#!/usr/local/bin/python3.3
import cgi
import cgitb
import pymysql
from subprocess import call
import datetime
import json
from functions import get_cookies, phead, ptail
cgitb.enable()
"""
The following issues need to be addressed:
-function does not work
"""

cookie = get_cookies()


if cookie:
    print(cookie)
    fname = cookie["fname"].value
    lname = cookie["lname"].value
    name = " ".join((fname, lname))
    admin = cookie["admin"].value
    uid = cookie["uid"].value
    uname = cookie["uname"].value
    
    
    form = cgi.FieldStorage()
    cb = form.getvalue("checkboxes")
    eid = form.getvalue("eid")
    #bid = form.getvalue("bid")
    print("Content-type: text/html\n")
    if cb != None:
        
        j = json.loads(cb)
        
        data = []
        #data should be in the order: user, passwd, host, db
        with open('./dbinfo.txt') as f:
            for line in f:
                line = line.strip('\n')
                data.append(line)      
        info = []
        for item in data:
            item = item.split(':')
            info.append(item)
 
        user=info[0][1]
        passwd=info[1][1]
        host=info[2][1]
        db=info[3][1]
        
        getcmid = """
        select cmid from ComputationalMethod
        where name ="bedtools intersect";
        """
        
        getwmid = """
        select wmid from WetlabMethod
        where name ="bedtools intersect";
        """
        
#         getbid = """
#         select bid from UserBEDfile
#         where name = 
#         """

        
        def runQuery(query, user, passwd):
            connection = pymysql.connect(host=host, user=user, db=db, passwd=passwd)
            cursor = connection.cursor()
            cursor.execute(query)
            res = cursor.fetchall()
            cursor.close()
            connection.close()
            return res
        
        def insert_copy_bed(name, location, command, uname):
            connection = pymysql.connect(host=host, user=user, db=db, passwd=passwd)
            cursor = connection.cursor()
            query1 = """INSERT INTO BEDfile (name, location,
            upload_date, bedtoolcommand, uploader, cmid, wmid)
                        VALUES ("%s", "%s", "%s", "%s", "%s", "%s", "%s");
                        """%(name, location, str(datetime.datetime.now())[:-7],
                             command, uname, runQuery(getcmid, user, passwd)[0][0],
                             runQuery(getwmid, user, passwd)[0][0])
            cursor.execute(query1)
            connection.commit()
            cursor.close()
            connection.close()
        
        def update_exp(bid,eid,uid):
            connection = pymysql.connect(host=host, user=user, db=db, passwd=passwd)
            cursor = connection.cursor()
            query2 = """INSERT INTO ExperimentBEDfile(eid,bid)
                  VALUES (%s,%s);"""%(eid,bid)
            query5 = """ INSERT INTO UserBEDfile (uid, bid)
                  VALUES (%s, %s)"""%(uid, bid)
            cursor.execute(query2)
            cursor.execute(query5)
            connection.commit()
            cursor.close()
            connection.close()
        
        def query_bedname(bid):
            connection = pymysql.connect(host=host, user=user, db=db, passwd=passwd)
            cursor = connection.cursor()
            query6 = """
                select name from BEDfile
                where bid = "%s"
                """ % bid
            cursor.execute(query6)
            res = cursor.fetchall()
            connection.close()
            return res
        
        dire = "/var/www/dapr_test/bedfiles/"
        
        
    
        
#         q2 = """select wmid,cmid,name,location,description1,description2,description3,bedtoolcommand, stringency, source from BEDfile where bid = "%s";"""%bid
#         q3 = """select bid from BEDfile order by bid DESC limit 1;"""
#         q4 = """select eid from Experiment where title = "%s";"""%eid
#         add_new = runQuery(q2,user,passwd)
#         nbid = runQuery(q3,user,passwd)
#         neid = runQuery(q4,user,passwd)
#         name = add_new[0] + "_" + str(nbid)
        #Copy(nbid,name, add_new[0][3], add_new[0][4], add_new[0][5], add_new[0][6], add_new[0][7], nuname, add_new[0][1], add_new[0][0],add_new[0][8], add_new[0][9],neid)

        f1_bid = j[0]    
        
        f1 = str(query_bedname(f1_bid))
        eid = int(form.getvalue("eid"))
        if f1 and eid:
            q3 = """
            select bid from BEDfile
            order by bid DESC
            limit 1;
            """
            nbid = int(runQuery(q3, user, passwd)[0][0])+1
            
            original = f1[3:-5] #+ ".bed"
            bedname = "Copy_of_"+f1[3:-9]+"_"+str(nbid) #+ ".bed"
        
            locpre = "dapr_test/bedfiles/"
            loc = locpre+bedname#+".bed"
            
            getbid = """
            select bid from BEDfile
            where name = "%s"
            """ % bedname
            
            getename = """
            select title from Experiment
            where eid = "%s"
            """ % eid
            
            
            command = "copyBED " + f1[3:-5] #+ ".bed"
        
            new_file = open('/var/www/dapr_test/bedfiles/' + bedname, "w+")
            with open('/var/www/dapr_test/bedfiles/' + original) as f:
                for line in f:
                    new_file.write(line)
                    
            new_file.close()
            
          
            #counting lines
#             original.seek(0)
#             if original:
#             # It's an uploaded file; count lines
#                 linecount = 0
#                 while 1:
#                     line = original.readline()
#                     if not line: break
#                 linecount = linecount + 1
        
            insert_copy_bed(bedname, loc, command, uname)
            #bid = runQuery(getbid, user, passwd)[0][0]
            update_exp(nbid, eid, uid)
            
              
              
          #  message = 'The file "' + f1 + '" was successfully copied'
#             location = '/dapr_test/bedfiles/' + fn_new
           # runQuery(nbid,fn_new , location, des1, des2, des3, command,uname, cmid, wmid,linecount)
            #runQuery2(nbid,eid, uid)
#               
            
            print("""<script type="text/javascript">
            window.alert("File was successfully copied. Click OK to be directed to new list of BED files.")
            </script>""") 
           
        
    else:
        print("Content-type: text/html\n")
        print("""
                <script type="text/javascript">
                window.alert("Invalid inputs! No file was generated! Please try again")
                location.href='BEDfunctions.py?eid=%s'; 
                </script>""" %eid) 
        
        

else:
    print("Location: login.py")
    print("Content-type: text/html\n")