def main ():
global args
# read PIF
if args.ifile is not None:
with open(args.ifile) as ifs:
pifdata = pif.load(ifs)
else:
pifdata = pif.load(sys.stdin)
# perform requested action
if args.action == 'property':
rval = str(property(pifdata))
elif args.action == 'uid':
rval = str(uid(pifdata))
elif args.action == 'sagittariidae':
if not isinstance(pifdata, list):
pifdata = [pifdata]
add_link = sagittariidae.link_factory(
projectID='nq3X4-concept-inconel718',
host='http://sagittariidae.adapt.mines.edu')
for p in pifdata:
add_link(p)
return json.dumps(pifdata)
else:
msg = '{} is not a recognized action.'.format(args.action)
raise ValueError(msg)
# write PIF
if args.ofile is not None:
if authorize_overwrite(args.ofile):
with open(args.ofile, 'w') as ofs:
ofs.write(rval)
else:
sys.stdout.write(rval)
def test_property_add_Ifile(self):
rval, out, err = execute('pifmod -i data/pif.json -o data/test.pif ' \
'property foo=bar')
with open('data/out.pif') as ifs:
expected = pif.load(ifs)
with open('data/test.pif') as ifs:
received = pif.load(ifs)
assert rval == 0
assert empty(out)
assert empty(err)
assert compare_dictionaries(expected.as_dictionary(),
received.as_dictionary()), \
'\n'.join(strdiff(pif.dumps(expected), pif.dumps(received)))
def test_property_add_volume_Ifile(self):
# with tags...
rval, out, err = execute('pifmod -i data/pif.json -o data/test.pif ' \
'property data/pore-distribution.json volume')
with open('data/out_volume.pif') as ifs:
expected = pif.load(ifs)
with open('data/test.pif') as ifs:
received = pif.load(ifs)
assert rval == 0
assert empty(out)
assert empty(err)
assert compare_dictionaries(expected.as_dictionary(),
received.as_dictionary()), \
'{}'.format(strdiff(pif.dumps(expected), pif.dumps(received)))
def test_property_add_tags_Ifile(self):
# with tags...
rval, out, err = execute('pifmod -i data/pif.json -o data/test.pif ' \
'property --tag="Hello World" foo=bar')
with open('data/out_tags.pif') as ifs:
expected = pif.load(ifs)
with open('data/test.pif') as ifs:
received = pif.load(ifs)
assert rval == 0
assert empty(out)
assert empty(err)
assert compare_dictionaries(expected.as_dictionary(),
received.as_dictionary()), \
'{}'.format(strdiff(pif.dumps(expected), pif.dumps(received)))
def test_property_add_contacts_Ifile(self):
# with contacts...
rval, out, err = execute('pifmod -i data/pif.json -o data/test.pif ' \
'property --contact="Branden Kappes,[email protected]" ' \
'foo=bar')
with open('data/out_contact.pif') as ifs:
expected = pif.load(ifs)
with open('data/test.pif') as ifs:
received = pif.load(ifs)
assert rval == 0
assert empty(out)
assert empty(err)
assert compare_dictionaries(expected.as_dictionary(),
received.as_dictionary()), \
'{}'.format(strdiff(pif.dumps(expected), pif.dumps(received)))
def test_linkages_sagittariidae(self):
# try:
with open('data/package.json') as ifs:
pifdata = pif.load(ifs)
add_link = sagittariidae.link_factory(
projectID='nq3X4-concept-inconel718',
host='http://sagittariidae.adapt.mines.edu')
for p in pifdata:
add_link(p)
with open('delme.json', 'w') as ofs:
pif.dump(pifdata, ofs)
def test_auto_dft():
"""Test that auto-format works"""
argv = "tests/dft/B.hR12".split()
args = get_cli().parse_args(args=argv)
main(args)
# Make sure both files are processed
assert exists(
"tests/dft/B.hR12/pif.json"), "Expected to find output pif for B.hR12"
assert not exists("tests/dft/B.hR105/pif.json"
), "Did not expect to find output pif for B.hR105"
# Check basic parsing
with open("tests/dft/B.hR12/pif.json", "r") as f:
bhr12 = pif.load(f)[0]
assert bhr12.chemical_formula == "B12"
def test_recursive_dft():
"""Test that recursive application of the DFT ingester works"""
argv = "tests/dft dft -r".split()
args = get_cli().parse_args(args=argv)
main(args)
# Make sure both files are processed
assert exists(
"tests/dft/B.hR12/pif.json"), "Expected to find output pif for B.hR12"
assert exists("tests/dft/B.hR105/pif.json"
), "Expected to find output pif for B.hR105"
# Check basic parsing
with open("tests/dft/B.hR12/pif.json", "r") as f:
bhr12 = pif.load(f)
assert bhr12.chemical_formula == "B12"
def test_recursive_dft():
"""Test that recursive application of the DFT ingester works"""
argv = "tests/dft -f dft -m tests/dft/metadata.json -r".split()
args = get_cli().parse_args(args=argv)
main(args)
# Make sure both files are processed
assert exists(
"tests/dft/B.hR12/pif.json"), "Expected to find output pif for B.hR12"
assert exists("tests/dft/B.hR105/pif.json"
), "Expected to find output pif for B.hR105"
# Check basic parsing
with open("tests/dft/B.hR12/pif.json", "r") as f:
bhr12 = pif.load(f)[0]
assert bhr12.chemical_formula == "B12"
assert len(bhr12.contacts) == 2
emails = set(["*****@*****.**", "*****@*****.**"])
assert set(x.email for x in bhr12.contacts) == emails
def test_csv_generator():
"""Test that generator-returning ingesters work"""
argv = "tests/csv/template_example.csv".split()
args = get_cli().parse_args(args=argv)
main(args)
# Make sure both files are processed
expected_name = "tests/csv/template_example.csv_pif.json"
assert exists(expected_name), "Expected to find output pif for template_example"
# Check basic parsing
with open(expected_name, "r") as f:
csv_pif = pif.load(f)
assert csv_pif[0].names[0] == 'P20 Tool steel'
assert csv_pif[0].sub_systems[0].names[0] == 'Martensite'
assert csv_pif[0].sub_systems[0].quantity.ideal_mass_percent.value == '80'
assert csv_pif[0].contacts[0].name == 'Jo Hill'
assert csv_pif[0].contacts[0].email == '*****@*****.**'
assert csv_pif[0].contacts[2].name == 'Mary'
assert csv_pif[0].contacts[2].url == 'http://jo'
def test_dft_csv_merge():
"""Test that merge works works"""
argv = "tests/merge/1000000.cif -f merge".split()
args = get_cli().parse_args(args=argv)
main(args)
# Make sure there is an output
assert exists("tests/merge/1000000.cif_pif.json"
), "Expected to find output pif for 1000000.cif"
# Check that one property from each ingester is included
with open("tests/merge/1000000.cif_pif.json", "r") as f:
merged = pif.load(f)[0]
# This is from the calphad tdb ingester
assert next(
(x for x in merged.properties if x.name == "Thermodynamic database"),
None) != None
# This is from the CIF ingester
space_group = next(
(x for x in merged.properties if x.name == "Space group symbol"), None)
assert (space_group.scalars[0].value == "P2_1/c")
from pypif import pif
from pypif.obj import *
import csv
import json
# Open the json file that contains the pifs
json_file = open("pifs.json")
# Load json with pif
pifs = pif.load(json_file)
# Find all the CSV headers
headers = []
for p in pifs:
props = p.properties
names = []
for i in props:
names.append(i.name)
if len(names) > len(headers):
headers = names
# Possible attributes associated with a pif:
pif_common_objs = []
header = []
# CSV outfile
csv_out = "pifs.csv"
with open(csv_out, 'w', newline='') as outfile:
csvwriter = csv.writer(outfile)
csvwriter.writerow(headers)
# Loop through each pif
def stress_dataframe():
with open(STRESS) as ifs:
pifobj = pif.load(ifs)
return pif_to_dataframe(pifobj)
def strain_dataframe():
with open(STRAIN) as ifs:
pifobj = pif.load(ifs)
return pif_to_dataframe(pifobj)
def test_key_error_case():
with open("./pypif_sdk/readview/tests/csv_pif.pif") as f:
test_case = load(f)
rv = ReadView(test_case)
assert len(rv.keys()) > 0
def sspif():
# stress-strain PIF
with open('{}/data/astm-mark10-aramis.json'.format(HERE)) as ifs:
rval = pif.load(ifs)
return rval