Merge branch 'dev' into nodejs-8

openaps · Aug 12, 2017 · 32c032a · 32c032a
2 parents 4b5b86b + 514fbfb
commit 32c032a
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diff --git a/bin/monitor-xdrip.sh b/bin/monitor-xdrip.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+date
+cp -rf xdrip/glucose.json xdrip/last-glucose.json
+curl --compressed -s http://localhost:5000/api/v1/entries?count=288 | json -e "this.glucose = this.sgv" > xdrip/glucose.json
+if ! cmp --silent xdrip/glucose.json xdrip/last-glucose.json; then
+    if cat xdrip/glucose.json | json -c "minAgo=(new Date()-new Date(this.dateString))/60/1000; return minAgo < 10 && minAgo > -5 && this.glucose > 38" | grep -q glucose; then
+        cp -up $directory/xdrip/glucose.json $directory/monitor/glucose.json
+    else
+        echo No recent glucose data downloaded from xDrip.
+        diff xdrip/glucose.json xdrip/last-glucose.json
+    fi
+fi
diff --git a/bin/ns-get.sh b/bin/ns-get.sh
@@ -23,6 +23,8 @@ $self host <NIGHTSCOUT_HOST|localhost:1337> <entries.json> [QUERY] [stdout|-]
 EOF
 }
 
+CURL_AUTH=""
+
 # use token authentication if the user has a token set in their API_SECRET environment variable
 if [[ "${API_SECRET,,}" =~ "token=" ]]; then
   if [[ -z ${QUERY} ]]; then
@@ -32,6 +34,7 @@ if [[ "${API_SECRET,,}" =~ "token=" ]]; then
   fi
 else
   REPORT_ENDPOINT=$NIGHTSCOUT_HOST/api/v1/${REPORT}'?'${QUERY}
+  CURL_AUTH='-H "api-secret: ${API_SECRET}"'
 fi
 
 case $1 in
@@ -54,7 +57,7 @@ case $1 in
     fi
     test -z "$NIGHTSCOUT_HOST" && usage && exit 1;
 
-    curl ${CURL_FLAGS} $REPORT_ENDPOINT | $NIGHTSCOUT_FORMAT
+    curl ${CURL_AUTH} ${CURL_FLAGS} $REPORT_ENDPOINT | $NIGHTSCOUT_FORMAT
 
     ;;
   type)
@@ -66,7 +69,7 @@ case $1 in
     ;;
   *)
     test -z "$NIGHTSCOUT_HOST" && usage && exit 1;
-    curl ${CURL_FLAGS} $REPORT_ENDPOINT | $NIGHTSCOUT_FORMAT
+    curl ${CURL_AUTH} ${CURL_FLAGS} $REPORT_ENDPOINT | $NIGHTSCOUT_FORMAT
     ;;
 esac
 

diff --git a/bin/oref0-autotune-export-to-xlsx.py b/bin/oref0-autotune-export-to-xlsx.py
@@ -137,9 +137,9 @@ def excel_init_workbook(workbook):
 # sort filenames. First on date and then on run number
 # put settings/profile.js
 def sortedFilenames():
-    filelist=glob.glob("settings/profile.json")
-    filelist=filelist+glob.glob("settings/pumpprofile.json")
-    profiles=glob.glob("autotune/profile*.json")
+    filelist=glob.glob("../settings/profile.json")
+    filelist=filelist+glob.glob("../settings/pumpprofile.json")
+    profiles=glob.glob("profile*.json")
     listdateandrun=[]
     for i in profiles:
         date, run = parseDateAndRun(i)
@@ -155,9 +155,9 @@ def sortedFilenames():
 
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description='Export oref0 autotune files to Microsoft Excel')
-    parser.add_argument('-d', '--dir', help='autotune directory', default='.')
+    parser.add_argument('-d', '--dir', help='openaps directory', default='.')
     parser.add_argument('-o', '--output', help='default autotune.xlsx', default='autotune.xlsx')
-    parser.add_argument('--version', action='version', version='%(prog)s 0.0.3-dev')
+    parser.add_argument('--version', action='version', version='%(prog)s 0.0.4-dev')
     args = parser.parse_args()
 
     # change to openaps directory
@@ -172,13 +172,20 @@ def sortedFilenames():
         f=open(filename, 'r')
         print "Adding %s to Excel" % filename
         j=json.load(f)
-        basalProfile=j['basalprofile']
-        isfProfile=j['isfProfile']['sensitivities']
-        expandedBasal=expandProfile(basalProfile, 'rate', 'minutes')
-        expandedIsf=expandProfile(isfProfile, 'sensitivity', 'offset')
-        write_timebased_profile(worksheetBasal, row, expandedBasal, excel_2decimals_format)
-        write_timebased_profile(worksheetIsf, row, expandedIsf, excel_integer_format)
-        write_profile(worksheetProfile, row, j, excel_integer_format)	
-        row=row+1
+        try:
+            basalProfile=j['basalprofile']
+            isfProfile=j['isfProfile']['sensitivities']
+            expandedBasal=expandProfile(basalProfile, 'rate', 'minutes')
+            expandedIsf=expandProfile(isfProfile, 'sensitivity', 'offset')
+            write_timebased_profile(worksheetBasal, row, expandedBasal, excel_2decimals_format)
+            write_timebased_profile(worksheetIsf, row, expandedIsf, excel_integer_format)
+            write_profile(worksheetProfile, row, j, excel_integer_format)	
+            row=row+1
+        except Exception as e:
+            if j.has_key('error'):
+               print "Skipping file. Error: %s " % j['error']
+            else:
+               print "Skipping file. Exception: %s" % e
+
     workbook.close()  
     print "Written %d lines to Excel" % row
diff --git a/bin/oref0-autotune-recommends-report.sh b/bin/oref0-autotune-recommends-report.sh
@@ -18,6 +18,9 @@
 #
 # Example usage: ~/src/oref0/bin/oref0-autotune-recommends-report.sh <OpenAPS Loop Directory Path>
 
+# fix problems with locales with printf output
+LC_NUMERIC=en_US.UTF-8
+
 die() {
   echo "$@"
   exit 1
@@ -65,16 +68,16 @@ printf "%-${parameter_width}s| %-${data_width}s| %-${data_width}s\n" "Parameter"
 printf "%s\n" "-------------------------------------" >> $report_file
 
 # Print ISF, CSF and Carb Ratio Recommendations
-printf "%-${parameter_width}s| %-${data_width}.3f| %-${data_width}.3f\n" "ISF" $isf_current $isf_new >> $report_file
+printf "%-${parameter_width}s| %-${data_width}.3f| %-${data_width}.3f\n" "ISF [mg/dL/U]" $isf_current $isf_new >> $report_file
 if [ $csf_current != null ]; then
-  printf "%-${parameter_width}s| %-${data_width}.3f| %-${data_width}.3f\n" "CSF" $csf_current $csf_new >> $report_file
+  printf "%-${parameter_width}s| %-${data_width}.3f| %-${data_width}.3f\n" "CSF [mg/dL/g]" $csf_current $csf_new >> $report_file
 else
-  printf "%-${parameter_width}s| %-${data_width}s| %-${data_width}.3f\n" "CSF" "n/a" $csf_new >> $report_file
+  printf "%-${parameter_width}s| %-${data_width}s| %-${data_width}.3f\n" "CSF [mg/dL/g]" "n/a" $csf_new >> $report_file
 fi
-printf "%-${parameter_width}s| %-${data_width}.3f| %-${data_width}.3f\n" "Carb Ratio" $carb_ratio_current $carb_ratio_new >> $report_file
+printf "%-${parameter_width}s| %-${data_width}.3f| %-${data_width}.3f\n" "Carb Ratio [g]" $carb_ratio_current $carb_ratio_new >> $report_file
 
 # Print Basal Profile Recommendations
-printf "%-${parameter_width}s| %-${data_width}s| %-${data_width}s\n" "Basal Profile" "" "" >> $report_file
+printf "%-${parameter_width}s| %-${data_width}s|\n" "Basal Profile  [unit/hour]" "-" >> $report_file
 
 # Build time_list array of H:M in 30 minute increments to mirror pump basal schedule
 time_list=()

diff --git a/bin/oref0-autotune.sh b/bin/oref0-autotune.sh
@@ -45,8 +45,13 @@ TERMINAL_LOGGING=true
 RECOMMENDS_REPORT=true
 UNKNOWN_OPTION=""
 
-if [ -n "${API_SECRET_READ}" ]; then
-	HASHED_API_SECRET_READ=`echo -n ${API_SECRET_READ}|sha1sum|cut -f1 -d '-'|cut -f1 -d ' '`
+if [ -n "${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 "ERROR: 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
@@ -134,12 +139,12 @@ fi
 
 # Get profile for testing copied to home directory. "openaps" is my loop directory name.
 cd $directory && mkdir -p autotune
-cp settings/pumpprofile.json autotune/profile.pump.json
+cp settings/pumpprofile.json autotune/profile.pump.json || die "Cannot copy settings/pumpprofile.json"
 # This allows manual users to be able to run autotune by simply creating a settings/pumpprofile.json file.
 if [[ `uname` == 'Darwin' ]] ; then
-    cp settings/pumpprofile.json settings/profile.json
+    cp settings/pumpprofile.json settings/profile.json || die "Cannot copy settings/pumpprofile.json"
 else
-    cp -up settings/pumpprofile.json settings/profile.json
+    cp -up settings/pumpprofile.json settings/profile.json || die "Cannot copy settings/pumpprofile.json"
 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 | json | grep -q start || cp autotune/profile.pump.json autotune/profile.json
@@ -156,13 +161,9 @@ fi
 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 $url
-if [ -n "${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
+query="find\[created_at\]\[\$gte\]=`date --date="$START_DATE -4 hours" -Iminutes`&find\[created_at\]\[\$lte\]=`date --date="$END_DATE +1 days" -Iminutes`"
+echo Query: $NIGHTSCOUT_HOST/$query
+ns-get host $NIGHTSCOUT_HOST treatments.json $query > ns-treatments.json || die "Couldn't download ns-treatments.json"
 ls -la ns-treatments.json || die "No ns-treatments.json downloaded"
 
 # Build date list for autotune iteration
@@ -183,14 +184,9 @@ echo "Grabbing NIGHTSCOUT entries/sgv.json for date range..."
 # Get Nightscout BG (sgv.json) Entries
 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 $url
-  if [ -n "${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
-
+  query="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 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"
 done
 

diff --git a/bin/oref0-pump-loop.sh b/bin/oref0-pump-loop.sh
@@ -196,6 +196,7 @@ function smb_verify_status {
     && if grep -q '"suspended": true' monitor/status.json; then
         echo -n "Pump suspended; "
         unsuspend_if_no_temp
+        gather
     fi
 }
 
@@ -316,7 +317,9 @@ function preflight {
 # reset radio, init world wide pump (if applicable), mmtune, and wait_for_silence 60 if no signal
 function mmtune {
     # TODO: remove reset_spi_serial.py once oref0_init_pump_comms.py is fixed to do it correctly
-    reset_spi_serial.py 2>/dev/null
+    if [[ $port == "/dev/spidev5.1" ]]; then
+        reset_spi_serial.py 2>/dev/null
+    fi
     oref0_init_pump_comms.py
     echo -n "Listening for 30s silence before mmtuning: "
     for i in $(seq 1 800); do

diff --git a/bin/oref0-setup.sh b/bin/oref0-setup.sh
@@ -522,6 +522,12 @@ if [[ $REPLY =~ ^[Yy]$ ]]; then
         mkdir -p xdrip || die "Can't mkdir xdrip"
     fi
 
+    # check whether decocare-0.0.31 has been installed
+    if ! ls /usr/local/lib/python2.7/dist-packages/decocare-0.0.31-py2.7.egg/ 2>/dev/null >/dev/null; then
+        # install decocare with setuptools since 0.0.31 (with the 6.4U/h fix) isn't published properly to pypi
+        sudo easy_install -U decocare || die "Can't easy_install decocare"
+    fi
+
     mkdir -p $HOME/src/
     if [ -d "$HOME/src/oref0/" ]; then
         echo "$HOME/src/oref0/ already exists; pulling latest"
@@ -547,12 +553,12 @@ if [[ $REPLY =~ ^[Yy]$ ]]; then
 #fi
 
     cd $directory || die "Can't cd $directory"
-    if [[ "$max_iob" == "0" && -z "$max_daily_safety_multiplier" && -z "&current_basal_safety_multiplier" && -z "$bolussnooze_dia_divisor" && -z "$min_5m_carbimpact" ]]; then
+    if [[ "$max_iob" == "0" && -z "$max_daily_safety_multiplier" && -z "$current_basal_safety_multiplier" && -z "$bolussnooze_dia_divisor" && -z "$min_5m_carbimpact" ]]; then
         oref0-get-profile --exportDefaults > preferences.json || die "Could not run oref0-get-profile"
     else
         preferences_from_args=()
         if [[ "$max_iob" != "0" ]]; then
-        preferences_from_args+="\"max_iob\":$max_iob "
+            preferences_from_args+="\"max_iob\":$max_iob "
         fi
         if [[ ! -z "$max_daily_safety_multiplier" ]]; then
             preferences_from_args+="\"max_daily_safety_multiplier\":$max_daily_safety_multiplier "
@@ -835,6 +841,8 @@ if [[ $REPLY =~ ^[Yy]$ ]]; then
             cd $HOME/src/EdisonVoltage
             make voltage
         fi
+        # Add module needed for EdisonVoltage to work on jubilinux 0.2.0
+        grep iio_basincove_gpadc /etc/modules-load.d/modules.conf || echo iio_basincove_gpadc >> /etc/modules-load.d/modules.conf
         cd $directory || die "Can't cd $directory"
         for type in edisonbattery; do
             echo importing $type file
@@ -959,7 +967,7 @@ if [[ $REPLY =~ ^[Yy]$ ]]; then
             (crontab -l; crontab -l | grep -q "cd $directory-cgm-loop && oref0-truncate-git-history" || echo "* * * * * cd $directory-cgm-loop && oref0-truncate-git-history") | crontab -
             (crontab -l; crontab -l | grep -q "cd $directory-cgm-loop && ps aux | grep -v grep | grep -q 'openaps monitor-cgm'" || echo "* * * * * cd $directory-cgm-loop && ps aux | grep -v grep | grep -q 'openaps monitor-cgm' || ( date; openaps monitor-cgm) | tee -a /var/log/openaps/cgm-loop.log; cp -up monitor/glucose-raw-merge.json $directory/cgm/glucose.json ; cp -up $directory/cgm/glucose.json $directory/monitor/glucose.json") | crontab -
         elif [[ ${CGM,,} =~ "xdrip" ]]; then
-            (crontab -l; crontab -l | grep -q "cd $directory && ps aux | grep -v grep | grep -q 'openaps monitor-xdrip'" || echo "* * * * * cd $directory && ps aux | grep -v grep | grep -q 'openaps monitor-xdrip' || ( date; cp -rf xdrip/glucose.json xdrip/last-glucose.json; openaps monitor-xdrip) | tee -a /var/log/openaps/xdrip-loop.log; cmp --silent xdrip/glucose.json xdrip/last-glucose.json || cp -up $directory/xdrip/glucose.json $directory/monitor/glucose.json") | crontab -
+            (crontab -l; crontab -l | grep -q "cd $directory && ps aux | grep -v grep | grep -q 'monitor-xdrip.sh'" || echo "* * * * * cd $directory && ps aux | grep -v grep | grep -q 'monitor-xdrip.sh' || monitor-xdrip.sh | tee -a /var/log/openaps/xdrip-loop.log") | crontab -
         (crontab -l; crontab -l | grep -q "xDripAPS.py" || echo "@reboot python $HOME/.xDripAPS/xDripAPS.py") | crontab -
         elif [[ $ENABLE =~ dexusb ]]; then
             (crontab -l; crontab -l | grep -q "@reboot .*dexusb-cgm" || echo "@reboot cd $directory && /usr/bin/python -u /usr/local/bin/oref0-dexusb-cgm-loop >> /var/log/openaps/cgm-dexusb-loop.log 2>&1" ) | crontab -

diff --git a/lib/bolus.js b/lib/bolus.js
@@ -9,7 +9,7 @@ function reduce (treatments) {
   function in_previous (ev) {
     var found = false;
     previous.forEach(function (elem) {
-      if (elem.timestamp == ev.timestamp && ev._type == elem._type) {
+      if (elem.timestamp === ev.timestamp && ev._type === elem._type) {
         found = true;
       }
     });
@@ -30,7 +30,7 @@ function reduce (treatments) {
 
   function bolus (ev, remaining) {
     if (!ev) { console.error('XXX', ev, remaining); return; }
-    if (ev._type == 'BolusWizard') {
+    if (ev._type === 'BolusWizard') {
       state.carbs = ev.carb_input.toString( );
       state.ratio = ev.carb_ratio.toString( );
       if (ev.bg) {
@@ -43,20 +43,22 @@ function reduce (treatments) {
       previous.push(ev);
     }
 
-    if (ev._type == 'Bolus') {
+    if (ev._type === 'Bolus') {
       state.duration = ev.duration.toString( );
       // if (state.square || state.bolus) { }
       // state.insulin = (state.insulin ? state.insulin : 0) + ev.amount;
       if (ev.duration && ev.duration > 0) {
         state.square = ev;
       } else {
-        state.bolus = ev;
+        if (state.bolus) {
+          state.bolus.amount = state.bolus.amount + ev.amount;
+        } else
+          state.bolus = ev;
       }
       state.created_at = state.timestamp = ev.timestamp;
       previous.push(ev);
     }
 
-
     if (remaining && remaining.length > 0) {
       if (state.bolus && state.wizard) {
         // skip to end
@@ -69,8 +71,8 @@ function reduce (treatments) {
       // console.error("remaining", remaining);
       state.eventType = '<none>';
 
-      state.insulin = (state.square ? state.square.amount : 0) +
-                      (state.bolus ? state.bolus.amount : 0);
+      state.insulin = (state.insulin ? state.insulin : 0) + (state.square ? state.square.amount : 0) +
+            (state.bolus ? state.bolus.amount : 0);
       var has_insulin = state.insulin && state.insulin > 0;
       var has_carbs = state.carbs && state.carbs > 0;
       var has_wizard = state.wizard ? true : false;
@@ -151,7 +153,7 @@ function reduce (treatments) {
     switch (current._type) {
       case 'Bolus':
       case 'BolusWizard':
-        var tail = within_minutes_from(current, treatments.slice(index+1), 4);
+        var tail = within_minutes_from(current, treatments.slice(index+1), 2);
         bolus(current, tail);
         break;
       default:

diff --git a/lib/determine-basal/determine-basal.js b/lib/determine-basal/determine-basal.js
@@ -261,15 +261,19 @@ var determine_basal = function determine_basal(glucose_status, currenttemp, iob_
     // disable SMB when a high temptarget is set
     if (profile.temptargetSet && target_bg > 100) {
         enableSMB=false;
-    // enable SMB (if enabled in preferences) for DIA hours after bolus
+    // enable SMB/UAM (if enabled in preferences) for DIA hours after bolus
     } else if (profile.enableSMB_with_bolus && bolusiob > 0.1) {
         enableSMB=true;
-    // enable SMB (if enabled in preferences) while we have COB
+    // enable SMB/UAM (if enabled in preferences) while we have COB
     } else if (profile.enableSMB_with_COB && meal_data.mealCOB) {
         enableSMB=true;
-    // enable SMB (if enabled in preferences) if a low temptarget is set
+    // enable SMB/UAM (if enabled in preferences) if a low temptarget is set
     } else if (profile.enableSMB_with_temptarget && (profile.temptargetSet && target_bg < 100)) {
         enableSMB=true;
+    // enable SMB/UAM (if enabled in preferences) for a full 6 hours after any carb entry
+    // (6 hours is defined in carbWindow in lib/meal/total.js)
+    } else if (profile.enableSMB_after_carbs && meal_data.carbs) {
+        enableSMB=true;
     }
     // enable UAM (if enabled in preferences) for DIA hours after bolus, or if SMB is enabled
     var enableUAM=(profile.enableUAM && (bolusiob > 0.1 || enableSMB));

diff --git a/lib/iob/history.js b/lib/iob/history.js
@@ -101,6 +101,15 @@ function calcTempTreatments (inputs) {
             temp.date = temp.started_at.getTime();
             temp.insulin = current.amount;
             tempBoluses.push(temp);
+        } else if (current.eventType == "Meal Bolus" || current.eventType == "Correction Bolus" || current.eventType == "Snack Bolus" || current.eventType == "Bolus Wizard") {
+            //imports treatments entered through Nightscout Care Portal
+            //"Bolus Wizard" refers to the Nightscout Bolus Wizard, not the Medtronic Bolus Wizard
+            var temp = {};
+            temp.timestamp = current.created_at;
+            temp.started_at = new Date(tz(temp.timestamp));
+            temp.date = temp.started_at.getTime();
+            temp.insulin = current.insulin;
+            tempBoluses.push(temp);
         } else if (current.enteredBy == "xdrip") {
             var temp = {};
             temp.timestamp = current.timestamp;