Merge pull request #259 from RADAR-base/release-0.6.1

Release 0.6.1

java-sdk/build.gradle

@@ -3,7 +3,7 @@
 //---------------------------------------------------------------------------//
 
 plugins {
-    id 'com.commercehub.gradle.plugin.avro-base' version '0.19.1'
+    id 'com.commercehub.gradle.plugin.avro-base' version '0.9.1'
 }
 
 subprojects {
@@ -14,7 +14,7 @@ subprojects {
     apply plugin: 'idea'
 
     // Configuration
-    version = '0.6.0'
+    version = '0.6.1'
     group = 'org.radarbase'
     ext.githubRepoName = 'RADAR-base/RADAR-Schemas'
 

java-sdk/gradle/publishing.gradle

@@ -27,7 +27,7 @@ assemble.dependsOn(javadocJar, sourcesJar)
 
 publishing {
     publications {
-        mavenJar(MavenPublication) { publication ->
+        mavenJar(MavenPublication) {
             from components.java
             artifact sourcesJar
             artifact javadocJar

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

@@ -1,4 +1,3 @@
-ext.artifactName = 'radar-schemas-commons'
 description = 'RADAR Schemas Commons SDK'
 
 sourceSets {

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

@@ -32,10 +32,9 @@ sourceSets {
     }
 }
 
-ext {
-    artifactName = 'radar-schemas-tools'
-    description = 'RADAR Schemas specification and validation tools.'
+description = 'RADAR Schemas specification and validation tools.'
 
+ext {
     argparseVersion = '0.8.1'
     jacksonVersion = '2.10.4'
     jacksonYamlVersion = '2.10.4'
@@ -103,8 +102,8 @@ run {
     classpath = sourceSets.application.runtimeClasspath
 }
 
-task createStartScripts(type: CreateStartScripts) {
-    applicationName = 'radar-schema'
+startScripts {
+    classpath = sourceSets.application.runtimeClasspath
 }
 
 //---------------------------------------------------------------------------//

specifications/active/aRMT-1.11.0.yml

@@ -0,0 +1,224 @@
+name: aRMT
+vendor: RADAR
+model: aRMT-App
+version: 1.11.0
+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
+    doc: A speech questionnaire that contain two parts, a scripted text part where users will record themselves reading a text aloud, and an unscripted text part where users will record themselves answering a question.
+    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
+    doc: A speech questionnaire that contain two parts, a scripted text part where users will record themselves reading a text aloud, and an unscripted text part where users will record themselves answering a question.
+    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
+    doc: A speech questionnaire that contain two parts, a scripted text part where users will record themselves reading a text aloud, and an unscripted text part where users will record themselves answering a question.
+    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: CNS_COVID19_FOLLOWUP_V3
+    topic: questionnaire_cns_covid19_followup_v3
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/cns_covid19_followup_v3/cns_covid19_followup_v3_armt.json
+  - type: ART_COVID19_FOLLOWUP
+    topic: questionnaire_art_covid19_followup
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/art_covid19_followup/art_covid19_followup_armt.json
+  - type: ADHD_MEDICATION_USE
+    topic: questionnaire_adhd_medication_use
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/adhd_medication_use/adhd_medication_use_armt.json
+  - type: QIDS
+    topic: questionnaire_qids
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/qids/qids_armt.json
+  - type: WSAS
+    topic: questionnaire_wsas
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/wsas/wsas_armt.json
+  - type: SLEEP_QUESTIONS
+    topic: questionnaire_rapid_sleep_questions
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/sleep_questions/sleep_questions_armt.json
+  - type: AUDIO_WITHOUT_UNSCRIPTED
+    doc: A speech questionnaire similar to the AUDIO questionnaire but without the second unscripted task.
+    topic: questionnaire_audio_without_unscripted
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio_without_unscripted/audio_without_unscripted_armt.json
+  - type: AUDIO_WITHOUT_UNSCRIPTED_2
+    doc: A speech questionnaire similar to the AUDIO questionnaire but without the second unscripted task.
+    topic: questionnaire_audio_without_unscripted_2
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio_without_unscripted_2/audio_without_unscripted_armt.json
+  - type: AUDIO_WITHOUT_UNSCRIPTED_3
+    doc: A speech questionnaire similar to the AUDIO questionnaire but without the second unscripted task.
+    topic: questionnaire_audio_without_unscripted_3
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio_without_unscripted_3/audio_without_unscripted_armt.json
+  - type: CAT
+    topic: questionnaire_cat
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/cat/cat_armt.json
+  - type: PSQI
+    topic: questionnaire_psqi
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/psqi/psqi_armt.json
+  - type: FSS
+    topic: questionnaire_fss
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/fss/fss_armt.json
+  - type: PCFS
+    topic: questionnaire_pcfs
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/pcfs/pcfs_armt.json
+  - type: RALPMH_COVID_SYMPTOMS
+    topic: questionnaire_ralpmh_covid_symptoms
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/ralpmh_covid_symptoms/ralpmh_covid_symptoms_armt.json
+  - type: LIPF
+    topic: questionnaire_lipf
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/lipf/lipf_armt.json
+  - type: ERS
+    topic: questionnaire_ers
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/ers/ers_armt.json
+  - type: VAS
+    topic: questionnaire_vas
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/vas/vas_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
+  - type: EPI_SEIZURE_DIARY
+    topic: questionnaire_epi_seizure_diary
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/epi_seizure_diary/epi_seizure_diary_armt.json
+  - type: EPI_EVENING_QUESTIONNAIRE
+    topic: questionnaire_epi_evening_questionnaire
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/epi_evening_questionnaire/epi_evening_questionnaire_armt.json
+  - type: EPI_WSAS
+    topic: questionnaire_epi_wsas
+    value_schema: .active.questionnaire.Questionnaire
+    questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/epi_wsas/epi_wsas_armt.json