//Sets the minimum values to a fastqEntry
void initializeFastqEntry (fastqEntry *newEntry) {
initializeString (&newEntry->title);
initializeString (&newEntry->sequence);
initializeString (&newEntry->quality);
newEntry->next = NULL;
return;
}
//Create a new node on a fasta entry list
void createFastaEntry (fastaEntry **newEntry) {
*newEntry = malloc (sizeof (**newEntry));
initializeString (&(*newEntry)->title);
initializeString (&(*newEntry)->seq);
initializeString (&(*newEntry)->output);
(*newEntry)->next = NULL;
return;
}
//(Re)Sets a node to empty values
void initializeNode (node *newNode) {
initializeString (&newNode->title);
initializeString (&newNode->sequence);
initializeString (&newNode->quality);
newNode->left = NULL;
newNode->right = NULL;
newNode->height = -1;
return;
}
void initializePatient(PatientT * patient) {
initializeString(patient->firstName, 30);
initializeString(patient->lastName, 30);
initializeString(patient->race, 30);
initializeString(patient->gender, 30);
initializeString(patient->uuid, 33);
initializeString(patient->ssn, 10);
initializeString(patient->dateOfBirth, 11);
patient->age = 0;
patient->smokes = 0;
patient->insurance = malloc(sizeof(InsuranceT));
initializeString(patient->insurance->name, 40);
initializeString(patient->insurance->name, 30);
patient->immunizations = malloc(sizeof(ImmunizationListT));
patient->immunizations->next = NULL;
patient->immunizations->item = NULL;
patient->medications = malloc(sizeof(MedicationListT));
patient->medications->next = NULL;
patient->medications->item = NULL;
patient->visits = malloc(sizeof(VisitListT));
patient->visits->next = NULL;
patient->visits->item = NULL;
patient->testResults = malloc(sizeof(TestResultListT));
patient->testResults->next = NULL;
patient->testResults->item = NULL;
}
//Prints the nodes
void printNodeList (node *firstNode, FILE *outFile) {
//Local variables
node *curNode = firstNode;
string curScaff;
initializeString (&curScaff);
copyString (&firstNode->scaffold, &curScaff);
fprintf (outFile, "##gff-version 3\n");
//One loop
while (curNode != NULL) {
//If it's a new scaffold print a "###" breaker line
if (strcmp (curNode->scaffold.str, curScaff.str) != 0) {
fprintf (outFile, "###\n");
copyString (&curNode->scaffold, &curScaff);
}
fprintf (outFile, "%s\n", curNode->entry.str);
curNode = curNode->next;
free (firstNode->entry.str);
free (firstNode->scaffold.str);
free (firstNode);
firstNode = curNode;
}
free (curScaff.str);
fprintf (outFile, "###");
return;
}
int main()
{
PString *p = initializeString(30);
strcpy(p->chars, "Hello");
printf("%d\n", p->length(p));
return 0;
}
//Check buffer with a particular. always stops at $
boolean WiFlyRNXV::checkBufferResponse(String compareValue,int timeout){
//NULL case
boolean noCase=false;
if(compareValue==NULL) noCase=true;
initializeString(responseBuffer,LONG_STRING);
//Variables
//char* responseBuffer; //Buffer for response
boolean bufRead = true; //Finish Reading
int bufpos = 0; //Buffer position
char chResponse = 'A'; //Initial character response
boolean compareSuccess=false; //Compare Success
//Fill the buffer
unsigned long startTime = millis();
while(bufRead){
//Start getting values
if(uart.available()){
chResponse = uart.read();
//Serial.print(chResponse);
//Keep reading until $ seen
if(noCase){
if(chResponse=='$'){
compareSuccess=true;
break;
}
}
//Place into String
if(bufpos<100){
responseBuffer[bufpos]=chResponse;
bufpos++;
}else{
Serial.println("Overflow");
bufpos=0;
}
}
//Check for existence of the comparison string, or if timeout stop
if(checkForString(compareValue,responseBuffer) && noCase==false){
compareSuccess=true;
bufRead=false;
}else if((millis()-startTime)>timeout){
compareSuccess=false;
bufRead=false;
}
}
uart.flush();
//if(compareSuccess)Serial.println("Found: "+compareValue);
//else Serial.println("Not found: "+compareValue);
return compareSuccess;
}
//main ()
int main (int argc, char *argv[]) {
//Call syntax check
if (argc != 3) {
printf ("Usage: %s Title_list_filename Sequence_list_filename\n", argv[0]);
exit (1);
}
//Main variables
string title, sequence;
FILE *titleInFile = NULL, *sequenceInFile = NULL, *outFile = NULL;
int count = 0;
//File creation and checks
printf ("Opening files..\n");
createFile (&titleInFile, argv[1], 'r');
createFile (&sequenceInFile, argv[2], 'r');
createFile (&outFile, "Combined.fasta", 'w');
//Combine entries
printf ("File opened. Combining...\n");
initializeString (&title);
initializeString (&sequence);
while (1) {
//Load the data, break the loop if either list runs out
loadString (&title, titleInFile);
loadString (&sequence, sequenceInFile);
if ((title.str == NULL) || (sequence.str == NULL)) {
break;
}
//Print the new fasta entry and reset for the next set
fprintf (outFile, ">%s\n%s\n", title.str, sequence.str);
reinitializeString (&title);
reinitializeString (&sequence);
//A counter so the user has some idea of how long it will take
if (++count % 1000000 == 0) {
printf ("%d entries combined...\n", count);
}
}
//Close everything and free memory
printf ("%d entries combined. Closing files and freeing memory...\n", count);
free (title.str);
free (sequence.str);
fclose (titleInFile);
fclose (sequenceInFile);
fclose (outFile);
return 0;
}
int main(int argc, char* argv[])
{
bool running = true;
struct SudokuBoard board = { 0 };
struct SudokuCommandInput commandInput = { 0 };
const struct SudokuCommand *command = NULL;
SudokuCommandResult status = SUDOKU_COMMAND_SUCCESS;
initializeSudokuBoard(&board);
initializeString(&commandInput.string);
puts("========== Sudoku Game ==========");
puts(showAllCommandsPrompt);
putchar('\n');
// if one argument was provided, go ahead and load sudoku board from textfile
if (argc > 1)
{
// if filename provided by argument cannot be found/read, loadSudokuBoard will
// print an error statement, and execution will continue with a blank board
loadSudokuBoard(argv[1], &board);
}
printSudokuBoard(&board);
while (running)
{
// put extra space between previous output and command prompt
putchar('\n');
command = getCommand(&commandInput);
status = command->commandFunction(&board, &commandInput);
if (status == SUDOKU_COMMAND_USAGE)
{
printf("Usage: '%s'\n", command->usagePrompt);
}
else if (status == SUDOKU_COMMAND_EXIT)
{
running = false;
}
}
freeHistory(&board.history);
return 0;
}
//ResponseBuffer will be updated
uint8_t WiFlyRNXV::sendTCPString(String data,uint8_t command){
bool status=false;
uint8_t resp=0;
initializeString(responseBuffer,LONG_STRING);
Serial.print("SEND:");
Serial.println(data);
if(!inCommandMode) EnterCommandMode();
delay(500);
uart.println("open");
if(checkBufferResponse("*OPEN*",5000)){
delay(300);
uart.print(command,DEC);
uart.print(":");
uart.println(data);
}
if(checkBufferResponse("*CLOS*",5000)){
Serial.print("RESP:");
//Serial.println("TEST: "+responseBuffer);
resp=processResponse(false);
Serial.println(resp,DEC);
Serial.print("RECV:");
Serial.println(responseBuffer);
status=true;
}else{
status=false;
}
//delete data;
inCommandMode=false;
return resp;
}
void WiFlyRNXV::EnterAdHoc(){
initializeString(ipValue,SHORT_STRING);
int delayW=500;
if(!inCommandMode) EnterCommandMode();
delay(1000);
// Setup adhoc network
Serial.println("set ip address 169.254.1.1"); uart.flush();
uart.println("set ip address 169.254.1.1"); delay(delayW);
Serial.println("set ip netmask 255.255.0.0"); uart.flush();
uart.println("set ip netmask 255.255.0.0"); delay(delayW);
Serial.println("set ip dhcp 0"); uart.flush();
uart.println("set ip dhcp 0"); delay(delayW);
Serial.println("set ip proto 2"); uart.flush();
uart.println("set ip proto 2"); delay(delayW);
Serial.println("set wlan ssid WiRED"); uart.flush();
uart.println("set wlan ssid WiRED"); delay(delayW);
Serial.println("set wlan channel 1"); uart.flush();
uart.println("set wlan channel 1"); delay(delayW);
// Create adhoc network
Serial.println("set wlan join 4"); uart.flush();
uart.println("set wlan join 4"); delay(delayW);
Serial.println("save"); uart.flush();
uart.println("save"); delay(delayW);
Serial.println("reboot"); uart.flush();
uart.println("reboot"); delay(delayW);
delay(2000);
inCommandMode=false;
uart.flush();
Serial.println("Done AdHoc");
}
//Resets a used string to an empty status
void reinitializeString (string *string) {
free (string->str);
initializeString (&(*string));
return;
}
//main ()
int main (int argc, char *argv[]) {
//Call syntax check
if (argc != 2) {
printf ("Usage: %s Input_filename\n", argv[0]);
exit (1);
}
//Main variables
FILE *inFile = NULL;
string source, type;
char in;
int maker_count = 0, augustus_count = 0, snap_count = 0, genemark_count = 0, blastn_count = 0, blastx_count = 0, est2genome_count = 0, protein2genome_count = 0, repeatmasker_count = 0, repeatrunner_count = 0, LTRharvest_count = 0, LTRfinder_count = 0, TRF_count = 0, tRNAscan_count = 0, gene_count = 0, TE_count = 0, count = 0;
//File creation and checks
printf ("Opening files...\n");
createFile (&inFile, argv[1], 'r');
//Collect stats
printf ("Files opened. Parsing stats...\n");
initializeString (&source);
initializeString (&type);
in = fgetc (inFile);
//Automate the rest
while (1) {
//Skip the title
while (in != '\t') {
if (((ferror (inFile)) || (feof (inFile)))) {
source.str = NULL;
break;
}
in = fgetc (inFile);
}
//Stop the loop if the list is done
if (source.str == NULL) {
break;
}
//Read the source
in = fgetc (inFile);
while (in != '\t') {
readValueToString (&source, in);
in = fgetc (inFile);
}
//Read the type
in = fgetc (inFile);
while (in != '\t') {
readValueToString (&type, in);
in = fgetc (inFile);
}
//Burn the rest of the line and reset the strings
while (in != '\n') {
in = fgetc (inFile);
}
//Increase the counts as they appear /*ADD NEW SOURCES HERE */
if ((strcmp (source.str, "maker") == 0) && (strcmp (type.str, "gene") == 0)) {
maker_count++;
} else if ((strcmp (source.str, "augustus_masked") == 0) && (strcmp (type.str, "match") == 0)) {
augustus_count++;
} else if ((strcmp (source.str, "snap_masked") == 0) && (strcmp (type.str, "match") == 0)) {
snap_count++;
} else if ((strcmp (source.str, "genemark_masked") == 0) && (strcmp (type.str, "match") == 0)) {
genemark_count++;
} else if ((strcmp (source.str, "blastn") == 0) && (strcmp (type.str, "expressed_sequence_match") == 0)) {
blastn_count++;
} else if ((strcmp (source.str, "blastx") == 0) && (strcmp (type.str, "protein_match") == 0)) {
blastx_count++;
} else if ((strcmp (source.str, "est2genome") == 0) && (strcmp (type.str, "expressed_sequence_match") == 0)) {
est2genome_count++;
} else if ((strcmp (source.str, "protein2genome") == 0) && (strcmp (type.str, "protein_match") == 0)) {
protein2genome_count++;
} else if ((strcmp (source.str, "repeatmasker") == 0) && (strcmp (type.str, "match") == 0)) {
repeatmasker_count++;
} else if ((strcmp (source.str, "repeatrunner") == 0) && (strcmp (type.str, "protein_match") == 0)) {
repeatrunner_count++;
} else if ((strcmp (source.str, "LTRharvest") == 0) && (strcmp (type.str, "repeat_region") == 0)) {
LTRharvest_count++;
} else if ((strcmp (source.str, "LTRfinder") == 0) && (strcmp (type.str, "repeat_region") == 0)) {
LTRfinder_count++;
} else if ((strcmp (source.str, "TRF") == 0) && (strcmp (type.str, "repeat_region") == 0)) {
TRF_count++;
} else if ((strcmp (source.str, "tRNAscan") == 0) && (strcmp (type.str, "tRNA") == 0)) {
tRNAscan_count++;
} else if (strcmp (type.str, "gene") == 0) {
gene_count++;
} else if (strcmp (type.str, "transposable_element") == 0) {
TE_count++;
}
//A counter so the user has some idea of how long it will take
if (++count % 100000 == 0) {
printf ("%d entries processed...\n", count);
}
reinitializeString (&source);
reinitializeString (&type);
}
//Display the stats
printf ("%d entries process. All stats Parsed.\n\t###MAKER Matches###\nMAKER Consensus Genes:\t%d\nAugustus Matches:\t%d\nsnap Matches:\t\t%d\nGenemark Matches:\t%d\nBLASTn Matches\t\t%d\nBLASTx Matches\t\t%d\nest2genome Matches:\t%d\nprotein2genome Matches:\t%d\nRepeatMasker Matches:\t%d\nRepeatrunner Matches:\t%d\n\t###Other Annotations###\nLTRharvest Matches:\t%d\nLTRfinder Matches:\t%d\nTRF Matches:\t\t%d\ntRNAscan Matches:\t%d\n\t###Generic Matches###\nGenes:\t\t\t%d\nTransposable Elements:\t%d\n", count, maker_count, augustus_count, snap_count, genemark_count, blastn_count, blastx_count, est2genome_count, protein2genome_count, repeatmasker_count, repeatrunner_count, LTRharvest_count, LTRfinder_count, TRF_count, tRNAscan_count, gene_count, TE_count);
//Close everything and free memory
free (source.str);
free (type.str);
fclose (inFile);
return 0;
}
void exportUser(PatientT * patient) {
if(patient == NULL) {
//Lol you boi
return;
}
char * uuid = patient->uuid;
char fileName[45];
initializeString(fileName, 45);
strncat(fileName, "records/", 8);
strncat(fileName, uuid, 32);
FILE * userRecords = fopen(fileName, "w+");
int err;
err = fprintf(userRecords, "%s,%s,%d,%s,%s,%d,%s,%s\n",
patient->firstName,
patient->lastName,
patient->smokes,
patient->race,
patient->gender,
patient->age,
patient->ssn,
patient->dateOfBirth
);
if(err < 0) {
//Error
}
err = fprintf(userRecords, "%s,%s\n",
patient->insurance->name,
patient->insurance->policyNumber
);
if(err < 0) {
//Error
}
ImmunizationListT * currentImmuList = patient->immunizations;
int numRecords = 1;
int i = 0;
while(currentImmuList->next != NULL) {
currentImmuList = currentImmuList->next;
numRecords++;
}
err = fprintf(userRecords, "IMMUNIZATIONS,%d\n", numRecords);
if(err < 0) {
//Error
}
currentImmuList = patient->immunizations;
for(i = 0; i < numRecords; i++) {
err = fprintf(userRecords, "%s,%s,%s\n",
currentImmuList->item->name,
currentImmuList->item->datePerformed,
currentImmuList->item->performingPerson
);
if(err < 0) {
//Error
}
currentImmuList = currentImmuList->next;
}
MedicationListT * currentMedList = patient->medications;
while(currentMedList->next != NULL) {
currentMedList = currentMedList->next;
numRecords++;
}
err = fprintf(userRecords, "MEDICATIONS,%d\n", numRecords);
if(err < 0) {
//Error
}
currentMedList = patient->medications;
for(i = 0; i < numRecords; i++) {
err = fprintf(userRecords, "%s,%d,%s\n",
currentMedList->item->name,
currentMedList->item->dosage,
currentMedList->item->prescribingPerson
);
if(err < 0) {
//Error
}
currentMedList = currentMedList->next;
}
VisitListT * currentVisitList = patient->visits;
while(currentVisitList->next != NULL) {
currentVisitList = currentVisitList->next;
numRecords++;
}
err = fprintf(userRecords, "VISITS,%d\n", numRecords);
if(err < 0) {
//Error
}
currentVisitList = patient->visits;
for(i = 0; i < numRecords; i++) {
err = fprintf(userRecords, "%d,%d,%s,%s\n",
currentVisitList->item->heartRate,
currentVisitList->item->bloodPressure,
currentVisitList->item->visitDateTime,
currentVisitList->item->personSeen
);
if(err < 0) {
//Error
}
currentVisitList = currentVisitList->next;
}
TestResultListT * currentTestList = patient->testResults;
while(currentTestList->next != NULL) {
currentTestList = currentTestList->next;
numRecords++;
}
err = fprintf(userRecords, "TESTRESULT,%d\n", numRecords);
if(err < 0) {
//Error
}
currentTestList = patient->testResults;
for(i = 0; i < numRecords; i++) {
err = fprintf(userRecords, "%s,%s\n",
currentTestList->item->testName,
currentTestList->item->testResults
);
if(err < 0) {
//Error
}
currentTestList = currentTestList->next;
}
fclose(userRecords);
}
void editPatient(char* uuid){
//TODO check if uuid is part of DOC's patients
PatientT * patient = fetchPatient(uuid);
fprintf(stderr, "found patient\n");
int choice=0;
char temp[2];
initializeString(temp,2);
//display edit menu
while(choice!=9){
displayPatient(uuid);
printf("\n****Edit Patient\n");
printf("[1] Insurance\n");
printf("[2] Add Immunization\n");
printf("[3] Add Medication\n");
printf("[4] Add Vitals\n");
printf("[5] Add Test Results\n");
printf("[6] Demographics\n");
printf("[9] EXIT\n");
//get input
if(fgets(temp,2,stdin));
choice = temp[0]-48;
//process choice
switch(choice){
case 1:
;
while(getchar()!='\n');//clean buffer
//edit insurance
char name[40];
char policyNumber[30];
initializeString(name,40);
initializeString(policyNumber,40);
while(getchar()!='\n');//clean buffer
printf("INSURANCE NAME: ");
if(fgets(name,40,stdin));
while(getchar()!='\n');//clean buffer
printf("\nPOLICY NO: ");
if(fgets(policyNumber,30,stdin));
printf("\n");
sanitizeInput(name,40);
sanitizeInput(policyNumber,30);
strncpy(patient->insurance->name,name,40);
strncpy(patient->insurance->policyNumber,policyNumber,30);
exportUser(patient);
printf("\nUPDATED!\n");
break;
case 2:
break;
case 3:
break;
case 4:
break;
case 5:
break;
case 6:
;
while(getchar()!='\n');//clean buffer
char firstName[30];
initializeString(firstName,30);
char lastName[30];
initializeString(lastName,30);
bool smokes=3;
char race[30];
initializeString(race,30);
char gender[30];
initializeString(gender,30);
int age=-1;
char tempAge[10];
initializeString(tempAge,10);
char ssn[10];
initializeString(ssn,10);
char dateOfBirth[11];
initializeString(dateOfBirth,11);
while(getchar()!='\n');//clean buffer
printf("FIRSTNAME: ");
if(fgets(firstName,30,stdin));
while(getchar()!='\n');//clean buffer
printf("\nLASTNAME: ");
if(fgets(lastName,30,stdin));
while(getchar()!='\n');//clean buffer
while(smokes!=0&&smokes!=1){
printf("\nSmoker?{1=YES,0=NO}");
if(fgets(temp,2,stdin));
sanitizeInt(temp,2);
smokes=temp[0]-48;
while(getchar()!='\n');//clean buffer
}
while(getchar()!='\n');//clean buffer
printf("\nGENDER: ");
if(fgets(gender,30,stdin));
while(getchar()!='\n');//clean buffer
printf("\nRACE: ");
if(fgets(race,30,stdin));
while(getchar()!='\n');//clean buffer
while(age<=0||age>=999){
printf("\nAGE {000}");
if(fgets(tempAge,3,stdin));
//sanitizeInt(tempAge,4);
//age+=((tempAge[0]+48)*1);
//age+=((tempAge[1]+48)*10);
//age+=((tempAge[2]+48)*100);
age= (int) strtol(tempAge,NULL,10);
while(getchar()!='\n');//clean buffer
}
while(getchar()!='\n');//clean buffer
printf("\nSSN: ");
if(fgets(ssn,10,stdin));
while(getchar()!='\n');//clean buffer
printf("\nDOB{MM/DD/YYYY}");
if(fgets(dateOfBirth,11,stdin));
sanitizeInput(firstName,30);
sanitizeInput(lastName,30);
sanitizeInput(race,30);
sanitizeInput(gender,30);
sanitizeInput(ssn,10);
sanitizeInput(dateOfBirth,11);
strncpy(patient->firstName,firstName,30);
strncpy(patient->lastName,lastName,30);
strncpy(patient->race,race,30);
strncpy(patient->gender,gender,30);
strncpy(patient->ssn,ssn,10);
strncpy(patient->dateOfBirth,dateOfBirth,11);
patient->smokes=smokes;
patient->age=age;
exportUser(patient);
printf("\nUPDATED!\n");
break;
case 9:
break;
default:
break;
}
}
}
//Sets minimum values to a node
void initializeNode (node *newNode) {
initializeString (&newNode->entry);
initializeString (&newNode->scaffold);
newNode->next = NULL;
return;
}
void initializeCommon(
)
{
initializeString();
initializeX11();
}
//Constructor-Start listen on uart
WiFlyRNXV::WiFlyRNXV(byte pinReceive, byte pinSend) : uart (pinReceive, pinSend),irSystem(IR_RECEIVEPIN){
initializeString(responseBuffer,LONG_STRING);
initializeString(ipValue,SHORT_STRING);
inCommandMode=false;
wifiStatus=false;
}
PatientT * fetchPatient(char * uuid) {
fprintf(stderr,"Fetching Patient INFO\n");
if(patientCache == NULL) {
patientCache = malloc(sizeof(PatientCacheT));
if(patientCache == NULL) {
//malloc error
}
else {
patientCache->item = NULL;
patientCache->next = NULL;
}
}
//First we need to search the cache for a proper user
PatientCacheT * currentRecord = patientCache;
while(true) {
if(currentRecord->item == NULL) {
//There is no record, ayyyyy
break;
}
//Match found
if(strncmp(currentRecord->item->uuid, uuid, 33)) {
return currentRecord->item;
}
else {
currentRecord = currentRecord->next;
}
}
//No record :c
fprintf(stderr,"NO RECORD SEARCHING FILE\n");
char fileName[45];
initializeString(fileName, 45);
strncat(fileName, "records/", 8);
strncat(fileName, uuid, 32);
FILE * userRecords = fopen(fileName, "r");
char line[500];
initializeString(line, 500);
//First thing we wanna read in is the basic information about the user
fprintf(stderr,"Reading Basic info\n");
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
PatientT * patient = malloc(sizeof(PatientT));
if(patient == NULL) {
//Error during malloc
}
initializePatient(patient);
if(feof(userRecords) && (line[0] == '\0' || line[0] == ' ' || line[1] == '\0')) {
fclose(userRecords);
return patient;
}
char csvData[10][50];
parseCSV(line, csvData);
strncpy(patient->uuid, uuid, 33);
strncpy(patient->firstName, csvData[0], 29);
strncpy(patient->lastName, csvData[1], 29);
patient->smokes = (strncmp(csvData[2], "1", 1) == 0) ? true : false;
strncpy(patient->race, csvData[3], 29);
strncpy(patient->gender, csvData[4], 29);
int age = (int) strtol(csvData[5], NULL, 10);
if(age == 0) {
//Errored out during conversion
printf("System errored during age import. Setting age to -1\n");
age = -1;
}
patient->age = age;
strncpy(patient->ssn, csvData[6], 10);
strncpy(patient->dateOfBirth, csvData[7], 10);
fprintf(stderr,"Read basic info\n");
fprintf(stderr,"Reading insuracne info");
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
parseCSV(line, csvData);
InsuranceT * insurance = malloc(sizeof(InsuranceT));
if(insurance == NULL) {
//Malloc error
}
strncpy(insurance->name, csvData[0], 40);
strncpy(insurance->policyNumber, csvData[1], 30);
patient->insurance = insurance;
//--------------------------------------------------------------------------------
//Immunization data
fprintf(stderr,"Read Immunization");
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
parseCSV(line, csvData);
int numberOfRecords = (int) strtol(csvData[1], NULL, 10);
if(numberOfRecords == 0) {
printf("System errored during Immunization import. Ignoring.");
numberOfRecords = 0;
}
int i = 0;
ImmunizationListT * lastRecordImmu = malloc(sizeof(ImmunizationListT));
if(lastRecordImmu == NULL) {
//Malloc error
}
ImmunizationListT * firstRecordImmu = lastRecordImmu;
for(i = 0; i < numberOfRecords; i++) {
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
parseCSV(line, csvData);
ImmunizationT * record = malloc(sizeof(ImmunizationT));
if(record == NULL) {
//Malloc error
}
initializeString(record->name, 40);
initializeString(record->datePerformed, 20);
initializeString(record->performingPerson, 33);
strncpy(record->name, csvData[0], 40);
strncpy(record->datePerformed, csvData[1], 20);
strncpy(record->performingPerson, csvData[2], 33);
lastRecordImmu->item = record;
if(i + 1 >= numberOfRecords) {
lastRecordImmu->next = NULL;
break;
}
lastRecordImmu->next = malloc(sizeof(ImmunizationListT));
if(lastRecordImmu->next == NULL) {
//Malloc error
}
lastRecordImmu = lastRecordImmu->next;
lastRecordImmu->next = NULL;
}
patient->immunizations = firstRecordImmu;
//--------------------------------------------------------------------------------
//Medication data
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
parseCSV(line, csvData);
numberOfRecords = (int) strtol(csvData[1], NULL, 10);
if(numberOfRecords == 0) {
printf("System errored during Medication import. Ignoring.");
numberOfRecords = 0;
}
MedicationListT * lastRecordMedi = malloc(sizeof(MedicationListT));
if(lastRecordMedi == NULL) {
//Malloc error
}
MedicationListT * firstRecordMedi = lastRecordMedi;
for(i = 0; i < numberOfRecords; i++) {
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
parseCSV(line, csvData);
MedicationT * record = malloc(sizeof(MedicationT));
if(record == NULL) {
//Malloc error
}
initializeString(record->prescribingPerson, 33);
strncpy(record->name, csvData[0], 40);
const int dosage = (int) strtol(csvData[1], NULL, 10);
if(dosage == 0) {
printf("System error during Medication import.");
record->dosage = -1;
}
else {
record->dosage = dosage;
}
strncpy(record->prescribingPerson, csvData[2], 33);
lastRecordMedi->item = record;
if(i + 1 >= numberOfRecords) {
lastRecordMedi->next = NULL;
break;
}
lastRecordMedi->next = malloc(sizeof(MedicationListT));
if(lastRecordMedi->next == NULL) {
//Malloc error
}
lastRecordMedi = lastRecordMedi->next;
lastRecordMedi->next = NULL;
}
patient->medications = firstRecordMedi;
//---------------------------------------------------------------------------------
//Visits data
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
parseCSV(line, csvData);
numberOfRecords = (int) strtol(csvData[1], NULL, 10);
if(numberOfRecords == 0) {
printf("System error during Visits import. Ignoring.");
numberOfRecords = 0;
}
VisitListT * lastVisitRecord = malloc(sizeof(VisitListT));
if(lastVisitRecord == NULL) {
//Malloc error
}
VisitListT * firstVisitRecord = lastVisitRecord;
for(i = 0; i < numberOfRecords; i++) {
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
parseCSV(line, csvData);
VisitT * record = malloc(sizeof(VisitT));
if(record == NULL) {
//Malloc error
}
initializeString(record->visitDateTime, 19);
initializeString(record->personSeen, 33);
const int heartRate = (int) strtol(csvData[0], NULL, 10);
if(heartRate == 0) {
printf("System error during Visit import");
record->heartRate = -1;
}
else {
record->heartRate = heartRate;
}
const int bloodPressure = (int) strtol(csvData[1], NULL, 10);
if(bloodPressure == 0) {
printf("System error during Visit import");
record->bloodPressure = -1;
}
else {
record->bloodPressure = bloodPressure;
}
strncpy(record->visitDateTime, csvData[2], 19);
strncpy(record->personSeen, csvData[3], 33);
lastVisitRecord->item = record;
if(i + 1 >= numberOfRecords) {
lastVisitRecord->next = NULL;
break;
}
lastVisitRecord->next = malloc(sizeof(VisitT));
if(lastVisitRecord->next == NULL) {
//Malloc error
}
lastVisitRecord = lastVisitRecord->next;
lastVisitRecord->next = NULL;
}
patient->visits = firstVisitRecord;
//---------------------------------------------------------------------------------
//Test Result data
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
parseCSV(line, csvData);
numberOfRecords = (int) strtol(csvData[1], NULL, 10);
if(numberOfRecords == 0) {
printf("System error during Test Results import. Ignoring.");
numberOfRecords = 0;
}
TestResultListT * lastTestRecord = malloc(sizeof(TestResultListT));
if(lastTestRecord == NULL) {
//Malloc error;
}
TestResultListT * firstTestRecord = lastTestRecord;
for(i = 0; i < numberOfRecords; i++) {
if(fgets(line, 500, userRecords) == NULL) {
//Error during reading
}
parseCSV(line, csvData);
TestResultT * record = malloc(sizeof(TestResultT));
if(record == NULL) {
//Malloc error
}
initializeString(record->testName, 30);
initializeString(record->testResults, 120);
strncpy(record->testName, csvData[0], 30);
strncpy(record->testResults, csvData[1], 120);
lastTestRecord->item = record;
if(i + 1 >= numberOfRecords) {
lastTestRecord->next = NULL;
break;
}
lastTestRecord->next = malloc(sizeof(TestResultT));
if(lastTestRecord->next == NULL) {
//Malloc error;
}
lastTestRecord = lastTestRecord->next;
lastTestRecord->next = NULL;
}
patient->testResults = firstTestRecord;
//I think we're done here.
patientCache->item = patient;
patientCache->next = malloc(sizeof(PatientCacheT));
if(patientCache->next == NULL) {
//Error;
}
fclose(userRecords);
return patient;
}
boolean WiFlyRNXV::getDataType(String& fillBuff,int action){
initializeString(fillBuff,SHORT_STRING);
if(!inCommandMode) EnterCommandMode();
String delimit;
if(action==GET_IP){
delimit="IP=";
uart.println("get ip");
}else if(action==GET_DEVID){
delimit="d=";
uart.println("show deviceid");
}
boolean bufRead = true; //Finish Reading
boolean ipReadMode = false; //Ready to write in IP
boolean ipReadOver = false; //Finished writing IP
int bufpos = 0; //Buffer position
char chResponse = 'A'; //Initial character response
boolean compareSuccess=false; //Compare Success
int timeout=5000; //Timeout value fixed
//Fill the buffer
unsigned long startTime = millis();
while(bufRead){
//Start getting values
if(uart.available()){
chResponse = uart.read();
//Serial.print(chResponse);
//Stop at character :
if(chResponse==':'){
ipReadOver=true;
break;
}
if(ipReadMode==false){
responseBuffer[bufpos]=chResponse;
}else{
fillBuff[bufpos]=chResponse;
}
bufpos++;
}
//Check for existence of the comparison string, or if timeout stop
if(checkForString(delimit,responseBuffer) && ipReadMode==false){
ipReadMode=true;
bufpos=0;
}else if((millis()-startTime)>timeout){
compareSuccess=false;
bufRead=false;
}
}
if(ipReadOver==true){
//ipValue.trim();
ipValue.replace(" ","");
Serial.print("IPVAL:");
Serial.println(fillBuff);
compareSuccess=true;
delay(200);
ExitCommandMode();
}
uart.flush();
return compareSuccess;
}
