Merge pull request #563 from PieterGit/201707_autotune2

autotune fixes (e.g. support for tokenbased authentication for autotune)

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
 

bin/oref0-autotune-export-to-xlsx.py

@@ -157,7 +157,7 @@ def sortedFilenames():
     parser = argparse.ArgumentParser(description='Export oref0 autotune files to Microsoft Excel')
     parser.add_argument('-d', '--dir', help='autotune 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

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=()

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
 

bin/oref0-setup.sh

@@ -523,7 +523,6 @@ if [[ $REPLY =~ ^[Yy]$ ]]; then
     fi
 
     # 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"
 
     mkdir -p $HOME/src/