dev branch - prepping next release

bin/mm-format-oref0-glucose.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+# Author: Ben West @bewest
+# Maintainer: @tghoward
+
+# Written for decocare v0.0.18. Will need updating the the decocare json format changes.
+HISTORY=${1-glucosehistory.json}
+OUTPUT=${2-/dev/fd/1}
+#TZ=${3-$(date +%z)}
+
+cat $HISTORY | \
+  json -e "this.medtronic = this._type;" | \
+  json -e "this.dateString = this.date + '$(date +%z)'" | \
+  json -e "this.date = new Date(this.dateString).getTime();" | \
+  json -e "this.type = (this.name == 'GlucoseSensorData') ? 'sgv' : 'pumpdata'" | \
+  json -e "this.device = 'openaps://medtronic/pump/cgm'" \
+  > $OUTPUT
+

bin/ns-dedupe-treatments.sh

@@ -76,6 +76,7 @@ done
 }
 
 export API_SECRET
+test -n "$3" && API_SECRET=$3
 case "$1" in
   --list)
     list $2

bin/ns-uploader-setup.sh

@@ -0,0 +1,134 @@
+#!/bin/bash
+
+# This script sets up a read-only openaps environment that uploads pump history data to nightscout
+# by defining the required devices, reports, and aliases.
+#
+# Released under MIT license. See the accompanying LICENSE.txt file for
+# full terms and conditions
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+# THE SOFTWARE.
+
+die() {
+  echo "$@"
+  exit 1
+}
+
+self=$(basename $0)
+if [[ $# -lt 2 ]]; then
+    openaps device show pump 2>/dev/null >/dev/null || die "Usage: $self <directory> <pump serial #>"
+fi
+directory=`mkdir -p $1; cd $1; pwd`
+serial=$2
+
+echo -n Setting up oref0 in $directory for pump $serial
+
+if [[ $# -gt 3 ]]; then
+	diyps_url=$4
+    echo -n ", DIYPS URL $diyps_url"
+fi
+echo
+
+read -p "Continue? " -n 1 -r
+echo
+if [[ $REPLY =~ ^[Yy]$ ]]; then
+
+( ( cd $directory 2>/dev/null && git status ) || ( openaps init $directory ) ) || die "Can't init $directory"
+cd $directory || die "Can't cd $directory"
+
+#sudo cp ~/src/oref0/logrotate.openaps /etc/logrotate.d/openaps
+sudo bash -c "curl -s https://raw.githubusercontent.com/openaps/oref0/master/logrotate.openaps > /etc/logrotate.d/openaps"
+#sudo cp ~/src/oref0/logrotate.rsyslog /etc/logrotate.d/rsyslog
+sudo bash -c "curl -s https://raw.githubusercontent.com/openaps/oref0/master/logrotate.rsyslog > /etc/logrotate.d/rsyslog"
+
+test -d /var/log/openaps || sudo mkdir /var/log/openaps && sudo chown $USER /var/log/openaps
+
+openaps vendor add openapscontrib.timezones
+
+# don't re-create devices if they already exist
+openaps device show 2>/dev/null > /tmp/openaps-devices
+
+# add devices
+grep -q pump.ini .gitignore 2>/dev/null || echo pump.ini >> .gitignore
+git add .gitignore
+grep pump /tmp/openaps-devices || openaps device add pump medtronic $serial || die "Can't add pump"
+grep cgm /tmp/openaps-devices || openaps device add cgm dexcom || die "Can't add CGM"
+git add cgm.ini
+grep ns-glucose /tmp/openaps-devices || openaps device add ns-glucose process 'bash -c "curl -s $NIGHTSCOUT_HOST/api/v1/entries/sgv.json | json -e \"this.glucose = this.sgv\""' || die "Can't add ns-glucose"
+git add ns-glucose.ini
+grep oref0 /tmp/openaps-devices || openaps device add oref0 process oref0 || die "Can't add oref0"
+git add oref0.ini
+grep iob /tmp/openaps-devices || openaps device add iob process --require "pumphistory profile clock" oref0 calculate-iob || die "Can't add iob"
+git add iob.ini
+grep tz /tmp/openaps-devices || openaps device add tz timezones || die "Can't add tz"
+git add tz.ini
+#grep latest-treatments /tmp/openaps-devices || openaps device add latest-treatments process nightscout 'latest-openaps-treatment $NIGHTSCOUT_HOST' || die "Can't add latest-treatments"
+#git add latest-treatments.ini
+
+# don't re-create reports if they already exist
+openaps report show 2>/dev/null > /tmp/openaps-reports
+
+# add reports for frequently-refreshed monitoring data
+ls monitor 2>/dev/null >/dev/null || mkdir monitor || die "Can't mkdir monitor"
+grep monitor/glucose.json /tmp/openaps-reports || openaps report add monitor/glucose.json JSON cgm iter_glucose 5 || die "Can't add glucose.json"
+grep monitor/ns-glucose.json /tmp/openaps-reports || openaps report add monitor/ns-glucose.json text ns-glucose shell || die "Can't add ns-glucose.json"
+grep settings/model.json /tmp/openaps-reports || openaps report add settings/model.json JSON pump model || die "Can't add model"
+grep monitor/clock.json /tmp/openaps-reports || openaps report add monitor/clock.json JSON pump read_clock || die "Can't add clock.json"
+grep monitor/clock-zoned.json /tmp/openaps-reports || openaps report add monitor/clock-zoned.json JSON tz clock monitor/clock.json || die "Can't add clock-zoned.json"
+grep monitor/temp_basal.json /tmp/openaps-reports || openaps report add monitor/temp_basal.json JSON pump read_temp_basal || die "Can't add temp_basal.json"
+grep monitor/reservoir.json /tmp/openaps-reports || openaps report add monitor/reservoir.json JSON pump reservoir || die "Can't add reservoir.json"
+grep monitor/pumphistory.json /tmp/openaps-reports || openaps report add monitor/pumphistory.json JSON pump iter_pump_hours 4 || die "Can't add pumphistory.json"
+grep monitor/pumphistory-zoned.json /tmp/openaps-reports || openaps report add monitor/pumphistory-zoned.json JSON tz rezone monitor/pumphistory.json || die "Can't add pumphistory-zoned.json"
+grep monitor/iob.json /tmp/openaps-reports || openaps report add monitor/iob.json text iob shell monitor/pumphistory-zoned.json settings/profile.json monitor/clock-zoned.json || die "Can't add iob.json"
+
+# add reports for infrequently-refreshed settings data
+ls settings 2>/dev/null >/dev/null || mkdir settings || die "Can't mkdir settings"
+grep settings/bg_targets.json /tmp/openaps-reports || openaps report add settings/bg_targets.json JSON pump read_bg_targets || die "Can't add bg_targets.json"
+grep settings/insulin_sensitivities.json /tmp/openaps-reports || openaps report add settings/insulin_sensitivities.json JSON pump read_insulin_sensitivities || die "Can't add insulin_sensitivities.json"
+grep settings/basal_profile.json /tmp/openaps-reports || openaps report add settings/basal_profile.json JSON pump read_selected_basal_profile || die "Can't add basal_profile.json"
+grep settings/settings.json /tmp/openaps-reports || openaps report add settings/settings.json JSON pump read_settings || die "Can't add settings.json"
+
+# add aliases to get data
+openaps alias add invoke "report invoke" || die "Can't add invoke"
+openaps alias add preflight '! bash -c "rm -f monitor/clock.json && openaps report invoke monitor/clock.json >/dev/null 2>/dev/null && grep -q T monitor/clock.json && echo PREFLIGHT OK || ( mm-stick warmup || sudo oref0-reset-usb; echo PREFLIGHT FAIL; sleep 120; exit 1 )"' || die "Can't add preflight"
+openaps alias add monitor-cgm "report invoke monitor/glucose.json" || die "Can't add monitor-cgm"
+openaps alias add get-ns-glucose "report invoke monitor/ns-glucose.json" || die "Can't add get-ns-glucose"
+openaps alias add monitor-pump "report invoke monitor/clock.json monitor/temp_basal.json monitor/pumphistory.json monitor/pumphistory-zoned.json monitor/clock-zoned.json" || die "Can't add monitor-pump"
+openaps alias add get-settings "report invoke settings/model.json settings/bg_targets.json settings/insulin_sensitivities.json settings/basal_profile.json settings/settings.json" || die "Can't add get-settings"
+openaps alias add get-bg '! bash -c "openaps monitor-cgm 2>/dev/null || ( openaps get-ns-glucose && grep -q glucose monitor/ns-glucose.json && mv monitor/ns-glucose.json monitor/glucose.json )"' || die "Can't add get-bg"
+openaps alias add gather '! bash -c "rm monitor/*; ( openaps get-bg && openaps get-settings >/dev/null && openaps monitor-pump ) 2>/dev/null"' || die "Can't add gather"
+openaps alias add wait-for-bg '! bash -c "cp monitor/glucose.json monitor/last-glucose.json; while(diff -q monitor/last-glucose.json monitor/glucose.json); do echo -n .; sleep 10; openaps get-bg >/dev/null; done"'
+
+# upload treatments to nightscout
+ls upload 2>/dev/null >/dev/null || mkdir upload || die "Can't mkdir upload"
+openaps alias add latest-ns-treatment-time '! bash -c "nightscout latest-openaps-treatment $NIGHTSCOUT_HOST | json created_at"' || die "Can't add latest-ns-treatment-time"
+openaps alias add format-latest-nightscout-treatments '! bash -c "nightscout cull-latest-openaps-treatments monitor/pumphistory-zoned.json settings/model.json $(openaps latest-ns-treatment-time) > upload/latest-treatments.json"' || die "Can't add format-latest-nightscout-treatments"
+openaps alias add upload-recent-treatments '! bash -c "openaps format-latest-nightscout-treatments && test $(json -f upload/latest-treatments.json -a created_at eventType | wc -l ) -gt 0 && (ns-upload $NIGHTSCOUT_HOST $API_SECRET treatments.json upload/latest-treatments.json ) || echo \"No recent treatments to upload\""' || die "Can't add upload-recent-treatments"
+openaps alias add upload '! bash -c "openaps preflight && ( openaps monitor-pump && openaps upload-recent-treatments && openaps get-settings) 2>/dev/null >/dev/null && echo -n \"Uploaded; most recent treatment event @ \" && openaps latest-ns-treatment-time || echo \"Error; could not upload\""' || die "Can't add upload"
+
+read -p "Schedule oref1 (openaps nightscout uploader) in cron? " -n 1 -r
+echo
+if [[ $REPLY =~ ^[Yy]$ ]]; then
+    read -p "Nightscout hostname? "
+    NIGHTSCOUT_HOST=$REPLY
+    read -p "Hashed API secret? "
+    API_SECRET=$REPLY
+    read -p "Upload to $NIGHTSCOUT_HOST using API secret $API_SECRET, correct? " -n 1 -r
+    if [[ $REPLY =~ ^[Yy]$ ]]; then
+        (crontab -l; echo NIGHTSCOUT_HOST=$NIGHTSCOUT_HOST) | crontab -
+        (crontab -l; echo API_SECRET=$API_SECRET) | crontab -
+    fi
+    # add crontab entries
+    (crontab -l; crontab -l | grep -q PATH || echo 'PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin') | crontab -
+    (crontab -l; crontab -l | grep -q killall || echo '* * * * * killall -g --older-than 10m openaps') | crontab -
+    (crontab -l; crontab -l | grep -q "reset-git" || echo "* * * * * cd $directory && oref0-reset-git") | crontab -
+    (crontab -l; crontab -l | grep -q uploader || echo "* * * * * cd $directory && ( ps aux | grep -v grep | grep -q 'openaps ' && echo OpenAPS already running || openaps upload ) 2>&1 | tee -a /var/log/openaps/uploader.log") | crontab -
+    crontab -l
+fi
+
+fi

bin/oref0-calculate-iob.js

@@ -21,16 +21,16 @@
 var generate = require('oref0/lib/iob');
 
 if (!module.parent) {
-  var iob_input = process.argv.slice(2, 3).pop()
-  var profile_input = process.argv.slice(3, 4).pop()
-  var clock_input = process.argv.slice(4, 5).pop()
+  var iob_input = process.argv.slice(2, 3).pop();
+  var profile_input = process.argv.slice(3, 4).pop();
+  var clock_input = process.argv.slice(4, 5).pop();
 
   if (!iob_input || !profile_input) {
     console.log('usage: ', process.argv.slice(0, 2), '<pumphistory.json> <profile.json> <clock.json>');
     process.exit(1);
   }
 
-  var cwd = process.cwd()
+  var cwd = process.cwd();
   var all_data = require(cwd + '/' + iob_input);
   var profile_data = require(cwd + '/' + profile_input);
   var clock_data = require(cwd + '/' + clock_input);

bin/oref0-determine-basal.js

@@ -163,11 +163,12 @@ function init() {
             console.log(JSON.stringify(rT));
             return rT;
         }
-        var threshold = profile.min_bg - 30;
+        // min_bg of 90 -> threshold of 70, 110 -> 80, and 130 -> 90
+        var threshold = profile.min_bg - 0.5*(profile.min_bg-50);
 
         if (bg < threshold) { // low glucose suspend mode: BG is < ~80
             rT.reason = "BG " + bg + "<" + threshold;
-            if ((glucose_status.delta < 0 && glucose_status.avgdelta < 0) || (glucose_status.delta < bgi && glucose_status.avgdelta < bgi)) {
+            if ((glucose_status.delta <= 0 && glucose_status.avgdelta <= 0) || (glucose_status.delta < bgi && glucose_status.avgdelta < bgi)) {
                 // BG is still falling / rising slower than predicted
                 console.error(rT.reason);
                 return determinebasal.setTempBasal(0, 30, profile, rT, offline);
@@ -191,7 +192,11 @@ function init() {
             rT.reason = "Eventual BG " + eventualBG + "<" + profile.min_bg;
             // if 5m or 15m avg BG is rising faster than BGI/2
             if (glucose_status.delta > bgi/2 && glucose_status.avgdelta > bgi/2) {
-                rT.reason += ", but Delta " + tick + " > BGI " + bgi + " / 2";
+                if (glucose_status.delta > glucose_status.avgdelta) {
+                    rT.reason += ", but Delta " + tick + " > BGI " + bgi + " / 2";
+                } else {
+                    rT.reason += ", but Avg. Delta " + glucose_status.avgdelta + " > BGI " + bgi + " / 2";
+                }
                 if (currenttemp.duration > 0) { // if there is currently any temp basal running
                     rT.reason = rT.reason += "; cancel";
                     return determinebasal.setTempBasal(0, 0, profile, rT, offline); // cancel temp
@@ -205,14 +210,14 @@ function init() {
             if (snoozeBG > profile.min_bg) { // if adding back in the bolus contribution BG would be above min
                 // if BG is falling and high-temped, or rising and low-temped, cancel
                 // compare against zero here, not BGI, because BGI will be highly negative from boluses and no carbs
-                if (glucose_status.delta < 0 && currenttemp.rate > profile.current_basal) {
+                if (glucose_status.delta < 0 && currenttemp.duration > 0 && currenttemp.rate > profile.current_basal) {
                     rT.reason += tick + ", and temp " + currenttemp.rate + " > basal " + profile.current_basal;
                     return determinebasal.setTempBasal(0, 0, profile, rT, offline); // cancel temp
-                } else if (glucose_status.delta > 0 && currenttemp.rate < profile.current_basal) {
+                } else if (glucose_status.delta > 0 && currenttemp.duration > 0 && currenttemp.rate < profile.current_basal) {
                     rT.reason += tick + ", and temp " + currenttemp.rate + " < basal " + profile.current_basal;
                     return determinebasal.setTempBasal(0, 0, profile, rT, offline); // cancel temp
                 }
-                rT.reason += "bolus snooze: eventual BG range " + eventualBG + "-" + snoozeBG;
+                rT.reason += ", bolus snooze: eventual BG range " + eventualBG + "-" + snoozeBG;
                 console.error(rT.reason);
                 console.log(JSON.stringify(rT));
                 return rT;
@@ -225,7 +230,7 @@ function init() {
             rate = Math.round( rate * 1000 ) / 1000;
             // if required temp < existing temp basal
             if (typeof currenttemp.rate !== 'undefined' && (currenttemp.duration > 0 && rate > currenttemp.rate - 0.1)) {
-                rT.reason += "temp " + currenttemp.rate + " <~ req " + rate + "U/hr";
+                rT.reason += ", temp " + currenttemp.rate + " <~ req " + rate + "U/hr";
                 console.error(rT.reason);
                 console.log(JSON.stringify(rT));
                 return rT;
@@ -235,7 +240,11 @@ function init() {
         }
         // if eventual BG is above min but BG is falling faster than BGI/2
         if (glucose_status.delta < bgi/2 || glucose_status.avgdelta < bgi/2) {
-            rT.reason = "Eventual BG " + eventualBG + ">" + profile.min_bg + " but Delta " + tick + " < BGI " + bgi + " / 2";
+            if (glucose_status.delta < glucose_status.avgdelta) {
+                rT.reason = "Eventual BG " + eventualBG + ">" + profile.min_bg + " but Delta " + tick + " < BGI " + bgi + " / 2";
+            } else {
+                rT.reason = "Eventual BG " + eventualBG + ">" + profile.min_bg + " but Avg. Delta " + glucose_status.avgdelta + " < BGI " + bgi + " / 2";
+            }
             if (currenttemp.duration > 0) { // if there is currently any temp basal running
                 rT.reason = rT.reason += "; cancel";
                 return determinebasal.setTempBasal(0, 0, profile, rT, offline); // cancel temp
@@ -292,7 +301,7 @@ function init() {
             rT.reason = currenttemp.duration + "@" + currenttemp.rate + " > req " + insulinReq + "U";
             return determinebasal.setTempBasal(rate, 30, profile, rT, offline);
         }
-        if (typeof currenttemp.rate == 'undefined' || currenttemp.rate == 0) { // no temp is set
+        if (typeof currenttemp.duration == 'undefined' || currenttemp.duration == 0) { // no temp is set
             rT.reason += "no temp, setting " + rate + "U/hr";
             return determinebasal.setTempBasal(rate, 30, profile, rT, offline);
         }

lib/iob/calculate.js

@@ -1,45 +1,40 @@
 
 function iobCalc(treatment, time, dia) {
-    var diaratio = dia / 3;
+    var diaratio = 3.0 / dia;
     var peak = 75 ;
     var end = 180 ;
     //var sens = profile_data.sens;
     if (typeof time === 'undefined') {
-        var time = new Date();
+        time = new Date();
     }
 
+    var results = {};
+
     if (treatment.insulin) {
-        var bolusTime=new Date(treatment.date);
-        var minAgo=(time-bolusTime)/1000/60 * diaratio;
+        var bolusTime = new Date(treatment.date);
+        var minAgo = diaratio * (time-bolusTime) / 1000 / 60;
+        var iobContrib = 0;
+        var activityContrib = 0;
 
-        if (minAgo < 0) { 
-            var iobContrib=0;
-            var activityContrib=0;
-        }
-        else if (minAgo < peak) {
+        if (minAgo < peak) {
             var x = (minAgo/5 + 1);
-            var iobContrib=treatment.insulin*(1-0.001852*x*x+0.001852*x);
-            //var activityContrib=sens*treatment.insulin*(2/dia/60/peak)*minAgo;
-            var activityContrib=treatment.insulin*(2/dia/60/peak)*minAgo;
-        }
-        else if (minAgo < end) {
-            var x = (minAgo-peak)/5;
-            var iobContrib=treatment.insulin*(0.001323*x*x - .054233*x + .55556);
-            //var activityContrib=sens*treatment.insulin*(2/dia/60-(minAgo-peak)*2/dia/60/(60*dia-peak));
-            var activityContrib=treatment.insulin*(2/dia/60-(minAgo-peak)*2/dia/60/(60*dia-peak));
-        }
-        else {
-            var iobContrib=0;
-            var activityContrib=0;
+            iobContrib = treatment.insulin * (1 - 0.001852 * x * x + 0.001852 * x);
+            //activityContrib=sens*treatment.insulin*(2/dia/60/peak)*minAgo;
+            activityContrib = treatment.insulin * (2 / dia / 60 / peak) * minAgo;
+        } else if (minAgo < end) {
+            var y = (minAgo-peak)/5;
+            iobContrib = treatment.insulin * (0.001323 * y * y - .054233 * y + .55556);
+            //activityContrib=sens*treatment.insulin*(2/dia/60-(minAgo-peak)*2/dia/60/(60*dia-peak));
+            activityContrib = treatment.insulin * (2 / dia / 60 - (minAgo - peak) * 2 / dia / 60 / (60 * dia - peak));
         }
-        return {
+
+        results = {
             iobContrib: iobContrib,
             activityContrib: activityContrib
         };
     }
-    else {
-        return '';
-    }
+
+    return results;
 }
 
 exports = module.exports = iobCalc;