Merge pull request #209 from RADAR-base/release-0.5.6

Release 0.5.6

commons/active/banking/BankingEvent.avsc

@@ -0,0 +1,23 @@
+{
+ "namespace": "org.radarcns.active.banking",
+ "type": "record",
+ "name": "BankingEvent",
+ "doc": "A Banking App Event, which is either a correct or wrong submission of a PIN number, an amount to withdraw, a cancelled or confirmed transaction. Notably, this allows us to distinguish between a wrong confirmed transaction or a correct cancelled transaction etc.",
+ "fields": [
+ { "name": "time", "type": "double", "doc": "Time since the Unix Epoch (seconds), time stores the time an event has started." },
+ { "name": "timeCompleted", "type": "double", "doc": "Time since the Unix Epoch (seconds), time stores the time an event has been completed." },
+ { "name": "duration", "type": "double", "doc": "Duration of the event (seconds), duration is essentially timeCompleted - time."},
+ { "name": "transactionId", "type":"string", "doc": "The uid of Transaction record that the event is related to." },
+ { "name": "isCorrect", "type": ["null","boolean"], "doc": "Describes if the input Pin or Amount is correct. Null if this event is a confirmation or cancellation.", "default": null },
+ { "name": "eventType", 
+ "type": {
+ "name": "EventType",
+ "type": "enum", 
+ "symbols": ["PIN", "AMOUNT", "TRANSACTION_CANCELLED", "TRANSACTION_CONFIRMED", "UNKNOWN"],
+ "doc": "PIN: PIN input, AMOUNT: Amount input, TRANSACTION_CANCELLED: the Transaction is canceled, TRANSACTION_CONFIRMED: the Transaction is confirmed, UNKNOWN: for any other input type."
+ },
+ "doc": "The type of submitted input: PIN or Amount.", 
+ "default": "UNKNOWN"
+ }
+ ]
+}

commons/active/banking/BankingTransaction.avsc

@@ -0,0 +1,38 @@
+{
+ "namespace": "org.radarcns.active.banking",
+ "type": "record",
+ "name": "BankingTransaction",
+ "doc": "Transaction in Banking App. This captures a full transaction: inputting a PIN number, then an amount and then a confirmation or cancellation. A transaction may also time out or end prematurely.",
+ "fields": [ {
+ "name": "transactionId",
+ "type": "string",
+ "doc": "Unique ID for an Transaction."
+ }, {
+ "name": "time",
+ "type": "double",
+ "doc": "Time since the Unix Epoch (seconds), time stores the time a transaction has started."
+ }, {
+ "name": "timeCompleted",
+ "type": "double",
+ "doc": "Time stores the time a transaction has been completed."
+ }, {
+ "name": "duration",
+ "type": "double",
+ "doc": "Duration of the transaction (seconds), duration is essentially timeCompleted - time."
+ }, {
+ "name": "isComplete",
+ "type": [ "null", "boolean" ],
+ "doc": "True if the result is CORRECT_CONFIRMED, WRONG_CONFIRMED, CORRECT_CANCELLED or WRONG_CANCELLED. False if TIME_OUT or EXIT.",
+ "default": null
+ }, {
+ "name": "transactionResult",
+ "type": {
+ "type": "enum",
+ "name": "TransactionResult",
+ "doc": "CORRECT_CONFIRMED: both inputs Correct- Confirmed Transaction, CORRECT_CANCELLED: Correct inputs - Cancelled Transaction, WRONG_CONFIRMED: (at least one of two inputs Wrong) - Confirmed Transaction, WRONG_CANCELLED: Wrong input Cancelled Transaction, TIME_OUT: Transaction timed Out, EXIT: Transaction Ended prematurely.",
+ "symbols" : [ "CORRECT_CONFIRMED", "CORRECT_CANCELLED", "WRONG_CONFIRMED", "WRONG_CANCELLED", "TIME_OUT", "EXIT", "UNKNOWN"]
+ },
+ "doc": "Shows the result of the Transaction which can be Correct Cancelled, Correct Cancelled, Wrong Confirmed, Wrong Cancelled, Timed Out, Ended.",
+ "default": "UNKNOWN"
+ } ]
+}

commons/connector/upload/axivity/axivity_battery.avsc → commons/connector/upload/axivity/axivity_battery_level.avsc

@@ -1,7 +1,7 @@
 {
  "namespace": "org.radarcns.connector.upload.axivity",
  "type": "record",
- "name": "AxivityBattery",
+ "name": "AxivityBatteryLevel",
  "doc": "Battery level data from Axivity device.",
  "fields": [
  {"name": "time", "type": "double", "doc": "Timestamp in unix time acquired locally from the device."},

commons/connector/upload/axivity/axivity_event.avsc

@@ -0,0 +1,15 @@
+{
+ "namespace": "org.radarcns.connector.upload.axivity",
+ "type": "record",
+ "name": "AxivityEvent",
+ "doc": "Event data available in a CWA block.",
+ "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": "event", "type": {
+ "name": "AxivityEventType",
+ "type": "enum",
+ "doc": "Event types recorded from the axivity device.",
+ "symbols": ["RESUME", "SINGLE_TAP", "DOUBLE_TAP", "FIFO_OVERFLOW", "BUFFER_OVERFLOW", "UNHANDLED_INTERRUPT", "UNKNOWN"]}, "doc": "Event of the block.", "default": "UNKNOWN"}
+ ]
+}

commons/connector/upload/axivity/axivity_metadata.avsc

@@ -6,9 +6,7 @@
  "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."}
+ {"name": "annotationName", "type": "string", "doc": "Name of the annotation from cwa metadata."},
+ {"name": "annotationData", "type": "string", "doc": "Value available for this annotation in the cwa metadata."}
  ]
 }

commons/monitor/questionnaire/questionnaire_application_interaction_event.avsc

@@ -9,7 +9,7 @@
  "name": "InteractionEventType",
  "doc": "NOTIFICATION_OPEN = When a user presses the notification to open the app, APP_OPEN = When a user opens the app directly, QUESTIONNAIRE_STARTED = When a user starts a questionnaire, QUESTIONNAIRE_FINISHED = When a user completes a questionnaire, QUESTIONNAIRE_CANCELLED = When a user closes a questionnaire without completing it.", 
  "type": "enum",
- "symbols": ["NOTIFICATION_OPEN", "APP_OPEN", "QUESTIONNAIRE_STARTED", "QUESTIONNAIRE_FINISHED", "QUESTIONNAIRE_CANCELLED", "OTHER", "UNKNOWN"]
+ "symbols": ["NOTIFICATION_OPEN", "APP_OPEN", "QUESTIONNAIRE_STARTED", "QUESTIONNAIRE_FINISHED", "QUESTIONNAIRE_CANCELLED", "OTHER", "UNKNOWN", "RECORDING_STARTED", "RECORDING_STOPPED"]
  },
  "doc": "Questionnaire app activity usage event type.",
  "default": "UNKNOWN"

java-sdk/README.md

@@ -9,10 +9,10 @@ repositories {
 
 dependencies {
  // Commons schemas (backend, passive remote monitoring app)
- compile 'org.radarcns:radar-schemas-commons:0.5.5'
+ compile 'org.radarcns:radar-schemas-commons:0.5.6'
 
  // Questionnaire schemas (active remote monitoring app)
- compile 'org.radarcns:radar-schemas-tools:0.5.5'
+ compile 'org.radarcns:radar-schemas-tools:0.5.6'
 }
 ```
 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 = '0.5.5'
+ version = '0.5.6'
  group = 'org.radarcns'
  ext.githubRepoName = 'RADAR-base/RADAR-Schemas'
 

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

@@ -31,14 +31,14 @@ ext {
  description = 'RADAR Schemas specification and validation tools.'
 
  argparseVersion = '0.8.1'
- jacksonVersion = '2.9.9.1'
- jacksonYamlVersion = '2.9.9'
- jerseyVersion = '2.28'
- jettyVersion = '9.4.17.v20190418'
+ jacksonVersion = '2.10.1'
+ jacksonYamlVersion = '2.10.1'
+ jerseyVersion = '2.29.1'
+ jettyVersion = '9.4.24.v20191120'
  junitVersion = '4.12'
- confluentVersion = '5.3.0'
+ confluentVersion = '5.3.1'
  kafkaVersion = '2.3.0'
- okHttpVersion = '4.0.0'
+ okHttpVersion = '4.2.2'
  radarCommonsVersion = '0.12.1'
  slf4jVersion = '1.7.26'
 }

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

@@ -171,8 +171,8 @@ public int execute(Namespace options, CommandLineApp app) {
  try {
  SchemaRegistry registration = new SchemaRegistry(url);
  boolean forced = options.getBoolean("force");
- if (forced) {
- forced = registration.putCompatibility(Compatibility.NONE);
+ if (forced && !registration.putCompatibility(Compatibility.NONE)) {
+ return 1;
  }
  boolean result;
  Pattern pattern = matchTopic(

java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/validation/rules/RadarSchemaRules.java

@@ -222,7 +222,10 @@ public Validator<Schema> validateAvroData() {
  org.apache.kafka.connect.data.Schema connectSchema = encoder
  .toConnectSchema(schema);
  Schema originalSchema = decoder.fromConnectSchema(connectSchema);
- return check(schema.equals(originalSchema), "Schema changed by validation");
+ return check(schema.equals(originalSchema),
+ () -> "Schema changed by validation: "
+ + schema.toString(true) + " is not equal to "
+ + originalSchema.toString(true));
  } catch (Exception ex) {
  return raise("Failed to convert schema back to itself");
  }

java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/validation/rules/Validator.java

@@ -20,6 +20,7 @@
 import java.util.Collection;
 import java.util.function.Function;
 import java.util.function.Predicate;
+import java.util.function.Supplier;
 import java.util.regex.Pattern;
 import java.util.stream.Stream;
 import org.radarcns.schema.validation.ValidationException;
@@ -32,6 +33,10 @@ static Stream<ValidationException> check(boolean test, String message) {
  return test ? valid() : raise(message);
  }
 
+ static Stream<ValidationException> check(boolean test, Supplier<String> message) {
+ return test ? valid() : raise(message.get());
+ }
+
  /**
  * TODO.
  * @param predicate TODO

specifications/active/aRMT-1.5.1.yml

@@ -0,0 +1,118 @@
+name: aRMT
+vendor: RADAR
+model: aRMT-App
+version: 1.5.1
+assessment_type: QUESTIONNAIRE
+doc: aRMT Questionnaires definition. Includes Personal Health Questionnaire Depression Scale (PHQ-8), Experience sampling method (ESM) and RSES and other data.
+data:
+ - type: THINC_IT
+ topic: notification_thinc_it
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://github.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/blob/master/questionnaires/thinc_it/thinc_it_armt.json
+ - type: ROMBERG_TEST
+ doc: The value of the task is in milliseconds (ms).
+ topic: task_romberg_test
+ value_schema: .active.task.Task
+ questionnaire_definition_url: https://github.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/blob/master/questionnaires/romberg_test/romberg_test_armt.json
+ - type: 2MW_TEST
+ doc: The value of the task is in milliseconds (ms).
+ topic: task_2MW_test
+ value_schema: .active.task.Task
+ questionnaire_definition_url: https://github.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/blob/master/questionnaires/2MW_test/2MW_test_armt.json
+ - type: TANDEM_WALKING_TEST
+ doc: The value of the task is in milliseconds (ms).
+ topic: task_tandem_walking_test
+ value_schema: .active.task.Task
+ questionnaire_definition_url: https://github.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/blob/master/questionnaires/tandem_walking_test/tandem_walking_test_armt.json
+ - type: PHQ8
+ topic: questionnaire_phq8
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/phq8/phq8_armt.json
+ - type: ESM
+ topic: questionnaire_esm
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/esm/esm_armt.json
+ - type: AUDIO
+ topic: questionnaire_audio
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio/audio_armt.json
+ - type: AUDIO_2
+ topic: questionnaire_audio
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio_2/audio_2_armt.json
+ - type: AUDIO_3
+ topic: questionnaire_audio
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio_3/audio_3_armt.json
+ - type: AUDIO_4
+ topic: questionnaire_audio
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio_4/audio_4_armt.json
+ - type: RSES
+ topic: questionnaire_rses
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/rses/rses_armt.json
+ - type: PERCEIVED_DEFICITS_QUESTIONNAIRE
+ topic: questionnaire_perceived_deficits_questionnaire
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/perceived_deficits_questionnaire/perceived_deficits_questionnaire_armt.json
+ - type: PATIENT_DETERMINED_DISEASE_STEP
+ topic: questionnaire_patient_determined_disease_step
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/patient_determined_disease_step/patient_determined_disease_step_armt.json
+ - type: ESM28Q
+ topic: questionnaire_esm28q
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/esm28q/esm28q_armt.json
+ - type: BIPQ
+ topic: questionnaire_bipq
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/bipq/bipq_armt.json
+ - type: ESM_EPI_MOD_1
+ topic: questionnaire_esm_epi_mod_1
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/esm_epi_mod_1/esm_epi_mod_1_armt.json
+ - type: EVENING_ASSESSMENT
+ topic: questionnaire_evening_assessment
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/evening_assessment/evening_assessment_armt.json
+ - type: MORNING_ASSESSMENT
+ topic: questionnaire_morning_assessment
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/morning_assessment/morning_assessment_armt.json
+ - type: TAM
+ topic: questionnaire_tam
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/tam/tam_armt.json
+ - type: BAARS_IV
+ topic: questionnaire_baars_iv
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/baars_iv/baars_iv_armt.json
+ - type: ARI_SELF
+ topic: questionnaire_ari_self
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/ari_self/ari_self_armt.json
+ - type: GAD7
+ topic: questionnaire_gad7
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/gad7/gad7_armt.json
+ - type: RPQ
+ topic: questionnaire_rpq
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/rpq/rpq_armt.json
+ - type: ART_COGNITIVE_TEST
+ topic: questionnaire_art_cognitive_test
+ value_schema: .active.questionnaire.Questionnaire
+ questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/art_cognitive_test/art_cognitive_test_armt.json
+ - type: COMPLETION_LOG
+ doc: Information about the completeness of each questionnaire.
+ topic: questionnaire_completion_log
+ value_schema: .monitor.questionnaire.QuestionnaireCompletionLog
+ - type: TIMEZONE
+ doc: Timezone information sent along with each questionnaire.
+ topic: questionnaire_timezone
+ value_schema: .monitor.application.ApplicationTimeZone
+ - type: APP_EVENT
+ doc: Questionnaire application interaction event.
+ topic: questionnaire_app_event
+ value_schema: .monitor.questionnaire.QuestionnaireApplicationInteractionEvent

specifications/active/banking-app-1.0.0.yml

@@ -0,0 +1,17 @@
+#==================== BankingApp Specification ======================#
+name: BankingApp
+vendor: CERTH
+model: BankingApp
+version: 1.0.0
+assessment_type: APP
+doc: Banking App schemas and topics
+data:
+ - type: APP_EVENT
+ doc: A Banking App Event, which is either a correct or wrong submission of a PIN number, an amount to withdraw, a cancelled or confirmed transaction. Notably, this allows us to distinguish between a wrong confirmed transaction or a correct cancelled transaction etc.
+ topic: certh_banking_app_event
+ value_schema: .active.banking.BankingEvent
+ - type: TRANSACTION
+ doc: Transaction in Banking App. This captures a full transaction inputting a PIN number, then an amount and then a confirmation or cancellation.
+ topic: certh_banking_app_transaction
+ value_schema: .active.banking.BankingTransaction
+

specifications/connector/radar-axivity-connector.yml

@@ -3,12 +3,28 @@ name: RADAR-AXIVITY-CONNECTOR
 vendor: Axivity
 model: Axivity.device
 version: 1.0.0
-doc: Spec for RADAR-base Axivity data upload connector. Schemas should be registered in the connector.
+doc: Spec for RADAR-base Axivity data upload connector. Schemas should be registered in the connector. Information on the raw data can be found at https://github.com/digitalinteraction/openmovement/tree/master/Docs/ax3.
 data:
  - doc: Data from 3-axis accelerometer sensor with gravitational constant g as unit. Data extracted from CWA binary file.
  topic: connect_upload_axivity_acceleration
  value_schema: .connector.upload.axivity.AxivityAcceleration
 
+ - doc: Battery level information of axivity device extracted from CWA Block.
+ topic: connect_upload_axivity_battery_level
+ value_schema: .connector.upload.axivity.AxivityBatteryLevel
+
+ - doc: Ambient light data extracted from a CWA Block.
+ topic: connect_upload_axivity_light
+ value_schema: .connector.upload.axivity.AxivityLight
+
+ - doc: Temperature data extracted from CWA Block.
+ topic: connect_upload_axivity_temperature
+ value_schema: .connector.upload.axivity.AxivityLight
+
+ - doc: Event data extracted from from a CWA Block.
+ topic: connect_upload_axivity_event
+ value_schema: .connector.upload.axivity.AxivityEvent
+
  # meta-data
  - doc: Data that contains additional meta-data of the recording. Data extracted from the header of CWA binary file.
  topic: connect_upload_axivity_metadata