<*>=
<Helper functions>
%%
parser CifParser:
<Regular expressions>
<Grammar specification>
%%
We have a monitor function which we can call to save the last parsed value (and print, if we are debugging). We also have functions for stripping off delimiters from strings. Finally, we match up our loops after reading them in. Note that we have function stripextras, which is only for semicolon strings, and stripstring, which is for getting rid of the inverted commas.
<Helper functions>= (<-U)
# An alternative specification for the Cif Parser, based on Yapps2
# by Amit Patel (http://theory.stanford.edu/~amitp/Yapps)
#
# helper code: we define our match tokens
lastval = ''
def monitor(location,value):
global lastval
#print 'At %s: %s' % (location,`value`)
lastval = `value`
return value
def stripextras(value):
# we get rid of semicolons and leading/trailing terminators etc.
import re
jj = re.compile("[\n\r\f \t\v]*")
semis = re.compile("[\n\r\f \t\v]*[\n\r\f]\n*;")
cut = semis.match(value)
if cut:
nv = value[cut.end():len(value)-2]
if nv[-1]=='\r': nv = nv[:-1]
else: nv = value
cut = jj.match(nv)
if cut:
return stripstring(nv[cut.end():])
return nv
# helper function to get rid of inverted commas etc.
def stripstring(value):
if value:
if value[0]== '\'' and value[-1]=='\'':
return value[1:-1]
if value[0]=='"' and value[-1]=='"':
return value[1:-1]
return value
# helper function to create a dictionary given a set of
# looped datanames and data values
def makeloop(namelist,itemlist,context):
noitems = len(namelist)
nopoints = divmod(len(itemlist),noitems)
if nopoints[1]!=0: #mismatch
raise "CifError:loop item mismatch"
nopoints = nopoints[0]
newdict = {}
for i in range(0,noitems):
templist = []
for j in range(0,nopoints):
templist.append(itemlist[j*noitems + i])
newdict.update({namelist[i]:templist})
context.append(newdict)
#print 'Contructed loop with items: '+`newdict`
return {} # to keep things easy
#
The regular expressions aren't quite as easy to deal with as in kjParsing; in kjParsing we could pass string variables as re arguments, but here we have to have a raw string. However, we can simplify the BNC specification of Nick Spadaccini. First of all, we do not have to have type I and type II strings, which are distinguished by the presence or absence of a line feed directly preceding them and thus by being allowed a semicolon at the front or not. We take care of this by treating as whitespace all terminators except for those with a following semicolon, so that a carriage-return-semicolon sequence matches the start_sc_line uniquely.
We include reserved words and save frames, although we semantically utterly ignore any save frames that we see - but no syntax error is flagged. The other reserved words have no rules defined, so will flag a syntax error. However, as yapps is a context-sensitive parser, it will by default make any word found starting with our reserved words into a data value if it occurs in the expected position, so we explicity exclude stuff starting with our words in the definition of data_value_1.
<Regular expressions>= (<-U)
# first handle whitespace and comments, keeping whitespace
# before a semicolon
ignore: "([ \t\n\r](?!;))|[ \t]"
ignore: "#.*[\n\r](?!;)"
ignore: "#.*"
# now the tokens
token LBLOCK: "(L|l)(O|o)(O|o)(P|p)_" # loop_
token save_heading: "(S|s)(A|a)(V|v)(E|e)_[][!%&\(\)*+,./:<=>?@0-9A-Za-z\\\\^`{}\|~\"#$';_-]+"
token save_end: "(S|s)(A|a)(V|v)(E|e)_"
token RESERVED: "((G|g)(L|l)(O|o)(B|b)(A|a)(L|l)_)|((S|s)(T|t)(O|o)(P|p)_)"
token data_name: "_[][!%&\(\)*+,./:<=>?@0-9A-Za-z\\\\^`{}\|~\"#$';_-]+" #_followed by stuff
token data_heading: "(D|d)(A|a)(T|t)(A|a)_[][!%&\(\)*+,./:<=>?@0-9A-Za-z\\\\^`{}\|~\"#$';_-]+"
token start_sc_line: "(\n|\r\n);([^\n\r])*(\r\n|\r|\n)+"
token sc_line_of_text: "[^;\r\n]([^\r\n])*(\r\n|\r|\n)+"
token end_sc_line: ";"
token data_value_1: "((?!(((S|s)(A|a)(V|v)(E|e)_[^\s]*)|((G|g)(L|l)(O|o)(B|b)(A|a)(L|l)_[^\s]*)|((S|s)(T|t)(O|o)(P|p)_[^\s]*)|((D|d)(A|a)(T|t)(A|a)_[^\s]*)))[^\s\"#$'_\[\]][^\s]*)|'(('(?=\S))|([^\n\r\f']))*'+|\"((\"(?=\S))|([^\n\r\"]))*\"+"
token END: '$'
The grammar specification is adapted from the kjParsing version. We now merge our actions in with the specification, rather than binding rules as we were doing. The final returned value is a dictionary, with each key a datablock name. The value attached to each key is an entire dictionary for that block, with special member 'loops' containing an array of dictionaries, one for each loop block. In order to construct this properly, we pass the current value of 'loops' to the data rule, so that when a loop is found it can be appended to this array.
<Grammar specification>= (<-U)
# now the rules
rule input: ((
dblock {{maindict = dblock }}
(
dblock {{maindict.update(monitor('input',dblock))}} #
)*
END
)
|
(
END {{maindict = {} }}
)) {{return maindict}}
rule dblock: (data_heading {{dict={data_heading[5:]:{"loops":[]} } }} # a data heading
(
dataseq<<dict[data_heading[5:]]["loops"]>> {{dict[data_heading[5:]].update(dataseq)}}
|
save_frame
)*
) {{return monitor('dblock',dict)}} # but may be empty
rule dataseq<<loop_array>>: data<<loop_array>> {{datadict=data}}
(
data<<loop_array>> {{datadict.update(data)}}
)* {{return monitor('dataseq',datadict)}}
rule data<<loop_array>>: data_loop<<loop_array>> {{return data_loop}}
|
datakvpair {{return datakvpair}} #kv pair
rule datakvpair: data_name data_value {{return {data_name:data_value} }} # name-value
rule data_value: (data_value_1 {{thisval = stripstring(data_value_1)}}
|
sc_lines_of_text {{thisval = stripextras(sc_lines_of_text)}}
) {{return monitor('data_value',thisval)}}
rule sc_lines_of_text: start_sc_line {{lines = start_sc_line}}
(
sc_line_of_text {{lines = lines+sc_line_of_text}}
)*
end_sc_line {{return monitor('sc_line_of_text',lines+end_sc_line)}}
rule data_loop<<loop_array>>: LBLOCK loopfield loopvalues {{return makeloop(loopfield,loopvalues,loop_array)}}
rule loopfield: data_name {{loop=[data_name]}}
(
data_name {{loop.append(data_name)}}
)* {{return loop}} # sequence of data names
rule loopvalues: ( data_value {{loop=[data_value]}}
(
data_value {{loop.append(monitor('loopval',data_value))}}
)*
) {{return loop}}
rule save_frame: save_heading
(
data<<{"dummydict":0}>>
)*
save_end