TST: 2 tests fail for mivot #701
Description
============================================================================== FAILURES ===============================================================================
_________________________________________________________________________ test_all_properties _________________________________________________________________________
@pytest.mark.usefixtures("mocked_fps_grvs", "mocked_fps_grp")
@pytest.mark.skipif(not check_astropy_version(), reason="need astropy 6+")
def test_all_properties():
votable_filename = get_pkg_data_filename("data/test.mango_annoter.xml")
votable = parse(votable_filename)
builder = InstancesFromModels(votable, dmid="DR3Name")
# pylint: disable=E501
builder.add_query_origin(
{"service_protocol": "ASU",
"request_date": "2024-03-21T15:16:08",
"request": ("https://vizier.cds.unistra.fr/viz-bin/votable?-oc.form=dec&-out.max=5&"
"-out.add=_r&-out.add=_RAJ,_DEJ&-sort=_r&-c.eq=J2000&-c.r= 2&"
"-c.u=arcmin&-c.geom=r&-source=I/355/gaiadr3&-order=I&"
"-out.orig=standard&-out=DR3Name&-out=RA_ICRS&-out=DE_ICRS&"
"-out=Source&-out=e_RA_ICRS&-out=e_DE_ICRS&-out=Plx&"
"-out=e_Plx&-out=PM&-out=pmRA&-out=e_pmRA&-out=pmDE&"
"-out=e_pmDE&-out=RADEcor&-out=RAPlxcor&-out=RApmRAcor&"
"-out=RApmDEcor&-out=DEPlxcor&-out=DEpmRAcor&-out=DEpmDEcor&"
"-out=PlxpmRAcor&-out=PlxpmDEcor&-out=pmRApmDEcor&-out=RV&"
"-out=e_RV&-out=Vbroad&-out=GRVSmag&-out=QSO&-out=Gal&-out=NSS&"
"-out=XPcont&-out=XPsamp&-out=RVS&-out=EpochPh&-out=EpochRV&"
"-out=MCMCGSP&-out=MCMCMSC&-out=And&-out=Teff&-out=logg&"
"-out=[Fe/H]&-out=Dist&-out=A0&-out=HIP&-out=PS1&-out=SDSS13&"
"-out=SKYM2&-out=TYC2&-out=URAT1&-out=AllWISE&-out=APASS9&"
"-out=GSC23&-out=RAVE5&-out=2MASS&-out=RAVE6&-out=RAJ2000&"
"-out=DEJ2000&"),
"contact": "cds-question@unistra.fr",
"server_software": "7.33.3",
"publisher": "CDS",
"dataOrigin": [{"ivoid": "ivo://cds.vizier/i/355",
"creators": ["Gaia collaboration"],
"cites": "bibcode:2022yCat.1355....0G, ""doi:10.26093/cds/vizier.1355",
"original_date": "2022",
"reference_url": "https://cdsarc.cds.unistra.fr/viz-bin/cat/I/355",
"rights_uri": "https://cds.unistra.fr/vizier-org/licences_vizier.html",
"articles": [{"identifier": "doi:10.1051/0004-6361/202039657e]",
"editor": "A&A"}]
}]
})
add_color(builder)
add_photometry(builder)
add_epoch_positon(builder)
> builder.pack_into_votable()
pyvo/mivot/tests/test_mango_annoter.py:155:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pyvo/mivot/writer/instances_from_models.py:721: in pack_into_votable
self._annotation.build_mivot_block()
pyvo/utils/prototype.py:150: in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
pyvo/mivot/writer/annotations.py:196: in build_mivot_block
self.check_xml()
pyvo/utils/prototype.py:150: in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
pyvo/mivot/writer/annotations.py:306: in check_xml
schema = xmlschema.XMLSchema11(os.path.dirname(__file__) + "/mivot-v1.xsd")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/local/lib/python3.11/site-packages/xmlschema/validators/schemas.py:481: in __init__
self.maps.loader.load_declared_schemas(self)
/usr/local/lib/python3.11/site-packages/xmlschema/loaders.py:149: in load_declared_schemas
self.import_namespace(schema, namespace, url)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <xmlschema.loaders.SchemaLoader object at 0x64f97b7d130>, schema = XMLSchema11(name='mivot-v1.xsd', namespace='http://www.ivoa.net/xml/mivot')
namespace = 'http://www.ivoa.net/xml/VOTable/v1.3', location = 'http://www.ivoa.net/xml/VOTable/v1.3'
def import_namespace(self, schema: SchemaType,
namespace: str,
location: Optional[str] = None) -> None:
import_error: Optional[Exception] = None
locations = self.get_locations(namespace, location)
for url in locations:
try:
logger.info("Import namespace %r from %r", namespace, url)
self.import_schema(schema, namespace, url, schema.base_url)
except (OSError, XMLResourceBlocked, XMLResourceForbidden) as err:
# It's not an error if the location access fails (ref. section 4.2.6.2):
# https://www.w3.org/TR/2012/REC-xmlschema11-1-20120405/#composition-schemaImport
#
# Also consider block or defuse of XML data as a location access fail.
self.missing_locations.add(url)
logger.debug('%s', err)
if import_error is None:
import_error = err
except (XMLSchemaParseError, XMLSchemaTypeError, XMLResourceParseError) as err:
if namespace:
msg = _("import of namespace {!r} failed: {}").format(namespace, err)
else:
msg = _("import of chameleon schema failed: {}").format(err)
if isinstance(err, (XMLSchemaParseError, XMLResourceParseError)):
schema.parse_error(msg)
else:
raise type(err)(msg)
except XMLSchemaValueError as err:
schema.parse_error(err)
else:
logger.info("Namespace %r imported from %r", namespace, url)
break
else:
if import_error is not None:
msg = _("Import of namespace {!r} from {!r} failed: {}.")
schema.warnings.append(msg.format(namespace, locations, str(import_error)))
> warnings.warn(schema.warnings[-1], XMLSchemaImportWarning, stacklevel=4)
E xmlschema.validators.exceptions.XMLSchemaImportWarning: Import of namespace 'http://www.ivoa.net/xml/VOTable/v1.3' from ['http://www.ivoa.net/xml/VOTable/v1.3'] failed: can't access to resource 'http://www.ivoa.net/xml/VOTable/v1.3': An attempt was made to connect to the internet by a test that was not marked `remote_data`. The requested host was: www.ivoa.net.
/usr/local/lib/python3.11/site-packages/xmlschema/loaders.py:244: XMLSchemaImportWarning
-------------------------------------------------------------------------- Captured log call --------------------------------------------------------------------------
WARNING root:instances_from_models.py:210 An instance with dmid=GAIA_GAIA3_Grvs_AB has already been stored in GLOBALS: skip
WARNING root:instances_from_models.py:77 Ref frame spaceRefFrame is not in ['eq_FK4', 'FK4', 'eq_FK5', 'FK5', 'ICRS', 'GALACTIC', 'SUPER_GALACTIC', 'ECLIPTIC'], make sure there is no typo
WARNING root:instances_from_models.py:77 Ref frame refPosition is not in ['BARYCENTER', 'GEOCENTER', 'TOPOCENTER'], make sure there is no typo
_________________________________________________________________ test_extraction_from_votable_header _________________________________________________________________
@pytest.mark.skipif(not check_astropy_version(), reason="need astropy 6+")
def test_extraction_from_votable_header():
""" test that the automatic mapping extraction is well connected with the annoter
"""
votable_filename = get_pkg_data_filename("data/test.header_extraction.1.xml")
votable = parse(votable_filename)
builder = InstancesFromModels(votable, dmid="URAT1")
builder.extract_frames()
builder.extract_data_origin()
epoch_position_mapping = builder.extract_epoch_position_parameters()
builder.add_mango_epoch_position(**epoch_position_mapping)
> builder.pack_into_votable()
pyvo/mivot/tests/test_mango_annoter.py:174:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
pyvo/mivot/writer/instances_from_models.py:721: in pack_into_votable
self._annotation.build_mivot_block()
pyvo/utils/prototype.py:150: in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
pyvo/mivot/writer/annotations.py:196: in build_mivot_block
self.check_xml()
pyvo/utils/prototype.py:150: in wrapper
return function(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^
pyvo/mivot/writer/annotations.py:306: in check_xml
schema = xmlschema.XMLSchema11(os.path.dirname(__file__) + "/mivot-v1.xsd")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
/usr/local/lib/python3.11/site-packages/xmlschema/validators/schemas.py:481: in __init__
self.maps.loader.load_declared_schemas(self)
/usr/local/lib/python3.11/site-packages/xmlschema/loaders.py:149: in load_declared_schemas
self.import_namespace(schema, namespace, url)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
self = <xmlschema.loaders.SchemaLoader object at 0x64f97b7c820>, schema = XMLSchema11(name='mivot-v1.xsd', namespace='http://www.ivoa.net/xml/mivot')
namespace = 'http://www.ivoa.net/xml/VOTable/v1.3', location = 'http://www.ivoa.net/xml/VOTable/v1.3'
def import_namespace(self, schema: SchemaType,
namespace: str,
location: Optional[str] = None) -> None:
import_error: Optional[Exception] = None
locations = self.get_locations(namespace, location)
for url in locations:
try:
logger.info("Import namespace %r from %r", namespace, url)
self.import_schema(schema, namespace, url, schema.base_url)
except (OSError, XMLResourceBlocked, XMLResourceForbidden) as err:
# It's not an error if the location access fails (ref. section 4.2.6.2):
# https://www.w3.org/TR/2012/REC-xmlschema11-1-20120405/#composition-schemaImport
#
# Also consider block or defuse of XML data as a location access fail.
self.missing_locations.add(url)
logger.debug('%s', err)
if import_error is None:
import_error = err
except (XMLSchemaParseError, XMLSchemaTypeError, XMLResourceParseError) as err:
if namespace:
msg = _("import of namespace {!r} failed: {}").format(namespace, err)
else:
msg = _("import of chameleon schema failed: {}").format(err)
if isinstance(err, (XMLSchemaParseError, XMLResourceParseError)):
schema.parse_error(msg)
else:
raise type(err)(msg)
except XMLSchemaValueError as err:
schema.parse_error(err)
else:
logger.info("Namespace %r imported from %r", namespace, url)
break
else:
if import_error is not None:
msg = _("Import of namespace {!r} from {!r} failed: {}.")
schema.warnings.append(msg.format(namespace, locations, str(import_error)))
> warnings.warn(schema.warnings[-1], XMLSchemaImportWarning, stacklevel=4)
E xmlschema.validators.exceptions.XMLSchemaImportWarning: Import of namespace 'http://www.ivoa.net/xml/VOTable/v1.3' from ['http://www.ivoa.net/xml/VOTable/v1.3'] failed: can't access to resource 'http://www.ivoa.net/xml/VOTable/v1.3': An attempt was made to connect to the internet by a test that was not marked `remote_data`. The requested host was: www.ivoa.net.
/usr/local/lib/python3.11/site-packages/xmlschema/loaders.py:244: XMLSchemaImportWarning
-------------------------------------------------------------------------- Captured log call --------------------------------------------------------------------------
WARNING root:instances_from_models.py:302 A spaceSys instance with dmid=_spaceframe_ICRS_BARYCENTER has already been stored in GLOBALS: skip
WARNING root:instances_from_models.py:302 A spaceSys instance with dmid=_spaceframe_eq_FK5_J2000_BARYCENTER has already been stored in GLOBALS: skip
======================================================================= short test summary info =======================================================================
SKIPPED [63] ../../../../../local/lib/python3.11/site-packages/pytest_remotedata/plugin.py:81: need --remote-data option to run
======================================================== 2 failed, 398 passed, 63 skipped, 1 xfailed in 10.04s ========================================================
*** Error code 1
Version: 1.7
Python-3.11
FreeBSd 14.3