From 3ca63aa266524740f68323960f00bb6d5fbb3e9c Mon Sep 17 00:00:00 2001 From: Yatharth Ranjan Date: Tue, 27 Jul 2021 19:07:47 +0530 Subject: [PATCH 01/18] Fix pulse_ox definitions path --- specifications/active/aRMT-1.14.0.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/specifications/active/aRMT-1.14.0.yml b/specifications/active/aRMT-1.14.0.yml index 0394a004..41373648 100644 --- a/specifications/active/aRMT-1.14.0.yml +++ b/specifications/active/aRMT-1.14.0.yml @@ -201,7 +201,7 @@ data: - type: PULSE_OX topic: questionnaire_pulse_ox value_schema: .active.questionnaire.Questionnaire - questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/pulse_ox_response/pulse_ox_response_armt.json + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/pulse_ox/pulse_ox_armt.json - type: AUDIO_WITHOUT_UNSCRIPTED_4 doc: A speech questionnaire that contains `The North Wind` scripted text where users will record themselves reading a text aloud. topic: questionnaire_audio_without_unscripted_4 From b91e69aeaa5b128385fe286b0125d2fb92cce416 Mon Sep 17 00:00:00 2001 From: Yatharth Ranjan Date: Fri, 30 Jul 2021 18:09:46 +0530 Subject: [PATCH 02/18] snapshot version --- java-sdk/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java-sdk/build.gradle b/java-sdk/build.gradle index c8656d59..fb0f57a4 100644 --- a/java-sdk/build.gradle +++ b/java-sdk/build.gradle @@ -8,7 +8,7 @@ plugins { } allprojects { - version = '0.7.2' + version = '0.7.3-SNAPSHOT' group = 'org.radarbase' } From c60ed10e6e3ed66e632f177ff7d0f9d51b23223d Mon Sep 17 00:00:00 2001 From: yatharthranjan Date: Wed, 4 Aug 2021 14:28:02 +0530 Subject: [PATCH 03/18] add new questionnaires to specs --- specifications/active/aRMT-1.15.0.yml | 263 ++++++++++++++++++++++++++ 1 file changed, 263 insertions(+) create mode 100644 specifications/active/aRMT-1.15.0.yml diff --git a/specifications/active/aRMT-1.15.0.yml b/specifications/active/aRMT-1.15.0.yml new file mode 100644 index 00000000..8e6439bf --- /dev/null +++ b/specifications/active/aRMT-1.15.0.yml @@ -0,0 +1,263 @@ +name: aRMT +vendor: RADAR +model: aRMT-App +version: 1.15.0 +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: PULSE_OX + topic: questionnaire_pulse_ox + value_schema: .active.questionnaire.Questionnaire + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/pulse_ox/pulse_ox_armt.json + - type: AUDIO_WITHOUT_UNSCRIPTED_4 + doc: A speech questionnaire that contains `The North Wind` scripted text where users will record themselves reading a text aloud. + topic: questionnaire_audio_without_unscripted_4 + value_schema: .active.questionnaire.Questionnaire + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio_without_unscripted_4/audio_without_unscripted_4_armt.json + - type: AUDIO_COUNT + doc: A speech questionnaire where users will record themselves count from 1 to 20 aloud. + topic: questionnaire_audio_count + value_schema: .active.questionnaire.Questionnaire + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio_count/audio_count_armt.json + - type: AUDIO_VOCALISATION + doc: A speech questionnaire where users will record themselves speak the vowels displayed on the screen aloud. + topic: questionnaire_audio_vocalisation + value_schema: .active.questionnaire.Questionnaire + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/audio_vocalisation/audio_vocalisation_armt.json + - type: EXACERBATION_DIARY + topic: questionnaire_exacerbation_diary + value_schema: .active.questionnaire.Questionnaire + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/exacerbation_diary/exacerbation_diary_armt.json + - type: NUVOAIR_SPIROMETRY + topic: notification_nuvoair_spirometry + value_schema: .active.questionnaire.Questionnaire + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/nuvoair_spirometry/nuvoair_spirometry_armt.json + - type: K_BUILD_PRIVATE + topic: questionnaire_k_build_private + value_schema: .active.questionnaire.Questionnaire + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions-Private/master/questionnaires/k_build_private/k_build_private_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 + - type: BP_QUESTIONNAIRE + topic: questionnaire_bp + value_schema: .active.questionnaire.Questionnaire + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/bp/bp_armt.json + - type: HLH_QUESTIONNAIRE + topic: questionnaire_hlh + value_schema: .active.questionnaire.Questionnaire + questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/hlh/hlh_armt.json From 27761736ad0d335f3e283dc12e1ac0bea06e1d92 Mon Sep 17 00:00:00 2001 From: Amos Folarin Date: Thu, 5 Aug 2021 19:06:35 +0100 Subject: [PATCH 04/18] Update garmin_stress_level_sample.avsc typo --- commons/push/garmin/garmin_stress_level_sample.avsc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/commons/push/garmin/garmin_stress_level_sample.avsc b/commons/push/garmin/garmin_stress_level_sample.avsc index 34331437..0128038c 100644 --- a/commons/push/garmin/garmin_stress_level_sample.avsc +++ b/commons/push/garmin/garmin_stress_level_sample.avsc @@ -2,11 +2,11 @@ "namespace": "org.radarcns.push.garmin", "name": "GarminStressLevelSample", "type": "record", - "doc": "Stress levels are provided as 3-minute averages of the real-time stress scores generated on the device with values ranging from 1 to 100. A value of -1 means there was not enough data to detect stress, and -2 means there was too much motion (e.g. the user was walking or running). Scores between 1 and 25 are considered “rest” (i.e. not stressful), 26-50 as “low” stress, 51-75 “medium” stress, and 76- 100 as “high” stress. These numbers are derived based on a combination of many device sensors and will automatically adjust to the wearer of the device and gain accuracy over time as the stress algorithms learn the user’s natural biometric norms. Usually assocaited with Stress Details Summary using the summaryId. Stress values from the Health API are exactly the stress values shown on Garmin Connect.", + "doc": "Stress levels are provided as 3-minute averages of the real-time stress scores generated on the device with values ranging from 1 to 100. A value of -1 means there was not enough data to detect stress, and -2 means there was too much motion (e.g. the user was walking or running). Scores between 1 and 25 are considered “rest” (i.e. not stressful), 26-50 as “low” stress, 51-75 “medium” stress, and 76- 100 as “high” stress. These numbers are derived based on a combination of many device sensors and will automatically adjust to the wearer of the device and gain accuracy over time as the stress algorithms learn the user’s natural biometric norms. Usually associated with Stress Details Summary using the summaryId. Stress values from the Health API are exactly the stress values shown on Garmin Connect.", "fields": [ {"name": "time", "type": "double", "doc": "Start time of the sample in seconds since January 1, 1970, 00:00:00 UTC (Unix timestamp)."}, {"name": "timeReceived", "type": "double", "doc": "Time this sample was recieved by the push service in seconds since January 1, 1970, 00:00:00 UTC (Unix timestamp)."}, {"name": "summaryId", "type": "string", "doc": "Unique identifier for the summary that this sample is associated with."}, {"name": "stressLevel", "type": ["null", "float"], "doc": "Stress level value recorded for the time..", "default": null} ] -} \ No newline at end of file +} From 533351e72f2a76a46f006cb5b9c6226b6723a144 Mon Sep 17 00:00:00 2001 From: Pauline Conde Date: Fri, 6 Aug 2021 14:34:23 +0100 Subject: [PATCH 05/18] Update aRMT HLH questionnaire specs --- specifications/active/aRMT-1.15.0.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/specifications/active/aRMT-1.15.0.yml b/specifications/active/aRMT-1.15.0.yml index 8e6439bf..a9904d21 100644 --- a/specifications/active/aRMT-1.15.0.yml +++ b/specifications/active/aRMT-1.15.0.yml @@ -253,11 +253,11 @@ data: 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 - - type: BP_QUESTIONNAIRE + - type: BP topic: questionnaire_bp value_schema: .active.questionnaire.Questionnaire questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/bp/bp_armt.json - - type: HLH_QUESTIONNAIRE + - type: HLH topic: questionnaire_hlh value_schema: .active.questionnaire.Questionnaire questionnaire_definition_url: https://raw.githubusercontent.com/RADAR-base/RADAR-REDCap-aRMT-Definitions/master/questionnaires/hlh/hlh_armt.json From f2fc55df651b1e5eda8710e676e1d5772055fbf7 Mon Sep 17 00:00:00 2001 From: farazkhalidamani <31991722+farazkhalidamani@users.noreply.github.com> Date: Thu, 12 Aug 2021 16:33:10 +0530 Subject: [PATCH 06/18] Create dreem-1.0.0.yml --- specifications/passive/dreem-1.0.0.yml | 1 + 1 file changed, 1 insertion(+) create mode 100644 specifications/passive/dreem-1.0.0.yml diff --git a/specifications/passive/dreem-1.0.0.yml b/specifications/passive/dreem-1.0.0.yml new file mode 100644 index 00000000..8b137891 --- /dev/null +++ b/specifications/passive/dreem-1.0.0.yml @@ -0,0 +1 @@ + From fe457a07a9f63e852ebd2b2b00a84b81aa82b523 Mon Sep 17 00:00:00 2001 From: farazkhalidamani <31991722+farazkhalidamani@users.noreply.github.com> Date: Thu, 12 Aug 2021 16:37:36 +0530 Subject: [PATCH 07/18] Update dreem-1.0.0.yml Updated the yml file for the topics and associated schemas. --- specifications/passive/dreem-1.0.0.yml | 22 +++++++++++++++++++++- 1 file changed, 21 insertions(+), 1 deletion(-) diff --git a/specifications/passive/dreem-1.0.0.yml b/specifications/passive/dreem-1.0.0.yml index 8b137891..19fd1934 100644 --- a/specifications/passive/dreem-1.0.0.yml +++ b/specifications/passive/dreem-1.0.0.yml @@ -1 +1,21 @@ - +#====================================== For DREEM device =====================================# +vendor: DREEM +model: NA +version: 1.0.0 +doc: DREEM data collected and uploaded by DREEM web application +data: + - type: DREEM SLEEP STAGE + unit: NON_DIMENSIONAL + processing_state: VENDOR + topic: dreem_sleep_stage + value_schema: .passive.dreem.DreemSleepStage + - type: DREEM SLEEP ENDPOINTS + unit: NON_DIMENSIONAL + processing_state: VENDOR + topic: dreem_sleep_endpoints + value_schema: .passive.dreem.DreemSleepEndpoints + - type: DREEM METRIC + unit: NON_DIMENSIONAL + processing_state: VENDOR + topic: dreem_metric + value_schema: .passive.dreem.DreemMetric From ac16b0ccfe56d21664088330636827c41f330e9c Mon Sep 17 00:00:00 2001 From: farazkhalidamani <31991722+farazkhalidamani@users.noreply.github.com> Date: Thu, 12 Aug 2021 18:40:32 +0530 Subject: [PATCH 08/18] Update dreem-1.0.0.yml Updated the YAML based on feedback. --- specifications/passive/dreem-1.0.0.yml | 17 +++++------------ 1 file changed, 5 insertions(+), 12 deletions(-) diff --git a/specifications/passive/dreem-1.0.0.yml b/specifications/passive/dreem-1.0.0.yml index 19fd1934..683fc874 100644 --- a/specifications/passive/dreem-1.0.0.yml +++ b/specifications/passive/dreem-1.0.0.yml @@ -1,21 +1,14 @@ -#====================================== For DREEM device =====================================# +#====================================== For Dreem 3 headband also known as Neuroband device =====================================# vendor: DREEM -model: NA +model: Dreem 3 headband also known as Neuroband version: 1.0.0 doc: DREEM data collected and uploaded by DREEM web application data: - - type: DREEM SLEEP STAGE - unit: NON_DIMENSIONAL + - unit: NON_DIMENSIONAL processing_state: VENDOR topic: dreem_sleep_stage value_schema: .passive.dreem.DreemSleepStage - - type: DREEM SLEEP ENDPOINTS - unit: NON_DIMENSIONAL + - unit: NON_DIMENSIONAL processing_state: VENDOR topic: dreem_sleep_endpoints - value_schema: .passive.dreem.DreemSleepEndpoints - - type: DREEM METRIC - unit: NON_DIMENSIONAL - processing_state: VENDOR - topic: dreem_metric - value_schema: .passive.dreem.DreemMetric + value_schema: .passive.dreem.DreemSleepEndpoints From d2f03a96b4c4f877608d77f45acf04a59337788e Mon Sep 17 00:00:00 2001 From: farazkhalidamani <31991722+farazkhalidamani@users.noreply.github.com> Date: Thu, 12 Aug 2021 20:51:03 +0530 Subject: [PATCH 09/18] Update dreem-1.0.0.yml Added doc field --- specifications/passive/dreem-1.0.0.yml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/specifications/passive/dreem-1.0.0.yml b/specifications/passive/dreem-1.0.0.yml index 683fc874..54d7228b 100644 --- a/specifications/passive/dreem-1.0.0.yml +++ b/specifications/passive/dreem-1.0.0.yml @@ -4,11 +4,13 @@ model: Dreem 3 headband also known as Neuroband version: 1.0.0 doc: DREEM data collected and uploaded by DREEM web application data: - - unit: NON_DIMENSIONAL + - doc: This is DREEM hypnogram data captured from Neuroband + unit: NON_DIMENSIONAL processing_state: VENDOR topic: dreem_sleep_stage value_schema: .passive.dreem.DreemSleepStage - - unit: NON_DIMENSIONAL + - doc: This is DREEM metrics data captured from Neuroband + unit: NON_DIMENSIONAL processing_state: VENDOR topic: dreem_sleep_endpoints - value_schema: .passive.dreem.DreemSleepEndpoints + value_schema: .passive.dreem.DreemSleepEndpoints From 00a960b1be7344affe32293b65d67eb1cad6e860 Mon Sep 17 00:00:00 2001 From: farazkhalidamani <31991722+farazkhalidamani@users.noreply.github.com> Date: Thu, 12 Aug 2021 20:55:03 +0530 Subject: [PATCH 10/18] Update dreem-1.0.0.yml Updated the model name --- specifications/passive/dreem-1.0.0.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/specifications/passive/dreem-1.0.0.yml b/specifications/passive/dreem-1.0.0.yml index 54d7228b..dc5494ff 100644 --- a/specifications/passive/dreem-1.0.0.yml +++ b/specifications/passive/dreem-1.0.0.yml @@ -1,6 +1,6 @@ #====================================== For Dreem 3 headband also known as Neuroband device =====================================# vendor: DREEM -model: Dreem 3 headband also known as Neuroband +model: Dreem Neuroband version: 1.0.0 doc: DREEM data collected and uploaded by DREEM web application data: From 6dd2839e6bc4f5f38b4c396069d227ac8350de50 Mon Sep 17 00:00:00 2001 From: farazkhalidamani <31991722+farazkhalidamani@users.noreply.github.com> Date: Thu, 12 Aug 2021 21:26:42 +0530 Subject: [PATCH 11/18] Update dreem-1.0.0.yml Updated the model --- specifications/passive/dreem-1.0.0.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/specifications/passive/dreem-1.0.0.yml b/specifications/passive/dreem-1.0.0.yml index dc5494ff..8c8283e8 100644 --- a/specifications/passive/dreem-1.0.0.yml +++ b/specifications/passive/dreem-1.0.0.yml @@ -1,6 +1,6 @@ #====================================== For Dreem 3 headband also known as Neuroband device =====================================# vendor: DREEM -model: Dreem Neuroband +model: Neuroband version: 1.0.0 doc: DREEM data collected and uploaded by DREEM web application data: From 5fc507a02c1c1fccdaef36fcc6ff59906995fb8e Mon Sep 17 00:00:00 2001 From: Pauline Conde Date: Wed, 18 Aug 2021 11:56:59 +0100 Subject: [PATCH 12/18] Bump version --- java-sdk/build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java-sdk/build.gradle b/java-sdk/build.gradle index fb0f57a4..5ad98e79 100644 --- a/java-sdk/build.gradle +++ b/java-sdk/build.gradle @@ -8,7 +8,7 @@ plugins { } allprojects { - version = '0.7.3-SNAPSHOT' + version = '0.7.3' group = 'org.radarbase' } From e6d5b3aa5d6ca19877b940eb306293de6a09355e Mon Sep 17 00:00:00 2001 From: Joris Borgdorff Date: Mon, 23 Aug 2021 16:42:09 +0200 Subject: [PATCH 13/18] Update Gradle --- java-sdk/build.gradle | 2 +- java-sdk/gradle/wrapper/gradle-wrapper.jar | Bin 59203 -> 59536 bytes .../gradle/wrapper/gradle-wrapper.properties | 2 +- java-sdk/gradlew | 257 +++++++++++------- 4 files changed, 155 insertions(+), 106 deletions(-) diff --git a/java-sdk/build.gradle b/java-sdk/build.gradle index fb0f57a4..63e61af1 100644 --- a/java-sdk/build.gradle +++ b/java-sdk/build.gradle @@ -73,5 +73,5 @@ nexusPublishing { } wrapper { - gradleVersion '7.0' + gradleVersion '7.2' } diff --git a/java-sdk/gradle/wrapper/gradle-wrapper.jar b/java-sdk/gradle/wrapper/gradle-wrapper.jar index e708b1c023ec8b20f512888fe07c5bd3ff77bb8f..7454180f2ae8848c63b8b4dea2cb829da983f2fa 100644 GIT binary patch delta 18435 zcmY&<19zBR)MXm8v2EM7ZQHi-#I|kQZfv7Tn#Q)%81v4zX3d)U4d4 zYYc!v@NU%|U;_sM`2z(4BAilWijmR>4U^KdN)D8%@2KLcqkTDW%^3U(Wg>{qkAF z&RcYr;D1I5aD(N-PnqoEeBN~JyXiT(+@b`4Pv`;KmkBXYN48@0;iXuq6!ytn`vGp$ 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z_dz(yKufo<=m71bZfLp^Ll#t3(IHkrgMcvx@~om%Ib(h(<$Da7urTI`x|%`wD--sN zJEEa>4DGSEG?0ulkosfj8IMNN4)B=ZtvGG{|4Fp=Xhg!wPNgYzS>{Bp%%Qa+624X@ X49Luk)baa85H9$5YCsTPT`SVRWMtMW diff --git a/java-sdk/gradle/wrapper/gradle-wrapper.properties b/java-sdk/gradle/wrapper/gradle-wrapper.properties index f371643e..ffed3a25 100644 --- a/java-sdk/gradle/wrapper/gradle-wrapper.properties +++ b/java-sdk/gradle/wrapper/gradle-wrapper.properties @@ -1,5 +1,5 @@ distributionBase=GRADLE_USER_HOME distributionPath=wrapper/dists -distributionUrl=https\://services.gradle.org/distributions/gradle-7.0-bin.zip +distributionUrl=https\://services.gradle.org/distributions/gradle-7.2-bin.zip zipStoreBase=GRADLE_USER_HOME zipStorePath=wrapper/dists diff --git a/java-sdk/gradlew b/java-sdk/gradlew index 4f906e0c..1b6c7873 100755 --- a/java-sdk/gradlew +++ b/java-sdk/gradlew @@ -1,7 +1,7 @@ -#!/usr/bin/env sh +#!/bin/sh # -# Copyright 2015 the original author or authors. +# Copyright © 2015-2021 the original authors. # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. @@ -17,67 +17,101 @@ # ############################################################################## -## -## Gradle start up script for UN*X -## +# +# Gradle start up script for POSIX generated by Gradle. +# +# Important for running: +# +# (1) You need a POSIX-compliant shell to run this script. If your /bin/sh is +# noncompliant, but you have some other compliant shell such as ksh or +# bash, then to run this script, type that shell name before the whole +# command line, like: +# +# ksh Gradle +# +# Busybox and similar reduced shells will NOT work, because this script +# requires all of these POSIX shell features: +# * functions; +# * expansions «$var», «${var}», «${var:-default}», «${var+SET}», +# «${var#prefix}», «${var%suffix}», and «$( cmd )»; +# * compound commands having a testable exit status, especially «case»; +# * various built-in commands including «command», «set», and «ulimit». +# +# Important for patching: +# +# (2) This script targets any POSIX shell, so it avoids extensions provided +# by Bash, Ksh, etc; in particular arrays are avoided. +# +# The "traditional" practice of packing multiple parameters into a +# space-separated string is a well documented source of bugs and security +# problems, so this is (mostly) avoided, by progressively accumulating +# options in "$@", and eventually passing that to Java. +# +# Where the inherited environment variables (DEFAULT_JVM_OPTS, JAVA_OPTS, +# and GRADLE_OPTS) rely on word-splitting, this is performed explicitly; +# see the in-line comments for details. +# +# There are tweaks for specific operating systems such as AIX, CygWin, +# Darwin, MinGW, and NonStop. +# +# (3) This script is generated from the Groovy template +# https://github.com/gradle/gradle/blob/master/subprojects/plugins/src/main/resources/org/gradle/api/internal/plugins/unixStartScript.txt +# within the Gradle project. +# +# You can find Gradle at https://github.com/gradle/gradle/. +# ############################################################################## # Attempt to set APP_HOME + # Resolve links: $0 may be a link -PRG="$0" -# Need this for relative symlinks. -while [ -h "$PRG" ] ; do - ls=`ls -ld "$PRG"` - link=`expr "$ls" : '.*-> \(.*\)$'` - if expr "$link" : '/.*' > /dev/null; then - PRG="$link" - else - PRG=`dirname "$PRG"`"/$link" - fi +app_path=$0 + +# Need this for daisy-chained symlinks. +while + APP_HOME=${app_path%"${app_path##*/}"} # leaves a trailing /; empty if no leading path + [ -h "$app_path" ] +do + ls=$( ls -ld "$app_path" ) + link=${ls#*' -> '} + case $link in #( + /*) app_path=$link ;; #( + *) app_path=$APP_HOME$link ;; + esac done -SAVED="`pwd`" -cd "`dirname \"$PRG\"`/" >/dev/null -APP_HOME="`pwd -P`" -cd "$SAVED" >/dev/null + +APP_HOME=$( cd "${APP_HOME:-./}" && pwd -P ) || exit APP_NAME="Gradle" -APP_BASE_NAME=`basename "$0"` +APP_BASE_NAME=${0##*/} # Add default JVM options here. You can also use JAVA_OPTS and GRADLE_OPTS to pass JVM options to this script. DEFAULT_JVM_OPTS='"-Xmx64m" "-Xms64m"' # Use the maximum available, or set MAX_FD != -1 to use that value. -MAX_FD="maximum" +MAX_FD=maximum warn () { echo "$*" -} +} >&2 die () { echo echo "$*" echo exit 1 -} +} >&2 # OS specific support (must be 'true' or 'false'). cygwin=false msys=false darwin=false nonstop=false -case "`uname`" in - CYGWIN* ) - cygwin=true - ;; - Darwin* ) - darwin=true - ;; - MINGW* ) - msys=true - ;; - NONSTOP* ) - nonstop=true - ;; +case "$( uname )" in #( + CYGWIN* ) cygwin=true ;; #( + Darwin* ) darwin=true ;; #( + MSYS* | MINGW* ) msys=true ;; #( + NONSTOP* ) nonstop=true ;; esac CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar @@ -87,9 +121,9 @@ CLASSPATH=$APP_HOME/gradle/wrapper/gradle-wrapper.jar if [ -n "$JAVA_HOME" ] ; then if [ -x "$JAVA_HOME/jre/sh/java" ] ; then # IBM's JDK on AIX uses strange locations for the executables - JAVACMD="$JAVA_HOME/jre/sh/java" + JAVACMD=$JAVA_HOME/jre/sh/java else - JAVACMD="$JAVA_HOME/bin/java" + JAVACMD=$JAVA_HOME/bin/java fi if [ ! -x "$JAVACMD" ] ; then die "ERROR: JAVA_HOME is set to an invalid directory: $JAVA_HOME @@ -98,7 +132,7 @@ Please set the JAVA_HOME variable in your environment to match the location of your Java installation." fi else - JAVACMD="java" + JAVACMD=java which java >/dev/null 2>&1 || die "ERROR: JAVA_HOME is not set and no 'java' command could be found in your PATH. Please set the JAVA_HOME variable in your environment to match the @@ -106,80 +140,95 @@ location of your Java installation." fi # Increase the maximum file descriptors if we can. -if [ "$cygwin" = "false" -a "$darwin" = "false" -a "$nonstop" = "false" ] ; then - MAX_FD_LIMIT=`ulimit -H -n` - if [ $? -eq 0 ] ; then - if [ "$MAX_FD" = "maximum" -o "$MAX_FD" = "max" ] ; then - MAX_FD="$MAX_FD_LIMIT" - fi - ulimit -n $MAX_FD - if [ $? -ne 0 ] ; then - warn "Could not set maximum file descriptor limit: $MAX_FD" - fi - else - warn "Could not query maximum file descriptor limit: $MAX_FD_LIMIT" - fi +if ! "$cygwin" && ! "$darwin" && ! "$nonstop" ; then + case $MAX_FD in #( + max*) + MAX_FD=$( ulimit -H -n ) || + warn "Could not query maximum file descriptor limit" + esac + case $MAX_FD in #( + '' | soft) :;; #( + *) + ulimit -n "$MAX_FD" || + warn "Could not set maximum file descriptor limit to $MAX_FD" + esac fi -# For Darwin, add options to specify how the application appears in the dock -if $darwin; then - GRADLE_OPTS="$GRADLE_OPTS \"-Xdock:name=$APP_NAME\" \"-Xdock:icon=$APP_HOME/media/gradle.icns\"" -fi +# Collect all arguments for the java command, stacking in reverse order: +# * args from the command line +# * the main class name +# * -classpath +# * -D...appname settings +# * --module-path (only if needed) +# * DEFAULT_JVM_OPTS, JAVA_OPTS, and GRADLE_OPTS environment variables. # 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"` - - # We build the pattern for arguments to be converted via cygpath - ROOTDIRSRAW=`find -L / -maxdepth 1 -mindepth 1 -type d 2>/dev/null` - SEP="" - for dir in $ROOTDIRSRAW ; do - ROOTDIRS="$ROOTDIRS$SEP$dir" - SEP="|" - done - OURCYGPATTERN="(^($ROOTDIRS))" - # Add a user-defined pattern to the cygpath arguments - if [ "$GRADLE_CYGPATTERN" != "" ] ; then - OURCYGPATTERN="$OURCYGPATTERN|($GRADLE_CYGPATTERN)" - fi +if "$cygwin" || "$msys" ; then + APP_HOME=$( cygpath --path --mixed "$APP_HOME" ) + CLASSPATH=$( cygpath --path --mixed "$CLASSPATH" ) + + JAVACMD=$( cygpath --unix "$JAVACMD" ) + # Now convert the arguments - kludge to limit ourselves to /bin/sh - i=0 - for arg in "$@" ; do - CHECK=`echo "$arg"|egrep -c "$OURCYGPATTERN" -` - CHECK2=`echo "$arg"|egrep -c "^-"` ### Determine if an option - - if [ $CHECK -ne 0 ] && [ $CHECK2 -eq 0 ] ; then ### Added a condition - eval `echo args$i`=`cygpath --path --ignore --mixed "$arg"` - else - eval `echo args$i`="\"$arg\"" + for arg do + if + case $arg in #( + -*) false ;; # don't mess with options #( + /?*) t=${arg#/} t=/${t%%/*} # looks like a POSIX filepath + [ -e "$t" ] ;; #( + *) false ;; + esac + then + arg=$( cygpath --path --ignore --mixed "$arg" ) fi - i=`expr $i + 1` + # Roll the args list around exactly as many times as the number of + # args, so each arg winds up back in the position where it started, but + # possibly modified. + # + # NB: a `for` loop captures its iteration list before it begins, so + # changing the positional parameters here affects neither the number of + # iterations, nor the values presented in `arg`. + shift # remove old arg + set -- "$@" "$arg" # push replacement arg 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" ;; - esac fi -# Escape application args -save () { - for i do printf %s\\n "$i" | sed "s/'/'\\\\''/g;1s/^/'/;\$s/\$/' \\\\/" ; done - echo " " -} -APP_ARGS=`save "$@"` +# Collect all arguments for the java command; +# * $DEFAULT_JVM_OPTS, $JAVA_OPTS, and $GRADLE_OPTS can contain fragments of +# shell script including quotes and variable substitutions, so put them in +# double quotes to make sure that they get re-expanded; and +# * put everything else in single quotes, so that it's not re-expanded. + +set -- \ + "-Dorg.gradle.appname=$APP_BASE_NAME" \ + -classpath "$CLASSPATH" \ + org.gradle.wrapper.GradleWrapperMain \ + "$@" + +# Use "xargs" to parse quoted args. +# +# With -n1 it outputs one arg per line, with the quotes and backslashes removed. +# +# In Bash we could simply go: +# +# readarray ARGS < <( xargs -n1 <<<"$var" ) && +# set -- "${ARGS[@]}" "$@" +# +# but POSIX shell has neither arrays nor command substitution, so instead we +# post-process each arg (as a line of input to sed) to backslash-escape any +# character that might be a shell metacharacter, then use eval to reverse +# that process (while maintaining the separation between arguments), and wrap +# the whole thing up as a single "set" statement. +# +# This will of course break if any of these variables contains a newline or +# an unmatched quote. +# -# 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" +eval "set -- $( + printf '%s\n' "$DEFAULT_JVM_OPTS $JAVA_OPTS $GRADLE_OPTS" | + xargs -n1 | + sed ' s~[^-[:alnum:]+,./:=@_]~\\&~g; ' | + tr '\n' ' ' + )" '"$@"' exec "$JAVACMD" "$@" From 0983f12f59fcfbc6c008ad98da0bb9ce47428418 Mon Sep 17 00:00:00 2001 From: Joris Borgdorff Date: Mon, 23 Aug 2021 16:59:34 +0200 Subject: [PATCH 14/18] Fix additional message in raw topic listing --- java-sdk/radar-schemas-tools/build.gradle | 2 +- .../schema/tools/CommandLineApp.java | 27 +++++++++++++++++++ 2 files changed, 28 insertions(+), 1 deletion(-) diff --git a/java-sdk/radar-schemas-tools/build.gradle b/java-sdk/radar-schemas-tools/build.gradle index 513b4010..c67faa75 100644 --- a/java-sdk/radar-schemas-tools/build.gradle +++ b/java-sdk/radar-schemas-tools/build.gradle @@ -28,7 +28,7 @@ dependencies { implementation group: 'net.sourceforge.argparse4j', name: 'argparse4j', version: argparseVersion - runtimeOnly group: 'ch.qos.logback', name: 'logback-classic', version: logbackVersion + implementation group: 'ch.qos.logback', name: 'logback-classic', version: logbackVersion } application { diff --git a/java-sdk/radar-schemas-tools/src/main/java/org/radarbase/schema/tools/CommandLineApp.java b/java-sdk/radar-schemas-tools/src/main/java/org/radarbase/schema/tools/CommandLineApp.java index 2f0e0c05..ad671ded 100644 --- a/java-sdk/radar-schemas-tools/src/main/java/org/radarbase/schema/tools/CommandLineApp.java +++ b/java-sdk/radar-schemas-tools/src/main/java/org/radarbase/schema/tools/CommandLineApp.java @@ -26,6 +26,8 @@ import java.util.function.Function; import java.util.stream.Collectors; import java.util.stream.Stream; + +import ch.qos.logback.classic.Level; import net.sourceforge.argparse4j.ArgumentParsers; import net.sourceforge.argparse4j.helper.HelpScreenException; import net.sourceforge.argparse4j.inf.ArgumentParser; @@ -89,6 +91,16 @@ public static void main(String... args) { return; } + Boolean isVerbose = ns.getBoolean("verbose"); + if (isVerbose != null && isVerbose) { + setLogLevel(org.slf4j.event.Level.DEBUG); + } + + Boolean isQuiet = ns.getBoolean("quiet"); + if (isQuiet != null && isQuiet) { + setLogLevel(org.slf4j.event.Level.ERROR); + } + CommandLineApp app; try { app = new CommandLineApp(Paths.get(ns.getString("root")).toAbsolutePath()); @@ -196,4 +208,19 @@ public Stream getTopicsVerbose(boolean prettyPrint, String source) { }) .collect(Collectors.joining("\n"))); } + + private static void setLogLevel(org.slf4j.event.Level level) { + Logger rootLogger = LoggerFactory.getLogger(org.slf4j.Logger.ROOT_LOGGER_NAME); + if (rootLogger instanceof ch.qos.logback.classic.Logger) { + ch.qos.logback.classic.Logger logbackLogger = (ch.qos.logback.classic.Logger) rootLogger; + switch (level) { + case ERROR: logbackLogger.setLevel(Level.ERROR); break; + case WARN: logbackLogger.setLevel(Level.WARN); break; + case INFO: logbackLogger.setLevel(Level.INFO); break; + case DEBUG: logbackLogger.setLevel(Level.DEBUG); break; + case TRACE: logbackLogger.setLevel(Level.TRACE); break; + } + } + + } } From b1d28c10c64b005bb7d913b2fe1ab26dc70e3a67 Mon Sep 17 00:00:00 2001 From: Joris Borgdorff Date: Tue, 24 Aug 2021 10:26:42 +0200 Subject: [PATCH 15/18] Unify topic listing with broker listing --- .../schema/registration/KafkaTopics.java | 74 +++++++++++-------- 1 file changed, 45 insertions(+), 29 deletions(-) diff --git a/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java b/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java index ce16007d..62fe7422 100644 --- a/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java +++ b/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java @@ -17,6 +17,8 @@ import java.util.concurrent.ExecutionException; import java.util.concurrent.TimeUnit; import java.util.concurrent.TimeoutException; +import java.util.function.Function; +import java.util.function.Supplier; import java.util.regex.Pattern; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -24,6 +26,7 @@ import org.apache.kafka.clients.admin.AdminClient; import org.apache.kafka.clients.admin.ListTopicsOptions; import org.apache.kafka.clients.admin.NewTopic; +import org.apache.kafka.common.KafkaFuture; import org.apache.kafka.common.Node; import org.radarbase.schema.specification.SourceCatalogue; import org.slf4j.Logger; @@ -78,30 +81,38 @@ public void initialize(int brokers) throws InterruptedException { public void initialize(int brokers, int numTries) throws InterruptedException { int sleep = 2; int numBrokers = 0; + long timeout = 5; - for (int tries = 0; tries < numTries && numBrokers < brokers; tries++) { - List hosts; + for (int tries = 0; tries < numTries; tries++) { + long start = System.currentTimeMillis(); + List hosts = Collections.emptyList(); try { hosts = kafkaClient.describeCluster() .nodes() - .get() + .get(timeout, TimeUnit.SECONDS) .stream() .map(Node::host) .collect(Collectors.toList()); } catch (ExecutionException ex) { logger.error("Failed to connect to bootstrap server {}", kafkaProperties.get(BOOTSTRAP_SERVERS_CONFIG), ex.getCause()); - hosts = Collections.emptyList(); + } catch (TimeoutException ex) { + logger.error("Failed to connect to bootstrap server {} within {} seconds", + kafkaProperties.get(BOOTSTRAP_SERVERS_CONFIG), timeout); } numBrokers = hosts.size(); - if (numBrokers >= brokers) { break; } else if (tries < numTries - 1) { logger.warn("Only {} out of {} Kafka brokers available. Waiting {} seconds.", numBrokers, brokers, sleep); - Thread.sleep(sleep * 1000L); + long timeTaken = System.currentTimeMillis() - start; + long sleepMillis = Math.max(sleep * 1000L - timeTaken, 0L); + if (sleepMillis > 0L) { + Thread.sleep(sleepMillis); + } sleep = Math.min(MAX_SLEEP, sleep * 2); + timeout = Math.min(5, sleep); } else { logger.error("Only {} out of {} Kafka brokers available." + " Failed to wait on all brokers.", numBrokers, brokers); @@ -176,7 +187,10 @@ public boolean createTopics(Stream topicsToCreate, int partitions, short }).map(t -> new NewTopic(t, partitions, replication)).collect(Collectors.toList()); if (!newTopics.isEmpty()) { - getKafkaClient().createTopics(newTopics).all().get(); + getKafkaClient() + .createTopics(newTopics) + .all() + .get(); logger.info("Created {} topics. Requesting to refresh topics", newTopics.size()); refreshTopics(); } else { @@ -193,40 +207,42 @@ public boolean createTopics(Stream topicsToCreate, int partitions, short public boolean refreshTopics() throws InterruptedException { ensureInitialized(); logger.info("Waiting for topics to become available."); - int sleep = 10; + int sleep = 2; + long timeout = 5; int numTries = 10; topics = null; - ListTopicsOptions opts = new ListTopicsOptions().listInternal(true); + ListTopicsOptions opts = new ListTopicsOptions() + .listInternal(true); + for (int tries = 0; tries < numTries; tries++) { + long start = System.currentTimeMillis(); try { - topics = getKafkaClient().listTopics(opts).names().get(sleep, TimeUnit.SECONDS); - } catch (ExecutionException e) { - logger.error("Failed to list topics from brokers: {}." - + " Trying again after {} seconds.", e, sleep); - Thread.sleep(sleep * 1000L); - sleep = Math.min(MAX_SLEEP, sleep * 2); - continue; - } catch (TimeoutException e) { - // do nothing + topics = getKafkaClient() + .listTopics(opts) + .names() + .get(sleep, TimeUnit.SECONDS); + } catch (ExecutionException ex) { + logger.error("Failed to list topics from brokers: {}", ex.getCause().toString()); + } catch (TimeoutException ex) { + logger.error("Failed to list topics within {} seconds", timeout); } if (topics != null && !topics.isEmpty()) { break; - } - if (tries < numTries - 1) { - logger.warn("Topics not listed yet after {} seconds", sleep); + } else if (tries < numTries - 1) { + logger.warn("Topics not listed yet. Trying again after {} seconds.", sleep); + long timeTaken = System.currentTimeMillis() - start; + long sleepMillis = Math.max(sleep * 1000L - timeTaken, 0L); + if (sleepMillis > 0L) { + Thread.sleep(sleepMillis); + } + sleep = Math.min(MAX_SLEEP, sleep * 2); + timeout = Math.min(5, sleep); } else { logger.error("Topics have not become available. Failed to wait on Kafka."); } - sleep = Math.min(MAX_SLEEP, sleep * 2); - } - - if (topics == null || topics.isEmpty()) { - return false; - } else { - Thread.sleep(5000L); - return true; } + return topics != null && !topics.isEmpty(); } @Override From dcae0734661f0a8ba1b10e46acba549cd2bb41b2 Mon Sep 17 00:00:00 2001 From: Joris Borgdorff Date: Tue, 24 Aug 2021 10:29:55 +0200 Subject: [PATCH 16/18] Fixed typo --- .../java/org/radarbase/schema/registration/KafkaTopics.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java b/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java index 62fe7422..aa3f271d 100644 --- a/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java +++ b/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java @@ -239,7 +239,7 @@ public boolean refreshTopics() throws InterruptedException { sleep = Math.min(MAX_SLEEP, sleep * 2); timeout = Math.min(5, sleep); } else { - logger.error("Topics have not become available. Failed to wait on Kafka."); + logger.error("Topics have not become available. Failed to list topics."); } } return topics != null && !topics.isEmpty(); From 0a201991da07ee196ff2ec856dd7484985527327 Mon Sep 17 00:00:00 2001 From: Joris Borgdorff Date: Tue, 24 Aug 2021 10:30:30 +0200 Subject: [PATCH 17/18] Remove unused imports --- .../java/org/radarbase/schema/registration/KafkaTopics.java | 3 --- 1 file changed, 3 deletions(-) diff --git a/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java b/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java index aa3f271d..39c37fad 100644 --- a/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java +++ b/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java @@ -17,8 +17,6 @@ import java.util.concurrent.ExecutionException; import java.util.concurrent.TimeUnit; import java.util.concurrent.TimeoutException; -import java.util.function.Function; -import java.util.function.Supplier; import java.util.regex.Pattern; import java.util.stream.Collectors; import java.util.stream.Stream; @@ -26,7 +24,6 @@ import org.apache.kafka.clients.admin.AdminClient; import org.apache.kafka.clients.admin.ListTopicsOptions; import org.apache.kafka.clients.admin.NewTopic; -import org.apache.kafka.common.KafkaFuture; import org.apache.kafka.common.Node; import org.radarbase.schema.specification.SourceCatalogue; import org.slf4j.Logger; From 5639f084bffa88a2483ae075d583dff304d28f01 Mon Sep 17 00:00:00 2001 From: Joris Borgdorff Date: Tue, 24 Aug 2021 12:15:39 +0200 Subject: [PATCH 18/18] Simplified initialization sleep (removed timeout) --- .../org/radarbase/schema/registration/KafkaTopics.java | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java b/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java index 39c37fad..f693e71e 100644 --- a/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java +++ b/java-sdk/radar-schemas-registration/src/main/java/org/radarbase/schema/registration/KafkaTopics.java @@ -78,7 +78,6 @@ public void initialize(int brokers) throws InterruptedException { public void initialize(int brokers, int numTries) throws InterruptedException { int sleep = 2; int numBrokers = 0; - long timeout = 5; for (int tries = 0; tries < numTries; tries++) { long start = System.currentTimeMillis(); @@ -86,7 +85,7 @@ public void initialize(int brokers, int numTries) throws InterruptedException { try { hosts = kafkaClient.describeCluster() .nodes() - .get(timeout, TimeUnit.SECONDS) + .get(sleep, TimeUnit.SECONDS) .stream() .map(Node::host) .collect(Collectors.toList()); @@ -95,7 +94,7 @@ public void initialize(int brokers, int numTries) throws InterruptedException { kafkaProperties.get(BOOTSTRAP_SERVERS_CONFIG), ex.getCause()); } catch (TimeoutException ex) { logger.error("Failed to connect to bootstrap server {} within {} seconds", - kafkaProperties.get(BOOTSTRAP_SERVERS_CONFIG), timeout); + kafkaProperties.get(BOOTSTRAP_SERVERS_CONFIG), sleep); } numBrokers = hosts.size(); if (numBrokers >= brokers) { @@ -109,7 +108,6 @@ public void initialize(int brokers, int numTries) throws InterruptedException { Thread.sleep(sleepMillis); } sleep = Math.min(MAX_SLEEP, sleep * 2); - timeout = Math.min(5, sleep); } else { logger.error("Only {} out of {} Kafka brokers available." + " Failed to wait on all brokers.", numBrokers, brokers); @@ -205,7 +203,6 @@ public boolean refreshTopics() throws InterruptedException { ensureInitialized(); logger.info("Waiting for topics to become available."); int sleep = 2; - long timeout = 5; int numTries = 10; topics = null; @@ -222,7 +219,7 @@ public boolean refreshTopics() throws InterruptedException { } catch (ExecutionException ex) { logger.error("Failed to list topics from brokers: {}", ex.getCause().toString()); } catch (TimeoutException ex) { - logger.error("Failed to list topics within {} seconds", timeout); + logger.error("Failed to list topics within {} seconds", sleep); } if (topics != null && !topics.isEmpty()) { break; @@ -234,7 +231,6 @@ public boolean refreshTopics() throws InterruptedException { Thread.sleep(sleepMillis); } sleep = Math.min(MAX_SLEEP, sleep * 2); - timeout = Math.min(5, sleep); } else { logger.error("Topics have not become available. Failed to list topics."); }