Merge pull request #238 from RADAR-base/release-0.5.12

Release 0.5.12
RADAR-base · Aug 11, 2020 · 44452cb · 44452cb
2 parents 88e299d + 47b7069
commit 44452cb
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Showing 6 changed files with 309 additions and 18 deletions.
diff --git a/Dockerfile b/Dockerfile
@@ -1,12 +1,12 @@
-FROM openjdk:11-jdk-slim
+FROM openjdk:11-jdk-slim as builder
 
 RUN mkdir -p /code/java-sdk
 WORKDIR /code/java-sdk
 
 COPY commons /code/commons
 COPY specifications /code/specifications
 COPY java-sdk/gradle /code/java-sdk/gradle
-COPY java-sdk/build.gradle java-sdk/settings.gradle  java-sdk/gradlew /code/java-sdk/
+COPY java-sdk/build.gradle java-sdk/settings.gradle java-sdk/gradlew /code/java-sdk/
 
 ENV GRADLE_OPTS -Dorg.gradle.daemon=false
 
@@ -20,8 +20,8 @@ RUN ./gradlew distTar && cd radar-schemas-tools/build/distributions && tar xzf r
 
 FROM openjdk:11-jre-slim
 
-COPY --from=0 /code/java-sdk/radar-schemas-tools/build/distributions/radar-schemas-tools-*/lib/* /usr/lib/
-COPY --from=0 /code/java-sdk/radar-schemas-tools/build/distributions/radar-schemas-tools-*/bin/radar-schemas-tools /usr/bin/
+COPY --from=builder /code/java-sdk/radar-schemas-tools/build/distributions/radar-schemas-tools-*/lib/* /usr/lib/
+COPY --from=builder /code/java-sdk/radar-schemas-tools/build/distributions/radar-schemas-tools-*/bin/radar-schemas-tools /usr/bin/
 
 WORKDIR /schemas
 VOLUME /schemas

diff --git a/Dockerfile.kafkaInit b/Dockerfile.kafkaInit
@@ -3,23 +3,21 @@ FROM openjdk:11-jdk-slim as builder
 RUN mkdir -p /code/java-sdk
 WORKDIR /code/java-sdk
 
-COPY ./commons /code/commons
-COPY ./specifications /code/specifications
-COPY ./java-sdk/gradle /code/java-sdk/gradle
-COPY ./java-sdk/build.gradle /code/java-sdk/build.gradle
-COPY ./java-sdk/settings.gradle java-sdk/gradlew /code/java-sdk/
+COPY commons /code/commons
+COPY specifications /code/specifications
+COPY java-sdk/gradle /code/java-sdk/gradle
+COPY java-sdk/build.gradle java-sdk/settings.gradle java-sdk/gradlew /code/java-sdk/
 
 ENV GRADLE_OPTS -Dorg.gradle.daemon=false
 
 RUN ./gradlew tasks
-COPY ./java-sdk/radar-schemas-commons/build.gradle /code/java-sdk/radar-schemas-commons/
-COPY ./java-sdk/radar-schemas-commons/src /code/java-sdk/radar-schemas-commons/src
+COPY java-sdk/radar-schemas-commons/build.gradle /code/java-sdk/radar-schemas-commons/
+COPY java-sdk/radar-schemas-commons/src /code/java-sdk/radar-schemas-commons/src
 RUN ./gradlew :radar-schemas-commons:jar
-COPY ./java-sdk/radar-schemas-tools/build.gradle /code/java-sdk/radar-schemas-tools/
-COPY ./java-sdk/radar-schemas-tools/src /code/java-sdk/radar-schemas-tools/src
+COPY java-sdk/radar-schemas-tools/build.gradle /code/java-sdk/radar-schemas-tools/
+COPY java-sdk/radar-schemas-tools/src /code/java-sdk/radar-schemas-tools/src
 RUN ./gradlew distTar && cd radar-schemas-tools/build/distributions && tar xzf radar-schemas-tools*.tar.gz
 
-
 FROM openjdk:11-jdk-slim
 
 ENV KAFKA_SCHEMA_REGISTRY=http://schema-registry-1:8081
@@ -50,8 +48,8 @@ COPY --from=builder /code ./original
 VOLUME /schema/conf
 VOLUME /etc/confluent/
 # Copy bash file
-COPY ./docker/specifications.exclude /etc/radar-schemas/specifications.exclude
-COPY ./docker/topic_init.sh ./docker/init.sh ./docker/cc_topic_init.sh ./docker/list_aggregated.sh ./docker/list_raw.sh /usr/bin/
+COPY docker/specifications.exclude /etc/radar-schemas/specifications.exclude
+COPY docker/topic_init.sh ./docker/init.sh ./docker/cc_topic_init.sh ./docker/list_aggregated.sh ./docker/list_raw.sh /usr/bin/
 RUN chmod +x /usr/bin/*.sh
 
 ENTRYPOINT ["init.sh"]

diff --git a/java-sdk/build.gradle b/java-sdk/build.gradle
@@ -17,7 +17,7 @@ subprojects {
     apply plugin: 'idea'
 
     // Configuration
-    version = '0.5.11.1'
+    version = '0.5.12'
     group = 'org.radarcns'
     ext.githubRepoName = 'RADAR-base/RADAR-Schemas'
 

diff --git a/java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/CommandLineApp.java b/java-sdk/radar-schemas-tools/src/main/java/org/radarcns/schema/CommandLineApp.java
@@ -153,6 +153,11 @@ public static void main(String... args) {
             System.exit(1);
         }
 
+        if (ns.getBoolean("help")) {
+            parser.printHelp();
+            System.exit(0);
+        }
+
         CommandLineApp app = null;
         try {
             app = new CommandLineApp(Paths.get(ns.getString("root")).toAbsolutePath());
@@ -172,7 +177,7 @@ public static void main(String... args) {
     }
 
     private static ArgumentParser getArgumentParser(SortedMap<String, SubCommand> subCommands) {
-        ArgumentParser parser = ArgumentParsers.newFor("radar-schema")
+        ArgumentParser parser = ArgumentParsers.newFor("radar-schemas-tools")
                 .addHelp(true)
                 .build()
                 .description("Schema tools");

diff --git a/specifications/active/aRMT-1.6.1.yml b/specifications/active/aRMT-1.6.1.yml
@@ -0,0 +1,138 @@
+name: aRMT
+vendor: RADAR
+model: aRMT-App
+version: 1.6.1
+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: COVID19_DIAGNOSIS
+    topic: questionnaire_covid19_diagnosis
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/covid19_diagnosis/covid19_diagnosis_armt.json
+  - type: COVID19_SYMPTOMS
+    topic: questionnaire_covid19_symptoms
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/covid19_symptoms/covid19_symptoms_armt.json
+  - type: CNS_COVID19_BASELINE
+    topic: questionnaire_cns_covid19_baseline
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/cns_covid19_baseline/cns_covid19_baseline_armt.json
+  - type: CNS_COVID19_FOLLOWUP
+    topic: questionnaire_cns_covid19_followup
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/cns_covid19_followup/cns_covid19_followup_armt.json
+  - type: CNS_COVID19_FOLLOWUP_V2
+    topic: questionnaire_cns_covid19_followup_v2
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/cns_covid19_followup_v2/cns_covid19_followup_v2_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