def initialize_material(self):
# setup input data
self.kwargs = self.material.kwargs
# setup the first, last indices
self.real_space_first = self.material.real_space_first
self.real_space_last = self.material.real_space_last
data = load_data(self.material.real_space_filename)
self.r = data[:, get_index_of_function("r", RealSpaceHeaders)]
self.gofr = data[:, get_index_of_function("g(r)", RealSpaceHeaders)]
self.GofR = data[:, get_index_of_function("G(r)", RealSpaceHeaders)]
self.GKofR = data[:, get_index_of_function("GK(r)", RealSpaceHeaders)]
# targets for 1st peaks
self.gofr_ff_target = self.material.gofr_ff_target
self.GofR_ff_target = self.material.GofR_ff_target
self.GKofR_ff_target = self.material.GKofR_ff_target
data = load_data(self.material.reciprocal_space_filename)
self.q = data[:, get_index_of_function("Q", ReciprocalSpaceHeaders)]
self.sq = data[:,
get_index_of_function("S(Q)", ReciprocalSpaceHeaders)]
self.fq = data[:,
get_index_of_function("Q[S(Q)-1]",
ReciprocalSpaceHeaders)]
self.fq_keen = data[:,
get_index_of_function("FK(Q)",
ReciprocalSpaceHeaders)]
self.dcs = data[:,
get_index_of_function("DCS(Q)", ReciprocalSpaceHeaders
)]
def test_sample3():
dir = Path('tests/sample_3')
gt_BoundingBoxes = load_data(dir / 'groundtruths.json')
pd_BoundingBoxes = load_data(dir / 'detections.json')
RESULT0_5 = json.load(open(dir / 'expected0_5.json'))
results = get_pascal_voc_metrics(gt_BoundingBoxes, pd_BoundingBoxes, .5)
assert_results(results, RESULT0_5, 'ap')
assert_results(results, RESULT0_5, 'precision')
assert_results(results, RESULT0_5, 'recall')
results = get_pascal_voc_metrics(gt_BoundingBoxes, pd_BoundingBoxes, .3)
assert_results(results, RESULT0_3, 'ap')
def test_get_signatures_with_digest_reference(hostname):
all_signatures = signatures_matching = json.loads(load_data("sigs_with_reference"))
signatures_matching["data"] = all_signatures["data"][0:2]
manifest_to_search = "sha256:dummy-manifest-digest-1"
reference_to_search = (
"registry.redhat.io/e2e-container/rhel-8-e2e-container-test-"
"product:latest,registry.access.redhat.com/e2e-container/rhel-8-e2e-container-test-"
"product:latest"
)
url_with_digest_ref = (
"{0}v1/signatures?filter=manifest_digest=in=({1}),reference=in=({2})".format(
hostname, manifest_to_search, reference_to_search
)
)
with requests_mock.Mocker() as m:
m.get(
url_with_digest_ref,
json=signatures_matching,
)
my_client = pyxis_client.PyxisClient(hostname, 5, None, 3, True)
res = my_client.get_container_signatures(
manifest_to_search, reference_to_search
)
assert res == signatures_matching["data"]
assert m.request_history[0].url == url_with_digest_ref
def initialize_material(self):
# setup input data
self.kwargs = self.material.kwargs
# setup the tolerance
self.first = self.material.reciprocal_space_first
self.last = self.material.reciprocal_space_last
data = load_data(self.material.reciprocal_space_filename)
self.q = data[:, get_index_of_function("Q", ReciprocalSpaceHeaders)]
self.sq = data[:,
get_index_of_function("S(Q)", ReciprocalSpaceHeaders)]
self.fq = data[:,
get_index_of_function("Q[S(Q)-1]",
ReciprocalSpaceHeaders)]
self.fq_keen = data[:,
get_index_of_function("FK(Q)",
ReciprocalSpaceHeaders)]
self.dcs = data[:,
get_index_of_function("DCS(Q)", ReciprocalSpaceHeaders
)]
# targets for 1st peaks
self.sq_target = self.material.sq_target
self.fq_target = self.material.fq_target
self.fq_keen_target = self.material.fq_keen_target
self.dcs_target = self.material.dcs_target
def test_get_signatures_manifests_file(capsys):
hostname = "https://pyxis.remote.host/"
data_file_path = "@tests/data/manifest_digests.json"
signatures_matching = json.loads(load_data("sigs_with_reference"))
manifest_digest = (
"sha256:dummy-manifest-digest-1,sha256:sha256:dummy-manifest-digest-2")
args = [
"dummy",
"--pyxis-server",
hostname,
"--manifest-digest",
data_file_path,
"--pyxis-ssl-crtfile",
"/root/name.crt",
"--pyxis-ssl-keyfile",
"/root/name.key",
]
expected = json.dumps(signatures_matching["data"],
sort_keys=True,
indent=4,
separators=(",", ": "))
with requests_mock.Mocker() as m:
m.get(
"{0}v1/signatures?filter=manifest_digest=in=({1})".format(
hostname, manifest_digest),
json=signatures_matching,
)
pyxis_ops.get_signatures_main(args)
out, _ = capsys.readouterr()
assert out == expected
def test_get_signatures(capsys, hostname):
all_signatures = signatures_matching = json.loads(
load_data("sigs_with_reference"))
manifest_digest = "sha256:dummy-manifest-digest-1"
reference = "registry.access.redhat.com/e2e-container/rhel-8-e2e-container-test-product:latest"
signatures_matching["data"] = all_signatures["data"][0:3]
args = [
"dummy",
"--pyxis-server",
hostname,
"--manifest-digest",
manifest_digest,
"--reference",
reference,
"--pyxis-ssl-crtfile",
"/root/name.crt",
"--pyxis-ssl-keyfile",
"/root/name.key",
]
expected = json.dumps(signatures_matching["data"],
sort_keys=True,
indent=4,
separators=(",", ": "))
with requests_mock.Mocker() as m:
m.get(
"{0}v1/signatures?filter=manifest_digest=in=({1}),reference=in=({2})"
.format(hostname, manifest_digest, reference),
json=signatures_matching,
)
pyxis_ops.get_signatures_main(args)
out, _ = capsys.readouterr()
assert out == expected
def test_upload_signature_error_timeout(capsys):
"""Test a connection error which persists after a few attempts."""
hostname = "https://pyxis.remote.host/"
data = load_data("signatures")
args = [
"dummy",
"--pyxis-server",
hostname,
"--pyxis-ssl-crtfile",
"/root/name.crt",
"--pyxis-ssl-keyfile",
"/root/name.key",
"--signatures",
data,
]
with requests_mock.Mocker() as m:
m.post("{0}v1/signatures".format(hostname),
exc=requests.exceptions.ConnectTimeout)
with pytest.raises(requests.exceptions.ConnectTimeout):
pyxis_ops.upload_signatures_main(args)
out, err = capsys.readouterr()
assert out == ""
assert err == ""
def test_upload_signature_json(capsys, hostname):
items_to_upload = load_data("signatures")
responses = json.loads(load_response("post_signatures_ok"))
args = [
"dummy",
"--pyxis-server",
hostname,
"--pyxis-ssl-crtfile",
"/root/name.crt",
"--pyxis-ssl-keyfile",
"/root/name.key",
"--signatures",
items_to_upload,
]
with requests_mock.Mocker() as m:
m.post(
urljoin(hostname, "/v1/signatures"),
[{
"status_code": 200,
"json": resp
} for resp in responses],
)
retval = pyxis_ops.upload_signatures_main(args)
assert len(retval) == len(responses)
assert all(ret_item in responses for ret_item in retval)
out, _ = capsys.readouterr()
assert all(resp["signature_data"] in out for resp in responses)
def test_sample2():
dir = Path('tests/sample_2')
gt_BoundingBoxes = load_data(dir / 'groundtruths.json')
pd_BoundingBoxes = load_data(dir / 'detections.json')
RESULT0_5 = json.load(open(dir / 'expected0_5.json'))
results = get_pascal_voc_metrics(gt_BoundingBoxes, pd_BoundingBoxes, .5)
assert_results(results, RESULT0_5, 'ap')
assert_results(results, RESULT0_5, 'precision')
assert_results(results, RESULT0_5, 'recall')
assert_results(results, RESULT0_5, 'tp')
assert_results(results, RESULT0_5, 'fp')
assert_results(results, RESULT0_5, 'num_groundtruth')
assert_results(results, RESULT0_5, 'num_detection')
mAP = MetricPerClass.mAP(results)
assert np.isclose(RESULT0_5['mAP'], mAP, 1e-3), mAP
def test_get_signatures_from_multiple_pages(hostname):
page_1_response = json.loads(load_data("signatures_page1"))
page_2_response = json.loads(load_data("signatures_page2"))
manifest_to_search = (
"sha256:dummy-manifest-digest-1, sha256:dummy-manifest-digest-2"
)
with requests_mock.Mocker() as m:
m.get(
"{0}v1/signatures?filter=manifest_digest=in=({1})".format(
hostname, manifest_to_search
),
json=page_1_response,
)
m.get(
"{0}v1/signatures?filter=manifest_digest=in=({1})&page=1".format(
hostname, manifest_to_search
),
json=page_2_response,
)
my_client = pyxis_client.PyxisClient(hostname, 5, None, 3, True)
res = my_client.get_container_signatures(manifest_to_search, None)
assert res == page_1_response["data"] + page_2_response["data"]
def initialize_material(self):
# setup input data
self.kwargs = self.material.kwargs
# setup the tolerance
self.first = self.material.real_space_first
self.last = self.material.real_space_last
data = load_data(self.material.real_space_filename)
self.r = data[:, get_index_of_function("r", RealSpaceHeaders)]
self.gofr = data[:, get_index_of_function("g(r)", RealSpaceHeaders)]
self.GofR = data[:, get_index_of_function("G(r)", RealSpaceHeaders)]
self.GKofR = data[:, get_index_of_function("GK(r)", RealSpaceHeaders)]
# targets for 1st peaks
self.gofr_target = self.material.gofr_target
self.GofR_target = self.material.GofR_target
self.GKofR_target = self.material.GKofR_target
def test_upload_signatures_server_error_json_detail(capsys):
"""
Test error response with additional details as JSON.
Verify that in case of an erroneus response from the server not only the
status code (e.g. 400) and reason (e.g. "Client Error") are displayed, but
also the response content, because it may contain crucial information.
"""
hostname = "https://pyxis.remote.host/"
data = load_data("signatures")
args = [
"dummy",
"--pyxis-server",
hostname,
"--pyxis-ssl-crtfile",
"/root/name.crt",
"--pyxis-ssl-keyfile",
"/root/name.key",
"--signatures",
data,
]
with requests_mock.Mocker() as m:
m.post(
"{0}v1/signatures".format(hostname),
status_code=400,
reason="Crunchy frog",
text='{"detail": "Extremely nasty"}',
)
err_msg = "400 Client Error: Crunchy frog for url: .+\nExtremely nasty"
with pytest.raises(requests.exceptions.HTTPError, match=err_msg):
pyxis_ops.upload_signatures_main(args)
out, err = capsys.readouterr()
assert out == ""
assert err == ""
def test_upload_signatures_server_error_content(capsys):
"""
Test error response with additional details as non-JSON content.
Verify that in case of an error the extra details from the response are
shown even if we failed to parse the content as JSON.
"""
hostname = "https://pyxis.remote.host/"
data = load_data("signatures")
args = [
"dummy",
"--pyxis-server",
hostname,
"--pyxis-ssl-crtfile",
"/root/name.crt",
"--pyxis-ssl-keyfile",
"/root/name.key",
"--signatures",
data,
]
with requests_mock.Mocker() as m:
m.post(
"{0}v1/signatures".format(hostname),
status_code=400,
reason="Crunchy frog",
text="Extra non-JSON info",
)
err_msg = "400 Client Error: Crunchy frog for url: .+\nExtra non-JSON info"
with pytest.raises(requests.exceptions.HTTPError, match=err_msg):
pyxis_ops.upload_signatures_main(args)
out, err = capsys.readouterr()
assert out == ""
assert err == ""
def busta_rhymes(path='data/shakespeare.txt'):
data = load_data(path)
rhymes = {}
pairs = []
rhyme_sets = []
for sonnet in data:
pairs.extend([(lw(sonnet[i]), lw(sonnet[i + 2]))
for i in range(0, 9, 4)])
pairs.append((lw(sonnet[-2]), lw(sonnet[-1])))
while pairs != []:
rhyme_set = set(pairs.pop())
for i, pair in enumerate(pairs):
if not rhyme_set.isdisjoint(set(pair)):
rhyme_set |= set(pair)
pairs.pop(i)
rhyme_sets.append(rhyme_set)
for rhyme_set in rhyme_sets:
for word in rhyme_set:
s = rhyme_set.copy()
s.discard(word)
rhymes[word] = list(s)
with open('data/rhyming_dictionary.json', 'w') as fh:
fh.write(json.dumps(rhymes))
import json
from pathlib import Path
from podm.podm import get_pascal_voc_metrics
from podm.visualize import plot_precision_recall_curve_all
from tests.utils import load_data
if __name__ == '__main__':
dir = Path('sample_2')
gt_BoundingBoxes = load_data(dir / 'groundtruths.json')
pd_BoundingBoxes = load_data(dir / 'detections.json')
results = get_pascal_voc_metrics(gt_BoundingBoxes, pd_BoundingBoxes, .5)
plot_precision_recall_curve_all(results,
dir / 'plots',
show_interpolated_precision=True)