Source Code for Module weblogolib._cgi

  1  #!/usr/bin/env python 
  2   
  3  #  Copyright (c) 2003-2004 The Regents of the University of California. 
  4  #  Copyright (c) 2005 Gavin E. Crooks 
  5  #  Copyright (c) 2006, The Regents of the University of California, through  
  6  #  Lawrence Berkeley National Laboratory (subject to receipt of any required 
  7  #  approvals from the U.S. Dept. of Energy).  All rights reserved. 
  8   
  9  #  This software is distributed under the new BSD Open Source License. 
 10  #  <http://www.opensource.org/licenses/bsd-license.html> 
 11  # 
 12  #  Redistribution and use in source and binary forms, with or without  
 13  #  modification, are permitted provided that the following conditions are met:  
 14  # 
 15  #  (1) Redistributions of source code must retain the above copyright notice,  
 16  #  this list of conditions and the following disclaimer.  
 17  # 
 18  #  (2) Redistributions in binary form must reproduce the above copyright  
 19  #  notice, this list of conditions and the following disclaimer in the  
 20  #  documentation and or other materials provided with the distribution.  
 21  # 
 22  #  (3) Neither the name of the University of California, Lawrence Berkeley  
 23  #  National Laboratory, U.S. Dept. of Energy nor the names of its contributors  
 24  #  may be used to endorse or promote products derived from this software  
 25  #  without specific prior written permission.  
 26  # 
 27  #  THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"  
 28  #  AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE  
 29  #  IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE  
 30  #  ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE  
 31  #  LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR  
 32  #  CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF  
 33  #  SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS  
 34  #  INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN  
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 36  #  ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE  
 37  #  POSSIBILITY OF SUCH DAMAGE.  
 38   
 39  import sys 
 40  import cgi as cgilib 
 41  import cgitb; cgitb.enable() 
 42   
 43  #print "Content-Type: text/html\n\n" 
 44  #print "HELLO WORLD" 
 45  #print __name__ 
 46   
 47  from StringIO import StringIO 
 48  from color import * 
 49  from colorscheme import ColorScheme, ColorGroup 
 50   
 51  import weblogolib 
 52  from corebio.utils import * 
 53  from corebio._future import Template 
 54   
 55   
 56  # TODO: Check units 
 57   
 58  # TODO: In WebLogo2: why slash create.cgi? I think this was a workaround 
 59  # for some browser quirk 
 60  #<form method="post" action="/create.cgi" enctype="multipart/form-data"> 
 61       
 62 -def resource_string(resource, basefilename) : 
 63      import os 
 64      fn =  os.path.join(os.path.dirname(basefilename), resource) 
 65      return open( fn ).read() 
 66   
 67  mime_type = { 
 68      'eps': 'application/postscript',  
 69      'pdf': 'application/pdf', 
 70      'png': 'image/png', 
 71      'png_print': 'image/png',     
 72      'txt' : 'text/plain',        
 73      'jpeg'  : 'image/jpeg', 
 74  } 
 75   
 76  extension = { 
 77      'eps': 'eps', 
 78      'pdf': 'pdf', 
 79      'png': 'png', 
 80      'png_print': 'png', 
 81      'txt' : 'txt',         
 82      'jpeg'  : 'png' 
 83  } 
 84   
 85   
 86  alphabets = { 
 87      'alphabet_auto': None,  
 88      'alphabet_protein': weblogolib.unambiguous_protein_alphabet,  
 89      'alphabet_rna': weblogolib.unambiguous_rna_alphabet, 
 90      'alphabet_dna': weblogolib.unambiguous_dna_alphabet} 
 91   
 92  color_schemes = {} 
 93  for k in weblogolib.std_color_schemes.keys(): 
 94      color_schemes[ 'color_'+k.replace(' ', '_')] = weblogolib.std_color_schemes[k] 
 95       
 96   
 97  composition = {'comp_none' : 'none', 
 98      'comp_auto' : 'auto', 
 99      'comp_equiprobable':'equiprobable', 
100      'comp_CG': 'percentCG', 
101      'comp_Celegans' : 'C. elegans', 
102      'comp_Dmelanogaster' : 'D. melanogaster', 
103      'comp_Ecoli' : 'E. coli', 
104      'comp_Hsapiens': 'H. sapiens', 
105      'comp_Mmusculus' : 'M. musculus', 
106      'comp_Scerevisiae': 'S. cerevisiae' 
107  } 
108   
109 -class Field(object) : 
110      """ A representation of an HTML form field.""" 
111 -    def __init__(self, name, default=None, conversion= None, options=None, errmsg="Illegal value.") : 
112          self.name = name 
113          self.default = default 
114          self.value = default 
115          self.conversion = conversion         
116          self.options = options 
117          self.errmsg = errmsg 
118   
119 -    def get_value(self) : 
120          if self.options : 
121              if not self.value in self.options : 
122                  raise ValueError, (self.name, self.errmsg) 
123                   
124          if self.conversion : 
125              try : 
126                  return self.conversion(self.value) 
127              except ValueError, e : 
128                  raise ValueError, (self.name, self.errmsg) 
129          else: 
130              return self.value 
131       
132       
133 -def string_or_none(value) : 
134      if value is None or value == 'auto': 
135          return None 
136      return str(value) 
137       
138 -def truth(value) : 
139      if value== "true" : return True 
140      return bool(value) 
141   
142 -def int_or_none(value) : 
143      if value =='' or value is None or value == 'auto': 
144          return None 
145      return int(value) 
146       
147 -def float_or_none(value) : 
148      if value =='' or value is None or value == 'auto': 
149          return None 
150      return float(value) 
151           
152   
153 -def main(htdocs_directory = None) : 
154    
155      logooptions = weblogolib.LogoOptions()  
156       
157      # A list of form fields. 
158      # The default for checkbox values must be False (irrespective of 
159      # the default in logooptions) since a checked checkbox returns 'true' 
160      # but an unchecked checkbox returns nothing. 
161      controls = [ 
162          Field( 'sequences', ''), 
163          Field( 'format', 'png', weblogolib.formatters.get , 
164              options=['png_print', 'png', 'jpeg', 'eps', 'pdf', 'txt'] ,  
165              errmsg="Unknown format option."), 
166          Field( 'stacks_per_line', logooptions.stacks_per_line , int,  
167              errmsg='Invalid number of stacks per line.'), 
168          Field( 'size','medium', weblogolib.std_sizes.get, 
169              options=['small', 'medium', 'large'], errmsg='Invalid logo size.'), 
170          Field( 'alphabet','alphabet_auto', alphabets.get, 
171              options=['alphabet_auto', 'alphabet_protein', 'alphabet_dna',  
172                          'alphabet_rna'], 
173              errmsg="Unknown sequence type."), 
174          Field( 'unit_name', 'bits',  
175              options=[ 'probability', 'bits', 'nats', 'kT', 'kJ/mol',  
176                          'kcal/mol']), 
177          Field( 'first_index', 1, int_or_none), 
178          Field( 'logo_start', '', int_or_none), 
179          Field( 'logo_end', '', int_or_none), 
180          Field( 'composition', 'comp_auto', composition.get, 
181              options=['comp_none','comp_auto','comp_equiprobable','comp_CG', 
182              'comp_Celegans','comp_Dmelanogaster','comp_Ecoli', 
183              'comp_Hsapiens','comp_Mmusculus','comp_Scerevisiae'],  
184              errmsg= "Illegal sequence composition."), 
185          Field( 'percentCG', '', float_or_none, errmsg="Invalid CG percentage."), 
186          Field( 'show_errorbars', False , truth), 
187          Field( 'logo_title', logooptions.logo_title ), 
188          Field( 'logo_label', logooptions.logo_label ), 
189          Field( 'show_xaxis', False, truth), 
190          Field( 'xaxis_label', logooptions.xaxis_label ), 
191          Field( 'show_yaxis', False, truth),   
192          Field( 'yaxis_label', logooptions.yaxis_label, string_or_none ), 
193          Field( 'yaxis_scale', logooptions.yaxis_scale , float_or_none, 
194              errmsg="The yaxis scale must be a positive number." ), 
195          Field( 'yaxis_tic_interval', logooptions.yaxis_tic_interval ,  
196                  float_or_none), 
197          Field( 'show_ends', False, truth),  
198          Field( 'show_fineprint', False , truth),  
199          Field( 'color_scheme', 'color_auto', color_schemes.get, 
200              options=color_schemes.keys() , 
201              errmsg = 'Unknown color scheme'), 
202          Field( 'color0', ''), 
203          Field( 'symbols0', ''), 
204          Field( 'desc0', ''), 
205          Field( 'color1', ''), 
206          Field( 'symbols1', ''), 
207          Field( 'desc1', ''), 
208          Field( 'color2', ''), 
209          Field( 'symbols2', ''), 
210          Field( 'desc2', ''), 
211          Field( 'color3', ''), 
212          Field( 'symbols3', ''), 
213          Field( 'desc3', ''), 
214          Field( 'color4', ''), 
215          Field( 'symbols4', ''), 
216          Field( 'desc4', ''), 
217          Field( 'ignore_lower_case', False, truth),  
218          Field( 'scale_width', False, truth),  
219          ] 
220       
221      form = {} 
222      for c in controls : 
223          form[c.name] = c 
224   
225   
226      form_values = cgilib.FieldStorage() 
227       
228      # Send default form? 
229      if len(form_values) ==0 or form_values.has_key("cmd_reset"): 
230          # Load default truth values now. 
231          form['show_errorbars'].value = logooptions.show_errorbars 
232          form['show_xaxis'].value = logooptions.show_xaxis 
233          form['show_yaxis'].value = logooptions.show_yaxis 
234          form['show_ends'].value = logooptions.show_ends 
235          form['show_fineprint'].value = logooptions.show_fineprint 
236          form['scale_width'].value = logooptions.scale_width 
237           
238          send_form(controls, htdocs_directory = htdocs_directory)  
239          return 
240       
241      # Get form content 
242      for c in controls : 
243          c.value = form_values.getfirst( c.name, c.default)  
244          
245          
246      options_from_form = ['format', 'stacks_per_line', 'size',  
247          'alphabet', 'unit_name', 'first_index', 'logo_start','logo_end', 
248           'composition',  
249          'show_errorbars', 'logo_title', 'logo_label', 'show_xaxis',  
250          'xaxis_label', 
251          'show_yaxis', 'yaxis_label', 'yaxis_scale', 'yaxis_tic_interval', 
252          'show_ends', 'show_fineprint', 'scale_width'] 
253       
254      errors = [] 
255      for optname in options_from_form : 
256          try : 
257              value =  form[optname].get_value() 
258              if value!=None : setattr(logooptions, optname, value) 
259          except ValueError, err : 
260              errors.append(err.args)             
261   
262       
263      # Construct custom color scheme 
264      custom = ColorScheme() 
265      for i in range(0,5) : 
266          color = form["color%d"%i].get_value() 
267          symbols = form["symbols%d"%i].get_value() 
268          desc = form["desc%d"%i].get_value()  
269   
270          if color : 
271              try : 
272                  custom.groups.append(weblogolib.ColorGroup(symbols, color, desc)) 
273              except ValueError, e :  
274                  errors.append( ('color%d'%i, "Invalid color: %s" % color) ) 
275       
276      if form["color_scheme"].value == 'color_custom' : 
277          logooptions.color_scheme =  custom 
278      else : 
279          try : 
280              logooptions.color_scheme = form["color_scheme"].get_value() 
281          except ValueError, err : 
282              errors.append(err.args)             
283   
284      sequences = None 
285   
286      # FIXME: Ugly fix: Must check that sequence_file key exists 
287      # FIXME: Sending malformed or missing form keys should not cause a crash 
288      # sequences_file = form["sequences_file"] 
289      if form_values.has_key("sequences_file") : 
290          sequences = form_values.getvalue("sequences_file")  
291          assert type(sequences) == str 
292   
293      if not sequences or len(sequences)  ==0: 
294          sequences = form["sequences"].get_value() 
295       
296      if not sequences or len(sequences)  ==0: 
297          errors.append( ("sequences", "Please enter a multiple-sequence alignment in the box above, or select a file to upload.")) 
298     
299   
300   
301      # If we have uncovered errors or we want the chance to edit the logo  
302      # ("cmd_edit" command from examples page) then we return the form now. 
303      # We do not proceed to the time consuming logo creation step unless 
304      # required by a 'create' or 'validate' command, and no errors have been 
305      # found yet. 
306      if form_values.has_key("cmd_edit") or errors : 
307          send_form(controls, errors, htdocs_directory) 
308          return     
309                   
310   
311      # We write the logo into a local buffer so that we can catch and 
312      # handle any errors. Once the "Content-Type:" header has been sent 
313      # we can't send any useful feedback 
314      logo = StringIO() 
315      try : 
316          comp = form["composition"].get_value() 
317          percentCG = form["percentCG"].get_value() 
318          ignore_lower_case = form_values.has_key("ignore_lower_case")  
319          seqs = weblogolib.read_seq_data(StringIO( sequences),  
320                                          alphabet=logooptions.alphabet, 
321                                          ignore_lower_case=ignore_lower_case 
322                                          ) 
323          if comp=='percentCG': comp = str(percentCG/100) 
324          prior = weblogolib.parse_prior(comp, seqs.alphabet) 
325          data = weblogolib.LogoData.from_seqs(seqs, prior)  
326          logoformat =  weblogolib.LogoFormat(data, logooptions) 
327          format = form["format"].value 
328          weblogolib.formatters[format](data, logoformat, logo)             
329      except ValueError, err : 
330          errors.append( err.args ) 
331      except IOError, err : 
332          errors.append( err.args) 
333      except RuntimeError, err : 
334          errors.append( err.args ) 
335                 
336      if form_values.has_key("cmd_validate") or errors : 
337          send_form(controls, errors, htdocs_directory)  
338          return     
339    
340    
341      # 
342      #  RETURN LOGO OVER HTTP 
343      # 
344   
345      print "Content-Type:", mime_type[format] 
346      # Content-Disposition: inline       Open logo in browser window 
347      # Content-Disposition: attachment   Download logo   
348      if form_values.has_key("download") : 
349          print 'Content-Disposition: attachment; ' \ 
350              'filename="logo.%s"' % extension[format]  
351      else :        
352          print 'Content-Disposition: inline; ' \ 
353              'filename="logo.%s"' % extension[format]         
354       
355           
356      # Seperate header from data 
357      print  
358           
359      # Finally, and at last, send the logo. 
360      print logo.getvalue()         
361   
362     
363 -def send_form(controls, errors=[], htdocs_directory=None) : 
364      if htdocs_directory is None : 
365          htdocs_directory = os.path.join( 
366              os.path.dirname(__file__, "htdocs") ) 
367   
368      subsitutions = {} 
369      subsitutions["version"] = weblogolib.release_description  
370       
371      for c in controls : 
372          if c.options : 
373              for opt in c.options : 
374                  subsitutions[opt.replace('/','_')] = '' 
375              subsitutions[c.value.replace('/','_')] = 'selected' 
376          else : 
377              value = c.value 
378              if value == None : value = 'auto' 
379              if value=='true': 
380                  subsitutions[c.name] = 'checked' 
381              elif type(value)==bool : 
382                  if value : 
383                      subsitutions[c.name] = 'checked' 
384                  else : 
385                      subsitutions[c.name] = '' 
386              else : 
387                  subsitutions[c.name] = str(value) 
388          subsitutions[c.name+'_err']  = '' 
389               
390      if errors : 
391          print >>sys.stderr, errors 
392          error_message = [] 
393          for e in errors : 
394              if type(e) is str : 
395                  msg = e 
396              elif len(e)==2: 
397                  subsitutions[e[0]+"_err"] = "class='error'"     
398                  msg = e[1] 
399              else : 
400                  msg = e[0] 
401   
402   
403              error_message +=  "ERROR: "  
404              error_message +=  msg 
405              error_message += ' <br />' 
406               
407          error_message += \ 
408              "<input style='float:right; font-size:small' type='submit' name='cmd_validate' value='Clear Error' /> " 
409          subsitutions["error_message"] = ''.join(error_message) 
410      else : 
411          subsitutions["error_message"] = "" 
412       
413           
414      template = resource_string("create_html_template.html", htdocs_directory) 
415      html = Template(template).safe_substitute(subsitutions) #FIXME 
416   
417      print "Content-Type: text/html\n\n" 
418      print html 
419   
420      # DEBUG 
421      # keys = subsitutions.keys() 
422      # keys.sort() 
423      # for k in keys : 
424      #    print k,"=", subsitutions[k], " <br />"  
425   
426      #for k in controls : 
427      #    print k.name,"=", k.get_value(), " <br />"  
428   
429   
430   
431  if __name__=="__main__" : 
432      main() 
433