Source Code for Module bmrblib.pystarlib.FileTest

  1  """Unit test 
  2  """ 
  3  from bmrblib.pystarlib.File import File 
  4  from bmrblib.pystarlib import Utils 
  5   
  6  import __init__ 
  7   
  8  import os    
  9  import zipfile 
 10  import urllib.request, urllib.parse, urllib.error 
 11  from unittest import TestCase 
 12   
 13   
 14 -class AllChecks(TestCase): 
 15          strf           = File(verbosity=2)         
 16           
 17 -        def testparse(self): 
 18              """STAR parse""" 
 19              text = """data_no_comments_here 
 20   
 21  save_comment 
 22     _Saveframe_category  comment 
 23     loop_ 
 24          _comment 
 25          _every_flag 
 26          _category 
 27   
 28  '#It has very upfield-shifted H5', H5" @ 3.935,4.012 ppm' 
 29  ; 
 30  ####################### 
 31  #  BOGUS              # 
 32  ####################### 
 33   
 34  ; 
 35           
 36      BOGUS_CATEGORY 
 37   
 38       stop_ 
 39  save_ 
 40  """ 
 41              self.assertFalse(self.strf.parse(text=text))                                     
 42              st = self.strf.star_text() 
 43  #            print "unparsed text:[" +st+ "]" 
 44   
 45              exp = """data_no_comments_here 
 46  save_comment   _Saveframe_category  comment   loop_ 
 47          _comment 
 48          _every_flag 
 49          _category 
 50  ; 
 51  #It has very upfield-shifted H5', H5" @ 3.935,4.012 ppm 
 52  ; 
 53  ; 
 54  ####################### 
 55  #  BOGUS              # 
 56  ####################### 
 57   
 58  ;    BOGUS_CATEGORY     stop_ save_ 
 59  """ 
 60              self.assertTrue(Utils.equalIgnoringWhiteSpace(exp, st)) 
 61   
 62 -        def testread2(self): 
 63              """STAR File read""" 
 64              testEntry('1edp') 
 65                 
 66  """ 
 67  Extra Test Routine going over some entries in the NMR Restraints Grid 
 68  """ 
 69 -def testEntry(entry): 
 70      print("Testing Entry") 
 71      strf = File()  
 72      __init__.verbosity = 2 
 73      # Freely available on the web so not included in package. 
 74      stage = "2-parsed" 
 75  #    stage = "3-converted-DOCR" 
 76      urlLocation = ("http://www.bmrb.wisc.edu/WebModule/MRGridServlet?"+ 
 77      "block_text_type=%s&file_detail=%s&pdb_id=%s"+ 
 78      "&program=STAR&request_type=archive&subtype=full&type=entry") % (stage, stage, entry) 
 79      fnamezip = entry+".zip" 
 80  #    print "DEBUG: downloading url:", urlLocation 
 81      urllib.request.urlretrieve(urlLocation, fnamezip) 
 82  #    print "DEBUG: opening local zip file:", fnamezip 
 83      zfobj = zipfile.ZipFile(fnamezip) 
 84      fname = None 
 85      for name in zfobj.namelist():     
 86          if name.endswith('.str'): 
 87              fname = name             
 88      orgWattosWrittenFile     = entry+"_org.str" 
 89      pystarlibWrittenFile     = entry+"_pystar.str" 
 90      wattosWrittenFile        = entry+"_wattos.str" 
 91      diffOrgPystarFile        = entry+"_diff_org_pystar.str" 
 92      diffPystarWattosFile     = entry+"_diff_pystar_wattos.str" 
 93      diffOrgWattosWattosFile  = entry+"_diff_org_wattos_wattos.str" 
 94   
 95      outfile = open(orgWattosWrittenFile, 'w') 
 96      outfile.write(zfobj.read(fname)) 
 97      outfile.close()       
 98      zfobj.close()           
 99      strf.filename  = orgWattosWrittenFile    
100           
101      strf.read() 
102      strf.filename  = pystarlibWrittenFile 
103      strf.write() 
104   
105      if False: 
106          # In order to make the tests below work you'll first need to install Wattos 
107          #  which is why this test is not standard. 
108          try: 
109      #        print "Most likely the below diff will fail because it depends on diff being installed" 
110              cmd = "diff --ignore-all-space --ignore-blank-lines %s %s > %s" % ( orgWattosWrittenFile, pystarlibWrittenFile, diffOrgPystarFile) 
111              os.system(cmd) 
112              if not os.path.exists(diffOrgPystarFile): 
113                  print("WARNING: failed to diff files: ", orgWattosWrittenFile, pystarlibWrittenFile) 
114               
115      #        print "Most likely the below check will fail because it depends on Wattos being installed" 
116              print("DEBUG: rewrite to Java formating for comparison") 
117              cmd = "java -Xmx256m Wattos.Star.STARFilter %s %s ." % ( pystarlibWrittenFile, wattosWrittenFile) 
118              os.system(cmd) 
119              if not os.path.exists(wattosWrittenFile): 
120                  print("WARNING: failed to rewrite file: " + pystarlibWrittenFile) 
121              else: 
122      #            print "Most likely the below diff will fail because it depends on diff being installed" 
123                  cmd = "diff --ignore-all-space --ignore-blank-lines %s %s > %s" % ( pystarlibWrittenFile, wattosWrittenFile, diffPystarWattosFile) 
124                  os.system(cmd) 
125                  if not os.path.exists(diffPystarWattosFile): 
126                      print("WARNING: failed to diff file: ", pystarlibWrittenFile, wattosWrittenFile) 
127      #            print "Most likely the below diff will fail because it depends on diff being installed" 
128                  cmd = "diff --ignore-all-space --ignore-blank-lines %s %s > %s" % ( orgWattosWrittenFile, wattosWrittenFile, diffOrgWattosWattosFile) 
129                  os.system(cmd) 
130                  if not os.path.exists(diffOrgWattosWattosFile): 
131                      print("WARNING: failed to diff file: ", orgWattosWrittenFile, wattosWrittenFile) 
132          except KeyboardInterrupt: 
133              raise 
134          except: 
135      #        print "DEBUG: failed the rewrite or diff but as mentioned that's totally understandable." 
136              pass 
137       
138      try: 
139          os.unlink(entry+".zip") 
140          os.unlink(orgWattosWrittenFile) 
141          os.unlink(pystarlibWrittenFile) 
142      except KeyboardInterrupt: 
143          raise 
144      except: 
145          pass 
146       
147       
148 -def testAllEntries(): 
149      """ No need to test all entries for the unit testing frame work""" 
150  #    pdbList = ('1edp', '1q56', '1brv', '2hgh') 
151      pdbList = ('1edp') 
152      try: 
153          from Wattos.Utils import PDBEntryLists #@UnresolvedImport 
154          print("Imported Wattos.Utils; but it's not essential") 
155          pdbList = PDBEntryLists.getBmrbNmrGridEntries()[0:1] # Decide on the range yourself. 
156      except KeyboardInterrupt: 
157          raise 
158      except: 
159          print("Skipping import of Wattos.Utils; it's not needed") 
160       
161      for entry in pdbList: 
162          print(entry) 
163          testEntry(entry) 
164  #        entry = '1edp' # 57 kb 
165      #    entry = '1q56' # 10 Mb takes 27 s to parse on 2GHz PIV CPU 
166      #    entry = '1brv' # 1 Mb  
167      #    entry = '1hue' # 6 Mb takes 26 s to parse on 2GHz PIV CPU 
168      #    entry = '2ihx' # ? Mb has weird quoted values 
169        
170  """ 
171  Extra Test Routine going over some entries in the NMR Restraints Grid 
172  """ 
173 -def testSingleFile( filename ): 
174      strf = File()  
175      strf.filename  = filename    
176      print("DEBUG: reading file ", strf.filename) 
177      strf.read() 
178      strf.filename  = strf.filename + "_new.str" 
179      print("DEBUG: writing file ", strf.filename) 
180      strf.write() 
181       
182           
183  if __name__ == "__main__": 
184      testAllEntries() 
185  #    testSingleFile("S:\\jurgen\\2hgh_small_new_google.str") 
186  #    unittest.main() 
187      print("Done with STAR.FileTest") 
188