def read(cls, fp, verbose=False):
chk = cls(verbose=verbose)
lex = sas.StarLexer(fp, bufsize=0, verbose=verbose)
p = sas.CifParser.parse(lexer=lex,
content_handler=chk,
error_handler=chk,
verbose=verbose)
return chk
def check_nmr_star(cls, fp, dictionary=None, verbose=False):
chk = cls(dictionary)
lex = sas.StarLexer(fp, bufsize=0, verbose=verbose)
p = sas.SansParser.parse(lexer=lex,
content_handler=chk,
error_handler=chk,
verbose=verbose)
return (not chk._errs)
def parse(cls, fp, verbose=False):
h = cls()
lex = sas.StarLexer(fp, bufsize=0)
p = sas.SansParser.parse(lexer=lex,
content_handler=h,
error_handler=h,
verbose=verbose)
if h._errs > 0: return None
return h._data
def update_chem_comps(cls, ligand_dir, dsn, verbose=False):
cifdir = os.path.realpath(ligand_dir)
if not os.path.isdir(cifdir):
raise IOError("Not found/not a dir: %s" % (cifdir, ))
db = psycopg2.connect(dsn)
curs = db.cursor()
curs2 = db.cursor()
qry = "select pdbx_initial_date,pdbx_modified_date from ligand_expo.chem_comp where upper(id)=%s"
ldr = cls(curs=curs2, verbose=verbose)
# keep IDs for clean-up later
#
compids = []
stats = {
"total": 0,
"new": 0,
"updated": 0,
"obsolete": 0,
"compound": 0,
"failed": 0
}
for (root, dirs, files) in os.walk(cifdir):
if "FULL" in dirs:
dirs.remove("FULL")
if "REMOVED" in dirs:
dirs.remove("REMOVED")
for comp in files:
(compid, ext) = os.path.splitext(comp)
if ext != ".cif": continue
compid = str(compid).upper()
infile = os.path.join(root, comp)
chk = UpdateChecker.read_file(filename=infile,
verbose=False) # verbose )
if verbose:
sys.stdout.write("CC: %s in %s-%s\n" % (
compid,
root,
comp,
))
pprint.pprint(chk.__data__)
stats["total"] += 1
if chk.has_errors:
stats["failed"] += 1
sys.stderr.write("Errors parsing %s\n" % (filename, ))
continue
if chk.is_compound:
stats["compound"] += 1
continue
if chk.is_obsolete:
stats["obsolete"] += 1
continue
compids.append(compid)
updated = False
if verbose:
sys.stdout.write(qry % (compid, ))
sys.stdout.write("\n")
curs.execute(qry, (compid, ))
row = curs.fetchone()
if verbose:
pprint.pprint(row)
if row is None:
updated = True
stats["new"] += 1
else:
if chk.modified_date is not None:
if row[1] is not None:
if chk.modified_date > row[1]: updated = True
else: updated = True
else:
if chk.initial_date is not None:
if row[0] is not None:
if chk.initial_date > row[0]: updated = True
else: updated = True
else:
sys.stderr.write(
"This should never happen: chem comp %s has no dates and we got here"
% (compid, ))
if updated:
if verbose:
sys.stdout.write("-- updated, loading\n")
for table in CifLoader.TABLES:
if table != "chem_comp":
sql = "delete from ligand_expo.%s " % (table, )
sql += "where upper(comp_id)=%s"
if verbose:
sys.stdout.write(sql % (compid, ))
curs.execute(sql, (compid, ))
if verbose:
sys.stdout.write(" : %d\n" % (curs.rowcount, ))
sql = "delete from ligand_expo.chem_comp where upper(id)=%s"
if verbose:
sys.stdout.write(sql % (compid, ))
curs.execute(sql, (compid, ))
if verbose:
sys.stdout.write(" : %d\n" % (curs.rowcount, ))
with open(infile, "rU") as inf:
lex = sas.StarLexer(inf, bufsize=0, verbose=verbose)
curs.execute("begin")
try:
p = sas.CifParser.parse(lexer=lex,
content_handler=ldr,
error_handler=ldr,
verbose=verbose)
except:
curs.execute("rollback")
sys.stderr.write(
"ERR: Rollback in %s: Exception:\n" % (infile))
pprint.pprint(sys.exc_info())
traceback.print_exc()
compids.append(compid)
if ldr.has_errors:
sys.stderr.write("ERR: Rollback: errors in %s\n" %
(compid, ))
curs.execute("rollback")
else:
curs.execute("commit")
if verbose: sys.stdout - write("--- Committed\n")
compids.append(compid)
curs2.close()
# done updating, collect garbage
#
obsolete = []
idstr = "','".join(i for i in compids)
qry = "select upper(id) from ligand_expo.chem_comp where upper(id) not in ('%s')" % (
idstr, )
curs.execute(qry)
while True:
row = curs.fetchone()
if row is None: break
obsolete.append(row[0])
stats["obsolete"] = len(obsolete)
# "on delete cascade" should take care of child tables
#
idstr = "','".join(i for i in obsolete)
sql = "delete from ligand_expo.chem_comp where upper(id) in ('%s')" % (
idstr, )
curs.execute(sql)
# if verbose :
sys.stdout.write("%s : %d rows\n" % (sql, curs.rowcount))
sql = """delete from chem_comp."Chem_comp" where "ID" in ('%s')""" % (
idstr, )
curs.execute(sql)
# if verbose :
sys.stdout.write("%s : %d rows\n" % (sql, curs.rowcount))
curs.close()
db.close()
pprint.pprint(stats)
def comment(self, line, text):
if self._verbose:
sys.stdout.write("Comment %s in line %d\n" % (
text,
line,
))
return False
def data(self, tag, tagline, val, valline, delim, inloop):
if self._verbose:
sys.stdout.write( "data item %s in line %d:%d, delim=%s, inloop=%s - " \
% (tag, tagline, valline, str( delim ), str( inloop ),) )
sys.stdout.write(val)
sys.stdout.write("\n")
return False
#
#
if __name__ == "__main__":
e = sas.ErrorHandler()
c = Ch(verbose=False)
l = sas.StarLexer(fp=sys.stdin, bufsize=0, verbose=False)
with sas.timer("DDL"):
p = Parser.parse(lexer=l,
content_handler=c,
error_handler=e,
verbose=False)
def comment(self, line, text):
if self._verbose:
sys.stdout.write("Comment %s in line %d\n" % (
text,
line,
))
return False
def data(self, tag, tagline, val, valline, delim, inloop):
if self._verbose:
sys.stdout.write( "data item %s in line %d:%d, delim=%s, inloop=%s - " \
% (tag, tagline, valline, str( delim ), str( inloop ),) )
sys.stdout.write(val)
sys.stdout.write("\n")
return False
#
#
if __name__ == "__main__":
e = sas.ErrorHandler()
c = Ch(verbose=False)
l = sas.StarLexer(fp=sys.stdin, bufsize=0) #, verbose = True )
with sas.timer("SANS"):
p = SansParser.parse(lexer=l,
content_handler=c,
error_handler=e,
verbose=False)