Oref0 determine basal arg parsing cleanup (openaps#1119)

* Update to cleanup oref0-determine-basal.js argument processing. * Fix syntax error. * fixed spelling error. * Fix null dereference error. * Fixed more null dereferences. * Check for too many arguments. * Removed determine-basal device and associated reports. * Removed invalid determine-basal report from setup. * Remove setup for enact/suggested.json report that no longer functions. * Modify oref0-determine-basal test to account for argument changes.
TwistaTim · Oct 7, 2018 · 26b9b8f · 26b9b8f
1 parent b29e55d
commit 26b9b8f
Show file tree

Hide file tree

Showing 11 changed files with 36 additions and 106 deletions.
diff --git a/README.md b/README.md
@@ -31,7 +31,6 @@ Valid commands:
   oref0 ifttt-notify
   oref0 get-profile
   oref0 calculate-iob
-  oref0 determine-basal
   oref0 help - this message
 ```
 

diff --git a/bin/oref0-determine-basal.js b/bin/oref0-determine-basal.js
@@ -20,81 +20,70 @@ var determine_basal = require('../lib/determine-basal/determine-basal');
 /* istanbul ignore next */
 if (!module.parent) {
     var argv = require('yargs')
-      .usage("$0 iob.json currenttemp.json glucose.json profile.json [[--auto-sens] autosens.json] [meal.json] [--reservoir reservoir.json] --currentTime [currentTime]")
+      .usage("$0 <iob.json> <currenttemp.json> <glucose.json> <profile.json> [--auto-sens <autosens.json>] [--meal <meal.json>] [--reservoir <reservoir.json>] [--currentTime <currentTime>]")
       .option('auto-sens', {
         alias: 'a',
+        nargs: 1,
         describe: "Auto-sensitivity configuration",
-        default: true
-
+        default: false
       })
       .option('currentTime', {
         alias: 'c',
+        nargs: 1,
         describe: "Override current time (for R&D only - disables safety checks)",
         default: false
-
       })
       .option('reservoir', {
         alias: 'r',
+        nargs: 1,
         describe: "Reservoir status file for SuperMicroBolus mode (oref1)",
         default: false
-
       })
       .option('meal', {
+        alias: 'm',
+        nargs: 1,
         describe: "json doc describing meals",
-        default: true
-
+        default: false
       })
       .option('missing-auto-sens-ok', {
         describe: "If auto-sens data is missing, try anyway.",
+        boolean: true,
         default: true
-
       })
       .option('missing-meal-ok', {
         describe: "If meal data is missing, try anyway.",
+        boolean: true,
         default: true
-
       })
       .option('microbolus', {
         describe: "Enable SuperMicroBolus mode (oref1)",
+        boolean: true,
         default: false
-
       })
       // error and show help if some other args given
+      .demand(4)
       .strict(true)
       .help('help')
     ;
-    function usage ( ) {
-      argv.showHelp( );
-    }
 
     var params = argv.argv;
+    var inputs = params._;
     var errors = [ ];
     var warnings = [ ];
 
-    var iob_input = params._[0];
-    if ([null, '--help', '-h', 'help'].indexOf(iob_input) > 0) {
-
-      usage( );
-      process.exit(0)
-    }
-    var currenttemp_input = params._[1];
-    var glucose_input = params._[2];
-    var profile_input = params._[3];
-    var meal_input = params._[4];
-    var autosens_input = params.autoSens;
-    if (params._.length > 5) {
-      autosens_input = params.autoSens ? params._[4] : false;
-      meal_input = params._[5];
-    }
-    if (params.meal && params.meal !== true && !meal_input) {
-      meal_input = params.meal;
+    if (inputs.length > 4) {
+      argv.showHelp( );
+      console.error('Too many arguments');
+      process.exit(1);
     }
-    var reservoir_input = params.reservoir;
 
-    if (!iob_input || !currenttemp_input || !glucose_input || !profile_input) {
-        usage( );
-        process.exit(1);
-    }
+    var iob_input = inputs[0];
+    var currenttemp_input = inputs[1];
+    var glucose_input = inputs[2];
+    var profile_input = inputs[3];
+    var meal_input = params.meal;
+    var autosens_input = params['auto-sens'];
+    var reservoir_input = params.reservoir;
 
     var fs = require('fs');
     try {
@@ -116,12 +105,12 @@ if (!module.parent) {
     //printing microbolus before attempting check
     //console.error("Microbolus var is currently set to: ",params['microbolus']);
 
-    if (params['microbolus']) {
+    if (params.microbolus) {
         if (fs.existsSync("autotune")) {
             console.error("Autotune exists! Hoorah! You can use microbolus-related features.")
         } else {
             console.error("Warning: Autotune has not been run. All microboluses will be disabled until you manually run autotune or add it to run nightly in your loop.");
-            params['microbolus'] = false;
+            params.microbolus = false;
             //console.error("Microbolus var is currently set to: ",params['microbolus']);
         }
     }

diff --git a/bin/oref0-pump-loop.sh b/bin/oref0-pump-loop.sh
@@ -268,9 +268,9 @@ function smb_suggest {
 function determine_basal {
     cat monitor/meal.json
     if ( grep -q 12 settings/model.json ); then
-      oref0-determine-basal monitor/iob.json monitor/temp_basal.json monitor/glucose.json settings/profile.json settings/autosens.json monitor/meal.json --reservoir monitor/reservoir.json > enact/smb-suggested.json
+      oref0-determine-basal monitor/iob.json monitor/temp_basal.json monitor/glucose.json settings/profile.json --auto-sens settings/autosens.json --meal monitor/meal.json --reservoir monitor/reservoir.json > enact/smb-suggested.json
     else
-      oref0-determine-basal monitor/iob.json monitor/temp_basal.json monitor/glucose.json settings/profile.json settings/autosens.json monitor/meal.json --microbolus --reservoir monitor/reservoir.json > enact/smb-suggested.json
+      oref0-determine-basal monitor/iob.json monitor/temp_basal.json monitor/glucose.json settings/profile.json --auto-sens settings/autosens.json --meal monitor/meal.json --microbolus --reservoir monitor/reservoir.json > enact/smb-suggested.json
     fi
     cp -up enact/smb-suggested.json enact/suggested.json
 }

diff --git a/bin/oref0-setup.sh b/bin/oref0-setup.sh
@@ -1132,8 +1132,6 @@ if [[ $REPLY =~ ^[Yy]$ ]]; then
         do_openaps_import $HOME/src/oref0/lib/oref0-setup/pancreabble.json
         sudo cp $HOME/src/oref0/lib/oref0-setup/pancreoptions.json $directory/pancreoptions.json
     fi
-    echo Running: openaps report add enact/suggested.json text determine-basal shell monitor/iob.json monitor/temp_basal.json monitor/glucose.json settings/profile.json settings/autosens.json monitor/meal.json
-    openaps report add enact/suggested.json text determine-basal shell monitor/iob.json monitor/temp_basal.json monitor/glucose.json settings/profile.json settings/autosens.json monitor/meal.json
 
     if is_edison; then
         sudo apt-get -y -t jessie-backports install jq

diff --git a/bin/oref0.sh b/bin/oref0.sh
@@ -21,7 +21,6 @@ Valid commands:
   oref0 get-profile
   oref0 calculate-iob
   oref0 meal
-  oref0 determine-basal
   oref0 export-loop [backup-loop.json] - Print a backup json representation of
                                          entire configuration. Optionally, if a
                                          filename is specified, listing is

diff --git a/examples/example.sh b/examples/example.sh
@@ -2,7 +2,7 @@
 
 oref0-calculate-iob pumphistory.json profile.json clock.json autosens.json > iob.json
 oref0-meal pumphistory.json profile.json clock.json glucose.json basal_profile.json carbhistory.json > meal.json
-oref0-determine-basal iob.json temp_basal.json glucose.json profile.json autosens.json meal.json --microbolus --currentTime 1527924300000 > suggested.json
+oref0-determine-basal iob.json temp_basal.json glucose.json profile.json --auto-sens autosens.json --meal meal.json --microbolus --currentTime 1527924300000 > suggested.json
 cat suggested.json | jq -C -c '. | del(.predBGs) | del(.reason)'
 cat suggested.json | jq -C -c .reason
 cat suggested.json | jq -C -c .predBGs
diff --git a/lib/determine-basal/determine-basal.js b/lib/determine-basal/determine-basal.js
@@ -149,7 +149,7 @@ var determine_basal = function determine_basal(glucose_status, currenttemp, iob_
         sensitivityRatio = Math.min(sensitivityRatio, profile.autosens_max);
         sensitivityRatio = round(sensitivityRatio,2);
         process.stderr.write("Sensitivity ratio set to "+sensitivityRatio+" based on temp target of "+target_bg+"; ");
-    } else if (typeof autosens_data !== 'undefined' ) {
+    } else if (typeof autosens_data !== 'undefined' && autosens_data) {
         sensitivityRatio = autosens_data.ratio;
         process.stderr.write("Autosens ratio: "+sensitivityRatio+"; ");
     }
@@ -166,7 +166,7 @@ var determine_basal = function determine_basal(glucose_status, currenttemp, iob_
     // adjust min, max, and target BG for sensitivity, such that 50% increase in ISF raises target from 100 to 120
     if (profile.temptargetSet) {
         //process.stderr.write("Temp Target set, not adjusting with autosens; ");
-    } else if (typeof autosens_data !== 'undefined' ) {
+    } else if (typeof autosens_data !== 'undefined' && autosens_data) {
         if ( profile.sensitivity_raises_target && autosens_data.ratio < 1 || profile.resistance_lowers_target && autosens_data.ratio > 1 ) {
             // with a target of 100, default 0.7-1.2 autosens min/max range would allow a 93-117 target range
             min_bg = round((min_bg - 60) / autosens_data.ratio) + 60;
@@ -213,7 +213,7 @@ var determine_basal = function determine_basal(glucose_status, currenttemp, iob_
 
     var profile_sens = round(profile.sens,1)
     var sens = profile.sens;
-    if (typeof autosens_data !== 'undefined' ) {
+    if (typeof autosens_data !== 'undefined' && autosens_data) {
         sens = profile.sens / sensitivityRatio;
         sens = round(sens, 1);
         if (sens != profile_sens) {

diff --git a/lib/oref0-setup/device.json b/lib/oref0-setup/device.json
@@ -86,19 +86,6 @@
       "extra": "detect-sensitivity.ini"
     }
   },
-  {
-    "determine-basal": {
-      "vendor": "openaps.vendors.process",
-      "extra": "determine-basal.ini"
-    },
-    "type": "device",
-    "name": "determine-basal",
-    "extra": {
-      "fields": "iob temp_basal glucose profile",
-      "cmd": "oref0",
-      "args": "determine-basal"
-    }
-  },
   {
     "pebble": {
       "vendor": "openaps.vendors.process",

diff --git a/lib/oref0-setup/report.json b/lib/oref0-setup/report.json
@@ -316,23 +316,6 @@
     "type": "report",
     "name": "settings/profile.json"
   },
-  {
-    "type": "report",
-    "name": "enact/suggested.json",
-    "enact/suggested.json": {
-      "profile": "settings/profile.json",
-      "use": "shell",
-      "temp_basal": "monitor/temp_basal.json",
-      "reporter": "text",
-      "json_default": "True",
-      "meal": "monitor/meal.json",
-      "autosens": "settings/autosens.json",
-      "device": "determine-basal",
-      "remainder": "",
-      "iob": "monitor/iob.json",
-      "glucose": "monitor/glucose.json"
-    }
-  },
   {
     "type": "report",
     "enact/enacted.json": {

diff --git a/lib/oref0-setup/supermicrobolus.json b/lib/oref0-setup/supermicrobolus.json
@@ -1,19 +1,4 @@
 [
-  {
-    "enact/smb-suggested.json": {
-      "profile": "settings/profile.json",
-      "use": "shell",
-      "temp_basal": "monitor/temp_basal.json",
-      "reporter": "JSON",
-      "json_default": "True",
-      "device": "determine-basal",
-      "remainder": "settings/autosens.json monitor/meal.json --microbolus --reservoir monitor/reservoir.json",
-      "iob": "monitor/iob.json",
-      "glucose": "monitor/glucose.json"
-    },
-    "type": "report",
-    "name": "enact/smb-suggested.json"
-  },
   {
     "enact/smb-enacted.json": {
       "device": "pump",

diff --git a/tests/command-behavior.tests.sh b/tests/command-behavior.tests.sh
@@ -220,7 +220,7 @@ test-detect-sensitivity () {
     cat stderr_output | grep -q "ISF adjusted from 100 to 100" || fail_test "oref0-detect-sensitivity error: \n$ERROR_LINES"
 
     # Make sure output has ratio
-    cat stdout_output | jq ".ratio" | grep -q "1" || fail_test "oref0-determine-sensitivity did not report correct sensitivity"
+    cat stdout_output | jq ".ratio" | grep -q "1" || fail_test "oref0-detect-sensitivity did not report correct sensitivity"
 
     # Run detect-sensitivity with carbhistory and capture output
     ../bin/oref0-detect-sensitivity.js glucose.json pumphistory_zoned.json insulin_sensitivities.json basal_profile.json profile.json carbhistory.json 2>stderr_output 1>stdout_output
@@ -230,7 +230,7 @@ test-detect-sensitivity () {
     cat stderr_output | grep -q "ISF adjusted from 100 to 100" || fail_test "oref0-detect-sensitivity error: \n$ERROR_LINES"
 
     # Make sure output has ratio
-    cat stdout_output | jq ".ratio" | grep -q "1" || fail_test "oref0-determine-sensitivity did not report correct sensitivity"
+    cat stdout_output | jq ".ratio" | grep -q "1" || fail_test "oref0-detect-sensitivity did not report correct sensitivity"
 
     # Run oref0-detect-sensitivity with carbhistory and temptargets and capture output
     ../bin/oref0-detect-sensitivity.js glucose.json pumphistory_zoned.json insulin_sensitivities.json basal_profile.json profile.json carbhistory.json temptargets.json 2>stderr_output 1>stdout_output
@@ -240,7 +240,7 @@ test-detect-sensitivity () {
     cat stderr_output | grep -q "ISF adjusted from 100 to 100" || fail_test "oref0-detect-sensitivity error: \n$ERROR_LINES"
 
     # Make sure output has ratio
-    cat stdout_output | jq ".ratio" | grep -q "1" || fail_test "oref0-determine-sensitivity did not report correct sensitivity"
+    cat stdout_output | jq ".ratio" | grep -q "1" || fail_test "oref0-detect-sensitivity did not report correct sensitivity"
 
     # If we made it here, the test passed
     echo "oref0-detect-sensitivites test passed"
@@ -258,7 +258,7 @@ test-determine-basal () {
     cat stdout_output | jq ".reason" | grep -q "BG data is too old" || fail_test "oref0-determine-basal did not report correct reason"
 
     # Run determine-basal with options
-    ../bin/oref0-determine-basal.js --reservoir reservoir.json iob.json --currentTime "2018-09-05T09:44:11-05:00" temp_basal.json glucose.json --auto-sens autosens.json profile.json meal.json 2>stderr_output 1>stdout_output
+    ../bin/oref0-determine-basal.js --reservoir reservoir.json iob.json --currentTime "2018-09-05T09:44:11-05:00" temp_basal.json glucose.json --auto-sens autosens.json profile.json --meal meal.json 2>stderr_output 1>stdout_output
 
     # Make sure stderr output contains expected time
     ERROR_LINES=$( cat stderr_output )
@@ -267,16 +267,6 @@ test-determine-basal () {
     # Make sure output has reason
     cat stdout_output | jq ".reason" | grep -q "BG data is too old" || fail_test "oref0-determine-basal with options did not report correct reason"
 
-    # Run determine-basal with alternate methods of arguments
-    ../bin/oref0-determine-basal.js iob.json temp_basal.json glucose.json profile.json autosens.json meal.json 2>stderr_output 1>stdout_output
-
-    # Make sure stderr output contains expected time
-    ERROR_LINES=$( cat stderr_output )
-    cat stderr_output | jq .time | grep -q "2018-09-05T14:44:11.000Z" || fail_test "oref0-determine-basal with alternate options error: \n$ERROR_LINES"
-
-    # Make sure output has reason
-    cat stdout_output | jq ".reason" | grep -q "BG data is too old" || fail_test "oref0-determine-basal with alternate options did not report correct reason"
-
     # If we made it here, the test passed
     echo "oref0-determine-basal test passed"
 }