# YASARA BioTools
# Visit www.yasara.org for more...
# Copyright by Elmar Krieger

# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA


import os,string,shutil,fnmatch,zipfile

#  ======================================================================
#                D I S C   F U N C T I O N   G R O U P  (D S C)
#  ======================================================================

# MAKE PATH ABSOLUTE
# ==================
def abspath(path):
  return(os.path.abspath(path))

# CALCULATE FILE CHECKSUM
# =======================
def checksum(path):
  checksum=0
  file=open(path)
  pos=1
  a=0
  b=0  
  while (1):
    data=file.read(1000000)
    datalen=len(data)
    i=0
    while (i<datalen):
      ch=ord(data[i])
      a=(a+ch)&0xffff
      b=(b+pos*ch)&0xffff
      i+=1
      pos+=1
    if (datalen<1000000): break
  return(a|(b<<16))

# COPY FILE
# =========
def copy(srcfilename,dstfilename,timespreserved=1,mod=None):
  if (timespreserved):
    # copy2 CAN FAIL ON FAT PARTITIONS
    try: shutil.copy2(srcfilename,dstfilename)
    except: timespreserved=0
  if (not timespreserved):
    try: shutil.copy(srcfilename,dstfilename)
    except: shutil.copyfile(srcfilename,dstfilename)
  if (mod!=None): chmod(dstfilename,mod)

# COPY DIRECTORY
# ==============
# - srcpath IS A WILDCARD MATCHING THE FILES TO COPY
# - dstpath IS THE NAME OF THE DESTINATION DIRECTORY
def copydir(srcpath,dstpath,mod=None):
  filelist=dirlist(srcpath)
  for srcfilename in filelist:
    dstfilename=os.path.join(dstpath,os.path.basename(srcfilename))
    copy(srcfilename,dstfilename)
    if (mod!=None): chmod(dstfilename,mod)

# GET FREE DISC SPACE
# ===================
def free():
  stat=os.statvfs(os.getcwd())
  return(stat.f_bsize*stat.f_bavail)

# GET THE LAST ELEMENTS IN A PATH
# ===============================
def lastpathelements(path,elements):
  result=None
  for i in range(elements):
    if (result==None): result=os.path.basename(path)
    else: result=os.path.join(os.path.basename(path),result)
    path=os.path.dirname(path)
  return(result)

# GET ALL FILES MATCHING A PATH+WILDCARD
# ======================================
def matchfilelist(path):
  path=os.path.split(path)
  wildcard=path[1]
  path=path[0]
  if (path==""): path="."
  try: files=os.listdir(path)
  except: return(None)
  matchfilelist=[]
  # CYCLE THROUGH ALL THE FILES
  for name in files:
    # CHECK IF FILENAME MATCHES WILDCARD
    filename=os.path.join(path,name)
    if (fnmatch.fnmatch(name,wildcard) and os.path.isfile(filename)):
      matchfilelist.append(filename)
  return(matchfilelist)

# REPLACE FILE
# ============
# dstfilename IS REPLACED WITH srcfilename, PERMISSIONS ARE SET TO mod.
def replace(srcfilename,dstfilename,mod=None):
  remove(dstfilename)
  os.rename(srcfilename,dstfilename)
  if (mod!=None): chmod(dstfilename,mod)

# GET SIZE OF FILE
# ================
def filesize(filename):
  if (not os.path.exists(filename)): return(0)
  return(os.stat(filename)[6])

# INCREASE FILE NAME
# ==================
def incfilename(filename):
  i=len(filename)-1
  while (i>0 and filename[i] not in string.digits): i=i-1
  while (i>=0):
    num=ord(filename[i])
    if (num<48 or num>57): break
    num=num+1
    if (num==58): num=48
    filename=filename[:i]+chr(num)+filename[i+1:]
    if (num!=48): break
    i=i-1
  return(filename)

# MAKE DIRECTORY CHAIN
# ====================
def makedirs(path,permissions=0x1ed):
  if (not os.path.exists(path)):
    os.makedirs(path,permissions)
  # THE PERMISSIONS ARE NOT ALWAYS SET CORRECTLY, DO IT AGAIN
  chmod(path,permissions)

# GET MD5SUM
# ==========
def md5sum(filename):
  content=open(filename).read()
  md5sum=md5.new(content).digest()
  md5str=""
  for ch in md5sum:
    hexstr=hex(ord(ch))
    if (len(hexstr)==3): md5str+='0'+hexstr[-1]
    else: md5str+=hexstr[-2:]
  return(md5str)

# GET THE MODIFICATION TIME OF A FILE
# ===================================
def modtime(filename):
  if (not os.path.exists(filename)): return(0)
  else: return(os.path.getmtime(filename))

# GET ALL MODIFICATION TIMES FOR A LIST OF FILES
# ==============================================
def modtimes(filelist):
  timelist=[]
  for filename in filelist:
    if (not os.path.exists(filename)): timelist.append(0)
    else: timelist.append(os.path.getmtime(filename))
  return(timelist)

# CHECK IF TWO FILES ARE THE SAME
# ===============================
def havesamecontent(filename1,filename2):
  if (not os.path.exists(filename1) or not os.path.exists(filename2)): return(0)
  content1=open(filename1,"r").read()
  content2=open(filename2,"r").read()
  return (content1==content2)

# BUILD TEMPORARY FILE NAME
# =========================
def tmpfilename(filename):
  dotpos=filename.rfind(".")
  slashpos=filename.rfind(os.sep)
  if (dotpos==-1 or dotpos<slashpos): dotpos=len(filename)
  filename=filename[:dotpos]+"_tmp%d"%os.getpid()+filename[dotpos:]
  return(filename)

# CHECK IF FILE(S) EXIST(S)
# =========================
def pathexists(path):
  # NORMALIZE PATH, IMPORTANT TO CONVERT UNIX FORWARD TO WINDOWS BACKWARD SLASHES
  path=os.path.normpath(os.path.normcase(path))
  # CREATE LIST OF ALL THE FILENAMES IN THE DIRECTORY SPECIFIED BY PATH
  path=os.path.split(path)
  wildcard=path[1]
  path=path[0]
  if (path==""): path="."
  try: files=os.listdir(path)
  except: return(0)
  # DELETE ALL LIST ENTRIES THAT DO NOT MATCH THE WILDCARD GIVEN IN PATH
  for name in files:
    # CHECK IF FILENAME MATCHES WILDCARD
    #   INCLUDING A POSSIBLE _MOD APPENDIX (LIKE EMBL DSSP FILES)
    if (fnmatch.fnmatch(name,wildcard)): return(1)
  return(0)

# CREATE DIRECTORY LISTING INCLUDING FULL PATH NAMES
# ==================================================
# all==0: ONLY FILES WILL BE RETURNED
# all==1: ALL ENTRIES WILL BE RETURNED, INCLUDING DIRECTORIES
# all==-1: ONLY DIRECTORIES WILL BE RETURNED
def dirlist(path,all=0):
  # NORMALIZE PATH, IMPORTANT TO CONVERT UNIX FORWARD TO WINDOWS BACKWARD SLASHES
  path=os.path.normpath(os.path.normcase(path))
  # CREATE LIST OF ALL THE FILENAMES IN THE DIRECTORY SPECIFIED BY PATH
  (path,wildcard)=os.path.split(path)
  if (path==""): path="."
  elif (path.find("?")!=-1):
    # PATH STILL CONTAINS A WILDCARD, E.G. /mnt/structure_data/raw/pdb/??/pdb????.ent.gz
    filelist=[]
    for dir in dirlist(path,-1):
      filelist+=dirlist(os.path.join(dir,wildcard))
    return(filelist)
  try: filelist=os.listdir(path)
  except: return([])
  # CYCLE THROUGH ALL FILES AND CHECK IF THEY MATCH WILDCARD
  i=0
  while (i<len(filelist)):
    if (filelist not in [".",".."] and fnmatch.fnmatch(filelist[i],wildcard)):
      filelist[i]=os.path.join(path,filelist[i])
      if (all==1 or 
          (all==0 and os.path.isfile(filelist[i])) or
          (all==-1 and os.path.isdir(filelist[i]))):
        i=i+1
        continue
    # NO MATCH
    del filelist[i]
  filelist.sort()
  return(filelist)

# CREATE RECURSIVE DIRECTORY LISTING INCLUDING FULL PATH NAMES
# ============================================================
def recursivedirlist(path):
  # NORMALIZE PATH, IMPORTANT TO CONVERT UNIX FORWARD TO WINDOWS BACKWARD SLASHES
  path=os.path.normpath(os.path.normcase(path))
  # LIST OF COMPLETE PATHS
  pathlist=[]
  # CREATE LIST OF ALL THE FILENAMES IN THE DIRECTORY SPECIFIED BY PATH
  (dir,wildcard)=os.path.split(path)
  if (dir==""): dir="."
  try: filenamelist=os.listdir(dir)
  except: return([])
  # CYCLE THROUGH ALL FILES AND CHECK IF THEY MATCH WILDCARD
  for filename in filenamelist:
    path=os.path.join(dir,filename)
    if (os.path.isfile(path)):
      if (fnmatch.fnmatch(filename,wildcard)):
        pathlist.append(path)
    else:
      # RECURSE DIRECTORY
      if (filename!="." and filename!=".."):
        subdirlist=recursivedirlist(os.path.join(path,wildcard))
        if (subdirlist==[]):
          # EMPTY SUBDIRECTORY
          pathlist.append(path)
        else:
          pathlist=pathlist+subdirlist
  pathlist.sort()
  return(pathlist)

# DELETE A FILE
# =============
def remove(filename):
  if (type(filename)==type([])):
    for filename2 in filename: remove(filename2)
  else:
    if (filename!=None and os.path.exists(filename)): os.remove(filename)

# DELETE ALL NEWER FILES AND DIRECTORIES
# ======================================
def removenewer(filename):
  modtime=modtime(filename)
  dellist=[]
  print("Looking for ",os.path.join(os.path.dirname(filename),"*"))
  print(dirlist(os.path.join(os.path.dirname(filename),"*"),1))
  for filename in dirlist(os.path.join(os.path.dirname(filename),"*"),1):
    if (modtime(filename)>=modtime): dellist.append(filename)
  print(dellist)
  raw_input("Press <RETURN> to delete everything listed above...")
  for filename in dellist:
    print("Removing ",filename)
    if (os.path.isdir(filename)): rmdir(filename)
    else: remove(filename)

# RENAME A FILE
# =============
def rename(srcfilename,dstfilename):
  if (srcfilename and dstfilename and os.path.exists(srcfilename)):
    os.rename(srcfilename,dstfilename)

# DELETE ALL MATCHING FILES
# =========================
def removematch(path):
  if (type(path)==type([])):
    for pathname in path: removematch(pathname)
  else:
    # NORMALIZE PATH, IMPORTANT TO CONVERT UNIX FORWARD TO WINDOWS BACKWARD SLASHES
    path=os.path.normpath(os.path.normcase(path))
    # CREATE LIST OF ALL THE FILENAMES IN THE DIRECTORY SPECIFIED BY PATH
    path=os.path.split(path)
    wildcard=path[1]
    dir=path[0]
    if (dir==""): dir="."
    try: files=os.listdir(dir)
    except: return(0)
    # DELETE ALL LIST ENTRIES THAT DO NOT MATCH THE WILDCARD GIVEN IN PATH
    for name in files:
      # CHECK IF FILENAME MATCHES WILDCARD
      #   INCLUDING A POSSIBLE _MOD APPENDIX (LIKE EMBL DSSP FILES)
      if (fnmatch.fnmatch(name,wildcard)): remove(os.path.join(dir,name))
  return(0)

# SET MODIFICATION TIME
# =====================
def setmodtime(filename,modtime):
  os.utime(filename,(modtime,modtime))
  
# COPY MODIFICATION TIME
# ======================
def copymodtime(srcfilename,dstfilename):
  setmodtime(dstfilename,modtime(srcfilename))

# CHMOD A FILE
# ============
def chmod(path,mods):
  if (type(path)==type([])):
    for pathname in path: chmod(pathname,mods)
  else:
    try: os.chmod(path,mods)
    except: print("Could not change permissions for ",path)

# DELETE AN ENTIRE DIRECTORY INCLUDING ALL THE FILES
# ==================================================
def rmdir(path):
  if (os.path.exists(path)): shutil.rmtree(path,1)

# REMOVE FILE EXTENSION
# =====================
def rmext(filename):
  dotpos=filename.rfind(".")
  if (dotpos!=-1): filename=filename[:dotpos]
  return(filename)

# GET FILE EXTENSION
# ==================
def ext(filename):
  dotpos=filename.rfind(".")
  if (dotpos!=-1): return(filename[dotpos+1:])
  return("")

# COUNT NUMBER OF FILENAMES PRESENT
# =================================
def countpresent(filenamelist):
  count=0
  for filename in filenamelist:
    if (os.path.exists(filename)): count=count+1
  return(count)

# UPDATE DIRECTORY
# ================
# - srcpath IS A WILDCARD MATCHING THE FILES TO UPDATE
# - dstdir IS THE NAME OF THE DESTINATION DIRECTORY
# - excludelist CONTAINS EXCLUDED FILENAMES OR, .* TO EXCLUDE HIDDEN FILES
def updatedir(srcpath,dstdir,contentchecked=1,recursive=0,obsoleted=0,mod=None,excludelist=[]):
  modfilelist=[]
  if (os.path.isdir(srcpath)): srcpath=os.path.join(srcpath,"*")
  srcfilelist=dirlist(srcpath,recursive)
  srcbaselist=[]
  for srcfilename in srcfilelist:
    srcbasename=os.path.basename(srcfilename)
    srcbaselist.append(srcbasename)
    if (srcbasename not in excludelist and (srcbasename[0]!='.' or ".*" not in excludelist)):
      dstfilename=os.path.join(dstdir,srcbasename)
      if (os.path.isdir(srcfilename)):
        if (recursive):
          if (not os.path.exists(dstfilename)): makedirs(dstfilename)
          updatedir(srcfilename,dstfilename,contentchecked,1,obsoleted,mod,excludelist)
      else:
        if ((contentchecked and not havesamecontent(srcfilename,dstfilename)) or
            (not contentchecked and modtime(srcfilename)>modtime(dstfilename))):
          copy(srcfilename,dstfilename,0,mod)
          modfilelist.append(dstfilename) 
  if (obsoleted):
    # ALSO DELETE OBSOLETE FILES
    dstfilelist=dirlist(os.path.join(dstdir,os.path.basename(srcpath)))
    for dstfilename in dstfilelist:
      dstbasename=os.path.basename(dstfilename)
      if (dstbasename not in srcbaselist): remove(dstfilename)
  return(modfilelist)

# ZIP A FILE
# ==========
def zip(filename):
  print("Deflating",filename)
  zipfilename=filename+".zip"
  zip=zipfile.ZipFile(zipfilename,"w",zipfile.ZIP_DEFLATED)
  zip.write(filename,os.path.basename(filename))
  zip.close()
  remove(filename)

# RETURN AN UNZIPPED FILE
# =======================
def unzipped(filename):
  zipfilename=filename+".zip"
  zip=zipfile.ZipFile(zipfilename,"r",zipfile.ZIP_DEFLATED)
  data=zip.read(os.path.basename(filename))
  zip.close()
  return(data)