import os
from os.path import join as join_path
help(os.getcwd)
print("----------------------------------------------------------")
help(os.chdir)
print("----------------------------------------------------------")
help(os.makedirs)
print("----------------------------------------------------------")
help(os.listdir)
print("----------------------------------------------------------")
help(os.remove)
print("----------------------------------------------------------")
help(join_path)
print("----------------------------------------------------------")
help(os.path.abspath)

# Change the curent directory to the location of the "Special_topics_part_1" directory
os.chdir("/Users/malastm/new_ACM_tutorials/ACM-Python-Tutorials-KAUST-2014/Special_topics_part_1/")

print("The current directory was       : " + os.getcwd())

tutorial_example_dir = os.path.join(os.getcwd(), "example")
os.chdir(tutorial_example_dir)
print("The current directory changed to: " + os.getcwd())

print("Files in this directory: ", os.listdir('.'))

import glob

help(glob.glob)

import shutil

help(shutil.rmtree)

def ensure_dir(d):
    """ Create a directory and ignore the error if the directory already exist"""
    import os, errno
    try:
        os.makedirs(d)
    except OSError as exc:
        if exc.errno == errno.EEXIST:
            pass
        else: raise

def clean_all():
    """This function removes any generated previous result at this tutorial's example"""
    import glob, shutil, os
    for f in glob.glob('results/*.*'):
        os.remove(f)
    shutil.rmtree('results/patients', ignore_errors=True)

clean_all()

help(open)
print("----------------------------------------------------------")
print("----------------------------------------------------------")
print(dir(file))
print("----------------------------------------------------------")
help(file.close)
print("----------------------------------------------------------")
help(file.read)
print("----------------------------------------------------------")
help(file.write)
print("----------------------------------------------------------")
help(file.readline)

def print_file(f_name):
    """Print the contents of a file. The same operation of 'cat', the shell command"""
    f = open(f_name, 'r')
    print(f.read())
    f.close()

print_file(join_path("scripts", "format_info.py") )

import subprocess

python_script = join_path("scripts", "format_info.py")
command = "Python " + python_script
arguments = " Ahmad 1.77 80 25"

ensure_dir('results')

print("We will run a process using this command: " + command + arguments)
sts = subprocess.check_call(command + arguments, shell=True)
print ("The return status of the process: " + str(sts))

print(os.listdir('results'))

print_file(join_path("results", "patient_Ahmad_25.txt"))
os.remove(join_path("results", "patient_Ahmad_25.txt"))

script_template_txt = """#!/usr/bin/env python

import sys

name = str(sys.argv[1])
height = float(sys.argv[2])
weight = float(sys.argv[3])
age = int(sys.argv[4])

val = $formula

f = open('results/patients/patient_' + name + '_' + str(age) + '.txt', 'w')

f.write( "patient's name: " + name + "\\n")
f.write( "patient's age: " + str(age) + " Years\\n")
f.write( "patient's Weight: " + str(weight) + " kgs\\n")
f.write( "patient's height: " + str(height) + " Meters\\n")

f.write( "patient's $name: %f \\n" % val)

f.close()
"""

from string import Template

script_template = Template(script_template_txt)
formula = "weight/height**2"
name = "BMI"
script_txt = script_template.substitute(formula=formula, name=name)

with open(join_path("results","calc_bmi.py"), 'w') as f:
    f.write(script_txt)

print_file(join_path("results","calc_bmi.py"))

ensure_dir(join_path("results", "patients"))

python_script = join_path("results","calc_bmi.py")
command = "Python " + python_script
arguments = " Ahmad 1.77 80 25"

print("Execute: " + command + arguments)
subprocess.check_call(command + arguments, shell=True)

print_file(join_path("results", "patients", "patient_Ahmad_25.txt"))
os.remove(join_path("results", "patients", "patient_Ahmad_25.txt"))

patients = [('Williams',19,84,1.74), ('Johnson',23,82, 1.65), 
            ('Jones', 25, 70, 1.8), ('Jones', 29, 85, 1.66),
            ('Smith', 30, 120, 1.9), ('ahmad', 35, 50.5, 1.5)]

for n, a, w, h in patients:
    arguments = " %s %f %f %d" % (n, h, w, a)
    subprocess.check_call(command + arguments, shell=True)

os.listdir(join_path('results', 'patients'))

from collections import OrderedDict
def parse_bmi(fp):
    fields = [("patient's name", "name", str),("patient's age", "age", int),
              ("patient's Weight", "weight", float),("patient's height", "height", float),("patient's BMI", "bmi", float)]
    record = OrderedDict()
    for f in fields:
        record[f[1]] = 0
    for ln in fp:
        for f in fields:
            if f[0] in ln:
                # Using naive string parsing:
                #val = ln.split(":")[1].strip().split(' ')[0]
                val = ln.split(":")[1]
                val = val.strip()
                val = val.split(' ')[0]
                val = map(f[2], [val])[0]
                
                record[f[1]] = val

    return record

files_list = glob.glob(join_path('results', 'patients', '*.txt') )
print (files_list)

entries =[]
for rf in files_list:    
    with open(rf, 'r') as fp: 
        record = parse_bmi(fp)
        entries.append(record)

for i in entries: print(i)

# We will use the itemgetter function to specify our soring key from the dictionary
from operator import itemgetter

d0 = entries[0]
print(d0)

ig = itemgetter('age', 'name')
print (ig(d0))
# This is equivalent to:
print(d0['age'], d0['name'])

from operator import itemgetter

entries = sorted(entries, key=itemgetter('age', 'name'))

for i in entries: print(i)

from csv import DictWriter
fields = entries[0].keys()

with open( join_path('results', 'records.csv'), 'w' ) as output_file:
        r = DictWriter(output_file,fieldnames=fields)
        r.writeheader()
        for k in entries:
            r.writerow(k)

print_file( join_path('results', 'records.csv') )

from csv import DictReader
with open(join_path('results', 'records.csv'), 'rb') as output_file:
    data = DictReader(output_file)
    data = [k for k in data]
print(data)

points = []
for d in data:
    points.append((d['age'], d['bmi']))
print(points)

import tarfile
f_list = [join_path("results", "patients", "*.txt"), join_path("results", "*.py"), 
          join_path("results", "patients", "*.csv"), join_path("..", "*.ipynb")]
f_list = [glob.glob(n) for n in f_list]
f_list = [n for nn in f_list for n in nn]

f_name = join_path("results", "bmi.tar.gz")
print "Writing project files to:" + f_name
with tarfile.open(f_name, "w:gz") as tar:
    for n in f_list:
        print "Adding to the tar file: " + n
        tar.add(n)

# Repeating some functions definitions if only the exercise is executed
def ensure_dir(d):
    """ Create a directory and ignore the error if the directory already exist"""
    import os, errno
    try:
        os.makedirs(d)
    except OSError as exc:
        if exc.errno == errno.EEXIST:
            pass
        else: raise
def print_file(f_name):
    """Print the contents of a file. The same operation of 'cat', the shell command"""
    f = open(f_name, 'r')
    print(f.read())
    f.close()

import os
from os.path import join as join_path
from string import Template

# Full path to the special topics part 1 directory
os.chdir("/Users/malastm/new_ACM_tutorials/ACM-Python-Tutorials-KAUST-2014/Special_topics_part_1/")

os.chdir(join_path(os.getcwd(), "exercise"))
print("The current directory changed to: " + os.getcwd())
print("Files in this directory: ", os.listdir('.'))

script_template_txt = """#!/usr/bin/env python

import sys

name = str(sys.argv[1])
height = float(sys.argv[2])
weight = float(sys.argv[3])
age = int(sys.argv[4])
path = str(sys.argv[5])

$comp

f = open( path + 'patient_' + name + '_' + str(age) + '.txt', 'w')

f.write( "patient's name: " + name + "\\n")
f.write( "patient's age: " + str(age) + " Years\\n")
f.write( "patient's Weight: " + str(weight) + " kgs\\n")
f.write( "patient's height: " + str(height) + " Meters\\n")

$file_write

f.close()
"""

# First we generate the script for the BMI and test it
script_template = Template(script_template_txt)
comp = "val = weight/height**2"
file_write = 'f.write( "patient\'s BMI: " + str(val) + "\\n")'
script_txt = script_template.substitute(comp=comp, file_write=file_write)

ensure_dir(join_path('results', 'bmi'))
with open(join_path("results", "bmi","calc_bmi.py"), 'w') as f:
    f.write(script_txt)

print_file(join_path("results", "bmi","calc_bmi.py"))

# Test the BMI script

import subprocess
bmi_results_path = join_path(os.getcwd(), "results", 'bmi', 'patients', '') 
command = "Python " + join_path("results", "bmi","calc_bmi.py")
arguments = " Ahmad 1.77 80 25 " + bmi_results_path
ensure_dir(join_path("results", 'bmi', 'patients'))


print("Execute: " + command + arguments)
subprocess.check_call(command + arguments, shell=True)

print_file(join_path("results", "bmi", "patients", "patient_Ahmad_25.txt"))
os.remove(join_path("results", "bmi", "patients", "patient_Ahmad_25.txt"))

# Generate the script for the Cholesterol and test it
comp = """cholesterol = float(sys.argv[6])
if cholesterol < 200:
    risk = 'Low risk'
elif cholesterol < 240:
    risk = 'Borderline high risk'
else:
    risk = 'High risk'
"""
file_write = 'f.write( "patient\'s Cholesterol: " + str(cholesterol) + " (" + risk + ")\\n")'

script_txt = script_template.substitute(comp=comp, file_write=file_write)

ensure_dir(join_path("results", 'cholesterol'))
with open(join_path("results", "cholesterol","calc_cholesterol.py"), 'w') as f:
    f.write(script_txt)

print_file(join_path("results", "cholesterol","calc_cholesterol.py"))


# Test the Cholesterol script
chol_results_path = join_path(os.getcwd(), "results", 'cholesterol', 'patients', '') 

command = "Python " + join_path("results", "cholesterol","calc_cholesterol.py")
arguments = " Ahmad 1.77 80 25 " + chol_results_path + " 100"
ensure_dir(join_path("results", 'cholesterol', 'patients'))


print("Execute: " + command + arguments)
subprocess.check_call(command + arguments, shell=True)

print_file(join_path("results", "cholesterol", "patients", "patient_Ahmad_25.txt"))
os.remove(join_path("results", "cholesterol", "patients", "patient_Ahmad_25.txt"))

# Generate the BMI results

patients = [('Williams',19,84,1.74), ('Johnson',23,82, 1.65), 
            ('Jones', 25, 70, 1.8), ('Jones', 29, 85, 1.66),
            ('Smith', 30, 120, 1.9), ('ahmad', 35, 50.5, 1.5)]

command = "Python " + join_path("results", "bmi","calc_bmi.py")

for n, a, w, h in patients:
    arguments = " %s %f %f %d " % (n, h, w, a) + bmi_results_path
    subprocess.check_call(command + arguments, shell=True)

os.listdir(bmi_results_path)

# Generate the Cholesterol results

patients = [('Williams',19,84,1.74, 150), ('Johnson',23,82, 1.65, 220), 
            ('Jones', 25, 70, 1.8, 200), ('Jones', 29, 85, 1.66, 250),
            ('Smith', 30, 120, 1.9, 210), ('ahmad', 35, 50.5, 1.5, 260)]

command = "Python " + join_path("results", "cholesterol","calc_cholesterol.py")

for n, a, w, h, c in patients:
    arguments = " %s %f %f %d " % (n, h, w, a) + chol_results_path + " %f" % (c)
    subprocess.check_call(command + arguments, shell=True)

os.listdir(chol_results_path)

def write_to_csv(data, f_name):
    from csv import DictWriter
    fields = data[0].keys()
    
    with open( f_name, 'w' ) as output_file:
            r = DictWriter(output_file,fieldnames=fields)
            r.writeheader()
            for k in data:
                r.writerow(k)

# Repeating this function from the example
from collections import OrderedDict
def parse_bmi(fp):
    fields = [("patient's name", "name", str),("patient's age", "age", int),
              ("patient's Weight", "weight", float),("patient's height", "height", float),("patient's BMI", "bmi", float)]
    record = OrderedDict()
    for f in fields:
        record[f[1]] = 0
    for ln in fp:
        for f in fields:
            if f[0] in ln:
                # Using naive string parsing:
                #val = ln.split(":")[1].strip().split(' ')[0]
                val = ln.split(":")[1]
                val = val.strip()
                val = val.split(' ')[0]
                val = map(f[2], [val])[0]
                
                record[f[1]] = val

    return record

# Parse the BMI results using the BMI parsing script then store to the CSV file
import glob
files_list = glob.glob(join_path("results", 'bmi', 'patients', '*.txt') )
print (files_list)

entries =[]
for rf in files_list:    
    with open(rf, 'r') as fp: 
        record = parse_bmi(fp)
        entries.append(record)

for i in entries: print(i)
    
write_to_csv(entries, join_path("results", 'bmi', 'patients', 'records.csv'))
print_file(join_path("results", 'bmi', 'patients', 'records.csv'))

# Create a parsing function for the cholesterol results
from collections import OrderedDict
def parse_cholesterol(fp):
    fields = [("patient's name", "name", str),("patient's age", "age", int),
              ("patient's Weight", "weight", float),("patient's height", "height", float),("patient's Cholesterol", "chol", float)]
    record = OrderedDict()
    for f in fields:
        record[f[1]] = 0
    for ln in fp:
        for f in fields:
            if f[0] in ln:
                # Using naive string parsing:
                #val = ln.split(":")[1].strip().split(' ')[0]
                val = ln.split(":")[1]
                val = val.strip()
                val = val.split(' ')[0]
                val = map(f[2], [val])[0]
                record[f[1]] = val
        
        # Handle the special case that extract the risk string from the cholestrol line
        if "patient's Cholesterol" in ln:
            val = ln.split(":")[1]
            val = val.strip()
            val = val.split(' ',1)[1][1:-1]
            val = map(str, [val])[0]
            record['chol risk'] = val        

    return record

# Parse the Cholesterol results using the Cholesterol parsing script
import glob
files_list = glob.glob(join_path("results", 'cholesterol', 'patients', '*.txt') )
print (files_list)

entries =[]
for rf in files_list:    
    with open(rf, 'r') as fp: 
        record = parse_cholesterol(fp)
        entries.append(record)

for i in entries: print(i)

write_to_csv(entries, join_path("results", 'cholesterol', 'patients', 'records.csv'))
print_file(join_path("results", 'cholesterol', 'patients', 'records.csv'))

# Read both CSV files, merge the tables, and store all the data in a single CSV file
from csv import DictReader
from operator import itemgetter

with open(join_path('results', 'bmi', 'patients', 'records.csv'), 'rb') as output_file:
    data = DictReader(output_file)
    bmi_data = [k for k in data]

with open(join_path('results', 'cholesterol', 'patients', 'records.csv'), 'rb') as output_file:
    data = DictReader(output_file)
    chol_data = [k for k in data]

d0 = entries[0]
print(d0)

commons = itemgetter('age', 'name' ,'weight' , 'height')
# for each record in the cholesterol results add the BMI field to it from the bmi record of the same patient
all_data = []
for dc in chol_data:
    for db in bmi_data:
        if commons(db) == commons(dc):
            dc['bmi'] = db['bmi']
    all_data.append(dc)

write_to_csv(all_data, join_path("results", 'records_all_data.csv'))

print_file("results/records_all_data.csv")