Power failure

Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino → archive/Teensey Code/MicroPET_Launch_code/MicroPET_Launch_code.ino

@@ -220,8 +220,8 @@ String experimenta_log = "";
 unsigned int whichsensor = 0;
 
 #define SECONDS_IN_DAY 86400
-//#define DELAY_SECONDS_PER_EXPERIMENT SECONDS_IN_DAY
-#define DELAY_SECONDS_PER_EXPERIMENT 120 // 2 mins for the functional testing
+#define DELAY_SECONDS_PER_EXPERIMENT SECONDS_IN_DAY
+//#define DELAY_SECONDS_PER_EXPERIMENT 120 // 2 mins for the functional testing
 #define SERIAL_TIMEOUT 10000 //milliseconds
 
 const unsigned int MAX_MESSAGE_LENGTH = 12;
@@ -453,10 +453,10 @@ void rtcInit() {
     Serial.println("RTC is NOT initialized, let's set the time!");
     // When time needs to be set on a new device, or after a power loss, the
     // following line sets the RTC to the date & time this sketch was compiled
-    rtc.adjust(DateTime(F(__DATE__), F(__TIME__)));
+    //rtc.adjust(DateTime(F(__DATE__), F(__TIME__)));
     // This line sets the RTC with an explicit date & time, for example to set
     // January 21, 2014 at 3am you would call:
-    // rtc.adjust(DateTime(2014, 1, 21, 3, 0, 0));
+    // rtc.adjust(DateTime(2022, 11, 10, 2, 3, 3));
     //
     // Note: allow 2 seconds after inserting battery or applying external power
     // without battery before calling adjust(). This gives the PCF8523's
@@ -521,22 +521,42 @@ void recoverSystemStart(){
   /* (1) check for hard faults */
   //  (1.1) if system failed during an experiment, generate fault
   if(systemStateStructVar.testDayComplete != 1){
-    Serial.println("System was interrupted during an experiment! No way to resume!");
-    while(1);
-    return;
+    Serial.print("System was interrupted during experiment: ");
+    Serial.println(systemStateStructVar.testDay);
+    saveExperimentalLog("System was interrupted during experiment: " + String(systemStateStructVar.testDay));
+
+    if(systemStateStructVar.testDay == 1){
+      Serial.print("Restarting entire experiment since lost power on day 1");
+      saveExperimentalLog("Restarting entire experiment since lost power on day 1");
+      day_1();
+      systemState = true;
+      return;
+    }
   }
 
   //  (1.2) if system paused for longer than test day interval, generate fault
   uint32_t timeSinceLastExperiment = rtc.now().unixtime() - systemStateStructVar.epoch;
+  uint16_t skipDays;
   if(timeSinceLastExperiment >= DELAY_SECONDS_PER_EXPERIMENT){
-    Serial.println("System was off for longer than experiment interval! No way to resume!");
-    while(1);
-    return;
+    Serial.println("System was off for longer than experiment interval!");
+
+    skipDays = int( timeSinceLastExperiment / DELAY_SECONDS_PER_EXPERIMENT );
+    for(int i = 0; i < skipDays; i++){
+      systemStateStructVar.testDay++;
+      Serial.print(" Skipping day: ");
+      Serial.println(systemStateStructVar.testDay);
+
+      saveExperimentalLog(" Skipping day: " + String(systemStateStructVar.testDay));
+    }
   }
 
+  timeSinceLastExperiment = int( timeSinceLastExperiment % DELAY_SECONDS_PER_EXPERIMENT );
   //  (1.3) check if tests had already ended
   if(systemStateStructVar.testDay == TOTAL_EXPERIMENTS - 1){
     Serial.println("Power failure occured after experiment finished! No reason to resume!");
+
+    saveExperimentalLog("Power failure occured after experiment finished! No reason to resume!");
+
     while(1);
     return;
   }
@@ -553,6 +573,8 @@ void recoverSystemStart(){
 //  }
 
   Serial.println("System has recovered gracefully!");
+
+  systemState = true;
 }
 
 
@@ -590,6 +612,8 @@ bool checkForStartSerialCommand() {
         //Print the message (or do other things)
         Serial.println("Executing Test Script");
 
+
+
         day_functionTest();
       }
 
@@ -602,19 +626,13 @@ bool checkForStartSerialCommand() {
 }
 
 void day_functionTest(){
-
-  // DUMMY TASK
-
-  //EXP1
-  moveLiquid (experimentOne, e_buffer, chamberA, 2000);  //buffer to chamber A - 2 ml (flexible)
-  //EXP2
-  moveLiquid (experimentTwo, e_buffer, chamberA, 2000);  //buffer to chamber A - 2 ml (flexible)
-
-Serial.println("revival pumping...");
-motorSensorBrdCtrl(1, forward);
-delay (5000);
-motorSensorBrdCtrl(1, halt);
-
+
+  /////DAYFUNCTION
+
+  /////DAYFUNCTION
+
+  /////DAYFUNCTION
+
 }
 
 
@@ -642,13 +660,20 @@ void day_1() {
   saveExperimentalLog("Executing Day 1");
 
 
- // =============== SAFETY MECHANISM ================
-  // DUMMY TASK
+ // =============== ENZYME EXP =====================
 
-  //EXP1
-  moveLiquid (experimentOne, e_buffer, chamberA, 2000);  //buffer to chamber A - 2 ml (flexible)
-  //EXP2
-  moveLiquid (experimentTwo, e_buffer, chamberA, 2000);  //buffer to chamber A - 2 ml (flexible)
+  //DUMMY CODE
+  moveLiquid (experimentOne, e_buffer, chamberA, 1000);  //buffer to chamber A - 1 ml (flexible)
+  moveLiquid (experimentTwo, e_buffer, chamberA, 1000);  //buffer to chamber A - 1 ml (flexible)
+  Serial.println("finish the dummy code...");
+  saveExperimentalLog("Finish dummy code!");
+
+  //EXP1 - liquid in dummy code
+  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentOne, e_buffer, chamberA, 1525);  //buffer to chamber A - 1.525 ml (flexible)
+  //EXP2 - liquid in dummy code
+  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
+  moveLiquid (experimentTwo, e_buffer, chamberA, 1525);  //buffer to chamber A - 1.525 ml (flexible)
 
 
  // =============== MICROBE EXP =====================
@@ -670,16 +695,6 @@ void day_1() {
   motorSensorBrdCtrl(3, halt);
 
 
- // =============== ENZYME EXP =====================
-
-  //EXP1
-  moveLiquid (experimentOne, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
-  moveLiquid (experimentOne, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
-  //EXP2
-  moveLiquid (experimentTwo, enzyme, chamberA, 75); //enzyme to chamber A - 0.075 ml
-  moveLiquid (experimentTwo, e_buffer, chamberA, 2525);  //buffer to chamber A - 2.925 ml (flexible)
-
-
  // =============== UPDATE STATUS ===================
   systemStateStructVar.testDayComplete = 1;
   saveStateToSD(&systemStateStructVar);
@@ -1767,23 +1782,23 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
   if (experiment == 1 && origin == 0)
   {
     switch_conn_pin(BASEBD_J10_PIN2, LOW); //Experiment 1 valveA
-    Serial.println("_E1_exp1 move from e_buffer");
-    saveExperimentalLog("_E1_move from e_buffer");
+    Serial.println("E1_exp1 move from e_buffer");
+    saveExperimentalLog("E1_move from e_buffer");
   }
 
   if (experiment == 1 && origin == 1)
   {
     switch_conn_pin(BASEBD_J10_PIN2, HIGH); //Experiment 1 valveA
-    Serial.println("_E1 move from enzyme");
-    saveExperimentalLog("_E1_move from enzyme");
+    Serial.println("E1 move from enzyme");
+    saveExperimentalLog("E1_move from enzyme");
   }
 
   if (experiment == 1 && target == 2)
   {
     switch_conn_pin(BASEBD_J9_PIN2, HIGH); //Experiment 1 valveB high, waste line open
     int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
     Serial.println("move to chamberA");
-    saveExperimentalLog("exp1_move to chamberA" + String(move_pulse * 25) + "uL");
+    saveExperimentalLog("E1_move to chamberA" + String(move_pulse * 25) + "uL");
     for (int i = 0; i <= move_pulse; i++) {
       switch_conn_pin(BASEBD_J10_PIN4, HIGH); //Experiment 1 pumpA
       digitalWrite(LED, HIGH);
@@ -1792,6 +1807,7 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
       digitalWrite(LED, LOW);
       delay(200);
       Serial.println( i * 25); //print out the moving volume
+      saveExperimentalLog("STEP_exp1_move to chamberA" + String(i * 25) + "uL");
     }
     switch_conn_pin(BASEBD_J10_PIN2, LOW); //Reset eperiment 1 valveA so enzyme is blocked
   }
@@ -1821,8 +1837,8 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
   if (experiment == 1 && origin == 3 && target == 4)
   {
     int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
-    Serial.println("_E1 move to chamberB");
-    saveExperimentalLog("_E1_move to chamberB " + String(move_pulse * 25) + "uL");
+    Serial.println("E1 move to chamberB");
+    saveExperimentalLog("E1_move to chamberB " + String(move_pulse * 25) + "uL");
     for (int i = 0; i <= move_pulse; i++) {
       switch_conn_pin(BASEBD_J9_PIN4, HIGH); //Experiment 1 pumpB
       digitalWrite(LED, HIGH);
@@ -1831,6 +1847,7 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
       digitalWrite(LED, LOW);
       delay(200);
       Serial.println( i * 25); //print out the moving volume
+      saveExperimentalLog("STEP_E1_move to chamberB " + String(i * 25) + "uL");
     }
   //  switch_conn_pin(BASEBD_J9_PIN2, LOW); //Reset experiment 1 valveB so chamberA is blocked
   }
@@ -1840,23 +1857,23 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
   if (experiment == 2 && origin == 0)
   {
     switch_conn_pin(BASEBD_J12_PIN2, LOW); //Experiment 2 valveA
-    Serial.println("_E2 move from e_buffer");
-    saveExperimentalLog("_E2_move from e_buffer");
+    Serial.println("E2 move from e_buffer");
+    saveExperimentalLog("E2_move from e_buffer");
   }
 
   if (experiment == 2 && origin == 1)
   {
     switch_conn_pin(BASEBD_J12_PIN2, HIGH); //Experiment 2 valveA
-    saveExperimentalLog("_E2_move from enzyme");
-    Serial.println("_E2 move from Enzyme");
+    saveExperimentalLog("E2_move from enzyme");
+    Serial.println("E2 move from Enzyme");
   }
 
   if (experiment == 2 && target == 2)
   {
     switch_conn_pin(BASEBD_J11_PIN2, HIGH); //Experiment 2 valveB high, waste line open
     int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 25uL at a time
-    Serial.println("_E2 move to chamberA");
-    saveExperimentalLog("_E2_move to chamberA " + String(move_pulse * 25) + "uL");
+    Serial.println("E2 move to chamberA");
+    saveExperimentalLog("E2_move to chamberA " + String(move_pulse * 25) + "uL");
     for (int i = 0; i <= move_pulse; i++) {
       switch_conn_pin(BASEBD_J12_PIN4, HIGH); //Experiment 2 pumpA
       digitalWrite(LED, HIGH);
@@ -1865,6 +1882,7 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
       digitalWrite(LED, LOW);
       delay(200);
       Serial.println( i * 25);
+      saveExperimentalLog("STEP_E2_move to chamberA " + String(i * 25) + "uL");
     }
     switch_conn_pin(BASEBD_J12_PIN2, LOW); //Reset xperiment 1 valveA so enzyme is blocked
   }
@@ -1895,8 +1913,8 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
   if (experiment == 2 && origin == 3 && target == 4)
    {
       int move_pulse = liquid_volume / 25; //1ml = 1000uL and the pump moves 35uL at a time
-      Serial.println("_E2 media move to chamberB");
-      saveExperimentalLog("_E2_media_move to chamberB " + String(move_pulse * 25) + "uL");
+      Serial.println("E2 media move to chamberB");
+      saveExperimentalLog("E2_media_move to chamberB " + String(move_pulse * 25) + "uL");
       for (int i = 0; i <= move_pulse; i++){
       switch_conn_pin(BASEBD_J11_PIN4, HIGH); //Experiment 2 pumpB
       digitalWrite(LED, HIGH);
@@ -1905,6 +1923,7 @@ void moveLiquid(int experiment, int origin, int target, float liquid_volume)
       digitalWrite(LED, LOW);
       delay(200);
       Serial.println( i * 25);
+      saveExperimentalLog("STEP_E2_media_move to chamberB " + String(i * 25) + "uL");
       }
     }
 }
@@ -1914,23 +1933,23 @@ void switchCollection(int experiment, int bag)
   if (experiment == 1 && bag == 0)
   {
     switch_conn_pin(BASEBD_J5_PIN4, LOW); //Experiment 1 waste V6
-    Serial.println("exp1 open waste bag");
-    saveExperimentalLog("exp1_opem waste bag");
+    Serial.println("E1 open waste bag");
+    saveExperimentalLog("E1_opem waste bag");
   }
   if (experiment == 1 && bag == 1)
   {
     switch_conn_pin(BASEBD_J5_PIN4, HIGH); //NOT V6
     switch_conn_pin(BASEBD_J5_PIN2, LOW); //Experiment 1 preservativeOne V5
-    Serial.println("exp1 open preservativeOne bag");
-    saveExperimentalLog("exp1_open preservativeOne bag");
+    Serial.println("E1 open preservativeOne bag");
+    saveExperimentalLog("E1_open preservativeOne bag");
   }
   if (experiment == 1 && bag == 2)
   {
     switch_conn_pin(BASEBD_J5_PIN4, HIGH); //NOT V6
     switch_conn_pin(BASEBD_J5_PIN2, HIGH); //NOT V5
     switch_conn_pin(BASEBD_J3_PIN4, LOW); ////Experiment 1 preservativeTwo V4
-    Serial.println("exp1 open preservativeTwo bag");
-    saveExperimentalLog("exp1_open preservativeTwo bag");
+    Serial.println("E1 open preservativeTwo bag");
+    saveExperimentalLog("E1_open preservativeTwo bag");
   }
   if (experiment == 1 && bag == 3)
   {
@@ -1939,7 +1958,7 @@ void switchCollection(int experiment, int bag)
     switch_conn_pin(BASEBD_J3_PIN4, HIGH); //NOT V4
     switch_conn_pin(BASEBD_J3_PIN2, LOW); //Experiment 1 preservativeThree V3
     Serial.println("open preservativeThree bag");
-    saveExperimentalLog("exp1_open preservativeThree bag");
+    saveExperimentalLog("E1_open preservativeThree bag");
   }
     if (experiment == 1 && bag == 4)
   {
@@ -1948,40 +1967,40 @@ void switchCollection(int experiment, int bag)
     switch_conn_pin(BASEBD_J3_PIN4, HIGH); //NOT V4
     switch_conn_pin(BASEBD_J3_PIN2, HIGH); //NOT V3
     switch_conn_pin(BASEBD_J1_PIN4, LOW); //Experiment 1 preservativeFour V2
-    Serial.println("open preservativeFour bag");
+    Serial.println("E1_open preservativeFour bag");
     }
 
   //experiment two collection
 
   if (experiment == 2 && bag == 0)
   {
     switch_conn_pin(BASEBD_J2_PIN2, LOW); //Experiment 2 waste V7
-    Serial.println("exp2 open waste bag");
-    saveExperimentalLog("exp2_opem waste bag");
+    Serial.println("E2 open waste bag");
+    saveExperimentalLog("E2_opem waste bag");
   }
   if (experiment == 2 && bag == 1)
   {
     switch_conn_pin(BASEBD_J2_PIN2, HIGH); //NOT V7
     switch_conn_pin(BASEBD_J2_PIN4, LOW); //Experiment 2 preservativeOne V8
-    Serial.println("exp2 open preservativeOne bag");
-    saveExperimentalLog("exp2_open preservativeOne bag");
+    Serial.println("E2 open preservativeOne bag");
+    saveExperimentalLog("E2_open preservativeOne bag");
   }
   if (experiment == 2 && bag == 2)
   {
     switch_conn_pin(BASEBD_J2_PIN2, HIGH); //NOT V7
     switch_conn_pin(BASEBD_J2_PIN4, HIGH); //NOT V8
     switch_conn_pin(BASEBD_J4_PIN2, LOW); ////Experiment 2 preservativeTwo V9
-    Serial.println("exp2 open preservativeTwo bag");
-    saveExperimentalLog("exp2_open preservativeTwo bag");
+    Serial.println("E2 open preservativeTwo bag");
+    saveExperimentalLog("E2_open preservativeTwo bag");
   }
   if (experiment == 2 && bag == 3)
   {
   switch_conn_pin(BASEBD_J2_PIN2, HIGH); //NOT V7
   switch_conn_pin(BASEBD_J2_PIN4, HIGH); //NOT V8
   switch_conn_pin(BASEBD_J4_PIN2, HIGH); //NOT V9
   switch_conn_pin(BASEBD_J4_PIN4, LOW); //Experiment 2 preservativeThree V10
-  Serial.println("open preservativeThree bag");
-  saveExperimentalLog("exp2_open preservativeThree bag");
+  Serial.println("E2_open preservativeThree bag");
+  saveExperimentalLog("E2_open preservativeThree bag");
   }
 if (experiment == 2 && bag == 4)
 {
@@ -1990,8 +2009,8 @@ if (experiment == 2 && bag == 4)
   switch_conn_pin(BASEBD_J4_PIN2, HIGH); //NOT V9
   switch_conn_pin(BASEBD_J4_PIN4, HIGH); //NOT V10
   switch_conn_pin(BASEBD_J6_PIN2, LOW); //Experiment 2 preservativeFour V11
-  Serial.println("open preservativeFour bag");
-  saveExperimentalLog("exp2_open preservativeFour bag");
+  Serial.println("E2_open preservativeFour bag");
+  saveExperimentalLog("E2_open preservativeFour bag");
 }
 }