def testcomments_strip8(self):
"""comments_strip 8"""
text = """
"quoted 'complications;' with embedded # comment" # real comment
"""
textExpected = """
"quoted 'complications;' with embedded # comment"
"""
textNew = comments_strip( text )
self.assertEqual( textNew, textExpected)
def testcomments_strip6(self):
"""comments_strip 6"""
text = """
"quoted value with embedded # comment" # real comment
"""
textExpected = """
"quoted value with embedded # comment"
"""
textNew = comments_strip( text )
self.assertEqual( textNew, textExpected)
def testcomments_strip3(self):
"""comments_strip 3"""
text = """
H#
"""
textExpected = """
H#
"""
textNew = comments_strip( text )
self.assertEqual( textNew, textExpected)
def testcomments_strip2(self):
"""comments_strip 2"""
text = """
H' # comment
H" # also
"""
textExpected = """
H'
H"
"""
textNew = comments_strip( text )
self.assertEqual( textNew, textExpected)
def testcomments_strip4(self):
"""comments_strip 4"""
text = """
;
test1 # no comment 1
;
;
test2 # no comment 2
;
"""
textExpected = """
;
test1 # no comment 1
;
;
test2 # no comment 2
;
"""
textNew = comments_strip( text )
self.assertEqual( textNew, textExpected)
def testcomments_strip(self):
"""comments_strip"""
text = """
# my comment exactly
foo # comment
value#stil a value
bar
; # actual data
;
"""
textExpected = """
foo
value#stil a value
bar
; # actual data
;
"""
textNew = comments_strip( text )
self.assertEqual( textNew, textExpected)
def test(self):
"""Text"""
# textExpectedAfterCollapse = ';<eol-string>mmy xie<eol-string>;\n_Test'
# text = """;
#mmy xie
#;
#_Test"""
# textCollapsed = semicolon_block_collapse( text )
# self.assertEqual( textExpectedAfterCollapse, textCollapsed)
#
# value, pos = tag_value_quoted_parse( textCollapsed, 0 )
# valueExpected = '\nmmy xie\n'
# posExpected = 34
# self.assertEqual( valueExpected, value )
# self.assertEqual( posExpected, pos)
t2 = """
# comment 1
"""
t2noComment = """
"""
self.assertEqual(t2noComment, comments_strip( t2 ))
def parse(self, text='', nmrView_type=0):
if self.verbosity > 2:
print('DEBUG: Parsing STAR file:', self.filename)
"""
'"Begin at the beginning," the King said, gravely,
"and go on till you come to the end; then stop."' (LC)
"""
# print "DEBUG taking care of EOL variations"
text = Utils.dos2unix(text) # \r\n -> \n
text = Utils.mac2unix(text) # \r -> \n
text = comments_strip(text)
## Collapse the semicolon block for ease of parsing
text = semicolon_block_collapse(text)
## For nmrView 'nmrStar' also compress { } into {}
## Wim 05/03/2003
if nmrView_type:
text = nmrView_compress(text)
## TITLE
match_data_tag = re.search(r'\s*data_(\S+)\s+', text, 0)
if not match_data_tag:
print("ERROR: found no 'data_title' string in ")
print("ERROR: file's text (first 100 chars):[%s] " % text[0:100])
return 1
self.title = match_data_tag.group(1)
pos = match_data_tag.end()
## Four quick searches for possible continuations
next_sf_begin = None # SAVE FRAME BEGIN
next_sf_end = None # SAVE FRAME END
next_free_tt = None # FREE TAGTABLE
next_loop_tt = None # LOOP TAGTABLE
sf_open = None # When a saveframe is open
text_length = len(text)
## Only break when parsed to the eof
while pos < text_length:
if self.verbosity >= 9:
print('Parse text from position:%s : [%s]' %
(pos, text[pos:pos + 10]))
match_save_begin_nws = pattern_save_begin_nws.search(
text, pos, pos + len('save_1'))
if match_save_begin_nws:
if match_save_begin_nws.start() == pos:
next_sf_begin = 1
if not next_sf_begin:
match_save_end_nws = pattern_save_end_nws.search(
text, pos, pos + len('save_ '))
if match_save_end_nws:
if match_save_end_nws.start() == pos:
next_sf_end = 1
if not (next_sf_begin or next_sf_end):
match_tag_name_nws = pattern_tag_name_nws.search(
text, pos, pos + len(' _X'))
if match_tag_name_nws:
if match_tag_name_nws.start() == pos:
next_free_tt = 1
if not (next_sf_begin or next_sf_end or next_free_tt):
match_tagtable_loop_nws = pattern_tagtable_loop_nws.search(
text, pos, pos + len('loop_ '))
if match_tagtable_loop_nws:
if match_tagtable_loop_nws.start() == pos:
next_loop_tt = 1
## Just checking
if not (next_sf_begin or next_sf_end or next_free_tt
or next_loop_tt):
print('ERROR: No new item found in data_nodes_parse.')
print('Items looked for are a begin or end of a saveframe, or')
print('a begin of a tagtable(free or looped).')
print()
print("At text (before pos=", pos, "):")
start = pos - 70
if start < 0:
start = 0
print("[" + text[start:pos] + "]")
print("At text (starting pos=", pos, "):")
print("[" + text[pos:pos + 70] + "]")
return None
## SAVE FRAME BEGIN
if next_sf_begin:
if sf_open:
print("ERROR: Found the beginning of a saveframe but")
print(
"ERROR: saveframe before is still open(not closed;-)")
return None
match_save_begin = pattern_save_begin.search(text, pos)
if not match_save_begin:
print("ERROR: Code error (no second match on sf begin)")
return None
if match_save_begin.start() != pos:
print("ERROR: Code error (wrong second match on sf begin)")
return None
self.datanodes.append(
SaveFrame(tagtables=[])) # Need resetting ?
self.datanodes[-1].title = match_save_begin.group(1)
sf_open = 1
next_sf_begin = None
pos = match_save_begin.end()
continue
## SAVE FRAME END
if next_sf_end:
if not sf_open:
print("ERROR: Found the end of a saveframe but")
print("ERROR: saveframe was not open")
return None
match_save_end = pattern_save_end.search(text, pos)
if not match_save_end:
print("ERROR: Code error (no second match on sf end)")
return None
if match_save_end.start() != pos:
print("ERROR: Code error (wrong second match on sf end)")
return None
sf_open = None
next_sf_end = None
pos = match_save_end.end()
continue
## FREE or LOOP TAGTABLE
if next_free_tt:
free = 1
next_free_tt = None
else: # next_loop_tt must be true as this was checked before
if not next_loop_tt:
print('ERROR: code bug in File.parse()')
return None
free = None
next_loop_tt = None
match_tagtable_loop = pattern_tagtable_loop.search(text, pos)
if not match_tagtable_loop:
print(
'ERROR: Code error, no second match on tagtable_loop')
return None
if match_tagtable_loop.start() != pos:
print(
"ERROR: Code error (wrong second match on tagtable_loop)"
)
return None
pos = match_tagtable_loop.end()
if sf_open:
dn = self.datanodes[
-1].tagtables # Insert in last saveframes' tagtables
else:
dn = self.datanodes
dn.append(
TagTable(free=free,
tagnames=[],
tagvalues=[],
verbosity=self.verbosity))
tt = dn[-1] # Just to be verbose for the beloved reader
pos = tt.parse(text=text, pos=pos)
if pos == None:
print("ERROR: In parsing tagtable")
return None
if self.verbosity >= 9:
print('Parsed tagtable up to pos: [%s]' % pos)
if self.verbosity > 2:
print('DEBUG Parsed: [%s] datanodes (top level count only)' % \
len(self.datanodes))
if self.check_integrity(recursive=0):
print("ERROR: integrity not ok")
return 1
# Save some memory
text = ''
return 0