add database script in c for creation and init

Code-C/CMakeLists.txt

@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 2.8)
 project(Traitement-signal-plantes C)
 
 include(CTest)
@@ -10,16 +10,21 @@ file(MAKE_DIRECTORY Executable)
 
 set (CMAKE_RUNTIME_OUTPUT_DIRECTORY Executable) #Set Executable directory as default exectutable file location
 
-add_executable(exect fileGestion.c getArray.c average.c growthRate.c power.c queue.c simulateFlux.c main.c)
+add_executable(exect fileGestion.c getArray.c average.c growthRate.c power.c queue.c simulateFlux.c database.c main.c)
 # add_executable(exect main.c simulateFlux.c queue.c power.c growthRate.c average.c getArray.c fileGestion.c)
 
+find_package (SQLite3)
+include_directories(${SQLite3_INCLUDE_DIRS})
+target_link_libraries (exect ${SQLite3_LIBRARIES} m)
+
+
 find_package(Threads)
 target_link_libraries(exect ${CMAKE_THREAD_LIBS_INIT} m)
 
 set(CTEST_MEMORYCHECK_TYPE "AddressSanitizer")
 set(CTEST_MEMORYCHECK_SANITIZER_OPTIONS "verbosity=1:symbolize=1:abort_on_error=1:detect_leaks=1")
 
-add_executable(ctest fileGestion.c getArray.c average.c growthRate.c queue.c simulateFlux.c ctest.c)
+add_executable(ctest fileGestion.c getArray.c average.c growthRate.c queue.c simulateFlux.c database.c ctest.c)
 target_link_libraries(ctest ${CMAKE_THREAD_LIBS_INIT} m)
 
 add_test(test_queueCreateEmpty ./ctest queueCreateEmpty)

Code-C/Include/database.h

@@ -0,0 +1,11 @@
+#include <sqlite3.h>
+#include <stdio.h>
+#include <string.h>
+#include <stdlib.h>
+#include <stdbool.h>
+#include <unistd.h>
+#include <math.h>
+
+int createDb();
+int initiaizeNewTrial(char *position, double frequency, bool *captorOneHot);
+int initiaizeNewTrial(char *position, double frequency, bool *captorOneHot);

Code-C/cmake/FindSQLite3.cmake

@@ -0,0 +1,37 @@
+# Copyright (C) 2007-2009 LuaDist.
+# Created by Peter Kapec <kapecp@gmail.com>
+# Redistribution and use of this file is allowed according to the terms of the MIT license.
+# For details see the COPYRIGHT file distributed with LuaDist.
+#	Note:
+#		Searching headers and libraries is very simple and is NOT as powerful as scripts
+#		distributed with CMake, because LuaDist defines directories to search for.
+#		Everyone is encouraged to contact the author with improvements. Maybe this file
+#		becomes part of CMake distribution sometimes.
+
+# - Find sqlite3
+# Find the native SQLITE3 headers and libraries.
+#
+# SQLITE3_INCLUDE_DIRS	- where to find sqlite3.h, etc.
+# SQLITE3_LIBRARIES	- List of libraries when using sqlite.
+# SQLITE3_FOUND	- True if sqlite found.
+
+# Look for the header file.
+FIND_PATH(SQLITE3_INCLUDE_DIR NAMES sqlite3.h)
+
+# Look for the library.
+FIND_LIBRARY(SQLITE3_LIBRARY NAMES sqlite)
+
+# Handle the QUIETLY and REQUIRED arguments and set SQLITE3_FOUND to TRUE if all listed variables are TRUE.
+INCLUDE(FindPackageHandleStandardArgs)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(SQLITE3 DEFAULT_MSG SQLITE3_LIBRARY SQLITE3_INCLUDE_DIR)
+
+# Copy the results to the output variables.
+IF(SQLITE3_FOUND)
+	SET(SQLITE3_LIBRARIES ${SQLITE3_LIBRARY})
+	SET(SQLITE3_INCLUDE_DIRS ${SQLITE3_INCLUDE_DIR})
+ELSE(SQLITE3_FOUND)
+	SET(SQLITE3_LIBRARIES)
+	SET(SQLITE3_INCLUDE_DIRS)
+ENDIF(SQLITE3_FOUND)
+
+MARK_AS_ADVANCED(SQLITE3_INCLUDE_DIRS SQLITE3_LIBRARIES)

Code-C/database.c

@@ -1,9 +1,9 @@
-#include "./database.h"
+#include "./Include/simulateFlux.h"
+#include "./Include/database.h"
 
-int initializeTrailsTable()
+int initializeTrialsTable()
 {
     sqlite3 *db;
-    char *err_msg;
     int rc;
     sqlite3_stmt *stmt;
 
@@ -18,12 +18,12 @@ int initializeTrailsTable()
     rc = sqlite3_step(stmt);
     rc = sqlite3_finalize(stmt);
     sqlite3_close(db);
+    return 0;
 }
 
 int initializeCaptorMetadataTable()
 {
     sqlite3 *db;
-    char *err_msg;
     int rc;
     sqlite3_stmt *stmt;
 
@@ -38,6 +38,7 @@ int initializeCaptorMetadataTable()
     rc = sqlite3_step(stmt);
     rc = sqlite3_finalize(stmt);
     sqlite3_close(db);
+    return 0;
 }
 
 char *generateDataTableName(int trialId, int captorNumber)
@@ -56,7 +57,6 @@ char *generateDataTableName(int trialId, int captorNumber)
 int createCaptorDataTable(int trialId, int captorNumber)
 {
     sqlite3 *db;
-    char *err_msg;
     int rc;
     sqlite3_stmt *stmt;
 
@@ -81,49 +81,13 @@ int createCaptorDataTable(int trialId, int captorNumber)
     return 0;
 }
 
-/**
- * @brief convert an interger N into a char*
- *
- * @param N
- * @return char*
- */
-char *convertIntegerToChar(int N)
-{
-    // Count digits in number N
-    int m = N;
-    int digit = 0;
-    while (m)
-    {
-        digit++;
-        m /= 10;
-    }
-    char *arr;
-    char arr1[digit];
-    arr = (char *)malloc(digit * sizeof(char));
-    int index = 0;
-    while (N)
-    {
-        arr1[++index] = N % 10 + '0';
-        N /= 10;
-    }
-    int i;
-    for (i = 0; i < index; i++)
-    {
-        arr[i] = arr1[index - i];
-    }
-    arr[i] = '\0';
-    return (char *)arr;
-}
-
 int insertTrailElement(char *position, int start, double frequency)
 {
 
     sqlite3 *db;
     sqlite3_stmt *stmt;
 
-    char *err_msg;
     int rc;
-    int idx;
 
     rc = sqlite3_open("robotgowest.db", &db);
 
@@ -140,6 +104,7 @@ int insertTrailElement(char *position, int start, double frequency)
     rc = sqlite3_step(stmt);
     rc = sqlite3_finalize(stmt);
     sqlite3_close(db);
+    return 0;
 }
 
 int updateTrailElement(int id, char *position, int start, double frequency)
@@ -148,9 +113,7 @@ int updateTrailElement(int id, char *position, int start, double frequency)
     sqlite3 *db;
     sqlite3_stmt *stmt;
 
-    char *err_msg;
     int rc;
-    int idx;
 
     rc = sqlite3_open("robotgowest.db", &db);
 
@@ -169,6 +132,7 @@ int updateTrailElement(int id, char *position, int start, double frequency)
     rc = sqlite3_step(stmt);
     rc = sqlite3_finalize(stmt);
     sqlite3_close(db);
+    return 0;
 }
 
 int insertCaptorMetadataElement(int captorNumber, int trialId)
@@ -177,9 +141,7 @@ int insertCaptorMetadataElement(int captorNumber, int trialId)
     sqlite3 *db;
     sqlite3_stmt *stmt;
 
-    char *err_msg;
     int rc;
-    int idx;
 
     rc = sqlite3_open("robotgowest.db", &db);
 
@@ -193,7 +155,9 @@ int insertCaptorMetadataElement(int captorNumber, int trialId)
 
     rc = sqlite3_step(stmt);
     rc = sqlite3_finalize(stmt);
+
     sqlite3_close(db);
+    return 0;
 }
 
 int insertCaptorDataElement(int trialId, int captorNumber, double lux, double mean, double power)
@@ -204,16 +168,13 @@ int insertCaptorDataElement(int trialId, int captorNumber, double lux, double me
     sqlite3 *db;
     sqlite3_stmt *stmt;
 
-    char *err_msg;
     int rc;
-    int idx;
 
     rc = sqlite3_open("robotgowest.db", &db);
 
     char sql[70] = "INSERT INTO ";
     strcat(sql, tableName);
     strcat(sql, "(Lux,Mean,Power) VALUES ( :lux , :mean , :power)");
-    printf(sql);
 
     rc = sqlite3_prepare_v2(db, sql, -1, &stmt, NULL);
     if (rc != SQLITE_OK)
@@ -226,19 +187,62 @@ int insertCaptorDataElement(int trialId, int captorNumber, double lux, double me
     rc = sqlite3_step(stmt);
     rc = sqlite3_finalize(stmt);
     sqlite3_close(db);
+    return 0;
 }
 
-int main(void)
+int createDb()
 {
-    sqlite3_initialize();
+    char *dbPosition = "./robotgowest.db";
+    if (access(dbPosition, F_OK))
+    {
+        initializeTrialsTable();
+        initializeCaptorMetadataTable();
+        return 0;
+    }
+    else
+    {
+        printf("Database already initialized");
+        return 1;
+    }
+}
 
-    initializeTrailsTable();
-    // initializeCaptorMetadataTable();
-    // createCaptorDataTable(12, 8);
-    // insertTrailElement("test", 1, 3.0);
-    // insertCaptorMetadataElement(1, 2);
-    // insertCaptorDataElement(12, 8, 10, 121, 1513);
-    updateTrailElement(1, "test2", 122, 22);
+int getMaxTrialIdRow()
+{
+    int rc;
+    sqlite3 *db;
+    sqlite3_stmt *stmt;
+    int data = -1;
 
-    sqlite3_shutdown();
+    rc = sqlite3_open("robotgowest.db", &db);
+    if (rc != SQLITE_OK)
+    {
+        return -1;
+    }
+
+    rc = sqlite3_prepare_v2(db, "SELECT MAX(Id) FROM Trials", -1, &stmt, NULL);
+
+    if (sqlite3_step(stmt) == SQLITE_ROW)
+    {
+        data = sqlite3_column_int(stmt, 0);
+    }
+
+    rc = sqlite3_finalize(stmt);
+    sqlite3_close(db);
+
+    return data;
+}
+
+int initiaizeNewTrial(char *position, double frequency, bool *captorOneHot)
+{
+    insertTrailElement(position, -1, frequency);
+    int trialId = getMaxTrialIdRow();
+    for (int i = 0; i < 8; i++)
+    {
+        if (captorOneHot[i])
+        {
+            insertCaptorMetadataElement(i, trialId);
+            createCaptorDataTable(trialId, i + 1);
+        }
+    }
+    return 0;
 }

Code-C/main.c

@@ -8,6 +8,7 @@
 #include "./Include/average.h"
 #include "./Include/growthRate.h"
 #include "./Include/getArray.h"
+#include "./Include/database.h"
 
 bool rawDataWriteFlag;
 int nRowRawData = 5000;
@@ -160,6 +161,11 @@ int main(int argc, char **argv)
     invTimeBandWidth = 1 / (nRowRawData * period);
     firstRawDataQueue = queueCreateEmpty(); // change this for create empty
 
+    // launch DB related function
+    sqlite3_initialize();
+    createDb();                                           // Created the Db if not exist
+    initiaizeNewTrial("test", freqEch, selectionCaptors); // Initialize Trials data and tables
+
     pthread_t rawData;
     if (pthread_create(&rawData, NULL, threadSimulateFlux, "threadSimulflux") != 0)
     {
@@ -182,4 +188,6 @@ int main(int argc, char **argv)
     // }
 
     pthread_exit(NULL);
+
+    sqlite3_shutdown();
 }

Code-C/simulateFlux.c

@@ -152,11 +152,11 @@ bool writeOneRawData(FILE *rawDataFile)
             {
                 if (selectionCaptors[i - 1])
                 {
-                    quartet value;
-                    value.octet1 = buff[3 * i + 1];
-                    value.octet2 = buff[3 * i + 2];
-                    value.octet3 = buff[3 * i + 3];
-                    value.octet4 = 0;
+                    // quartet value;
+                    // value.octet1 = buff[3 * i + 1];
+                    // value.octet2 = buff[3 * i + 2];
+                    // value.octet3 = buff[3 * i + 3];
+                    // value.octet4 = 0;
 
                     valbin[i] = buff[3 * i + 1] * 256 * 256 * 256 + buff[3 * i + 2] * 256 * 256 + buff[3 * i + 3] * 256;
                     memcpy(&values[i], &valbin[i], sizeof(uint32_t));

Db-Script/database.h

@@ -1,14 +0,0 @@
-#include <sqlite3.h>
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
-
-// Duplication from simulFlux.c
-
-/**
- * @brief convert an interger N into a char*
- *
- * @param N
- * @return char*
- */
-char *convertIntegerToChar(int N);

Db-Script/database.py

@@ -1 +1,3 @@
-##This mist include all fetch function and also init and insert function for nn training annd testing result 
+##This mist include all fetch function and also init and insert function for nn training annd testing result 
+
+import numpy