def LGM1_verification(input_file, output_file, new_update, table_name):

##################################
    
    #file check variables
    column_length_counter = 0
    check_line_length_list = []
    check_blank_entry_list = []
    check_column_label_flag = False
    check_column_labels = []
    check_column_label_index = []
    missing_column_label = []
    
    #post file check variables
    matrix = {}
    rows = 0
    columns = 11
    repeat_marker_counter=0
    failure_counter = 0
    failure_list = []
    warning_list = []
    warning_counter = 0
    
##################################

    try:
        check_file = open(input_file)


        while True:
            check_line = check_file.readline()
            if check_line == '':
                break
            if '\n' in check_line:
                check_line = check_line[:-1]
            if '\r' in check_line:
                check_line = check_line[:-1]
            check_line = check_line.split('\t')
            check_line_length_list.append(len(check_line))

            
            for i in range (0,len(check_line)):
                if (check_line[i] == ''):
                    check_blank_entry =  column_length_counter +1, i+1
                    check_blank_entry_list.append(check_blank_entry)

            
            if (column_length_counter == 0):
                check_column_labels = check_line
                for i in range (0, len(check_line) ):
                    if (check_line[i] in lgm_dictionary_005.column_label_lgm1):
                        continue
                    else:
                        check_column_label_index.append(i)
                        check_column_label_flag = True



            column_length_counter = column_length_counter + 1

    except:
        print "DID NOT FIND FILE!:  " + input_file
        return
    
    check_file.close()


    #Blank entries were found
    if (len(check_blank_entry_list) != 0):
        print "\nBlank entries were found at the following locations\n\n"
        for i in range (0, len(check_blank_entry_list)):
            print "Row", repr(check_blank_entry_list[i][0]), ", Column" , lgm_dictionary_005.excel_column_label_dictionary[check_blank_entry_list[i][1]]
        return

    #the following code checks that all lines in the file have an equal length.
    #Matrices handed to the script must be rectangular
    for i in range (0, len(check_line_length_list)):
        for j in range (i+1 , len(check_line_length_list)):
            if (check_line_length_list[i] != check_line_length_list[j]):
                print "\nThe matrix is not rectangular check the list of lines for discrepancies\n\n"
                for k in range (0, len(check_line_length_list)):
                    print "line", k+1, "has", check_line_length_list[k], "entries" 
                print "All lines must have the same number of entries"
                return


    #The column labels do not match the defined column labels in column_label_lgm1
    if (check_column_label_flag == True):
        print "\nThe following column labels are incorrect\n\n"
        
        for i in check_column_label_index:        
            print "Column", lgm_dictionary_005.excel_column_label_dictionary[i+1], "The label is", check_column_labels[i], "it should be", lgm_dictionary_005.column_label_lgm1[i], '\n'
        return

    #Checks that all columns are in the file 
    for i in lgm_dictionary_005.column_label_lgm1:
        if i in check_column_labels:
            continue
        else:
            check_column_label_flag = True
            missing_column_label.append(i)
    if (check_column_label_flag == True):
        print "\nThe following columns are missing or they are not in the correct order.\n\n"
        for i in range (0,len(missing_column_label)):
            print missing_column_label[i]
        return



    #After file is checked for serious errors 
    #The file is read line by line into a 2d matrix
    try:
        text_file = open(input_file)
        
        while True:
            line = text_file.readline()
            if line == '':
                break
            if '' in line:
                line = line[:-1]
            if '\r' in line:
                line = line[:-1]
            line = line.split('\t')

            #removes all whitespace characters from the front and rear of the entry
            for i in range (0, len(line)):
                line[i].lstrip()
                line[i].rstrip()
            if (line[0] != '-'):
                for i in range (0,len(line)):
                    matrix[rows,i] = line[i]
                                 
            else:
                failure_string = (rows + 1) , "Row " +  repr(rows + 1)  +  " was ignored because it had no marker_id" 
                failure_list.append(failure_string)
                failure_counter = failure_counter + 1
                for j in range(0,columns):
                    matrix[rows, j] = "ignored_row"
            rows = rows + 1
        text_file.close()
    except:
            print "DID NOT FIND FILE:  " + input_file
            return

    while (repeat_marker_counter != rows):
        for i in range (repeat_marker_counter + 1, rows):
            if (matrix[i,0] == "ignored_row"):
                continue
                
            if (matrix[repeat_marker_counter,0] == matrix [i,0]):
                failure_string = (repeat_marker_counter+ 1) , "Row " + repr(repeat_marker_counter+ 1) + ", marker_id " +  repr(matrix[repeat_marker_counter,0]) + " has been repeated in row " + repr(i+1)  
                failure_list.append(failure_string)
                failure_counter = failure_counter + 1
        repeat_marker_counter= repeat_marker_counter + 1

    #marker_type
    for i in range(1, rows):
        if (matrix[i,0] == "ignored_row"):
            continue
        if (matrix[i,2] in lgm_dictionary_005.marker_type):
            continue

        else:       
                failure_string = (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " has a marker_type which is not recognized."
                failure_list.append(failure_string)
                failure_counter = failure_counter + 1
                    


    #marker_origin
    for i in range(1, rows):
        if (matrix[i,0] == "ignored_row"):
            continue

        if matrix[i,3]in lgm_dictionary_005.marker_origin:
            continue
        else:
            failure_string = (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " has a marker_origin which is not recognized."
            failure_list.append(failure_string)
            failure_counter = failure_counter + 1
                    

    #Later should log in and check that est_id is valid
    #marker_origin, marker_type, est_id
    for i in range(1, rows):
        if (matrix[i,0] == "ignored_row"):
            continue
        if matrix[i,3] in lgm_dictionary_005.marker_origin:
            if (matrix[i,3] == lgm_dictionary_005.marker_origin[0]):# marker_origin = CGPDB
                if (matrix[i,2] == lgm_dictionary_005.marker_type[0]):#marker_type = EST
                    if (matrix[i,1] == '-'):
                        failure_string = (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " requires an est_id."#works assuming all fields at least have a -
                        failure_list.append(failure_string)
                        failure_counter = failure_counter + 1
        

    #COS
    for i in range(1, rows):
        if (matrix[i,0] == "ignored_row"):
            continue

        if matrix[i,4]in lgm_dictionary_005.cos:
            continue
        else:
            failure_string =  (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " has a cos label which is not recognized."
            failure_list.append(failure_string)
            failure_counter = failure_counter + 1
    #Class
    for i in range(1, rows):
        if (matrix[i,0] == "ignored_row"):
            continue

        if matrix[i,5] in lgm_dictionary_005._class:
            continue
        else:
            failure_string = (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " has a class which is not recognized."
            failure_list.append(failure_string)
            failure_counter = failure_counter + 1
     
   #Annotations
    for i in range (1, rows):
        if (matrix[i,0] == "ignored_row"):
            continue

        annotation_string = matrix[i,6]
        if (annotation_string.count(' ') > 11):
            failure_string = (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " has an annotation which is too long. Only 12 words are allowed."
            failure_list.append(failure_string)
            failure_counter = failure_counter + 1

    #should login and check status
    #Status
    for i in range (1, rows):
        if (matrix[i,0] == "ignored_row"):
            continue

        if matrix[i,7] in lgm_dictionary_005.status: 
            continue
        else:            
            failure_string = (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " has a status which is not recognized."
            failure_list.append(failure_string)
            failure_counter = failure_counter + 1
        
    #Sender
    for i in range (1, rows):
        if (matrix[i,0] == "ignored_row"):
            continue

        if matrix[i,8] in lgm_dictionary_005.sender:
            continue
        else:            
            failure_string = (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " has a sender which is not recognized."
            failure_list.append(failure_string)
            failure_counter = failure_counter + 1


    #Date
    for i in range (1,rows):
        if (matrix[i,0] == "ignored_row"):
            continue

        date = matrix[i,9]
        for j in range (0, len(date)):
            if date[j].isdigit():
                continue
            elif date[j] == '/':
                continue
            elif date[j] == '\\':
                matrix[i,9] = string.replace(date,'\\','/')         
                warning_string = (i+1) , "Row " +  repr(i+1) + "  Date used backslashes, use foward slashes in your dates!" 
                warning_list.append(warning_string)
                warning_counter = warning_counter + 1
                break
            
            else:
                failure_string = (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " date is not in the correct format, date should be mm/dd/yyyy."
                failure_list.append(failure_string)
                failure_counter = failure_counter + 1
                break

    ### REFORMAT DUMMY DATE
    for i in range (1,rows):
        if (matrix[i,0] == "ignored_row"):
            continue
        date = matrix[i,9]
	### REFORMAT INTO MYSQL 
	date = date.split('/')
	mm = date[0]
	dd = date[1]
	yy = date[2]
	############
	if len(mm) == 1:
	    mm = "0" + mm
	if len(dd) == 1:
	    dd = "0" + dd
	matrix[i,9] = yy + "-" + mm + "-" + dd
	print matrix[i,9]
            
    #Public/Private
    for i in range (1,rows):
        if (matrix[i,0] == "ignored_row"):
            continue

        if matrix[i,10] in lgm_dictionary_005.public_private:
            continue
        elif matrix[i,10] == '-':
            matrix[i,10] = "public"
            warning_string = (i+1) , "Row " +  repr(i+1) + "  public_private entry '-' was changed to public, enter public or private!" 
            warning_list.append(warning_string)
            warning_counter = warning_counter + 1
            
        else:
            failure_string = (i+1) , "Row " + repr(i+1)  + ", marker_id " +  matrix[i,0] + " public_private label is not recognized check row  " + repr(i) + ''
            failure_list.append(failure_string)
            failure_counter = failure_counter + 1


    if (os.name == 'nt'):
        _newline = '\r\n'
    elif (os.name == 'mac'):
        _newline = '\r'
    else:
        _newline = '\n'
                  
                
    #Stops file output and outputs failure file       
    if (failure_counter != 0):
        failure_file = open(output_file + ".failure" , "wbU")
        failure_list.sort()
        for i in range (0,len(failure_list)):
            failure_file.write(failure_list[i][1])
            failure_file.write(_newline)
        print "\nOutput file was not created, check the failure file."
        failure_file.close()
        return


    #Output warning file
    if (warning_counter !=0):
        warning_file = open(output_file + ".warning" , "wbU")
        warning_list.sort()
        for j in range (0, len(warning_list)):
            warning_file.write(warning_list[j][1])
            warning_file.write(_newline)
        print "\nWarning file was created, please check for data entry mistakes."
        warning_file.close()
    #Create output file
    file_output = open(output_file + ".clean", "wbU")
    
    for i in range (0,rows):
        if (matrix[i,0] == "ignored_row"):
            continue
        for j in range (0,columns):
            file_output.write(matrix[i,j])
            file_output.write('\t')
        file_output.write(_newline)
    file_output.close()

    if new_update == "UPDATE":
    	file_mysql = open(output_file + ".update.table", "wbU")
	file_mysql.write("table_name" + '\t' + "marker_id" + '\t' + "field" + '\t' + "new_value" + '\n')
	for i in range (0,rows):
	    for j in range (0,columns):
		### WRITE DATA TO FILE ###
		### i AND j > 0 TO SKIP REPLACEMENT OF MARKER_ID
		if matrix[i,j] != "X" and i > 0 and j > 0:
		    file_mysql.write(table_name + '\t' + matrix[i,0] + '\t' + matrix[0,j] + '\t' + matrix[i,j] + '\n')
	file_mysql.close()

    print "\nprogram exited succesfully"




import array
import string
import os
import sys
import string
import lgm_dictionary_005
if __name__ == "__main__":
        
    if len(sys.argv) <= 4 or len(sys.argv) > 5:
        print "Program usage: "
        print "Input_file, Output_file, NEW/UPDATE, Table_Name"
	exit
    else:
        input_file  = sys.argv[1]
	output_file = sys.argv[2]
	new_update  = sys.argv[3]
	table_name  = sys.argv[4]
        LGM1_verification(input_file, output_file, new_update, table_name)