Merge branch 'release/v1.0.2'

.travis.yml

@@ -0,0 +1,6 @@
+language: java
+jdk:
+- oraclejdk8
+notifications:
+  slack:
+    secure: UjSpOIXxnH3JLZc109j+EzVwzVVvlNPsFoTRUf9uSfkwSCcAU/UQGOennJANOgloFychYl+YytWF9+Qi9AfF5OyFsXWqs4cx8CylQlN9YbEzUkCtGt4CX1AZqUCiH9oAzSExIS8FTpn/Viu8YtF91djaMdX5s+Nfj9IcVwWbrUE=

README.md

@@ -1,14 +1,17 @@
 # Open mHealth Schema Repository
+
 A repository of Open mHealth [schemas](http://www.openmhealth.org/developers/schemas/). This repository also includes sample test data, a validator for that data, and a Java schema SDK.
 
+[![Build Status](https://travis-ci.org/openmhealth/schemas.svg?branch=develop)](https://travis-ci.org/openmhealth/schemas)
+
 ## Schemas
 The schemas are located in the [schema](schema) directory.
 
 ## Validator and test data
 The [validator](test-data-validator) is a simple application that validates test data against schemas. The test data 
 that it uses is located in the [test-data](test-data) directory.  
 
-## Java SDK
+## Java SDK 
 The [Java SDK](java-schema-sdk) helps you produce and consume Open mHealth compliant data in your Java, Groovy, and Scala applications. 
 
 ## Tooling

java-schema-sdk/build.gradle

@@ -28,7 +28,7 @@ apply plugin: 'maven-publish'
 apply plugin: 'com.jfrog.bintray' // see https://github.com/bintray/gradle-bintray-plugin for details
 
 archivesBaseName = 'omh-schema-sdk'
-version = '1.0.1'
+version = '1.0.2'
 
 ext {
     jacksonVersion = '2.5.3'

schema/omh/minutes-moderate-activity-1.0.json

@@ -2,7 +2,12 @@
     "$schema": "http://json-schema.org/draft-04/schema#",
     "type": "object",
     "description": "This schema represents a single measurement of minutes of moderate-intensity activity performed. The ability to represent descriptive statistics (e.g., mean, median) will be added shortly.",
-
+    "references": [
+        {
+            "description": "The SNOMED code represents Physical activity target moderate exercise (finding)",
+            "url": "http://purl.bioontology.org/ontology/SNOMEDCT/408581006"
+        }
+    ],
     "definitions": {
         "duration_unit_value": {
             "$ref": "duration-unit-value-1.x.json"

test-data-validator/build.gradle

@@ -25,7 +25,7 @@ buildscript {
     }
 
     ext {
-        springBootVersion = '1.2.4.RELEASE'
+        springBootVersion = '1.2.5.RELEASE'
     }
 
     dependencies {
@@ -81,4 +81,9 @@ dependencies {
     testCompile 'junit:junit'
     testCompile 'org.mockito:mockito-core'
     testCompile 'org.springframework:spring-test'
+    testCompile 'org.testng:testng:6.8.21'
+}
+
+test {
+    useTestNG()
 }

test-data-validator/src/main/java/org/openmhealth/schema/configuration/Application.java

@@ -67,6 +67,7 @@ public class Application {
     @Autowired
     private ValidationService validationService;
 
+
     public static void main(String[] args) throws IOException, ProcessingException {
 
         ConfigurableApplicationContext applicationContext = SpringApplication.run(Application.class, args);

test-data-validator/src/main/java/org/openmhealth/schema/domain/DataFile.java

@@ -42,6 +42,7 @@ public class DataFile {
 
     private String name;
     private URI location;
+    private String path;
     private SchemaId schemaId;
     private DataFileValidationResult expectedValidationResult;
     private JsonNode data;
@@ -55,6 +56,7 @@ public DataFile(URI location, JsonNode data) {
 
         this.name = matcher.group(5);
         this.location = location;
+        this.path = matcher.group(0);
         this.schemaId = new SchemaId(matcher.group(1), matcher.group(2), new SchemaVersion(matcher.group(3)));
         this.expectedValidationResult = matcher.group(4).equals("shouldPass") ? PASS : FAIL;
         this.data = data;
@@ -68,6 +70,10 @@ public URI getLocation() {
         return location;
     }
 
+    public String getPath() {
+        return path;
+    }
+
     public SchemaId getSchemaId() {
         return schemaId;
     }
@@ -79,4 +85,9 @@ public DataFileValidationResult getExpectedValidationResult() {
     public JsonNode getData() {
         return data;
     }
+
+    @Override
+    public String toString() {
+        return getPath();
+    }
 }

test-data-validator/src/main/java/org/openmhealth/schema/domain/SchemaFile.java

@@ -71,4 +71,10 @@ public URI getLocation() {
     public JsonSchema getJsonSchema() {
         return jsonSchema;
     }
+
+
+    @Override
+    public String toString() {
+        return getSchemaId().toString();
+    }
 }

test-data-validator/src/test/java/org/openmhealth/schema/TestDataValidationIntegrationTests.java

@@ -0,0 +1,142 @@
+/*
+ * Copyright 2015 Open mHealth
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package org.openmhealth.schema;
+
+
+import com.github.fge.jackson.JacksonUtils;
+import com.github.fge.jsonschema.core.report.ProcessingMessage;
+import com.github.fge.jsonschema.core.report.ProcessingReport;
+import org.openmhealth.schema.configuration.Application;
+import org.openmhealth.schema.domain.DataFile;
+import org.openmhealth.schema.domain.DataFileValidationResult;
+import org.openmhealth.schema.domain.SchemaFile;
+import org.openmhealth.schema.domain.omh.SchemaVersion;
+import org.openmhealth.schema.service.DataFileService;
+import org.openmhealth.schema.service.SchemaFileService;
+import org.slf4j.Logger;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.boot.test.IntegrationTest;
+import org.springframework.boot.test.SpringApplicationConfiguration;
+import org.springframework.test.context.testng.AbstractTestNGSpringContextTests;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import java.io.File;
+import java.net.URI;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.List;
+
+import static org.hamcrest.CoreMatchers.equalTo;
+import static org.hamcrest.MatcherAssert.assertThat;
+import static org.openmhealth.schema.domain.DataFileValidationResult.FAIL;
+import static org.openmhealth.schema.domain.DataFileValidationResult.PASS;
+import static org.slf4j.LoggerFactory.getLogger;
+
+
+/**
+ * A test suite that dynamically creates a test for each combination of schema and applicable test data file.
+ *
+ * @author Emerson Farrugia
+ */
+@SpringApplicationConfiguration(classes = Application.class)
+@IntegrationTest
+public class TestDataValidationIntegrationTests extends AbstractTestNGSpringContextTests {
+
+    private static final Logger logger = getLogger(TestDataValidationIntegrationTests.class);
+
+    @Autowired
+    private SchemaFileService schemaFileService;
+
+    @Autowired
+    private DataFileService dataFileService;
+
+    @Value("${schemaFiles.baseDirectory}")
+    private String schemaFileBaseDirectory;
+
+    @Value("${testDataFiles.baseDirectory}")
+    private String testDataFileBaseDirectory;
+
+
+    @Test(dataProvider = "validationPairProvider")
+    public void validateTestData(SchemaFile schemaFile, DataFile dataFile) throws Exception {
+
+        ProcessingReport report = schemaFile.getJsonSchema().validate(dataFile.getData());
+        DataFileValidationResult validationResult = report.isSuccess() ? PASS : FAIL;
+
+        if (validationResult != dataFile.getExpectedValidationResult()) {
+            for (ProcessingMessage processingMessage : report) {
+                logger.error(JacksonUtils.prettyPrint(processingMessage.asJson()));
+            }
+        }
+
+        assertThat(dataFile.getExpectedValidationResult(), equalTo(validationResult));
+    }
+
+    /**
+     * @return an iterator over all pairs of schema files and applicable test data files
+     */
+    @DataProvider(name = "validationPairProvider")
+    public Iterator<Object[]> newValidationPairProvider() {
+
+        List<SchemaFile> schemaFiles = schemaFileService.getSchemaFiles(asUri(schemaFileBaseDirectory));
+
+        if (schemaFiles.size() == 0) {
+            return Collections.emptyIterator();
+        }
+
+        List<DataFile> dataFiles = dataFileService.getDataFiles(asUri(testDataFileBaseDirectory));
+
+        if (dataFiles.size() == 0) {
+            return Collections.emptyIterator();
+        }
+
+        List<Object[]> validationPairs = new ArrayList<>();
+
+        for (SchemaFile schemaFile : schemaFiles) {
+
+            for (DataFile dataFile : dataFiles) {
+
+                if (!dataFile.getSchemaId().getName().equals(schemaFile.getSchemaId().getName())) {
+                    continue;
+                }
+
+                SchemaVersion dataFileVersion = dataFile.getSchemaId().getVersion();
+                SchemaVersion schemaFileVersion = schemaFile.getSchemaId().getVersion();
+
+                if (dataFileVersion.getMajor() != schemaFileVersion.getMajor()) {
+                    continue;
+                }
+
+                // a data point conforms to the schema listed in its header and newer minor versions of that schema
+                if (dataFileVersion.getMinor() > schemaFileVersion.getMinor()) {
+                    continue;
+                }
+
+                validationPairs.add(new Object[]{schemaFile, dataFile});
+            }
+        }
+
+        return validationPairs.iterator();
+    }
+
+    private URI asUri(String filename) {
+        return new File(filename).toURI();
+    }
+}