def extract_cif(infile, folder, nodes_export_subfolder="nodes",
aiida_export_subfolder="aiida", silent=False):
"""
Extract the nodes to be imported from a TCOD CIF file. TCOD CIFs,
exported by AiiDA, may contain an importable subset of AiiDA database,
which can be imported. This function prepares SandboxFolder with files
required for import.
:param infile: file path
:param folder: a SandboxFolder, used to extract the file tree
:param nodes_export_subfolder: name of the subfolder for AiiDA nodes
:param aiida_export_subfolder: name of the subfolder for AiiDA data
inside the TCOD CIF internal file tree
:param silent: suppress debug print
"""
import os
import urllib2
import CifFile
from aiida.common.exceptions import ValidationError
from aiida.common.utils import md5_file, sha1_file
from aiida.tools.dbexporters.tcod import decode_textfield
values = CifFile.ReadCif(infile)
values = values[values.keys()[0]] # taking the first datablock in CIF
for i in range(0,len(values['_tcod_file_id'])-1):
name = values['_tcod_file_name'][i]
if not name.startswith(aiida_export_subfolder+os.sep):
continue
dest_path = os.path.relpath(name,aiida_export_subfolder)
if name.endswith(os.sep):
if not os.path.exists(folder.get_abs_path(dest_path)):
folder.get_subfolder(folder.get_abs_path(dest_path),create=True)
continue
contents = values['_tcod_file_contents'][i]
if contents == '?' or contents == '.':
uri = values['_tcod_file_uri'][i]
if uri is not None and uri != '?' and uri != '.':
contents = urllib2.urlopen(uri).read()
encoding = values['_tcod_file_content_encoding'][i]
if encoding == '.':
encoding = None
contents = decode_textfield(contents,encoding)
if os.path.dirname(dest_path) != '':
folder.get_subfolder(os.path.dirname(dest_path)+os.sep,create=True)
with open(folder.get_abs_path(dest_path),'w') as f:
f.write(contents)
f.flush()
md5 = values['_tcod_file_md5sum'][i]
if md5 is not None:
if md5_file(folder.get_abs_path(dest_path)) != md5:
raise ValidationError("MD5 sum for extracted file '{}' is "
"different from given in the CIF "
"file".format(dest_path))
sha1 = values['_tcod_file_sha1sum'][i]
if sha1 is not None:
if sha1_file(folder.get_abs_path(dest_path)) != sha1:
raise ValidationError("SHA1 sum for extracted file '{}' is "
"different from given in the CIF "
"file".format(dest_path))
def check_gzip_base64(self, text):
from aiida.tools.dbexporters.tcod import (
encode_textfield_gzip_base64, decode_textfield_gzip_base64)
encoded = encode_textfield_gzip_base64(text)
decoded = decode_textfield_gzip_base64(encoded)
decoded_universal = decode_textfield(encoded, 'gzip+base64')
self.assertEquals(text, decoded)
self.assertEquals(text, decoded_universal)
def check_base64(self, inp, out):
from aiida.tools.dbexporters.tcod import (encode_textfield_base64,
decode_textfield_base64)
encoded = encode_textfield_base64(inp)
decoded = decode_textfield_base64(out)
decoded_universal = decode_textfield(out, 'base64')
self.assertEquals(encoded, out)
self.assertEquals(decoded, inp)
self.assertEquals(decoded_universal, inp)
def check_ncr(self, inp, out):
from aiida.tools.dbexporters.tcod import (encode_textfield_ncr,
decode_textfield_ncr)
encoded = encode_textfield_ncr(inp)
decoded = decode_textfield_ncr(out)
decoded_universal = decode_textfield(out, 'ncr')
self.assertEquals(encoded, out)
self.assertEquals(decoded, inp)
self.assertEquals(decoded_universal, inp)
def test_quoted_printable(self, inp, out):
from aiida.tools.dbexporters.tcod import (encode_textfield_quoted_printable,
decode_textfield_quoted_printable)
encoded = encode_textfield_quoted_printable(inp)
decoded = decode_textfield_quoted_printable(out)
decoded_universal = decode_textfield(out, 'quoted-printable')
self.assertEquals(encoded, out)
self.assertEquals(decoded, inp)
self.assertEquals(decoded_universal, inp)
