"""
python/ui/web.py: CCP4MG Molecular Graphics Program
Copyright (C) 2001-2008 University of York, CCLRC
Copyright (C) 2009 University of York
This library is free software: you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public License
version 3, modified in accordance with the provisions of the
license to address the requirements of UK law.
You should have received a copy of the modified GNU Lesser General
Public License along with this library. If not, copies may be
downloaded from http://www.ccp4.ac.uk/ccp4license.php
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 Lesser General Public License for more details.
"""
from global_definitions import *
#---------------------------------------------------------------------------
#---------------------------------------------------------------------------
#---------------------------------------------------------------------------
class web:
#---------------------------------------------------------------------------
#---------------------------------------------------------------------------
#---------------------------------------------------------------------------
insts = None
def __init__(self):
import sys
web.insts = self
self.scheduler = None
if sys.platform == 'win32':
self.browserlist = ['netscape','firefox','explorer']
elif sys.platform == 'darwin':
self.browserlist = ['netscape','firefox','open']
else:
self.browserlist = ['netscape','firefox','konqueror']
import services
self.params = services.ParamsManager ( \
name='web_address', \
title='Browser/Web Tools', \
gui=['internal','browser','browser_command', 'EBI_Download_PDB','EBI_OCA','RCSB_Search','RCSB_Download_PDB','PDBJapan_Download_PDB','PDBJapan_Search'], \
default = {
'internal' : 1,
'browser' : self.set_default_browser(),
'browser_command' : '',
'EBI_OCA' : "http://www.ebi.ac.uk/msd-srv/msdlite/index.html",
'RCSB_Search': "http://www.rcsb.org/pdb",
'RCSB_Download_PDB': "'http://www.rcsb.org/pdb/cgi/export.cgi/' + pdbid + '.pdb?job=download;pdbId=' + pdbid +';opt=show;format=PDB;pre=1&compression=gz'" ,
'EBI_Download_PDB' : "'ftp://ftp.ebi.ac.uk/pub/databases/msd/pdb_uncompressed/pdb'+pdbid+'.ent' " ,
'PDBJapan_Download_PDB' : "'ftp://www.pdbj.org/pdb_nc/pdb'+pdbid+'.ent'" , 'PDBJapan_Search' : "http://pdbjs3.protein.osaka-u.ac.jp/xPSSS/index.html" }, \
#'EBI_Download_PDB' : "'http://oca.ebi.ac.uk/oca-bin/send-x-pdb?id=' + pdbid " ,
definition = {
'internal' : [ 'bool', 'Use internal browser (Linux only)'],
'browser': [str,'Web browser',['TYPEDEF','menu',self.browserlist,self.browserlist]],
'browser_command': [str,'Browser executable path'],
'EBI_OCA' : [str,'EBI OCA search page'], \
'RCSB_Search' : [str,'RCSB search page'], \
'RCSB_Download_PDB' : [str,'RSCB PDB download command'] ,
'EBI_Download_PDB' : [str,'EBI PDB download command'] ,
'PDBJapan_Download_PDB' : [str,' PDBJapan download command'],
'PDBJapan_Search' : [str,' PDBJapan search page']
}, \
help = 'web' )
self.default_server = 'EBI'
#---------------------------------------------------------------------------
def GetPDBFile(self,pdbid,server='EBI'):
#---------------------------------------------------------------------------
import urllib
import socket
import timeoutsocket
if server == 'RCSB':
exec "urlname = "+self.params.params['RCSB_Download_PDB']
elif server == 'EBI':
exec "urlname = "+self.params.params['EBI_Download_PDB']
elif server == 'PDBjapan':
exec "urlname = "+self.params.params['PDBJapan_Download_PDB']
#print "server",server,"urlname",urlname
ret = []
dto = timeoutsocket.getDefaultSocketTimeout()
timeoutsocket.setDefaultSocketTimeout(10)
try:
try:
url = urllib.urlopen(urlname)
pdbdata = url.read()
#print "pdbdata",pdbdata
url.close()
except socket.error, msg:
#print "timeout"
ret = [2,"Timeout waiting?"]
except:
ret = [3,'No data called '+pdbid+'?']
finally:
timeoutsocket.setDefaultSocketTimeout(dto)
if not ret:
return [0,pdbdata]
else:
return ret
#--------------------------------------------------------------------
def downloadpdb_handler ( self, ID='',local_file='', DIR_local_file='', \
view_server='',server='',**keywords):
#--------------------------------------------------------------------
import string
import utils
if view_server:
if server == 'EBI':
self.launch_browser( url=self.params.params['EBI_OCA'],internal=-1)
elif server == 'RCSB':
self.launch_browser( url=self.params.params['RCSB_Search'],internal=-1)
else:
self.launch_browser( url=self.params.params['PDBJapan_Search'],internal=-1)
if ID and not local_file:
ID=string.lower(string.strip(ID))
name = string.split(ID,',')[0]+'.pdb'
fullname = utils.get_filename('',name)
MGGUI().insts.UpdateGUIWindow ('downloadpdbfile', [
['OBJECT','local_file',
['CONFIGURE',
['filename',name],
['fullname',fullname]]] ])
#-----------------------------------------------------------------------
def downloadpdbfile (self,server='EBI',ID='',local_file='', DIR_local_file='',
compress=1, drawing_style='all_atoms',show_gui_on_loading='',
exit='', **keywords):
#-----------------------------------------------------------------------
import utils
if exit == 'dismiss': return
if ['EBI','PDBjapan'].count(server): compress = 0
if ['EBI','PDBjapan','RCSB'].count(server): self.default_server = server
if not ID:
MGGUI().WarningMessage('You must enter a four-letter code', \
parent='downloadpdbfile')
return
import gzip
import string
import os
import re
# Remove the '.pdb'
ID=string.lower(string.strip(ID))
ID = string.split(ID,'.')[0]
if not local_file:
local_file = ID+'.pdb'
DIR_local_file = CCP4DATABASE().get_current_project()
filn = utils.get_filename(DIR_local_file,local_file)
#print "filn",filn
if os.path.exists(filn):
MGGUI().WarningMessage('A file called '+filn+' already exists', \
parent='downloadpdbfile')
return
status,pdbdata = self.GetPDBFile(ID,server=server)
if status:
MGGUI().WarningMessage(pdbdata,parent='downloadpdbfile')
return
if not pdbdata:
MGGUI().WarningMessage('No data returned from server', \
parent='downloadpdbfile')
if compress:
try:
output = utils.openFile(filn+'.gz','wb')
output.write(pdbdata)
output.close()
except:
MGGUI().WarningMessage('Error saving compressed data to file ' \
+filn+'.gz',parent='downloadpdbfile')
return
try:
input = gzip.open(filn+'.gz')
uncomp_output = open(filn,'wb')
uncomp_output.write(input.read())
except:
MGGUI().WarningMessage('Error saving data to file '+filn, \
parent='downloadpdbfile')
return
try:
input.close()
uncomp_output.close()
os.remove(filn+'.gz')
except:
pass
else:
# Try saving uncompressed data
if re.search("<HTML>",pdbdata):
MGGUI().WarningMessage('Error reported from download site', \
parent='downloadpdbfile')
return
try:
output = utils.openFile(filn,'w')
output.write(pdbdata)
output.close()
except:
MGGUI().insts.WarningMessage('Error saving data to file ' \
+filn,parent='downloadpdbfile')
return
# Only delete the GUI window when we're sure it all worked
MGGUI().DeleteGUIWindow ('downloadpdbfile')
# Load the data from the local PDB file
import model
model.openpdbfile(pdbin=local_file,DIR_pdbin=DIR_local_file,
drawing_style=drawing_style,show_gui_on_loading=show_gui_on_loading,
exit=exit)
#---------------------------------------------------------------------------
def set_default_browser(self):
#---------------------------------------------------------------------------
import sys
import re
import string
import glob
import os
separator = ':'
if re.search('darwin',sys.platform):
return 'open'
elif re.search('win',sys.platform):
return 'explorer'
else:
browser_list = ['firefox','konqueror','mozilla','netscape']
for browser in browser_list:
for path in string.split(os.environ['PATH'],separator):
if glob.glob(os.path.join(path,browser)):
return browser
else:
# Looks bad but just try this
return "netscape"
#-------------------------------------------------------------------------
def launch_browser ( self, url = '', file = '', target ='',
max_retry=0,retry=-1, internal = 0, **keywords) :
#-------------------------------------------------------------------------
import os,sys,string
# It should be..
# internal == -1: Use external browser
# internal == 1: Use internal browser
# internal == 0: Check user preference
if string.find(sys.platform,'nux')>0:
if internal == 0: internal = self.params.params.get('internal')
else:
internal = -1
#print "launch_browser internal",internal
#print "launch_browser file",file,self.scheduler
# First make sure we have a file to display
if file:
# Retry >0 implies launch_browser has
# been invoked from the scheduler - we want to stop it if
# file exists or we've tried max_retry times
if self.scheduler and (retry>max_retry or os.path.exists(file)):
self.scheduler.RemoveTask(self.launch_browser,[], \
{ 'file' : file,
'target' : target })
if not os.path.exists(file):
if retry<0 and self.scheduler:
self.scheduler.AddTask(self.launch_browser,[], \
{ 'file' : file,
'target' : target },
max_retry= max_retry-1 )
return
elif retry>max_retry or not self.scheduler:
print "Error attempting to display file:",file,' file does not exist'
return [1,'Error attempting to display file: '+file+ \
'\\n file does not exist']
return
if url:
cmd = 'browser '+url
elif file:
cmd = 'browser '+file
# Default is send to internal (hv3) browser
if internal>0:
import guiUtils
guiUtils.guiHelp(file=file)
return
args = []
browser = self.params.params.get('browser')
browser_command = self.params.params.get('browser_command')
#print "browser_command",browser_command
if sys.platform != 'win32':
if not browser_command: browser_command = browser
# The -url argument causes problems on Linux if the browser is
# already open
#if re.search('firefox|mozilla|netscape',browser_command) and not re.search('-url',browser_command):
# browser_command =browser_command+' -url'
if url:
cmd = browser_command +' '+url+' &'
elif file:
cmd = browser_command +' '+file
if target and not ['open','firefox'].count(browser_command): cmd=cmd+'#'+target
cmd = cmd + ' &'
print 'launch_browser cmd',cmd
try:
os.system(cmd)
except:
return [1,'Error launching '+browser+' browser']
else:
#Windows specific
import _winreg
import string
import utils
import re
# Try to get browser executable from registry
if not browser_command:
key = None
ii = -1
trythese = ['HTTP','http','https']
while key == None and ii < len(trythese):
try:
ii = ii+1
key = _winreg.OpenKey(_winreg.HKEY_CLASSES_ROOT,trythese[ii]+'\\shell\\open\\command')
except:
key = None
if key:
browser_command = _winreg.QueryValueEx( key, "") [0]
if not key or not browser_command:
MGGUI().WarningMessage('Failed to find executable for browser'+browser+'//nPlease use the Preferences, Web Tools interface to choose another browser//n or enter the full path name for the executable')
return
if re.search('IREF|iref',browser_command) :
browser = 'firefox'
elif re.search('ETSC|etsc',browser_command) :
browser = 'netscape'
else:
browser = 'explorer'
print "launch_browser key",key,browser_command
print 'treat as browser',browser
comd_words = utils.splitWords0(browser_command)
#print "comd_words",comd_words
browser_command = string.strip(comd_words[0],'"')
for word in comd_words[1:]:
if re.match('%',word)<0:
args.append(string.strip(word,'"'))
if ['firefox','netscape','mozilla'].count(browser):
if not args.count('-url'):args.append('-url')
file = re.sub(r'\\',r'/',file)
if not re.match('file',file): file = 'file:///'+file
args.append(utils.msvcescape(file))
print "launch browser cmd",browser_command,"args",args
try:
os.spawnv(os.P_NOWAIT,browser_command,args)
except:
return [2,'Error launching '+browser]
return [0,'']
def display_ani_gif (self, file = '', internal=1, **keywords ) :
import sys,string
if string.find(sys.platform,'nux')>0 :
MGGUI().Send('run_anigif '+file)
else:
# Try using external browser
self.launch_browser(file=file,internal = -1)