#!/usr/local/bin/python3.3 import cgi import os import cgitb import pymysql import datetime import subprocess import DAPRfunctions as dapr #dapr.loadConfiguration() cookie = dapr.get_cookies() db=dapr.DBConnection() cgitb.enable() if 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 ceid = cookie["ck_eid"].value dire = "/var/www/dapr_test/bedfiles/" form = cgi.FieldStorage() eid = form.getvalue("exp") if eid: cookie["ck_eid"]=eid print(cookie) else: if ceid != "0": eid=ceid else: eid_error_flag=True eid_error="there is no experiment set" geneFile = form.getvalue("file") # sid = form.getvalue("study") if geneFile == None: message="there is no file" print("Location: upload_v0.2.py") print("Content-type: text/html\n\n") else: #print("Content-type: text/html\n\n") #print("there is a file") message="There is a file" def insertBEDfile(bid,name, location, des1, des2, des3, command, uname, cmid, wmid,peaknumber,colnames): query1 = """INSERT INTO BEDfile (bid,name, location, description1, description2, description3, upload_date, bedtoolcommand, uploader, cmid, wmid,peaknumber,fieldnames) VALUES (%s, "%s", "%s", "%s", "%s", "%s", "%s", "%s", "%s", %s, %s, %s,"%s") """%(int(bid),name, location, des1, des2, des3, str(datetime.datetime.now())[:-7], command, uname, int(cmid), int(wmid),int(peaknumber),colnames) db.runInsert(query1) def updateBEDAssignment(bid,eid,uid): query2 = """INSERT INTO ExperimentBEDfile(eid,bid) VALUES (%s,%s);"""%(eid,bid) #query3 = """ INSERT INTO ComputationalMethod (cmid, name, bid) #VALUES (%s, %s, %s)"""(cmid, cname, bid) #query4 = """ INSERT INTO WetlabMethod (bid, wimid, name) #VALUES (%s, %s, %s)"""(bid, wimid, cname) query5 = """ INSERT INTO UserBEDfile (uid, bid) VALUES (%s, %s)"""%(uid, bid) db.runInsert(query2) db.runInsert(query5) fileitem = form['file'] givenname = form.getvalue("givenname") des1 = form.getvalue("des1") des2 = form.getvalue("des2") des3 = form.getvalue("des3") command = form.getvalue("command") cmid = form.getvalue('comp') wmid = form.getvalue('wet') sid = form.getvalue('study') plid = form.getvalue('plt') colnames = form.getvalue('BEDcols') if cmid == None: cmid = 0 if wmid == None: wmid == 0 colnamestr = None if colnames: colnamestr=",".join([ _.strip() for _ in colnames.strip().split('\n')]) else: colnamestr="NULL" if des1 == None: des1 = "NULL" if des2 == None: des2 = "NULL" if des3 == None: des3 = "NULL" q5 = """select plid from Platform join Study using(plid) where sid="%s" Group by plid order by date desc;""" %sid if fileitem.filename: if givenname == None: (givenname,ext)=os.path.splitext(os.path.basename(fileitem.filename)) else: if len(givenname)<1: (givenname,ext)=os.path.splitext(os.path.basename(fileitem.filename)) q3="""SHOW TABLE STATUS where Name='BEDfile';""" nbid=db.runQueryFetchOne(q3) nbid = int(nbid[10]) fn_new = givenname +"_"+ str(nbid) location = dire + fn_new + ".bed" location_temp= dire + fn_new+"_temp.bed" location_temp_eol = dire + fn_new + "_tempeol.bed" location_sorted = dire + fn_new + "_sorted.bed" ff=open(dire+"upload_logfile","w") open(location_temp, 'wb').write(fileitem.file.read()) #TODO: don't load the whole file into memory #location_temp_f=open(location_temp) #command_for_test = "head %s "%(location_temp) #split into 2 commands command_for_bedtools_sort = "sort -k 1,1 -k2,2n %s"%(location_temp) #command_for_bedtools_sort = "sortBed -i %s"%(location_temp) #f1=open(location_temp_eol,"wb") #subprocess.call(command_for_eol_conversion.split(" "), stdin=location_temp_f,stdout=f1) #can't split by space #f1.close() #subprocess.call(command_for_test.split(" "), stdout=ff) #can't split by space with open(location_sorted,"wb") as f2: subprocess.call(command_for_bedtools_sort.split(" "), stdout=f2) #can't split by space f2.close() command_for_rm = "rm -f %s"%(location_temp_eol) subprocess.call(command_for_rm.split(" "), stdout=ff) #counting lines and adding ID #fileitem.file.seek(0) sorted_bed = open(location_sorted) sorted_bed_w_id = open(location,"w") id_prefix = "id_"+str(nbid)+"_" if sorted_bed: # It's an uploaded file; count lines linecount = 0 while True: line = sorted_bed.readline() if not line: break linecount = linecount + 1 line_spl = line.strip().split("\t") if len(line_spl)<4: #add id line_spl.append(id_prefix+ str(linecount)) sorted_bed_w_id.write("\t".join(line_spl)+"\n") else: sorted_bed_w_id.write(line) sorted_bed_w_id.close() command_for_rm = "rm -f %s"%(location_sorted) subprocess.call(command_for_rm.split(" "), stdout=ff) ff.close() #linecount2=len(fileitem.file.readlines()) #print("Content-type: text/html\n") #print("%s %s %s"%(eid,sid,plid)) #TODO: validate that bed file meets constraints of genome if eid and sid: insertBEDfile(nbid,fn_new , location, des1, des2, des3, command,uname, cmid, wmid,linecount,colnamestr) updateBEDAssignment(nbid,eid, uid) #TODO use function to display success or error messages #print("Content-type: text/html\n") message=""" File was successfully uploaded, with %s lines Click OK to be directed to list of BED files. """ #change location on callback of message box print("Location: BEDfunctions.py?eid=%s"%eid) print("Content-type: text/html\n") else: #print("Content-type: text/html\n") message=""" File failed to upload, please try again """ else: print("Location: login.py") print("Content-type: text/html\n")