#!/usr/local/bin/python3.3
import cgi
import cgitb
import pymysql
import re
import subprocess
#from subprocess import call
#from subprocess import Popen
import datetime
import json
import DAPRfunctions as dapr


cgitb.enable()
dapr.loadConfiguration()
cookie = dapr.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
    
    db=dapr.DBConnection()
    
    #define functions that connect to the db
    def insert_bedtools_output(bid,name, location, command, uname,peak_count):
        getcmid = """
        select cmid from ComputationalMethod
        where name ="bedtools intersect";
        """      
        
        getwmid = """
        select wmid from WetlabMethod
        where name ="derived computationally";
        """
        
        (wmid,)=db.runQueryFetchOne(getwmid)
        (cmid,)=db.runQueryFetchOne(getcmid)
        date_str=str(datetime.datetime.now())[:-7]
        
        query1 = """INSERT INTO BEDfile (bid,name, location,
        upload_date, bedtoolcommand, uploader, cmid, wmid,peaknumber)
                    VALUES (%s,"%s", "%s", "%s", "%s", "%s", "%s", "%s", %s);
                    """%(bid,name, location, date_str,
                         command, uname,cmid,wmid,peak_count)
                         
        db.runInsert(query1)
    

    def update_exp(bid,eid,uid):
        query2 = """INSERT INTO ExperimentBEDfile(eid,bid)
              VALUES (%s,%s);"""%(eid,bid)
        query5 = """ INSERT INTO UserBEDfile (uid, bid)
              VALUES (%s, %s)"""%(uid, bid)
        db.runInsert(query2)
        db.runInsert(query5)
        
        
    #this should return only one value
    def query_bedname(bid):
        query6 = """
            select name from BEDfile
            where bid = "%s"
            """ % bid
        res=db.runQueryFetchOne(query6)

        return res


    dire = "/var/www/dapr_test/bedfiles/"
    locpre = "/dapr_test/bedfiles/"
        
    #get values from the HTTP request
    form = cgi.FieldStorage()
    eid = int(form.getvalue("eid"))
    bedtools_cmd = form.getvalue("tool")
    cmd_template = form.getvalue("cmd")
    bedtools_cmd_label = form.getvalue("cmd_label")
    cb = form.getvalue("checkboxes")

    # example of the values these variables have
    #bedtools_cmd_label="Intersection"
    #bedtools_cmd="intersect"
    #cmd_template="bedtools %s -a %s.bed -b %s.bed"
    
    j = json.loads(cb)
    
    f1_bid = j[0]    
    f2_bid = j[1]
    
    #get names with .bed extension
    (f1,) = query_bedname(f1_bid)
    (f2,) = query_bedname(f2_bid)

    #get names without .bed extension
    f1_no_bed = re.sub("\.bed$","",f1)
    f2_no_bed = re.sub("\.bed$","",f2)
    
    #get names without _bid suffix, using regular expressions ### might not use these names
    f1_no_id = re.sub("_[0-9]+$","",f1)
    f2_no_id = re.sub("_[0-9]+$","",f2)
        
    if f1 and f2 and eid:
        #get the next available bid from the database, and use that for the name of the new file
        getbid="""SHOW TABLE STATUS where Name='BEDfile'"""
        bid = db.runQueryFetchOne(getbid)[10]
        
        new_bedname_in_db ="%s %s and %s_%s"%(bedtools_cmd_label,f1_no_bed,f2_no_bed,str(bid))
        new_bedfile_name="%s%s.bed"%(dire,new_bedname_in_db)
        
        f1_w_path=dire+f1
        f2_w_path=dire+f2
        
        getename = """
        select title from Experiment
        where eid = "%s"
        """ % eid
        
        # ename = runQuery(getename, user, passwd)[0][0]
        command_for_desc = cmd_template%(f1,f2)
        
        f1_w_path=re.sub(" ","#",f1_w_path)#need to deal with spaces in names
        f2_w_path=re.sub(" ","#",f2_w_path)#need to deal w spaces

        command_for_bedtools_sp_call=cmd_template%(f1_w_path,f2_w_path)
        
        #example of what it's supposed to look like
        #command_for_bedtools_sp_call =["bedtools", "intersect", "-a", f1_w_path,"-b",f2_w_path]
                
        ff=open(dire+"BEDfuncions_logfile","w")
        
        with open(new_bedfile_name, "w") as f:
            #call(command_for_bedtools_sp_call.split("\s"), stdout=f) 
            #can't split by space because file names have spaces, so the file names would get split too
            
            #converted the spaces in fnames to # then split by space, then converted # back to escaped spaces
            subprocess.call([cp.replace("#"," ") for cp in command_for_bedtools_sp_call.split(" ")], stdout=f) #can't split by space 

        ff.close()
                
        with open(new_bedfile_name) as f:
            peak_count=sum(1 for line in f)
        
        #insert new bedfile entry to db table
        insert_bedtools_output(str(bid),new_bedname_in_db, new_bedfile_name, command_for_desc, uname,str(peak_count))
        
        #insert link between bedfile and experiment and user tables
        update_exp(bid, eid, uid)
        
        print("Content-type: text/html\n")
        print("""<script type="text/javascript">
            window.alert("Files were successfully intersected. Click OK to be directed to new list of BED files.")
            location.href='BEDfunctions.py?eid=%s';
            </script>"""%eid) 
       
    
    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")