def test_get_provenance_document_for_id(tmpdir):
asdf_filename = os.path.join(tmpdir.strpath, "test.h5")
data_set = ASDFDataSet(asdf_filename)
filename = os.path.join(data_dir,
"example_schematic_processing_chain.xml")
doc = prov.read(filename)
data_set.provenance["test_provenance"] = doc
assert data_set.provenance.get_provenance_document_for_id(
'{http://seisprov.org/seis_prov/0.1/#}sp002_dt_f87sf7sf78') == \
{"name": "test_provenance", "document": doc}
assert data_set.provenance.get_provenance_document_for_id(
'{http://seisprov.org/seis_prov/0.1/#}sp004_lp_f87sf7sf78') == \
{"name": "test_provenance", "document": doc}
# Id not found.
with pytest.raises(ASDFValueError) as err:
data_set.provenance.get_provenance_document_for_id(
'{http://seisprov.org/seis_prov/0.1/#}bogus_id')
assert err.value.args[0] == (
"Document containing id "
"'{http://seisprov.org/seis_prov/0.1/#}bogus_id'"
" not found in the data set.")
# Not a qualified id.
with pytest.raises(ASDFValueError) as err:
data_set.provenance.get_provenance_document_for_id("bla")
assert err.value.args[0] == ("Not a valid qualified name.")
data_set.__del__()
def __validate_seis_prov(file_object):
"""
Core validation function.
:param file_object: Open file or file-like object.
"""
original_position = file_object.tell()
# Step 1: Check and read the JSON schema.
json_schema = _check_json_schema()
# Determine file type.
is_json = _is_json_file(file_object)
file_object.seek(original_position, 0)
is_xml = _is_xml_file(file_object)
file_object.seek(original_position, 0)
if is_json is False and is_xml is False:
_log_error("File is neither a valid JSON nor a valid XML file.")
elif is_json is True and is_xml is True:
# Should not happen for obvious reasons...
raise NotImplementedError
elif is_json:
fileformat = "json"
elif is_xml:
fileformat = "xml"
# Step 2: Attempt to read the provenance file with the prov Python package.
try:
doc = prov.read(file_object, format=fileformat)
except Exception as e:
_log_error("Could not parse the file with the prov Python library due"
" to: the following PROV error message: %s" % (repr(e)))
# Step 3: Validate against the PROV XML XSD Scheme.
_validate_against_xsd_scheme(doc)
# Find the seis prov namespace.
for ns in doc.namespaces:
if ns.uri == SEIS_PROV_NAMESPACE:
break
else:
_log_error("SEIS-PROV namespace not found in document!")
# Step 4: Custom validation against the JSON schema. Validate the root
# document as well as any bundles.
seis_prov_ids = _validate_prov_bundle(doc, json_schema, ns=ns)
for bundle in doc.bundles:
seis_prov_ids.extend(
_validate_prov_bundle(bundle, json_schema, ns=ns))
if not seis_prov_ids:
_log_warning("The document is a valid W3C PROV document but not a "
"single SEIS-PROV record has been found.")
# Find duplicate ids.
duplicates = set([i for i in seis_prov_ids
if sum([1 for a in seis_prov_ids if a == i]) > 1])
if duplicates:
_log_error("One or more ids have been used more than once: %s" %
", ".join(["'%s'" % _i for _i in duplicates]))
def init():
f = open('plan.json', 'r')
doc = prov.read(f)
f.close()
doc.add_namespace('alg', 'https://data-mechanics.s3.amazonaws.com/linshan_luoty/algorithm/') # The scripts in <folder>/<filename> format.
doc.add_namespace('dat', 'https://data-mechanics.s3.amazonaws.com/linshan_luoty/data/') # The data sets in <user>/<collection> format.
doc.add_namespace('ont', 'https://data-mechanics.s3.amazonaws.com/ontology#') # 'Extension', 'DataResource', 'DataSet', 'Retrieval', 'Query', or 'Computation'.
doc.add_namespace('log', 'https://data-mechanics.s3.amazonaws.com/log#') # The event log.
doc.add_namespace('bdp', 'https://data.cityofboston.gov/resource/')
return doc
def test_get_ids_from_prov_document():
filename = os.path.join(data_dir, "example_schematic_processing_chain.xml")
doc = prov.read(filename, format="xml")
ids = get_all_ids_for_prov_document(doc)
assert ids == [
'{http://seisprov.org/seis_prov/0.1/#}sp001_wf_a34j4didj3',
'{http://seisprov.org/seis_prov/0.1/#}sp002_dt_f87sf7sf78',
'{http://seisprov.org/seis_prov/0.1/#}sp003_wf_js83hf34aj',
'{http://seisprov.org/seis_prov/0.1/#}sp004_lp_f87sf7sf78',
'{http://seisprov.org/seis_prov/0.1/#}sp005_wf_378f8ks8kd',
'{http://seisprov.org/seis_prov/0.1/#}sp006_dc_f87sf7sf78',
'{http://seisprov.org/seis_prov/0.1/#}sp007_wf_jude89du8l']
def test_provenance_list_command(tmpdir):
asdf_filename = os.path.join(tmpdir.strpath, "test.h5")
data_set = ASDFDataSet(asdf_filename)
filename = os.path.join(data_dir,
"example_schematic_processing_chain.xml")
# Add it as a document.
doc = prov.read(filename, format="xml")
data_set.add_provenance_document(doc, name="test_provenance")
assert data_set.provenance.list() == ["test_provenance"]
def test_get_ids_from_prov_document():
filename = os.path.join(data_dir, "example_schematic_processing_chain.xml")
doc = prov.read(filename, format="xml")
ids = get_all_ids_for_prov_document(doc)
assert ids == [
'{http://seisprov.org/seis_prov/0.1/#}sp001_wf_a34j4didj3',
'{http://seisprov.org/seis_prov/0.1/#}sp002_dt_f87sf7sf78',
'{http://seisprov.org/seis_prov/0.1/#}sp003_wf_js83hf34aj',
'{http://seisprov.org/seis_prov/0.1/#}sp004_lp_f87sf7sf78',
'{http://seisprov.org/seis_prov/0.1/#}sp005_wf_378f8ks8kd',
'{http://seisprov.org/seis_prov/0.1/#}sp006_dc_f87sf7sf78',
'{http://seisprov.org/seis_prov/0.1/#}sp007_wf_jude89du8l']
def test_wps_subset_cmip6_prov():
client = client_for(Service(processes=[Subset()], cfgfiles=[PYWPS_CFG]))
datainputs = "collection=CMIP6.CMIP.IPSL.IPSL-CM6A-LR.historical.r1i1p1f1.Amon.rlds.gr.v20180803"
datainputs += ";time=1860-01-01/1900-12-30;area=1,1,300,89"
resp = client.get(
"?service=WPS&request=Execute&version=1.0.0&identifier=subset&datainputs={}"
.format(datainputs))
assert_response_success(resp)
doc = prov.read(get_output(resp.xml)["prov"][len("file://"):])
assert ('roocs:time="1860-01-01/1900-12-30", roocs:area="1,1,300,89"'
in doc.get_provn())
assert (
"wasDerivedFrom(roocs:rlds_Amon_IPSL-CM6A-LR_historical_r1i1p1f1_gr_18600116-19001216.nc, roocs:CMIP6.CMIP.IPSL.IPSL-CM6A-LR.historical.r1i1p1f1.Amon.rlds.gr.v20180803" # noqa
in doc.get_provn())
def test_prov(path):
def drop_blank(lines):
return set(line for line in lines if line.strip())
provenance = prov.read(path, format='json')
output = StringIO()
# In production, we won't output PROV-N,
# but for tests, it's easy for a human to read, and easy to compare.
serializer = prov.serializers.provn.ProvNSerializer(provenance)
serializer.serialize(output)
actual = output.getvalue()
actual_lines = drop_blank(actual.split('\n'))
with open(Path(path).parent.parent / 'expected.prov') as prov_fixture:
expected_lines = drop_blank(prov_fixture.read().split('\n'))
assert actual_lines == expected_lines
def test_adding_a_provenance_record(tmpdir):
"""
Tests adding a provenance record.
"""
asdf_filename = os.path.join(tmpdir.strpath, "test.h5")
data_set = ASDFDataSet(asdf_filename)
filename = os.path.join(data_dir, "example_schematic_processing_chain.xml")
# Add it as a document.
doc = prov.read(filename, format="xml")
data_set.add_provenance_document(doc, name="test_provenance")
del data_set
# Read it again.
data_set = ASDFDataSet(asdf_filename)
assert data_set.provenance.test_provenance == doc
def test_wps_subset_cmip6_multiple_files_prov():
client = client_for(Service(processes=[Subset()], cfgfiles=[PYWPS_CFG]))
datainputs = "collection=CMIP6.CMIP.MPI-M.MPI-ESM1-2-HR.historical.r1i1p1f1.SImon.siconc.gn.latest"
datainputs += ";time=1850-01-01/2013-12-30"
resp = client.get(
"?service=WPS&request=Execute&version=1.0.0&identifier=subset&datainputs={}"
.format(datainputs))
assert_response_success(resp)
doc = prov.read(get_output(resp.xml)["prov"][len("file://"):])
print(doc.get_provn())
assert 'roocs:time="1850-01-01/2013-12-30"' in doc.get_provn()
assert (
"wasDerivedFrom(roocs:siconc_SImon_MPI-ESM1-2-HR_historical_r1i1p1f1_gn_18500116-18960316.nc, roocs:CMIP6.CMIP.MPI-M.MPI-ESM1-2-HR.historical.r1i1p1f1.SImon.siconc.gn.latest" # noqa
in doc.get_provn())
assert (
"wasDerivedFrom(roocs:siconc_SImon_MPI-ESM1-2-HR_historical_r1i1p1f1_gn_18960416-19420616.nc, roocs:CMIP6.CMIP.MPI-M.MPI-ESM1-2-HR.historical.r1i1p1f1.SImon.siconc.gn.latest" # noqa
in doc.get_provn())
def init():
f = open('plan.json', 'r')
doc = prov.read(f)
f.close()
doc.add_namespace(
'alg',
'https://data-mechanics.s3.amazonaws.com/linshan_luoty/algorithm/'
) # The scripts in <folder>/<filename> format.
doc.add_namespace(
'dat', 'https://data-mechanics.s3.amazonaws.com/linshan_luoty/data/'
) # The data sets in <user>/<collection> format.
doc.add_namespace(
'ont', 'https://data-mechanics.s3.amazonaws.com/ontology#'
) # 'Extension', 'DataResource', 'DataSet', 'Retrieval', 'Query', or 'Computation'.
doc.add_namespace(
'log',
'https://data-mechanics.s3.amazonaws.com/log#') # The event log.
doc.add_namespace('bdp', 'https://data.cityofboston.gov/resource/')
return doc
def test_trying_to_add_provenance_record_with_invalid_name_fails(tmpdir):
"""
The name must be valid according to a particular regular expression.
"""
asdf_filename = os.path.join(tmpdir.strpath, "test.h5")
data_set = ASDFDataSet(asdf_filename)
filename = os.path.join(data_dir, "example_schematic_processing_chain.xml")
# First try adding it as a prov document.
doc = prov.read(filename, format="xml")
with pytest.raises(ASDFValueError) as err:
data_set.add_provenance_document(doc, name="a-b-c")
assert err.value.args[0] == (
"Name 'a-b-c' is invalid. It must validate against the regular "
"expression '^[0-9a-z][0-9a-z_]*[0-9a-z]$'.")
# Must sometimes be called to get around some bugs.
data_set.__del__()
def test_provenance_dicionary_behaviour(tmpdir):
asdf_filename = os.path.join(tmpdir.strpath, "test.h5")
data_set = ASDFDataSet(asdf_filename)
filename = os.path.join(data_dir,
"example_schematic_processing_chain.xml")
# Add it as a document.
doc = prov.read(filename, format="xml")
# Setting via setitem.
data_set.provenance["test_provenance"] = doc
data_set.__del__()
del data_set
new_data_set = ASDFDataSet(asdf_filename)
assert new_data_set.provenance.list() == ["test_provenance"]
assert new_data_set.provenance["test_provenance"] == doc
assert getattr(new_data_set.provenance, "test_provenance") == doc
assert list(new_data_set.provenance.keys()) == ["test_provenance"]
assert list(new_data_set.provenance.values()) == [doc]
assert list(new_data_set.provenance.items()) == [("test_provenance", doc)]
elif o in ("-o", "--outfile"):
outfile = a
elif o in ("-i", "--infile"):
infile = a
elif o in ("-b", "--bindings"):
bindings = a
elif o in ("-3", "--bindver3"):
v3=True
else:
assert False, "unhandled option"
if not infile or not bindings:
sys.exit()
template=prov.read(infile)
bindings_dict=None
if v3:
bindings_dict=dict()
v3_dict=json.load(open(bindings, "r"))
if "context" in v3_dict:
print v3_dict["context"]
namespaces=set()
for k in v3_dict["context"]:
namespaces.add(prov.model.Namespace(k, v3_dict["context"][k]))
template=provconv.set_namespaces(namespaces, template)
if "var" in v3_dict:
for v in v3_dict["var"]:
