6 @@ blue-button-fhir
 [Mocha](http://mochajs.org/) and [Grunt](http://gruntjs.com/) are used for testing this project.  Simply run `grunt` in the project directory to run all the tests.
+
+## License
+
+Licensed under [Apache 2.0](./LICENSE).
+

RELEASENOTES.md

@@ -0,1 +1,5 @@
+# v1.4.1 - March 8, 2015
+
+- Move template based json tranformations to blue-button-json2jsom 
+
 # v1.4.0 - February 27, 2015
@@ -2,0 +6,0 @@

test/fixtures/unit/allergyIntolerance.js

@@ -10,5 +10,4 @@ "use strict";
 cases[0].resources = [{
-    "type": "AdverseReaction",
-    "id": "a-0-0",
-    "body": {
+    "id": "AdverseReaction/a-0-0",
+    "content": {
         "resourceType": "AdverseReaction",
@@ -30,5 +29,4 @@ "subject": na,
 }, {
-    "type": "AllergyIntolerance",
-    "id": "a-0-1",
-    "body": {
+    "id": "AllergyIntolerance/a-0-1",
+    "content": {
         "resourceType": "AllergyIntolerance",
@@ -50,5 +48,4 @@ "criticality": "medium",
 }, {
-    "type": "Substance",
-    "id": "a-0-2",
-    "body": {
+    "id": "Substance/a-0-2",
+    "content": {
         "resourceType": "Substance",
@@ -114,5 +111,4 @@ "text": na,
 cases[1].resources = [{
-    "type": "AdverseReaction",
-    "id": "a-1-0",
-    "body": {
+    "id": "AdverseReaction/a-1-0",
+    "content": {
         "resourceType": "AdverseReaction",
@@ -134,5 +130,4 @@ "subject": na,
 }, {
-    "type": "AllergyIntolerance",
-    "id": "a-1-1",
-    "body": {
+    "id": "AllergyIntolerance/a-1-1",
+    "content": {
         "resourceType": "AllergyIntolerance",
@@ -139,0 +134,0 @@ "criticality": "medium",

test/fixtures/unit/condition.js

@@ -10,5 +10,4 @@ "use strict";
 cases[0].resources = [{
-    "type": "Condition",
-    "id": "c-0-0",
-    "body": {
+    "id": "Condition/c-0-0",
+    "content": {
         "resourceType": "Condition",
@@ -55,5 +54,4 @@ "status": "confirmed",
 cases[1].resources = [{
-    "type": "Condition",
-    "id": "c-1-0",
-    "body": {
+    "id": "Condition/c-1-0",
+    "content": {
         "resourceType": "Condition",
@@ -96,5 +94,4 @@ "status": "confirmed",
 cases[2].resources = [{
-    "type": "Condition",
-    "id": "c-2-0",
-    "body": {
+    "id": "Condition/c-2-0",
+    "content": {
         "resourceType": "Condition",
@@ -101,0 +98,0 @@ "status": "confirmed",

test/fixtures/unit/medicationAdministration.js

@@ -10,5 +10,4 @@ "use strict";
 cases[0].resources = [{
-    "type": "MedicationPrescription",
-    "id": "ma-0-0",
-    "body": {
+    "id": "MedicationPrescription/ma-0-0",
+    "content": {
         "resourceType": "MedicationPrescription",
@@ -76,5 +75,4 @@ "status": "active",
 }, {
-    "type": "MedicationAdministration",
-    "id": "ma-0-1",
-    "body": {
+    "id": "MedicationAdministration/ma-0-1",
+    "content": {
         "resourceType": "MedicationAdministration",
@@ -81,0 +79,0 @@ "status": "completed",

test/fixtures/unit/medicationPrescription.js

@@ -10,5 +10,4 @@ "use strict";
 cases[0].resources = [{
-    "type": "MedicationPrescription",
-    "id": "mp-0-0",
-    "body": {
+    "id": "MedicationPrescription/mp-0-0",
+    "content": {
         "resourceType": "MedicationPrescription",
@@ -62,5 +61,4 @@ "status": "completed",
 }, {
-    "type": "Medication",
-    "id": "mp-0-1",
-    "body": {
+    "id": "Medication/mp-0-1",
+    "content": {
         "resourceType": "Medication",
@@ -146,5 +144,4 @@ "text": {
 cases[1].resources = [{
-    "type": "MedicationPrescription",
-    "id": "mp-1-0",
-    "body": {
+    "id": "MedicationPrescription/mp-1-0",
+    "content": {
         "resourceType": "MedicationPrescription",
@@ -199,5 +196,4 @@ "status": "active",
 cases[2].resources = [{
-    "type": "MedicationPrescription",
-    "id": "mp-2-0",
-    "body": {
+    "id": "MedicationPrescription/mp-2-0",
+    "content": {
         "resourceType": "MedicationPrescription",
@@ -271,5 +267,4 @@ "status": "completed",
 cases[3].resources = [{
-    "type": "MedicationPrescription",
-    "id": "mp-3-0",
-    "body": {
+    "id": "MedicationPrescription/mp-3-0",
+    "content": {
         "resourceType": "MedicationPrescription",
@@ -276,0 +271,0 @@ "status": "active",

test/fixtures/unit/observation-result-single.js

@@ -10,5 +10,4 @@ "use strict";
 cases[0].resources = [{
-    "type": "Observation",
-    "id": "ors-0-0",
-    "body": {
+    "id": "Observation/ors-0-0",
+    "content": {
         "resourceType": "Observation",
@@ -15,0 +14,0 @@ "name": {

test/fixtures/unit/observation-result.js

@@ -10,5 +10,4 @@ "use strict";
 cases[0].resources = [{
-    "type": "Observation",
-    "id": "or-0-0",
-    "body": {
+    "id": "Observation/or-0-0",
+    "content": {
         "resourceType": "Observation",
@@ -62,5 +61,4 @@ "name": {
 }, {
-    "type": "Observation",
-    "id": "or-0-1",
-    "body": {
+    "id": "Observation/or-0-1",
+    "content": {
         "resourceType": "Observation",
@@ -125,5 +123,4 @@ "name": {
 }, {
-    "type": "Observation",
-    "id": "or-0-2",
-    "body": {
+    "id": "Observation/or-0-2",
+    "content": {
         "resourceType": "Observation",
@@ -188,5 +185,4 @@ "name": {
 }, {
-    "type": "Observation",
-    "id": "or-0-3",
-    "body": {
+    "id": "Observation/or-0-3",
+    "content": {
         "resourceType": "Observation",
@@ -205,3 +201,3 @@ "name": {
         "related": [{
-            "type": "has-component",
+            "id": "has-component",
             "target": {
@@ -211,3 +207,3 @@ "reference": "Observation/or-0-0"
         }, {
-            "type": "has-component",
+            "id": "has-component",
             "target": {
@@ -217,3 +213,3 @@ "reference": "Observation/or-0-1"
         }, {
-            "type": "has-component",
+            "id": "has-component",
             "target": {
@@ -311,1 +307,98 @@ "reference": "Observation/or-0-2"
 };
+
+cases[1] = {};
+
+cases[1].resources = [{
+    "type": "Observation",
+    "id": "Observation/or-1-0",
+    "content": {
+        "resourceType": "Observation",
+        "name": {
+            "coding": [{
+                "system": "http://loinc.org",
+                "code": "26515-7",
+                "display": "Copy of BLOOD COUNT, PLATELET, AUTOMATED"
+            }],
+            "text": "Copy of BLOOD COUNT, PLATELET, AUTOMATED"
+        },
+        "valueQuantity": {
+            "value": 170
+        },
+        "issued": "2013-05-30T21:25:23.000Z",
+        "status": "final",
+        "reliability": "ok",
+        "extension": [{
+            "url": "http://amida.com/fhir/Profile/extensions#observation-type",
+            "valueCoding": {
+                "code": "11502-2",
+                "display": "Laboratory report",
+                "system": "http://loinc.org"
+            }
+        }],
+        "interpretation": {
+            "coding": [{
+                "system": "http://hl7.org/fhir/v2/0078",
+                "code": "N",
+                "display": "Normal"
+            }],
+            "text": "Normal"
+        }
+    }
+}, {
+    "id": "Observation/or-1-1",
+    "content": {
+        "resourceType": "Observation",
+        "name": {
+            "coding": [{
+                "system": "urn:oid:2.16.840.1.113883.6.12",
+                "code": "85049",
+                "display": "Copy of BLOOD COUNT, PLATELET, AUTOMATED (85049)"
+            }],
+            "text": "Copy of BLOOD COUNT, PLATELET, AUTOMATED (85049)"
+        },
+        "status": "final",
+        "reliability": "ok",
+        "related": [{
+            "type": "has-component",
+            "target": {
+                "reference": "Observation/or-1-0"
+            }
+        }],
+        "extension": [{
+            "url": "http://amida.com/fhir/Profile/extensions#observation-type",
+            "valueCoding": {
+                "code": "11502-2",
+                "display": "Laboratory report",
+                "system": "http://loinc.org"
+            }
+        }]
+    }
+}];
+
+cases[1].input = cases[1].resources[1];
+
+cases[1].result = {
+    "result_set": {
+        "name": "Copy of BLOOD COUNT, PLATELET, AUTOMATED (85049)",
+        "code": "85049",
+        "code_system_name": "CPT"
+    },
+    "results": [{
+        "result": {
+            "name": "Copy of BLOOD COUNT, PLATELET, AUTOMATED",
+            "code": "26515-7",
+            "code_system_name": "LOINC"
+        },
+        "value": 170,
+        "interpretations": [
+            "Normal"
+        ],
+        "date_time": {
+            "point": {
+                "date": "2013-05-30T00:00:00.000Z",
+                "precision": "day"
+            }
+        },
+        "status": "completed"
+    }]
+};

test/fixtures/unit/observation-vital.js

@@ -5,10 +5,9 @@ "use strict";
 
+var na = null;
+
 cases[0] = {};
 
-var na = null;
-
 cases[0].resources = [{
-    "type": "Observation",
-    "id": "ov-0-0",
-    "body": {
+    "id": "Observation/ov-0-0",
+    "content": {
         "resourceType": "Observation",
@@ -76,5 +75,4 @@ "name": {
 cases[1].resources = [{
-    "type": "Observation",
-    "id": "ov-1-0",
-    "body": {
+    "id": "Observation/ov-1-0",
+    "content": {
         "resourceType": "Observation",
@@ -142,5 +140,4 @@ "name": {
 cases[2].resources = [{
-    "type": "Observation",
-    "id": "ov-2-0",
-    "body": {
+    "id": "Observation/ov-2-0",
+    "content": {
         "resourceType": "Observation",
@@ -208,5 +205,4 @@ "name": {
 cases[3].resources = [{
-    "type": "Observation",
-    "id": "ov-3-0",
-    "body": {
+    "id": "Observation/ov-3-0",
+    "content": {
         "resourceType": "Observation",
@@ -274,5 +270,4 @@ "name": {
 cases[4].resources = [{
-    "type": "Observation",
-    "id": "ov-4-0",
-    "body": {
+    "id": "Observation/ov-4-0",
+    "content": {
         "resourceType": "Observation",
@@ -340,5 +335,4 @@ "name": {
 cases[5].resources = [{
-    "type": "Observation",
-    "id": "ov-5-0",
-    "body": {
+    "id": "Observation/ov-5-0",
+    "content": {
         "resourceType": "Observation",
@@ -406,5 +400,4 @@ "name": {
 cases[6].resources = [{
-    "type": "Observation",
-    "id": "ov-6-0",
-    "body": {
+    "id": "Observation/ov-6-0",
+    "content": {
         "resourceType": "Observation",
@@ -472,5 +465,4 @@ "name": {
 cases[7].resources = [{
-    "type": "Observation",
-    "id": "0",
-    "body": {
+    "id": "Observation/0",
+    "content": {
         "resourceType": "Observation",
@@ -477,0 +469,0 @@ "name": {

New alerts

Dynamic require

Supply chain risk

Dynamic require can indicate the package is performing dangerous or unsafe dynamic code execution.

Found 1 instance in 1 package

Improved metrics

Number of lines in readme file

54

increased by10.2%

Worsened metrics

Total package byte prevSize

93235

decreased by-6.96%

Dependency count

5

increased by25%

Number of package files

32

decreased by-13.51%

Lines of code

2650

decreased by-7.02%

Number of low supply chain risk alerts

2

increased by100%

Dependency changes

• + Addedblue-button-json2json@~1.4.0

• + Addedblue-button-json2json@1.4.0(transitive)

• + Addedlodash@3.3.1(transitive)

• Updatedblue-button-util@~1.4.1