PR for dev to master in prep for 0.5.0 release

.gitignore

@@ -20,3 +20,4 @@ static/bower_components/
 coverage/
 
 npm-debug.log
+bin/__pycache__

Makefile

@@ -8,7 +8,7 @@ all: test
 report:
  # report results to community
 test:
- ./node_modules/.bin/mocha ${TESTS}
+ ./node_modules/.bin/mocha -c ${TESTS}
 
 travis:
  ${ISTANBUL} cover ${MOCHA} --include-all-sources true --report lcovonly -- -R tap ${TESTS}

bin/mm-format-ns-pump-history.sh

@@ -24,11 +24,10 @@ OUTPUT=${2-/dev/fd/1}
 #TZ=${3-$(date +%z)}
 
 cat $HISTORY | \
- json -e "this.medtronic = this._type;" | \
- #json -e "this.dateString = this.timestamp + '$(TZ=TZ date +%z)'" | \
- json -e "this.dateString = this.timestamp + '$(date +%z)'" | \
- json -e "this.type = 'medtronic'" | \
- json -e "this.date = this.date ? this.date : new Date(Date.parse(this.dateString)).getTime( )" \
+ json -e "this.medtronic = this._type;" \
+ -e "this.dateString = this.timestamp + '$(date +%z)'" \
+ -e "this.type = 'medtronic'" \
+ -e "this.date = this.date ? this.date : new Date(Date.parse(this.dateString)).getTime( )" \
  > $OUTPUT
 
 

bin/mm-format-ns-treatments.sh

@@ -27,12 +27,11 @@ model=$(json -f $MODEL)
 
 oref0-normalize-temps $HISTORY \
  | json -e "this.medtronic = 'mm://openaps/$self/' + (this._type || this.eventType);" \
- | json -e "this.created_at = this.created_at ? this.created_at : this.timestamp" \
- | json -e "this.enteredBy = 'openaps://medtronic/$model'" \
- | json -e "if (this.glucose && !this.glucoseType && this.glucose > 0) { this.glucoseType = this.enteredBy }" \
- | json -e "this.eventType = (this.eventType ? this.eventType : 'Note')" \
- | json -e "if (this._type == 'AlarmSensor' && this.alarm_description) {this.notes = this.alarm_description}" \
- | json -e "if (this.eventType == 'Note' && !this.alarm_description) { this.notes = this._type + ' $model ' + (this.notes ? this.notes : '')}" \
- | json > $OUTPUT
-
+ -e "this.created_at = this.created_at ? this.created_at : this.timestamp" \
+ -e "this.enteredBy = 'openaps://medtronic/$model'" \
+ -e "if (this.glucose && !this.glucoseType && this.glucose > 0) { this.glucoseType = this.enteredBy }" \
+ -e "this.eventType = (this.eventType ? this.eventType : 'Note')" \
+ -e "if (this._type == 'AlarmSensor' && this.alarm_description) {this.notes = this.alarm_description}" \
+ -e "if (this.eventType == 'Note' && !this.alarm_description) { this.notes = this._type + ' $model ' + (this.notes ? this.notes : '')}" \
+ > $OUTPUT
 

bin/nightscout.sh

@@ -319,7 +319,11 @@ hash-api-secret)
 autoconfigure-device-crud)
  NIGHTSCOUT_HOST=$1
  PLAIN_NS_SECRET=$2
- API_SECRET=$($self hash-api-secret $2)
+ if [[ "${PLAIN_NS_SECRET,,}" =~ "token=" ]]; then
+ API_SECRET=$2 # store token as API_SECRET
+ else
+ API_SECRET=$($self hash-api-secret $2)
+ fi
  case $1 in
  help|-h|--help)
  setup_help
@@ -331,8 +335,8 @@ autoconfigure-device-crud)
  test -z "$API_SECRET" && setup_help && exit 1;
  openaps device add ns process --require "oper" nightscout ns "NIGHTSCOUT_HOST" "API_SECRET"
  openaps device show ns --json | json \
- | json -e "this.extra.args = this.extra.args.replace(' NIGHTSCOUT_HOST ', ' $NIGHTSCOUT_HOST ')" \
- | json -e "this.extra.args = this.extra.args.replace(' API_SECRET', ' $API_SECRET')" \
+ -e "this.extra.args = this.extra.args.replace(' NIGHTSCOUT_HOST ', ' $NIGHTSCOUT_HOST ')" \
+ -e "this.extra.args = this.extra.args.replace(' API_SECRET', ' $API_SECRET')" \
  | openaps import
  ;;
 cull-latest-openaps-treatments)
@@ -348,4 +352,4 @@ help|--help|-h)
 *)
  test -n "$COMMAND" && exec $COMMAND $*
  ;;
-esac
+esac

bin/ns-dedupe-treatments.sh

@@ -11,7 +11,7 @@ EOF
 }
 
 function fetch ( ) {
- curl -s -g $ENDPOINT.json
+ curl --compressed -s -g $ENDPOINT.json
 }
 
 function flatten ( ) {
@@ -22,7 +22,7 @@ function flatten ( ) {
 function find_dupes_on ( ) {
  count=$1
  date=$2
- test $count -gt 1 && curl -g -s ${ENDPOINT}.json"?count=$(($count-1))&find[created_at]=$date"
+ test $count -gt 1 && curl --compressed -g -s ${ENDPOINT}.json"?count=$(($count-1))&find[created_at]=$date"
 }
 function debug_cmd ( ) {
 tid=$1
@@ -45,8 +45,8 @@ export NIGHTSCOUT_HOST ENDPOINT
 fetch | flatten | while read count date; do
  test $count -gt 1 && echo "{}" \
  | json -e "this.count = $count" \
- | json -e "this.date = '$date'" \
- | json -e "this.created_at = '$date'"
+ -e "this.date = '$date'" \
+ -e "this.created_at = '$date'"
 done | json -g
 }
 

bin/ns-get.sh

@@ -8,7 +8,7 @@ NIGHTSCOUT_HOST=${NIGHTSCOUT_HOST-${2-localhost:1337}}
 QUERY=${3}
 OUTPUT=${4-/dev/fd/1}
 
-CURL_FLAGS="-g -s"
+CURL_FLAGS="--compressed -g -s"
 NIGHTSCOUT_FORMAT=${NIGHTSCOUT_FORMAT-json}
 test "$NIGHTSCOUT_DEBUG" = "1" && CURL_FLAGS="${CURL_FLAGS} -iv"
 test "$NIGHTSCOUT_DEBUG" = "1" && set -x
@@ -20,42 +20,47 @@ Usage: $self <entries.json> [NIGHTSCOUT_HOST|localhost:1337] [QUERY] [stdout|-]
 $self type <entries.json> <NIGHTSCOUT_HOST|localhost:1337] [QUERY] [stdout|-]
 $self host <NIGHTSCOUT_HOST|localhost:1337> <entries.json> [QUERY] [stdout|-]
 
-$self --config <device> <entries.json> <NIGHTSCOUT_HOST> <monitor/entries.json>
 EOF
 }
 
-REPORT_ENDPOINT=$NIGHTSCOUT_HOST/api/v1/${REPORT}'?'${QUERY}
+# use token authentication if the user has a token set in their API_SECRET environment variable
+if [[ "${API_SECRET,,}" =~ "token=" ]]; then
+ if [[ -z ${QUERY} ]]; then
+ REPORT_ENDPOINT=$NIGHTSCOUT_HOST/api/v1/${REPORT}'?'${API_SECRET}
+ else
+ REPORT_ENDPOINT=$NIGHTSCOUT_HOST/api/v1/${REPORT}'?'${API_SECRET}'&'${QUERY}
+ fi
+else
+ REPORT_ENDPOINT=$NIGHTSCOUT_HOST/api/v1/${REPORT}'?'${QUERY}
+fi
+
 case $1 in
- --config)
- test -z $2 && echo "Device name missing." && usage && exit 1;
- devicename=${2-${self}}
- test -z $3 && echo "Type is missing" && usage && exit 1;
- # echo openaps device add $2 process $self $3
- cat <<EOF
-openaps device add $devicename process $self $3 $self-NIGHTSCOUT_HOST
-sed -i -e "s/$self-NIGHTSCOUT_HOST/$4/g" $devicename.ini
-openaps report add $5 text $devicename shell 
-EOF
- exit 0;
- ;;
  host)
  # $self
  NIGHTSCOUT_HOST=${NIGHTSCOUT_HOST-${2-localhost:1337}}
  REPORT=${3-entries.json}
  QUERY=${4}
  OUTPUT=${5-/dev/fd/1}
- REPORT_ENDPOINT=$NIGHTSCOUT_HOST/api/v1/${REPORT}'?'${QUERY}
+
+ # use token authentication if the user has a token set in their API_SECRET environment variable
+ if [[ "${API_SECRET,,}" =~ "token=" ]]; then
+ if [[ -z ${QUERY} ]]; then
+ REPORT_ENDPOINT=$NIGHTSCOUT_HOST/api/v1/${REPORT}'?'${API_SECRET}
+ else
+ REPORT_ENDPOINT=$NIGHTSCOUT_HOST/api/v1/${REPORT}'?'${API_SECRET}'&'${QUERY}
+ fi
+ else
+ REPORT_ENDPOINT=$NIGHTSCOUT_HOST/api/v1/${REPORT}'?'${QUERY}
+ fi
  test -z "$NIGHTSCOUT_HOST" && usage && exit 1;
+
  curl ${CURL_FLAGS} $REPORT_ENDPOINT | $NIGHTSCOUT_FORMAT
 
  ;;
  type)
  shift
  exec $self $*
  ;;
- --noop)
- echo "curl -s $REPORT_ENDPOINT | json"
- ;;
  help|--help|-h)
  usage
  ;;

bin/ns-upload-entries.sh

@@ -6,7 +6,6 @@
 self=$(basename $0)
 ENTRIES=${1-entries.json}
 NIGHTSCOUT_HOST=${NIGHTSCOUT_HOST-localhost:1337}
-#TZ=${3-$(date +%z)}
 OUTPUT=${2}
 
 function usage ( ) {
@@ -24,11 +23,21 @@ case "$1" in
 esac
 
 export ENTRIES API_SECRET NIGHTSCOUT_HOST
+
+# use token authentication if the user has a token set in their API_SECRET environment variable
+if [[ "${API_SECRET,,}" =~ "token=" ]]; then
+ API_SECRET_HEADER=""
+ REST_ENDPOINT="${NIGHTSCOUT_HOST}/api/v1/entries.json?${API_SECRET}"
+else
+ REST_ENDPOINT="${NIGHTSCOUT_HOST}/api/v1/entries.json"
+ API_SECRET_HEADER='-H "API-SECRET: ${API_SECRET}"'
+fi
+
+
 # requires API_SECRET and NIGHTSCOUT_HOST to be set in calling environment (i.e. in crontab)
 (
-curl -m 30 -s -X POST --data-binary @$ENTRIES \
- -H "API-SECRET: $API_SECRET" \
- -H "content-type: application/json" \
- $NIGHTSCOUT_HOST/api/v1/entries.json
-) && ( test -n "$OUTPUT" && touch $OUTPUT ; logger "Uploaded $ENTRIES to $NIGHTSCOUT_HOST" ) || logger "Unable to upload to $NIGHTSCOUT_HOST"
+curl -m 30 -s -X POST --data-binary @${ENTRIES} \
+ ${API_SECRET_HEADER} -H "content-type: application/json" \
+ ${REST_ENDPOINT}
+) && ( test -n "${OUTPUT}" && touch ${OUTPUT} ; logger "Uploaded ${ENTRIES} to ${NIGHTSCOUT_HOST}" ) || logger "Unable to upload to ${NIGHTSCOUT_HOST}"
 

bin/ns-upload.sh

@@ -7,7 +7,6 @@ NIGHTSCOUT_HOST=${NIGHTSCOUT_HOST-${1-localhost:1337}}
 API_SECRET=${2-${API_SECRET}}
 TYPE=${3-entries.json}
 ENTRIES=${4-entries.json}
-#TZ=${3-$(date +%z)}
 OUTPUT=${5}
 
 REST_ENDPOINT="${NIGHTSCOUT_HOST}/api/v1/${TYPE}"
@@ -16,32 +15,19 @@ function usage ( ) {
 cat <<EOF
 Usage: $self <NIGHTSCOUT_HOST|localhost:1337> <API_SECRET> [API-TYPE|entries.json] <monitor/entries-to-upload.json> [stdout|-]
 
-$self --config <NIGHTSCOUT_HOST> <PLAIN_API_SECRET> <API-TYPE|entries.json> <monitor/entries-to-upload.json> output-report.json
-
 $self help - This message.
 EOF
 }
 
 case $1 in
- --config)
- test -z $3 && usage && exit 1;
- # echo openaps device add $2 process $self $3
-API_SECRET=$(echo -n $3 | sha1sum | cut -d ' ' -f 1 | tr -d "\n")
- cat <<EOF
-openaps device add $self process --require "type report" $self "$self-NIGHTSCOUT" "$self-APIKEY"
-sed -i -e "s/$self-NIGHTSCOUT/$2/g" $self.ini
-sed -i -e "s/$self-APIKEY/$API_SECRET/g" $self.ini
-openaps report add $6 text $self shell "$4" "$5"
-EOF
- exit 0;
- ;;
  help)
  usage
  ;;
  *)
- # curl -s $REPORT_ENDPOINT | json
+ # curl -s ${REPORT_ENDPOINT} | json
  ;;
 esac
+
 export ENTRIES API_SECRET NIGHTSCOUT_HOST REST_ENDPOINT
 if [[ -z $API_SECRET ]] ; then
  echo "$self: missing API_SECRET"
@@ -60,10 +46,20 @@ if [[ "$ENTRIES" != "-" ]] ; then
  exit 1;
  fi
 fi
-(test "$ENTRIES" != "-" && cat $ENTRIES || cat )| (
-curl -m 30 -s -X POST --data-binary @- \
- -H "API-SECRET: $API_SECRET" \
- -H "content-type: application/json" \
- $REST_ENDPOINT
-) && ( test -n "$OUTPUT" && touch $OUTPUT ; logger "Uploaded $ENTRIES to $NIGHTSCOUT_HOST" ) || logger "Unable to upload to $NIGHTSCOUT_HOST"
 
+# use token authentication if the user has a token set in their API_SECRET environment variable
+if [[ "${API_SECRET,,}" =~ "token=" ]]; then
+ REST_ENDPOINT="${REST_ENDPOINT}?${API_SECRET}"
+ (test "$ENTRIES" != "-" && cat $ENTRIES || cat )| (
+ curl -m 30 -s -X POST --data-binary @- \
+ -H "content-type: application/json" \
+ $REST_ENDPOINT
+ ) && ( test -n "$OUTPUT" && touch $OUTPUT ; logger "Uploaded $ENTRIES to $NIGHTSCOUT_HOST" ) || logger "Unable to upload to $NIGHTSCOUT_HOST"
+else
+ (test "$ENTRIES" != "-" && cat $ENTRIES || cat )| (
+ curl -m 30 -s -X POST --data-binary @- \
+ -H "API-SECRET: $API_SECRET" \
+ -H "content-type: application/json" \
+ $REST_ENDPOINT
+ ) && ( test -n "$OUTPUT" && touch $OUTPUT ; logger "Uploaded $ENTRIES to $NIGHTSCOUT_HOST" ) || logger "Unable to upload to $NIGHTSCOUT_HOST"
+fi

bin/oref0-autotune.sh

@@ -34,6 +34,7 @@ die() {
 }
 
 # defaults
+CURL_FLAGS="--compressed"
 DIR=""
 NIGHTSCOUT_HOST=""
 START_DATE=""
@@ -44,6 +45,10 @@ TERMINAL_LOGGING=true
 RECOMMENDS_REPORT=true
 UNKNOWN_OPTION=""
 
+if [ -n "${API_SECRET_READ}" ]; then
+ HASHED_API_SECRET_READ=`echo -n ${API_SECRET_READ}|sha1sum|cut -f1 -d '-'|cut -f1 -d ' '`
+fi
+
 # If we are running OS X, we need to use a different version
 # of the 'date' command; the built-in 'date' is BSD, which
 # has fewer options than the linux version. So the user
@@ -153,7 +158,11 @@ echo "Grabbing NIGHTSCOUT treatments.json for date range..."
 # Get Nightscout carb and insulin Treatments
 url="$NIGHTSCOUT_HOST/api/v1/treatments.json?find\[created_at\]\[\$gte\]=`date --date="$START_DATE -4 hours" -Iminutes`&find\[created_at\]\[\$lte\]=`date --date="$END_DATE +1 days" -Iminutes`"
 echo $url
-curl -s $url > ns-treatments.json || die "Couldn't download ns-treatments.json"
+if [ -n "${HASHED_API_SECRET_READ}" ]; then 
+ curl ${CURL_FLAGS} -H "api-secret: ${HASHED_API_SECRET_READ}" -s $url > ns-treatments.json || die "Couldn't download ns-treatments.json"
+else
+ curl ${CURL_FLAGS} -s $url > ns-treatments.json || die "Couldn't download ns-treatments.json"
+fi
 ls -la ns-treatments.json || die "No ns-treatments.json downloaded"
 
 # Build date list for autotune iteration
@@ -176,7 +185,12 @@ for i in "${date_list[@]}"
 do 
  url="$NIGHTSCOUT_HOST/api/v1/entries/sgv.json?find\[date\]\[\$gte\]=`(date -d $i +%s | tr -d '\n'; echo 000)`&find\[date\]\[\$lte\]=`(date --date="$i +1 days" +%s | tr -d '\n'; echo 000)`&count=1000"
  echo $url
- curl -s $url > ns-entries.$i.json || die "Couldn't download ns-entries.$i.json"
+ if [ -n "${HASHED_API_SECRET_READ}" ]; then 
+ curl ${CURL_FLAGS} -H "api-secret: ${HASHED_API_SECRET_READ}" -s $url > ns-entries.$i.json || die "Couldn't download ns-entries.$i.json"
+ else
+ curl ${CURL_FLAGS} -s $url > ns-entries.$i.json || die "Couldn't download ns-entries.$i.json"
+ fi
+
  ls -la ns-entries.$i.json || die "No ns-entries.$i.json downloaded"
 done
 
@@ -201,10 +215,18 @@ do
  # Autotune (required args, <autotune/glucose.json> <autotune/autotune.json> <settings/profile.json>), 
  # output autotuned profile or what will be used as <autotune/autotune.json> in the next iteration
  echo "oref0-autotune-core autotune.$run_number.$i.json profile.json profile.pump.json > newprofile.$run_number.$i.json"
- oref0-autotune-core autotune.$run_number.$i.json profile.json profile.pump.json > newprofile.$run_number.$i.json || die "Could not run oref0-autotune-core autotune.$run_number.$i.json profile.json profile.pump.json"
-
- # Copy tuned profile produced by autotune to profile.json for use with next day of data
- cp newprofile.$run_number.$i.json profile.json
+ if ! oref0-autotune-core autotune.$run_number.$i.json profile.json profile.pump.json > newprofile.$run_number.$i.json; then
+ if cat profile.json | jq --exit-status .carb_ratio==null; then
+ echo "ERROR: profile.json contains null carb_ratio: using profile.pump.json"
+ cp profile.pump.json profile.json
+ exit
+ else
+ die "Could not run oref0-autotune-core autotune.$run_number.$i.json profile.json profile.pump.json"
+ fi
+ else
+ # Copy tuned profile produced by autotune to profile.json for use with next day of data
+ cp newprofile.$run_number.$i.json profile.json
+ fi
 
  done # End Date Range Iteration
 done # End Number of Runs Loop

bin/oref0-detect-sensitivity.js

@@ -37,6 +37,7 @@ if (!module.parent) {
  try {
  var cwd = process.cwd();
  var glucose_data = require(cwd + '/' + glucose_input);
+ // require 6 hours of data to run autosens
  if (glucose_data.length < 72) {
  console.error("Optional feature autosens disabled: not enough glucose data to calculate sensitivity");
  return console.log('{ "ratio": 1, "reason": "not enough glucose data to calculate autosens" }');