Merge pull request #92 from RADAR-base/release-0.3.1

Release 0.3.1

README.md

@@ -60,5 +60,4 @@ docker-compose run --rm tools radar-schemas-tools register http://schema-registr
 docker-compose run --rm tools radar-schemas-tools create zookeeper-1:2181
 # run source-catalogue webservice
 docker-compose run --rm tools radar-schemas-tools serve -p <portnumber>
-
 ```

commons/catalogue/unit.avsc

@@ -20,6 +20,7 @@
  "RADAIAN_PER_SEC",
  "RMSSD_IN_MILLI_SEC",
  "SECOND",
+ "MICRO_VOLT",
  "UNKNOWN"
  ]
 }

commons/passive/emotion/emotion_faros_acceleration.avsc

@@ -0,0 +1,13 @@
+{
+ "namespace": "org.radarcns.passive.emotion",
+ "type": "record",
+ "name": "EmotionFarosAcceleration",
+ "doc": "Data from 3-axis accelerometer sensor of a eMotion Faros device.",
+ "fields": [
+ { "name": "time", "type": "double", "doc": "Device timestamp in UTC (s)." },
+ { "name": "timeReceived", "type": "double", "doc": "Device receiver timestamp in UTC (s)." } ,
+ { "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/passive/emotion/emotion_faros_battery_level.avsc

@@ -0,0 +1,11 @@
+{
+ "namespace": "org.radarcns.passive.emotion",
+ "type": "record",
+ "name": "EmotionFarosBatteryLevel",
+ "doc": "Battery level of a eMotion Faros device.",
+ "fields": [
+ { "name": "time", "type": "double", "doc": "Device timestamp in UTC (s)." },
+ { "name": "timeReceived", "type": "double", "doc": "Device receiver timestamp in UTC (s)." },
+ { "name": "batteryLevel", "type": "float", "doc": "Battery level from 0 to 1. Note that the battery level is a rough estimate." }
+ ]
+}

commons/passive/emotion/emotion_faros_ecg.avsc

@@ -0,0 +1,13 @@
+{
+ "namespace": "org.radarcns.passive.emotion",
+ "type": "record",
+ "name": "EmotionFarosEcg",
+ "doc": "Data from eMotion Faros' multi-channel electrocardiography electrodes. Not all Faros models possess the same number of channels, so the second and third channels are optional.",
+ "fields": [
+ { "name": "time", "type": "double", "doc": "Device timestamp in UTC (s)." },
+ { "name": "timeReceived", "type": "double", "doc": "Device receiver timestamp in UTC (s)." } ,
+ { "name": "ecgChannel1", "type": "float", "doc": "ECG signal from the first channel (µV)." },
+ { "name": "ecgChannel2", "type": ["null", "float"], "doc": "ECG signal from the second channel (µV). Null if the device does not have at least two channels.", "default": null },
+ { "name": "ecgChannel3", "type": ["null", "float"], "doc": "ECG signal from the first channel (µV). Null if the device does not have at least two three channels.", "default": null }
+ ]
+}

commons/passive/emotion/emotion_faros_inter_beat_interval.avsc

@@ -0,0 +1,11 @@
+{
+ "namespace": "org.radarcns.passive.emotion",
+ "type": "record",
+ "name": "EmotionFarosInterBeatInterval",
+ "doc": "Time between two successive R-peaks (RR-interval), as calculated by a eMotion Faros device from the ECG signal. You can compute the heart rate as (60 / ibi).",
+ "fields": [
+ {"name": "time", "type": "double", "doc": "Device timestamp in UTC (s)." },
+ {"name": "timeReceived", "type": "double", "doc": "Device receiver timestamp in UTC (s)." },
+ {"name": "interBeatInterval", "type": "float", "doc": "Duration (s) of the detected inter beat interval." }
+ ]
+}

commons/passive/emotion/emotion_faros_temperature.avsc

@@ -0,0 +1,11 @@
+{
+ "namespace": "org.radarcns.passive.emotion",
+ "type": "record",
+ "name": "EmotionFarosTemperature",
+ "doc": "Data from an eMotion Faros' temperature sensor.",
+ "fields": [
+ {"name": "time", "type": "double", "doc": "Device timestamp in UTC (s)." },
+ {"name": "timeReceived", "type": "double", "doc": "Device receiver timestamp in UTC (s)." },
+ {"name": "temperature", "type": "float", "doc": "Skin temperature (°C) converted from analog-to-digital converter (ADC) values. Conversion is reliable between 35 and 45 degrees Celcius." }
+ ]
+}

commons/stream/source_statistics.avsc

@@ -0,0 +1,11 @@
+{
+ "namespace": "org.radarcns.stream",
+ "type": "record",
+ "name": "SourceStatistics",
+ "doc": "Statistics about single sources.",
+ "version": "1.0.0",
+ "fields": [
+ { "name": "timeStart", "type": "double", "doc": "First time (seconds since the UNIX Epoch) that a source streamed any data." },
+ { "name": "timeEnd", "type": "double", "doc": "Last time (seconds since the UNIX Epoch) that a source streamed any data." }
+ ]
+}

java-sdk/README.md

@@ -9,13 +9,13 @@ repositories {
 
 dependencies {
  // Commons schemas (backend, passive remote monitoring app)
- compile 'org.radarcns:radar-schemas-commons:0.3'
+ compile 'org.radarcns:radar-schemas-commons:0.3.1'
 
  // REST API schemas (REST API, testing)
- compile 'org.radarcns:radar-schemas-restapi:0.3'
+ compile 'org.radarcns:radar-schemas-restapi:0.3.1'
 
  // Questionnaire schemas (active remote monitoring app)
- compile 'org.radarcns:radar-schemas-tools:0.3'
+ compile 'org.radarcns:radar-schemas-tools:0.3.1'
 }
 ```
 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 = '0.3'
+ version = '0.3.1'
  group = 'org.radarcns'
  ext.githubRepoName = 'RADAR-CNS/RADAR-Schemas'
 
@@ -128,17 +128,17 @@ subprojects {
  downloadSources = true
  }
  }
-}
 
-task downloadDependencies {
- description "Pre-downloads *most* dependencies"
- doLast {
- configurations.getAsMap().each { name, config ->
- println "Retrieving dependencies for $name"
- try {
- config.files
- } catch (e) {
- project.logger.info e.message // some cannot be resolved, silentlyish skip them
+ task downloadDependencies {
+ description "Pre-downloads *most* dependencies"
+ doLast {
+ configurations.getAsMap().each { name, config ->
+ println "Retrieving dependencies for $name"
+ try {
+ config.files
+ } catch (e) {
+ project.logger.info e.message // some cannot be resolved, silentlyish skip them
+ }
  }
  }
  }

java-sdk/radar-schemas-tools/README.md

@@ -1,5 +1,9 @@
 # RADAR Schemas tools
 
+A number of tools are provided with RADAR-Schemas. They are most easily accessed by using the docker
+image as described in the main readme. Below is more information about the schema validation that
+the tools can perform.
+
 The RADAR Schemas Validator checks if the `Schema Catalog` is in a valid state.
 
 It first checks the folder structure, it has to be compliant with:
@@ -70,9 +74,8 @@ All tests are enable by default.
 
 ```yaml
 validation:
- schema_to_skip:
- - record_name_check: [ ENABLE | DISABLE ]
- fields:
+ org.radarcns.passive.biovotion.BiovotionVSMSpO2:
+ - fields:
  - fieldnameOne
  - fieldnameTwo
 ``` 

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

@@ -3,10 +3,9 @@ plugins {
  id 'checkstyle'
  id 'pmd'
  id 'application'
+ id 'com.jfrog.artifactory'
 }
 
-apply plugin: 'com.jfrog.artifactory'
-
 ext.artifactName = 'radar-schemas-tools'
 ext.description = 'RADAR Schemas specification and validation tools.'
 
@@ -23,8 +22,9 @@ sourceSets {
 
 ext.junitVersion = '4.12'
 ext.slf4jVersion = '1.7.25'
-ext.jettyVersion = '9.4.7.v20170914'
-ext.jerseyVersion = '2.9'
+ext.jettyVersion = '9.4.8.v20171121'
+ext.jerseyVersion = '2.26'
+
 dependencies {
  api group: 'com.fasterxml.jackson.core', name: 'jackson-databind', version: '2.8.10'
  api group: 'javax.validation', name: 'validation-api', version: '2.0.0.Final'
@@ -116,6 +116,11 @@ publishing {
  root.appendNode('name', artifactName)
  root.appendNode('url', githubUrl)
  root.children().last() + pomConfig
+ root.dependencies.'*'.findAll() {
+ it.artifactId.text() == 'slf4j-simple'
+ }.each() {
+ it.parent().remove(it)
+ }
  }
  }
  }

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

@@ -50,7 +50,7 @@
 import static java.util.stream.Collectors.toList;
 
 /**
- * TODO.
+ * Command line app containing a source catalogue.
  */
 @SuppressWarnings("PMD.SystemPrintln")
 public class CommandLineApp {
@@ -60,6 +60,12 @@ public class CommandLineApp {
  private final SourceCatalogue catalogue;
  private final Path root;
 
+ /**
+ * Command line app started at a RADAR-Schemas root. The source catalogue is read from the
+ * {@code specifications} directory in that root.
+ * @param root path to the root of a RADAR-Schemas directory.
+ * @throws IOException if the source catalogue cannot be loaded.
+ */
  public CommandLineApp(Path root) throws IOException {
  this.root = root;
  this.catalogue = SourceCatalogue.load(root);
@@ -163,6 +169,7 @@ private Map<String, Map<String, String>> getTopicsInfoVerbose(boolean prettyPrin
  DataTopic::getTopic, d -> d.toString(prettyPrint)))));
  }
 
+ /** Command to execute. */
  public static void main(String... args) {
  SortedMap<String, SubCommand> subCommands = commandsToMap(
  KafkaTopics.command(),
@@ -221,6 +228,7 @@ private static SortedMap<String, SubCommand> commandsToMap(SubCommand... command
  return map;
  }
 
+ /** Command to list the topics. */
  private static SubCommand listCommand() {
  return new SubCommand() {
  @Override
@@ -262,13 +270,21 @@ public void addParser(ArgumentParser parser) {
  };
  }
 
+ /**
+ * Create a pattern to match given topic. If the exact match is non-null, it is returned
+ * as an exact match, otherwise if regex is non-null, it is used, and otherwise
+ * {@code null} is returned.
+ * @param exact string that should be exactly matched.
+ * @param regex string that should be matched as a regex.
+ * @return pattern or {@code null} if both exact and regex are {@code null}.
+ */
  public static Pattern matchTopic(String exact, String regex) {
  if (exact != null) {
  return Pattern.compile("^" + Pattern.quote(exact) + "$");
- }
- if (regex != null) {
+ } else if (regex != null) {
  return Pattern.compile(regex);
+ } else {
+ return null;
  }
- return null;
  }
 }

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

@@ -1,5 +1,11 @@
 package org.radarcns.schema.registration;
 
+import static org.radarcns.schema.CommandLineApp.matchTopic;
+
+import java.io.Closeable;
+import java.util.Optional;
+import java.util.Properties;
+import java.util.regex.Pattern;
 import kafka.admin.AdminUtils;
 import kafka.admin.RackAwareMode;
 import kafka.utils.ZKStringSerializer;
@@ -8,22 +14,15 @@
 import net.sourceforge.argparse4j.inf.Namespace;
 import org.I0Itec.zkclient.ZkClient;
 import org.I0Itec.zkclient.ZkConnection;
+import org.I0Itec.zkclient.exception.ZkException;
 import org.I0Itec.zkclient.exception.ZkMarshallingError;
 import org.I0Itec.zkclient.serialize.ZkSerializer;
-import org.apache.zookeeper.KeeperException;
 import org.radarcns.schema.CommandLineApp;
 import org.radarcns.schema.specification.SourceCatalogue;
 import org.radarcns.schema.util.SubCommand;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.Closeable;
-import java.util.Optional;
-import java.util.Properties;
-import java.util.regex.Pattern;
-
-import static org.radarcns.schema.CommandLineApp.matchTopic;
-
 /**
  * Registers Kafka topics with Zookeeper.
  */
@@ -60,10 +59,11 @@ public Object deserialize(byte[] bytes) throws ZkMarshallingError {
  * waiting for at most 200 seconds.
  * @param brokers number of brokers to wait for
  * @return whether the brokers where available
- * @throws InterruptedException
- * @throws KeeperException
+ * @throws InterruptedException when waiting for the brokers is interrepted.
+ * @throws ZkException if the Zookeeper instance cannot be reached or returns an unexpected
+ * result.
  */
- public boolean waitForBrokers(int brokers) throws InterruptedException, KeeperException {
+ public boolean waitForBrokers(int brokers) throws InterruptedException, ZkException {
  boolean brokersAvailable = false;
  int sleep = 2;
  for (int tries = 0; tries < 10; tries++) {
@@ -124,7 +124,7 @@ public boolean createTopic(String topic, int partitions, int replication) {
  }
  }
 
- public int getNumberOfBrokers() throws KeeperException, InterruptedException {
+ public int getNumberOfBrokers() throws ZkException {
  return zkUtils.getAllBrokersInCluster().length();
  }
 
@@ -185,8 +185,8 @@ public int execute(Namespace options, CommandLineApp app) {
  return result.get() ? 0 : 1;
  }
  }
- } catch (InterruptedException | KeeperException e) {
- logger.error("Cannot retrieve number of active Kafka brokers."
+ } catch (InterruptedException | ZkException e) {
+ logger.error("Cannot retrieve number of addActive Kafka brokers."
  + " Please check that Zookeeper is running.");
  return 1;
  }