Merge pull request #707 from openaps/dev

Prep for oref0 0.6.0 release dev to master

.gitignore

@@ -21,3 +21,7 @@ coverage/
 
 npm-debug.log
 bin/__pycache__
+
+package-lock.json
+
+*.pyc

bin/ns-get.sh

@@ -57,7 +57,7 @@ case $1 in
     fi
     test -z "$NIGHTSCOUT_HOST" && usage && exit 1;
 
-    curl ${CURL_AUTH} ${CURL_FLAGS} $REPORT_ENDPOINT | $NIGHTSCOUT_FORMAT
+    curl -m 30 ${CURL_AUTH} ${CURL_FLAGS} $REPORT_ENDPOINT | $NIGHTSCOUT_FORMAT
 
     ;;
   type)
@@ -69,7 +69,7 @@ case $1 in
     ;;
   *)
     test -z "$NIGHTSCOUT_HOST" && usage && exit 1;
-    curl ${CURL_AUTH} ${CURL_FLAGS} $REPORT_ENDPOINT | $NIGHTSCOUT_FORMAT
+    curl -m 30 ${CURL_AUTH} ${CURL_FLAGS} $REPORT_ENDPOINT | $NIGHTSCOUT_FORMAT
     ;;
 esac
 

bin/openaps-bootstrap.sh

@@ -29,6 +29,6 @@ ifdown wlan0; ifup wlan0
 sleep 10
 echo -ne "\nWifi SSID: "; iwgetid -r
 sleep 5
-# TODO check for options to fix the certificate activation error message for https
-cd /tmp/; wget --no-check-certificate https://raw.githubusercontent.com/openaps/docs/dev/scripts/openaps-install.sh; bash ./openaps-install.sh
+curl https://raw.githubusercontent.com/openaps/oref0/master/bin/openaps-install.sh > /tmp/openaps-install.sh
+bash /tmp/openaps-install.sh
 )

bin/openaps-install.sh

@@ -1,31 +1,50 @@
 #!/bin/bash
 set -e
 
-read -p "Enter your Edison's new hostname (this will be your rig's "name" in the future, so make sure to write it down): " -r
-myedisonhostname=$REPLY
-echo $myedisonhostname > /etc/hostname
-sed -r -i"" "s/localhost( jubilinux)?$/localhost $myedisonhostname/" /etc/hosts
+read -p "Enter your rig's new hostname (this will be your rig's "name" in the future, so make sure to write it down): " -r
+myrighostname=$REPLY
+echo $myrighostname > /etc/hostname
+sed -r -i"" "s/localhost( jubilinux)?$/localhost $myrighostname/" /etc/hosts
+sed -r -i"" "s/127.0.1.1.*$/127.0.1.1       $myrighostname/" /etc/hosts
 
 # if passwords are old, force them to be changed at next login
-passwd -S edison | grep 20[01][0-6] && passwd -e root
+passwd -S edison 2>/dev/null | grep 20[01][0-6] && passwd -e root
 # automatically expire edison account if its password is not changed in 3 days
-passwd -S edison | grep 20[01][0-6] && passwd -e edison -i 3
+passwd -S edison 2>/dev/null | grep 20[01][0-6] && passwd -e edison -i 3
+
+if [ -e /run/sshwarn ] ; then
+    echo Please select a secure password for ssh logins to your rig:
+    echo 'For the "root" account:'
+    passwd root
+    echo 'And for the "pi" account (same password is fine):'
+    passwd pi
+fi
+
+grep "PermitRootLogin yes" /etc/ssh/sshd_config || echo "PermitRootLogin yes" > /etc/ssh/sshd_config
 
 # set timezone
 dpkg-reconfigure tzdata
 
 #dpkg -P nodejs nodejs-dev
 # TODO: remove the `-o Acquire::ForceIPv4=true` once Debian's mirrors work reliably over IPv6
 apt-get -o Acquire::ForceIPv4=true update && apt-get -o Acquire::ForceIPv4=true -y dist-upgrade && apt-get -o Acquire::ForceIPv4=true -y autoremove
-apt-get -o Acquire::ForceIPv4=true install -y sudo strace tcpdump screen acpid vim python-pip locate
-adduser edison sudo
-adduser edison dialout
+apt-get -o Acquire::ForceIPv4=true install -y sudo strace tcpdump screen acpid vim python-pip locate ntpdate
+#check if edison user exists before trying to add it to groups
+
+if  getent passwd edison > /dev/null; then
+  echo "Adding edison to sudo users"
+  adduser edison sudo
+  echo "Adding edison to dialout users"
+  adduser edison dialout
+ # else
+  # echo "User edison does not exist. Apparently, you are runnning a non-edison setup."
+fi
 
 sed -i "s/daily/hourly/g" /etc/logrotate.conf
 sed -i "s/#compress/compress/g" /etc/logrotate.conf
 
-# TODO: change back to master after docs release
-curl -s https://raw.githubusercontent.com/openaps/docs/dev/scripts/quick-packages.sh | bash -
+# TODO: change to dev and then master after PR and release
+curl -s https://raw.githubusercontent.com/openaps/oref0/dev/bin/openaps-packages.sh | bash -
 mkdir -p ~/src; cd ~/src && git clone git://github.com/openaps/oref0.git || (cd oref0 && git checkout master && git pull)
 echo "Press Enter to run oref0-setup with the current release (master branch) of oref0,"
 read -p "or press ctrl-c to cancel. " -r

bin/openaps-packages.sh

@@ -3,7 +3,7 @@
 # TODO: remove the `-o Acquire::ForceIPv4=true` once Debian's mirrors work reliably over IPv6
 apt-get -o Acquire::ForceIPv4=true install -y sudo
 sudo apt-get -o Acquire::ForceIPv4=true update && sudo apt-get -o Acquire::ForceIPv4=true -y upgrade
-sudo apt-get -o Acquire::ForceIPv4=true install -y git python python-dev python-software-properties python-numpy python-pip nodejs-legacy npm watchdog strace tcpdump screen acpid vim locate jq lm-sensors && \
+sudo apt-get -o Acquire::ForceIPv4=true install -y git python python-dev software-properties-common python-numpy python-pip nodejs-legacy npm watchdog strace tcpdump screen acpid vim locate jq lm-sensors && \
 sudo pip install -U openaps && \
 sudo pip install -U openaps-contrib && \
 sudo openaps-install-udev-rules && \

bin/oref0-append-local-temptarget.sh

@@ -0,0 +1,15 @@
+#!/bin/bash
+
+if [[ ! -z "$2" ]]; then
+    input=$(oref0-set-local-temptarget $@)
+elif [[ ! -z "$1" ]]; then
+    input=$(cat $1)
+else
+    input=$(cat /dev/stdin)
+fi
+#cat "${1:-/dev/stdin}" \
+echo $input \
+    | tee /tmp/temptarget.json \
+    && jq -s '[.[0]] + .[1]' /tmp/temptarget.json settings/local-temptargets.json \
+    | tee settings/local-temptargets.json.new \
+    && mv settings/local-temptargets.json.new settings/local-temptargets.json

bin/oref0-autosens-loop.sh

@@ -0,0 +1,57 @@
+#!/bin/bash
+main() {
+    echo
+    echo Starting oref0-autosens-loop at $(date):
+    overtemp && exit 1
+    if highload && completed_recently; then
+        echo Load high at $(date): waiting up to 30m to continue
+        exit 2
+    fi
+
+    autosens 2>&1
+    touch /tmp/autons-completed
+    echo Completed oref0-autons-loop at $(date)
+}
+
+function overtemp {
+    # check for CPU temperature above 85°C
+    sensors -u 2>/dev/null | awk '$NF > 85' | grep input \
+    && echo Edison is too hot: waiting for it to cool down at $(date)\
+    && echo Please ensure rig is properly ventilated
+}
+
+function highload {
+    # check whether system load average is high
+    uptime | awk '$NF > 2' | grep load
+}
+
+function completed_recently {
+    find /tmp/ -mmin -30 | egrep -q "autosens-completed"
+}
+
+# find settings/ -newer settings/autosens.json | grep -q pumphistory-24h-zoned.json || find settings/ -size -5c | grep -q autosens.json || ! find settings/ | grep -q autosens || ! find settings/autosens.json
+# openaps use detect-sensitivity shell monitor/glucose.json settings/pumphistory-24h-zoned.json settings/insulin_sensitivities.json settings/basal_profile.json settings/profile.json monitor/carbhistory.json settings/temptargets.json
+function autosens {
+    # only run autosens if pumphistory-24h is newer than autosens
+    if find settings/ -newer settings/autosens.json | grep -q pumphistory-24h-zoned.json \
+        || find settings/ -size -5c | grep -q autosens.json \
+        || ! find settings/ | grep -q autosens \
+        || ! find settings/autosens.json >/dev/null; then
+        if oref0-detect-sensitivity monitor/glucose.json settings/pumphistory-24h-zoned.json settings/insulin_sensitivities.json settings/basal_profile.json settings/profile.json monitor/carbhistory.json settings/temptargets.json > settings/autosens.json.new && cat settings/autosens.json.new | jq .ratio | grep -q [0-9]; then
+            mv settings/autosens.json.new settings/autosens.json
+            echo -n "Autosens refreshed: "
+        else
+            echo -n "Failed to refresh autosens: using old autosens.json: "
+        fi
+    else
+        echo -n "No need to refresh autosens yet: "
+    fi
+    cat settings/autosens.json | jq . -C -c
+}
+
+die() {
+    echo "$@"
+    exit 1
+}
+
+main "$@"

bin/oref0-autotune-recommends-report.sh

@@ -85,16 +85,14 @@ minutes_list=()
 end_time=23:30
 time=00:00
 minutes=0
-while :
-do
-  time_list+=( "$time" )
-  minutes_list+=( "$minutes" )
-  if [ $time != "$end_time" ]; then
-    time="$(date --date="$time 30 minutes" +%R)";
-    minutes=$(expr $minutes + 30)
-  else
-    break
-  fi
+for h in $(seq -w 0 23); do
+    for m in 00 30; do
+        time="$h:$m"
+        minutes=$(echo "60 * $h + $m" | bc)
+        #echo $time $minutes
+        time_list+=( "$time" )
+        minutes_list+=( "$minutes" )
+    done
 done
 
 for (( i=0; i<${#minutes_list[@]}; i++ ))

bin/oref0-autotune.sh

@@ -27,8 +27,13 @@
 # THE SOFTWARE.
 
 die() {
-  echo "$@"
-  exit 1
+    if [[ -z "$API_SECRET" ]]; then
+        echo "Warning: API_SECRET is not set when calling oref0-autotune.sh"
+        echo "(this is only a problem if you have locked down read-only access to your NS)."
+    fi
+
+    echo "$@"
+    exit 1
 }
 
 # defaults
@@ -48,11 +53,6 @@ if [ -n "${API_SECRET_READ}" ]; then
    echo "WARNING: API_SECRET_READ is deprecated starting with oref 0.6.x. The Nightscout authentication information is now used from the API_SECRET environment variable"
 fi
 
-if [[ -z "$API_SECRET" ]]; then
-  echo "Warning: API_SECRET is not set when calling oref0-autotune.sh"
-  # exit 1
-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
@@ -155,7 +155,6 @@ fi
 # If a previous valid settings/autotune.json exists, use that; otherwise start from settings/profile.json
 cp settings/autotune.json autotune/profile.json && cat autotune/profile.json | jq . | grep -q start || cp autotune/profile.pump.json autotune/profile.json
 cd autotune
-# TODO: Need to think through what to remove in the autotune folder...
 
 # Turn on stderr logging, if enabled (default to true)
 if [[ $TERMINAL_LOGGING = "true" ]]; then
@@ -176,12 +175,23 @@ do
   fi
 done
 
+echo "Compressing old json and log files to save space..."
+gzip -f ns-*.json
+gzip -f autotune*.json
+# only gzip autotune log files more than 2 days old
+find autotune.*.log -mtime +2 | while read file; do gzip -f $file; done
+echo "Autotune disk usage:"
+du -h .
+echo "Overall disk used/avail:"
+df -h .
+
 echo "Grabbing NIGHTSCOUT treatments.json and entries/sgv.json for date range..."
 
 # Get Nightscout BG (sgv.json) Entries
 for i in "${date_list[@]}"
 do 
-    query="find%5Bdate%5D%5B%24gte%5D=`(date -d $i +%s | tr -d '\n'; echo 000)`&find%5Bdate%5D%5B%24lte%5D=`(date --date="$i +1 days" +%s | tr -d '\n'; echo 000)`&count=1000"
+    # pull CGM data from 4am-4am
+    query="find%5Bdate%5D%5B%24gte%5D=`(date -d "$i +4 hours " +%s | tr -d '\n'; echo 000)`&find%5Bdate%5D%5B%24lte%5D=`(date --date="$i +28 hours" +%s | tr -d '\n'; echo 000)`&count=1000"
     echo Query: $NIGHTSCOUT_HOST $query
     ns-get host $NIGHTSCOUT_HOST entries/sgv.json $query > ns-entries.$i.json || die "Couldn't download ns-entries.$i.json"
     ls -la ns-entries.$i.json || die "No ns-entries.$i.json downloaded"
@@ -190,8 +200,8 @@ do
     # echo $i $START_DATE;
     #query="find%5Bdate%5D%5B%24gte%5D=`(date -d $i +%s | tr -d'\n'; echo 000)`&find%5Bdate%5D%5B%24lte%5D=`(date --date="$i +1 days" +%s | tr -d '\n'; echo 000)`&count=1000"
     # to capture UTC-dated treatments, we need to capture an extra 12h on either side, plus the DIA lookback
-    # 18h = 12h for timezones + 6h for DIA; 36h = 24h for end-of-day + 12h for timezones
-    query="find%5Bcreated_at%5D%5B%24gte%5D=`date --date="$i -18 hours" -Iminutes`&find%5Bcreated_at%5D%5B%24lte%5D=`date --date="$i +36 hours" -Iminutes`"
+    # 18h = 12h for timezones + 6h for DIA; 40h = 28h for 4am + 12h for timezones
+    query="find%5Bcreated_at%5D%5B%24gte%5D=`date --date="$i -18 hours" -Iminutes`&find%5Bcreated_at%5D%5B%24lte%5D=`date --date="$i +42 hours" -Iminutes`"
     echo Query: $NIGHTSCOUT_HOST/$query
     ns-get host $NIGHTSCOUT_HOST treatments.json $query > ns-treatments.$i.json || die "Couldn't download ns-treatments.$i.json"
     ls -la ns-treatments.$i.json || die "No ns-treatments.$i.json downloaded"

bin/oref0-calculate-iob.js

@@ -20,7 +20,7 @@
 
 var generate = require('oref0/lib/iob');
 function usage ( ) {
-    console.log('usage: ', process.argv.slice(0, 2), '<pumphistory-zoned.json> <profile.json> <clock-zoned.json>');
+    console.log('usage: ', process.argv.slice(0, 2), '<pumphistory-zoned.json> <profile.json> <clock-zoned.json> [autosens.json]');
 
 }
 
@@ -32,6 +32,7 @@ if (!module.parent) {
   }
   var profile_input = process.argv.slice(3, 4).pop();
   var clock_input = process.argv.slice(4, 5).pop();
+  var autosens_input = process.argv.slice(5, 6).pop();
 
   if (!pumphistory_input || !profile_input) {
     usage( );
@@ -43,13 +44,24 @@ if (!module.parent) {
   var profile_data = require(cwd + '/' + profile_input);
   var clock_data = require(cwd + '/' + clock_input);
 
+  var autosens_data = null;
+  if (autosens_input) {
+    try {
+        var autosens_data = require(cwd + '/' + autosens_input);
+    } catch (e) {}
+    //console.error(autosens_input, JSON.stringify(autosens_data));
+  }
+
   // all_data.sort(function (a, b) { return a.date > b.date });
 
   var inputs = {
     history: all_data
   , profile: profile_data
   , clock: clock_data
   };
+  if ( autosens_data ) {
+    inputs.autosens = autosens_data;
+  }
 
   var iob = generate(inputs);
   console.log(JSON.stringify(iob));