Merge pull request #199 from RADAR-base/release-0.5.5

Release 0.5.5

commons/connector/upload/altoida/altoida_summary.avsc

@@ -9,9 +9,21 @@
  {"name": "label", "type": "string", "doc": "Label name of session as entered in the app."},
  {"name": "age", "type": "int", "doc": "Age of the participant in years."},
  {"name": "yearsOfEducation", "type": "int", "doc": "Years of education in years."},
- {"name": "gender", "type": "int", "doc": "Gender of the participant 0=male, 1=female, 2=other."},
- {"name": "class", "type": "int", "doc": "Classification based on the analysis 0=healthy, 1=at risk, 2=MCI due to AD."},
+ {"name": "gender", "type": {
+ "name": "GenderType",
+ "type": "enum",
+ "doc": "Gender types provided by Altoida.",
+ "symbols": ["MALE", "FEMALE", "OTHER", "UNKNOWN"]}, "doc": "Gender of the participant.", "default": "UNKNOWN"},
+ {"name": "classification", "type": ["null", {
+ "name": "Classification",
+ "type": "enum",
+ "doc": "Classifications provided by Altoida.",
+ "symbols": ["HEALTHY", "AT_RISK", "MCI_DUE_TO_AD"]}], "doc": "Classification based on the analysis 0=healthy, 1=at risk, 2=MCI due to AD.", "default": null},
  {"name": "nmi", "type": "double", "doc": "NMI value of the test,a value in 0-100, where 0-33.3 is class 2, 33.3-66.6 is class 1, 66.6-100 is class 0."},
- {"name": "groundTruth", "type": "int", "doc": "If the test is based on additional biomarkers -1=unknown, 0=healthy, 1= at risk, 2=MCI/AB+, 3=MCI/AB-."}
+ {"name": "groundTruth", "type": {
+ "name": "GroundTruth",
+ "type": "enum",
+ "doc": "GroundTruth supported by Altoida.",
+ "symbols": ["UNKNOWN", "HEALTHY", "AT_RISK", "MCI_OR_AB_PLUS", "MCI_OR_AB_MINUS"]}, "doc": "If the test is based on additional biomarkers -1=unknown, 0=healthy, 1= at risk, 2=MCI/AB+, 3=MCI/AB-.", "default": "UNKNOWN"}
  ]
 }

commons/connector/upload/altoida/altoida_trial.avsc

@@ -6,8 +6,8 @@
  "fields": [
  {"name": "placeDuration", "type": "float", "doc": "Time the user required to place the object (s)."},
  {"name": "findDuration", "type": "float", "doc": "Time the user required to find the object (s)."},
- {"name": "stepAngularChange", "type": "float", "doc": "Mean angle the user turned during one step when finding the object (s)."},
+ {"name": "stepAngularChange", "type": ["null", "float"], "doc": "Mean angle the user turned during one step when finding the object (s).", "default": null},
  {"name": "totalAngularChange", "type": "float", "doc": "Accumulated angular change when finding the object (radians)."},
- {"name": "pathComplexity", "type": "float", "doc": "Path complexity when finding the object (m)."}
+ {"name": "pathComplexity", "type": ["null", "float"], "doc": "Path complexity when finding the object (m).", "default": null}
  ]
 }

commons/connector/upload/axivity/axivity_acceleration.avsc

@@ -0,0 +1,13 @@
+{
+ "namespace": "org.radarcns.connector.upload.axivity",
+ "type": "record",
+ "name": "AxivityAcceleration",
+ "doc": "Data from 3-axis accelerometer sensor with gravitational constant g as unit.",
+ "fields": [
+ {"name": "time", "type": "double", "doc": "Interpolated Timestamp in unix time from the CWA data."},
+ {"name": "timeReceived", "type": "double", "doc": "Timestamp in unix time received from upload."},
+ {"name": "x", "type": "float", "doc": "Acceleration in the x-axis (g)."},
+ {"name": "y", "type": "float", "doc": "Acceleration in the y-axis (g)."},
+ {"name": "z", "type": "float", "doc": "Acceleration in the z-axis (g)."}
+ ]
+}

commons/connector/upload/axivity/axivity_battery.avsc

@@ -0,0 +1,11 @@
+{
+ "namespace": "org.radarcns.connector.upload.axivity",
+ "type": "record",
+ "name": "AxivityBattery",
+ "doc": "Battery level data from Axivity device.",
+ "fields": [
+ {"name": "time", "type": "double", "doc": "Timestamp in unix time acquired locally from the device."},
+ {"name": "timeReceived", "type": "double", "doc": "Timestamp in unix time received from upload."},
+ {"name": "batteryLevel", "type": "float", "doc": "Battery level of the Axivity device ." }
+ ]
+}

commons/connector/upload/axivity/axivity_light.avsc

@@ -0,0 +1,11 @@
+{
+ "namespace": "org.radarcns.connector.upload.axivity",
+ "type": "record",
+ "name": "AxivityLight",
+ "doc": "Light data from axivity.",
+ "fields": [
+ {"name": "time", "type": "double", "doc": "Timestamp in unix time acquired locally from the device."},
+ {"name": "timeReceived", "type": "double", "doc": "Timestamp in unix time received from upload."},
+ {"name": "light", "type": "float", "doc": "Light." }
+ ]
+}

commons/connector/upload/axivity/axivity_metadata.avsc

@@ -0,0 +1,14 @@
+{
+ "namespace": "org.radarcns.connector.upload.axivity",
+ "type": "record",
+ "name": "AxivityMetadata",
+ "doc": "Data that contains one column with the version name as type string.",
+ "fields": [
+ {"name": "time", "type": "double", "doc": "Timestamp in unix time acquired locally from the device."},
+ {"name": "timeReceived", "type": "double", "doc": "Timestamp in unix time received from upload."},
+ {"name": "deviceId", "type": "string", "doc": "Version number."},
+ {"name": "exerciseCode", "type": "string", "doc": "Exercise code from axivity."},
+ {"name": "bodyLocation", "type": "int", "doc": "Body location recorded on the axivity device."},
+ {"name": "studyCode", "type": "string", "doc": "Study code recorded on the axivity device."}
+ ]
+}

commons/connector/upload/axivity/axivity_temperature.avsc

@@ -0,0 +1,11 @@
+{
+ "namespace": "org.radarcns.connector.upload.axivity",
+ "type": "record",
+ "name": "AxivityTemperature",
+ "doc": "Temperature data from axivity.",
+ "fields": [
+ {"name": "time", "type": "double", "doc": "Timestamp in unix time acquired locally from the device."},
+ {"name": "timeReceived", "type": "double", "doc": "Timestamp in unix time received from upload."},
+ {"name": "temperature", "type": "float", "doc": "Temperature (°C)." }
+ ]
+}

commons/connector/upload/oxford/oxford_camera_axes.avsc

@@ -0,0 +1,11 @@
+{
+ "namespace": "org.radarcns.connector.upload.oxford",
+ "type": "record",
+ "name": "OxfordCameraAxes",
+ "doc": "Three-axes reference system.",
+ "fields": [
+ {"name": "x", "type": "float", "doc": "X coordinate value."},
+ {"name": "y", "type": "float", "doc": "Y coordinate value."},
+ {"name": "z", "type": "float", "doc": "Z coordinate value."}
+ ]
+}

commons/connector/upload/oxford/oxford_camera_data.avsc

@@ -0,0 +1,21 @@
+{
+ "namespace": "org.radarcns.connector.upload.oxford",
+ "type": "record",
+ "name": "OxfordCameraData",
+ "doc": "Entry for an image captured by Oxford's wearable camera.",
+ "fields": [
+ {"name": "time", "type": "double", "doc": "Time since Unix Epoch as reported by the device (s)."},
+ {"name": "timeReceived", "type": "double", "doc": "Time this record was processed (s)."},
+ {"name": "name", "type": "string", "doc": "Image name."},
+ {"name": "infraredProximity", "type": "boolean", "doc": "True if a the infrared sensor detected an warm object (e.g. part of a human body) closeby when the image was captured."},
+ {"name": "acceleration", "type": "OxfordCameraAxes", "doc": "Acceleration of the camera when the image was captured (g)."},
+ {"name": "magneticField", "type": "OxfordCameraAxes", "doc": "Magnetic field of the camera when the image was captured (100 µT)."},
+ {"name": "orientation", "type": "OxfordCameraAxes", "doc": "Orientation of the camera when the image was captured (unknown unit, unknown interpretation)."},
+ {"name": "temperature", "type": "float", "doc": "Ambient temperature when the image was recorded (celcius)."},
+ {"name": "colorMean", "type": "OxfordCameraRgb", "doc": "Mean color saturation over all pixels of the image in the sRGB color space (range 0-1)."},
+ {"name": "luminanceMean", "type": "float", "doc": "Mean luminance over all pixels of the image (0 - 1). Calculation unknown but assumed to match sum of RGB values."},
+ {"name": "exposure", "type": "int", "doc": "Physical exposure of the captured image (unknown unit, unknown range)."},
+ {"name": "gain", "type": "float", "doc": "Gain applied to raw photo sensor values. Amplification factor of the signal (unknown range)."},
+ {"name": "colorBalance", "type": "OxfordCameraRgb", "doc": "Relative distribution of gain applied in the captured image (uncertain interpretation)."}
+ ]
+}

commons/connector/upload/oxford/oxford_camera_image.avsc

@@ -0,0 +1,12 @@
+{
+ "namespace": "org.radarcns.connector.upload.oxford",
+ "type": "record",
+ "name": "OxfordCameraImage",
+ "doc": "Image captured by Oxford's wearable camera. This only contains a URL reference to the actual image data.",
+ "fields": [
+ {"name": "time", "type": "double", "doc": "Time since Unix Epoch as reported by the device (s)."},
+ {"name": "timeReceived", "type": "double", "doc": "Time this record was processed (s)."},
+ {"name": "name", "type": "string", "doc": "Image name."},
+ {"name": "url", "type": "string", "doc": "URL where image is stored."}
+ ]
+}

commons/connector/upload/oxford/oxford_camera_rgb.avsc

@@ -0,0 +1,11 @@
+{
+ "namespace": "org.radarcns.connector.upload.oxford",
+ "type": "record",
+ "name": "OxfordCameraRgb",
+ "doc": "Color in sRGB color space.",
+ "fields": [
+ {"name": "red", "type": "float", "doc": "Red value."},
+ {"name": "green", "type": "float", "doc": "Green value."},
+ {"name": "blue", "type": "float", "doc": "Blue value."}
+ ]
+}

java-sdk/README.md

@@ -9,10 +9,10 @@ repositories {
 
 dependencies {
  // Commons schemas (backend, passive remote monitoring app)
- compile 'org.radarcns:radar-schemas-commons:0.4.3'
+ compile 'org.radarcns:radar-schemas-commons:0.5.5'
 
  // Questionnaire schemas (active remote monitoring app)
- compile 'org.radarcns:radar-schemas-tools:0.4.3'
+ compile 'org.radarcns:radar-schemas-tools:0.5.5'
 }
 ```
 Usually, you only need to include the schemas you actually need in your dependencies.

java-sdk/build.gradle

@@ -17,7 +17,7 @@ subprojects {
  apply plugin: 'idea'
 
  // Configuration
- version = '0.5.4'
+ version = '0.5.5'
  group = 'org.radarcns'
  ext.githubRepoName = 'RADAR-base/RADAR-Schemas'
 
@@ -128,5 +128,5 @@ subprojects {
 }
 
 wrapper {
- gradleVersion '5.5.1'
+ gradleVersion '6.0.1'
 }

java-sdk/gradle/wrapper/gradle-wrapper.properties

@@ -1,5 +1,5 @@
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-5.4-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-6.0.1-bin.zip
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists

java-sdk/gradlew

@@ -7,7 +7,7 @@
 # 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
+# https://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,
@@ -125,8 +125,8 @@ if $darwin; then
  GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\""
 fi
 
-# For Cygwin, switch paths to Windows format before running java
-if $cygwin ; then
+# For Cygwin or MSYS, switch paths to Windows format before running java
+if [ "$cygwin" = "true" -o "$msys" = "true" ] ; then
  APP_HOME=`cygpath --path --mixed "$APP_HOME"`
  CLASSPATH=`cygpath --path --mixed "$CLASSPATH"`
  JAVACMD=`cygpath --unix "$JAVACMD"`
@@ -154,19 +154,19 @@ if $cygwin ; then
  else
  eval `echo args$i`="\"$arg\""
  fi
- i=$((i+1))
+ i=`expr $i + 1`
  done
  case $i in
- (0) set -- ;;
- (1) set -- "$args0" ;;
- (2) set -- "$args0" "$args1" ;;
- (3) set -- "$args0" "$args1" "$args2" ;;
- (4) set -- "$args0" "$args1" "$args2" "$args3" ;;
- (5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
- (6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
- (7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
- (8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
- (9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
+ 0) set -- ;;
+ 1) set -- "$args0" ;;
+ 2) set -- "$args0" "$args1" ;;
+ 3) set -- "$args0" "$args1" "$args2" ;;
+ 4) set -- "$args0" "$args1" "$args2" "$args3" ;;
+ 5) set -- "$args0" "$args1" "$args2" "$args3" "$args4" ;;
+ 6) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" ;;
+ 7) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" ;;
+ 8) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" ;;
+ 9) set -- "$args0" "$args1" "$args2" "$args3" "$args4" "$args5" "$args6" "$args7" "$args8" ;;
  esac
 fi
 
@@ -175,14 +175,9 @@ save () {
  for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done
  echo " "
 }
-APP_ARGS=$(save "$@")
+APP_ARGS=`save "$@"`
 
 # Collect all arguments for the java command, following the shell quoting and substitution rules
 eval set -- $DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS "\"-Dorg.gradle.appname=$APP_BASE_NAME\"" -classpath "\"$CLASSPATH\"" org.gradle.wrapper.GradleWrapperMain "$APP_ARGS"
 
-# by default we should be in the correct project dir, but when run from Finder on Mac, the cwd is wrong
-if [ "$(uname)" = "Darwin" ] && [ "$HOME" = "$PWD" ]; then
- cd "$(dirname "$0")"
-fi
-
 exec "$JAVACMD" "$@"

java-sdk/gradlew.bat

@@ -5,7 +5,7 @@
 @rem you may not use this file except in compliance with the License.
 @rem You may obtain a copy of the License at
 @rem
-@rem http://www.apache.org/licenses/LICENSE-2.0
+@rem https://www.apache.org/licenses/LICENSE-2.0
 @rem
 @rem Unless required by applicable law or agreed to in writing, software
 @rem distributed under the License is distributed on an "AS IS" BASIS,

java-sdk/radar-schemas-tools/build.gradle

@@ -45,7 +45,7 @@ ext {
 
 repositories {
  jcenter()
- maven { url 'http://packages.confluent.io/maven/' }
+ maven { url 'https://packages.confluent.io/maven/' }
  maven { url "https://dl.bintray.com/radar-base/org.radarbase" }
  maven { url 'https://oss.jfrog.org/artifactory/oss-snapshot-local' }
 }

java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/registration/SchemaTopicManager.java

@@ -20,6 +20,8 @@
 import net.sourceforge.argparse4j.impl.action.StoreConstArgumentAction;
 import net.sourceforge.argparse4j.inf.ArgumentParser;
 import net.sourceforge.argparse4j.inf.Namespace;
+import org.apache.kafka.clients.admin.AlterConfigOp;
+import org.apache.kafka.clients.admin.AlterConfigOp.OpType;
 import org.apache.kafka.clients.admin.AlterConfigsResult;
 import org.apache.kafka.clients.consumer.Consumer;
 import org.apache.kafka.clients.consumer.ConsumerConfig;
@@ -380,7 +382,9 @@ private void resetSchemaRegistryId() throws KeeperException, InterruptedExceptio
  private void commitBackup(SchemaTopicBackup backup)
  throws ExecutionException, InterruptedException, KeeperException {
  AlterConfigsResult alterResult = topics.getKafkaClient()
- .alterConfigs(Map.of(topicResource, backup.getConfig()));
+ .incrementalAlterConfigs(Map.of(topicResource, backup.getConfig().entries().stream()
+ .map(e -> new AlterConfigOp(e, OpType.SET))
+ .collect(Collectors.toList())));
 
  try (KafkaProducer<byte[], byte[]> producer = new KafkaProducer<>(getProducerProps())) {
  List<Future<RecordMetadata>> futures = backup.getRecords().stream()

java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/service/SourceCatalogueServer.java

@@ -40,7 +40,6 @@ public void close() {
 
  @SuppressWarnings("PMD.SignatureDeclareThrowsException")
  private void start(SourceCatalogue sourceCatalogue) throws Exception {
-
  ResourceConfig config = new ResourceConfig();
  config.register(new SourceCatalogueService(sourceCatalogue));
  ServletHolder servlet = new ServletHolder(new ServletContainer(config));