Python Bank.update方法代码示例

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_computed_ref_release(self):
   b = Bank('computed2')
   res = b.update(True)
   self.assertTrue(b.session.get('update'))
   b2 = Bank('computed2')
   res = b2.update(True)
   self.assertFalse(b2.session.get('update'))

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_update_hardlinks(self):
   """
   Update a bank twice with hard links^. Files copied from previous release
   must be links.
   """
   b = Bank('local')
   b.config.set('keep.old.version', '3')
   b.config.set('use_hardlinks', '1')
   # First update
   b.update()
   self.assertTrue(b.session.get('update'))
   old_release = b.session.get_full_release_directory()
   # Update test.fasta to force update (not that this file is modified in the
   # source tree)
   remote_file = b.session.config.get('remote.dir') + 'test.fasta.gz'
   stat = os.stat(remote_file)
   one_day = 3600 * 24
   os.utime(remote_file, (stat.st_atime + one_day, stat.st_atime + one_day))
   # Second update
   b.update()
   self.assertTrue(b.session.get('update'))
   new_release = b.session.get_full_release_directory()
   # Test that test2.fasta in both release are the same file (we can't use
   # test.fasta because it is uncompressed and then not the same file)
   file_old_release = os.path.join(old_release, 'flat', 'test2.fasta')
   file_new_release = os.path.join(new_release, 'flat', 'test2.fasta')
   try:
       self.assertTrue(os.path.samefile(file_old_release, file_new_release))
   except AssertionError:
       msg = "In %s: copy worked but hardlinks were not used." % self.id()
       logging.info(msg)
   # Restore date (otherwise repeated tests fail)
   os.utime(remote_file, (stat.st_atime, stat.st_atime))

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_removeAll(self):
   b = Bank('local')
   b.update()
   b.removeAll()
   self.assertFalse(os.path.exists(b.get_data_dir()))
   bdb = b.banks.find_one({'name': b.name})
   self.assertTrue(bdb is None)

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_stats(self):
     b = Bank("local")
     b.update()
     rel = b.session.get("release")
     stats = Bank.get_banks_disk_usage()
     self.assertTrue(stats[0]["size"] > 0)
     for release in stats[0]["releases"]:
         if release["name"] == rel:
             self.assertTrue(release["size"] > 0)

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_stats(self):
   b = Bank('local')
   b.update()
   rel = b.session.get('release')
   stats = Bank.get_banks_disk_usage()
   self.assertTrue(stats[0]['size']>0)
   for release in stats[0]['releases']:
     if release['name'] == rel:
       self.assertTrue(release['size']>0)

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_no_update(self):
     '''
     Try updating twice, at second time, bank should not be updated
     '''
     b = Bank('local')
     b.update()
     self.assertTrue(b.session.get('update'))
     b.update()
     self.assertFalse(b.session.get('update'))
     self.assertFalse(b.session.get_status(Workflow.FLOW_POSTPROCESS))

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_reupdate_from_task_wrong_release(self):
     b = Bank("local")
     b.options.stop_after = "download"
     b.update()
     self.assertFalse(b.session.get_status("postprocess"))
     b2 = Bank("local")
     b2.options.from_task = "postprocess"
     b2.options.release = "wrongrelease"
     res = b2.update()
     self.assertFalse(res)

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_reupdate_from_task_error(self):
     b = Bank("local")
     b.options.stop_after = "check"
     b.update()
     self.assertFalse(b.session.get_status("postprocess"))
     b2 = Bank("local")
     b2.options.from_task = "postprocess"
     b2.options.release = b.session.get("release")
     res = b2.update()
     self.assertFalse(res)

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_reupdate_from_task_error(self):
   b = Bank('local')
   b.options.stop_after = 'check'
   b.update()
   self.assertFalse(b.session.get_status('postprocess'))
   b2 = Bank('local')
   b2.options.from_task = 'postprocess'
   b2.options.release = b.session.get('release')
   res = b2.update()
   self.assertFalse(res)

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_no_update(self):
     """
   Try updating twice, at second time, bank should not be updated
   """
     b = Bank("local")
     b.update()
     self.assertTrue(b.session.get("update"))
     b.update()
     self.assertFalse(b.session.get("update"))
     self.assertFalse(b.session.get_status(Workflow.FLOW_POSTPROCESS))

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_reupdate_from_task_wrong_release(self):
   b = Bank('local')
   b.options.stop_after = 'download'
   b.update()
   self.assertFalse(b.session.get_status('postprocess'))
   b2 = Bank('local')
   b2.options.from_task = 'postprocess'
   b2.options.release = 'wrongrelease'
   res = b2.update()
   self.assertFalse(res)

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_computed(self):
   b = Bank('computed')
   res = b.update(True)
   self.assertTrue(res)
   self.assertTrue(os.path.exists(b.session.get_full_release_directory()+'/sub1/flat/test_100.txt'))
   self.assertTrue(b.session.get('update'))
   # Check that, with depends non updated, bank is not updated itself
   nextb = Bank('computed')
   res = nextb.update(True)
   self.assertFalse(nextb.session.get('update'))

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_reupdate_from_task(self):
     b = Bank("local")
     b.options.stop_after = "download"
     b.update()
     self.assertFalse(b.session.get_status("postprocess"))
     b2 = Bank("local")
     b2.options.from_task = "postprocess"
     b2.options.release = b.session.get("release")
     b2.update()
     self.assertTrue(b2.session.get_status("postprocess"))
     self.assertEqual(b.session.get_full_release_directory(), b2.session.get_full_release_directory())

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_search(self):
   b = Bank('localprocess')
   b.update()
   search_res = Bank.search(['blast'],[])
   self.assertTrue(len(search_res)==1)
   search_res = Bank.search([],['nucleic'])
   self.assertTrue(len(search_res)==1)
   search_res = Bank.search(['blast'],['nucleic'])
   self.assertTrue(len(search_res)==1)
   search_res = Bank.search(['blast'],['proteic'])
   self.assertTrue(len(search_res)==0)

# 需要导入模块: from biomaj.bank import Bank [as 别名]
# 或者: from biomaj.bank.Bank import update [as 别名]
 def test_search(self):
     b = Bank("localprocess")
     b.update()
     search_res = Bank.search(["blast"], [])
     self.assertTrue(len(search_res) == 1)
     search_res = Bank.search([], ["nucleic"])
     self.assertTrue(len(search_res) == 1)
     search_res = Bank.search(["blast"], ["nucleic"])
     self.assertTrue(len(search_res) == 1)
     search_res = Bank.search(["blast"], ["proteic"])
     self.assertTrue(len(search_res) == 0)