def dataset2trace(dataset, headonly=False):
"""Load trace from dataset."""
stats = AttribDict(dataset.attrs)
for key, val in stats.items():
# decode bytes to utf-8 string for py3
if isinstance(val, bytes):
stats[key] = val = val.decode('utf-8')
if _is_utc(val):
stats[key] = UTC(val)
elif key == 'processing':
# this block is only necessary for files written with old obspyh5
# versions (< 0.5.0)
stats[key] = json.loads(val)
jsondata = stats.pop('_json', None)
if jsondata is not None:
for k, v in json.loads(jsondata).items():
stats[k] = v
if headonly:
stats['npts'] = len(dataset)
trace = Trace(header=stats)
else:
trace = Trace(data=dataset[...], header=stats)
return trace
def test_write_with_extra_tags_and_read(self):
"""
Tests that a QuakeML file with additional custom "extra" tags gets
written correctly and that when reading it again the extra tags are
parsed correctly.
"""
filename = os.path.join(self.path, "quakeml_1.2_origin.xml")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
cat = _read_quakeml(filename)
self.assertEqual(len(w), 0)
# add some custom tags to first event:
# - tag with explicit namespace but no explicit ns abbreviation
# - tag without explicit namespace (gets obspy default ns)
# - tag with explicit namespace and namespace abbreviation
my_extra = AttribDict(
{'public': {'value': False,
'namespace': 'http://some-page.de/xmlns/1.0',
'attrib': {'some_attrib': 'some_value',
'another_attrib': 'another_value'}},
'custom': {'value': 'True',
'namespace': 'http://test.org/xmlns/0.1'},
'new_tag': {'value': 1234,
'namespace': 'http://test.org/xmlns/0.1'},
'tX': {'value': UTCDateTime('2013-01-02T13:12:14.600000Z'),
'namespace': 'http://test.org/xmlns/0.1'},
'dataid': {'namespace': 'http://anss.org/xmlns/catalog/0.1',
'type': 'attribute', 'value': '00999999'},
# some nested tags :
'quantity': {'namespace': 'http://some-page.de/xmlns/1.0',
'attrib': {'attrib1': 'attrib_value1',
'attrib2': 'attrib_value2'},
'value': {
'my_nested_tag1': {
'namespace': 'http://some-page.de/xmlns/1.0',
'value': 1.23E10},
'my_nested_tag2': {
'namespace': 'http://some-page.de/xmlns/1.0',
'value': False}}}})
nsmap = {'ns0': 'http://test.org/xmlns/0.1',
'catalog': 'http://anss.org/xmlns/catalog/0.1'}
cat[0].extra = my_extra.copy()
# insert a pick with an extra field
p = Pick()
p.extra = {'weight': {'value': 2,
'namespace': 'http://test.org/xmlns/0.1'}}
cat[0].picks.append(p)
with NamedTemporaryFile() as tf:
tmpfile = tf.name
# write file
cat.write(tmpfile, format='QUAKEML', nsmap=nsmap)
# check contents
with open(tmpfile, 'rb') as fh:
# enforce reproducible attribute orders through write_c14n
obj = etree.fromstring(fh.read()).getroottree()
buf = io.BytesIO()
obj.write_c14n(buf)
buf.seek(0, 0)
content = buf.read()
# check namespace definitions in root element
expected = [b'<q:quakeml',
b'xmlns:catalog="http://anss.org/xmlns/catalog/0.1"',
b'xmlns:ns0="http://test.org/xmlns/0.1"',
b'xmlns:ns1="http://some-page.de/xmlns/1.0"',
b'xmlns:q="http://quakeml.org/xmlns/quakeml/1.2"',
b'xmlns="http://quakeml.org/xmlns/bed/1.2"']
for line in expected:
self.assertIn(line, content)
# check additional tags
expected = [
b'<ns0:custom>True</ns0:custom>',
b'<ns0:new_tag>1234</ns0:new_tag>',
b'<ns0:tX>2013-01-02T13:12:14.600000Z</ns0:tX>',
b'<ns1:public '
b'another_attrib="another_value" '
b'some_attrib="some_value">false</ns1:public>'
]
for line in expected:
self.assertIn(line, content)
# now, read again to test if it's parsed correctly..
cat = _read_quakeml(tmpfile)
# when reading..
# - namespace abbreviations should be disregarded
# - we always end up with a namespace definition, even if it was
# omitted when originally setting the custom tag
# - custom namespace abbreviations should attached to Catalog
self.assertTrue(hasattr(cat[0], 'extra'))
def _tostr(x):
if isinstance(x, bool):
if x:
return str('true')
else:
return str('false')
elif isinstance(x, AttribDict):
for key, value in x.items():
x[key].value = _tostr(value['value'])
return x
else:
return str(x)
for key, value in my_extra.items():
my_extra[key]['value'] = _tostr(value['value'])
self.assertEqual(cat[0].extra, my_extra)
self.assertTrue(hasattr(cat[0].picks[0], 'extra'))
self.assertEqual(
cat[0].picks[0].extra,
{'weight': {'value': '2',
'namespace': 'http://test.org/xmlns/0.1'}})
self.assertTrue(hasattr(cat, 'nsmap'))
self.assertEqual(getattr(cat, 'nsmap')['ns0'], nsmap['ns0'])
def test_write_with_extra_tags_and_read(self):
"""
Tests that a QuakeML file with additional custom "extra" tags gets
written correctly and that when reading it again the extra tags are
parsed correctly.
"""
filename = os.path.join(self.path, "quakeml_1.2_origin.xml")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
cat = readQuakeML(filename)
self.assertEqual(len(w), 0)
# add some custom tags to first event:
# - tag with explicit namespace but no explicit ns abbreviation
# - tag without explicit namespace (gets obspy default ns)
# - tag with explicit namespace and namespace abbreviation
my_extra = AttribDict(
{'public': {'value': False,
'namespace': r"http://some-page.de/xmlns/1.0",
'attrib': {u"some_attrib": u"some_value",
u"another_attrib": u"another_value"}},
'custom': {'value': u"True",
'namespace': r'http://test.org/xmlns/0.1'},
'new_tag': {'value': 1234,
'namespace': r"http://test.org/xmlns/0.1"},
'tX': {'value': UTCDateTime('2013-01-02T13:12:14.600000Z'),
'namespace': r'http://test.org/xmlns/0.1'},
'dataid': {'namespace': r'http://anss.org/xmlns/catalog/0.1',
'type': 'attribute', 'value': '00999999'}})
nsmap = {"ns0": r"http://test.org/xmlns/0.1",
"catalog": r'http://anss.org/xmlns/catalog/0.1'}
cat[0].extra = my_extra.copy()
# insert a pick with an extra field
p = Pick()
p.extra = {'weight': {'value': 2,
'namespace': r"http://test.org/xmlns/0.1"}}
cat[0].picks.append(p)
with NamedTemporaryFile() as tf:
tmpfile = tf.name
# write file
cat.write(tmpfile, format="QUAKEML", nsmap=nsmap)
# check contents
with open(tmpfile, "r") as fh:
content = fh.read()
# check namespace definitions in root element
expected = ['<q:quakeml',
'xmlns:catalog="http://anss.org/xmlns/catalog/0.1"',
'xmlns:ns0="http://test.org/xmlns/0.1"',
'xmlns:ns1="http://some-page.de/xmlns/1.0"',
'xmlns:q="http://quakeml.org/xmlns/quakeml/1.2"',
'xmlns="http://quakeml.org/xmlns/bed/1.2"']
for line in expected:
self.assertTrue(line in content)
# check additional tags
expected = [
'<ns0:custom>True</ns0:custom>',
'<ns0:new_tag>1234</ns0:new_tag>',
'<ns0:tX>2013-01-02T13:12:14.600000Z</ns0:tX>',
'<ns1:public '
'another_attrib="another_value" '
'some_attrib="some_value">false</ns1:public>'
]
for lines in expected:
self.assertTrue(line in content)
# now, read again to test if its parsed correctly..
cat = readQuakeML(tmpfile)
# when reading..
# - namespace abbreviations should be disregarded
# - we always end up with a namespace definition, even if it was
# omitted when originally setting the custom tag
# - custom namespace abbreviations should attached to Catalog
self.assertTrue(hasattr(cat[0], "extra"))
def _tostr(x):
if isinstance(x, bool):
if x:
return str("true")
else:
return str("false")
return str(x)
for key, value in my_extra.items():
my_extra[key]['value'] = _tostr(value['value'])
self.assertEqual(cat[0].extra, my_extra)
self.assertTrue(hasattr(cat[0].picks[0], "extra"))
self.assertEqual(
cat[0].picks[0].extra,
{'weight': {'value': '2',
'namespace': r'http://test.org/xmlns/0.1'}})
self.assertTrue(hasattr(cat, "nsmap"))
self.assertTrue(getattr(cat, "nsmap")['ns0'] == nsmap['ns0'])
def test_write_with_extra_tags_and_read(self):
"""
Tests that a QuakeML file with additional custom "extra" tags gets
written correctly and that when reading it again the extra tags are
parsed correctly.
"""
filename = os.path.join(self.path, "quakeml_1.2_origin.xml")
with warnings.catch_warnings(record=True) as w:
warnings.simplefilter("always")
cat = _read_quakeml(filename)
self.assertEqual(len(w), 0)
# add some custom tags to first event:
# - tag with explicit namespace but no explicit ns abbreviation
# - tag without explicit namespace (gets obspy default ns)
# - tag with explicit namespace and namespace abbreviation
my_extra = AttribDict(
{
"public": {
"value": False,
"namespace": "http://some-page.de/xmlns/1.0",
"attrib": {"some_attrib": "some_value", "another_attrib": "another_value"},
},
"custom": {"value": "True", "namespace": "http://test.org/xmlns/0.1"},
"new_tag": {"value": 1234, "namespace": "http://test.org/xmlns/0.1"},
"tX": {"value": UTCDateTime("2013-01-02T13:12:14.600000Z"), "namespace": "http://test.org/xmlns/0.1"},
"dataid": {"namespace": "http://anss.org/xmlns/catalog/0.1", "type": "attribute", "value": "00999999"},
# some nested tags :
"quantity": {
"namespace": "http://some-page.de/xmlns/1.0",
"attrib": {"attrib1": "attrib_value1", "attrib2": "attrib_value2"},
"value": {
"my_nested_tag1": {"namespace": "http://some-page.de/xmlns/1.0", "value": 1.23e10},
"my_nested_tag2": {"namespace": "http://some-page.de/xmlns/1.0", "value": False},
},
},
}
)
nsmap = {"ns0": "http://test.org/xmlns/0.1", "catalog": "http://anss.org/xmlns/catalog/0.1"}
cat[0].extra = my_extra.copy()
# insert a pick with an extra field
p = Pick()
p.extra = {"weight": {"value": 2, "namespace": "http://test.org/xmlns/0.1"}}
cat[0].picks.append(p)
with NamedTemporaryFile() as tf:
tmpfile = tf.name
# write file
cat.write(tmpfile, format="QUAKEML", nsmap=nsmap)
# check contents
with open(tmpfile, "rb") as fh:
# enforce reproducible attribute orders through write_c14n
obj = etree.fromstring(fh.read()).getroottree()
buf = io.BytesIO()
obj.write_c14n(buf)
buf.seek(0, 0)
content = buf.read()
# check namespace definitions in root element
expected = [
b"<q:quakeml",
b'xmlns:catalog="http://anss.org/xmlns/catalog/0.1"',
b'xmlns:ns0="http://test.org/xmlns/0.1"',
b'xmlns:ns1="http://some-page.de/xmlns/1.0"',
b'xmlns:q="http://quakeml.org/xmlns/quakeml/1.2"',
b'xmlns="http://quakeml.org/xmlns/bed/1.2"',
]
for line in expected:
self.assertIn(line, content)
# check additional tags
expected = [
b"<ns0:custom>True</ns0:custom>",
b"<ns0:new_tag>1234</ns0:new_tag>",
b"<ns0:tX>2013-01-02T13:12:14.600000Z</ns0:tX>",
b"<ns1:public " b'another_attrib="another_value" ' b'some_attrib="some_value">false</ns1:public>',
]
for line in expected:
self.assertIn(line, content)
# now, read again to test if it's parsed correctly..
cat = _read_quakeml(tmpfile)
# when reading..
# - namespace abbreviations should be disregarded
# - we always end up with a namespace definition, even if it was
# omitted when originally setting the custom tag
# - custom namespace abbreviations should attached to Catalog
self.assertTrue(hasattr(cat[0], "extra"))
def _tostr(x):
if isinstance(x, bool):
if x:
return str("true")
else:
return str("false")
elif isinstance(x, AttribDict):
for key, value in x.items():
x[key].value = _tostr(value["value"])
return x
else:
return str(x)
for key, value in my_extra.items():
my_extra[key]["value"] = _tostr(value["value"])
self.assertEqual(cat[0].extra, my_extra)
self.assertTrue(hasattr(cat[0].picks[0], "extra"))
self.assertEqual(cat[0].picks[0].extra, {"weight": {"value": "2", "namespace": "http://test.org/xmlns/0.1"}})
self.assertTrue(hasattr(cat, "nsmap"))
self.assertEqual(getattr(cat, "nsmap")["ns0"], nsmap["ns0"])
