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 +} diff --git a/java-sdk/build.gradle b/java-sdk/build.gradle index c8656d59..3460efa2 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' group = 'org.radarbase' } @@ -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 e708b1c0..7454180f 100644 Binary files a/java-sdk/gradle/wrapper/gradle-wrapper.jar and b/java-sdk/gradle/wrapper/gradle-wrapper.jar differ 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 "$JAVACMD" "$@" 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..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 @@ -79,28 +79,34 @@ public void initialize(int brokers, int numTries) throws InterruptedException { int sleep = 2; int numBrokers = 0; - 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(sleep, 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), sleep); } 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); } else { logger.error("Only {} out of {} Kafka brokers available." @@ -176,7 +182,10 @@ 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 +202,40 @@ 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; 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", sleep); } 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); } else { - logger.error("Topics have not become available. Failed to wait on Kafka."); + logger.error("Topics have not become available. Failed to list topics."); } - 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 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; + } + } + + } } 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 diff --git a/specifications/active/aRMT-1.15.0.yml b/specifications/active/aRMT-1.15.0.yml new file mode 100644 index 00000000..a9904d21 --- /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 + 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 + 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 diff --git a/specifications/passive/dreem-1.0.0.yml b/specifications/passive/dreem-1.0.0.yml new file mode 100644 index 00000000..8c8283e8 --- /dev/null +++ b/specifications/passive/dreem-1.0.0.yml @@ -0,0 +1,16 @@ +#====================================== For Dreem 3 headband also known as Neuroband device =====================================# +vendor: DREEM +model: Neuroband +version: 1.0.0 +doc: DREEM data collected and uploaded by DREEM web application +data: + - doc: This is DREEM hypnogram data captured from Neuroband + unit: NON_DIMENSIONAL + processing_state: VENDOR + topic: dreem_sleep_stage + value_schema: .passive.dreem.DreemSleepStage + - doc: This is DREEM metrics data captured from Neuroband + unit: NON_DIMENSIONAL + processing_state: VENDOR + topic: dreem_sleep_endpoints + value_schema: .passive.dreem.DreemSleepEndpoints