def _attach_attribute_annotation(node, record):
# Adding a node to show all attributes
attributes = list(
(attr_name, value) for attr_name, value in record.attributes
if attr_name not in PROV_ATTRIBUTE_QNAMES
)
if not attributes:
return # No attribute to display
# Sort the attributes.
attributes = sorted_attributes(record.get_type(), attributes)
ann_rows = [ANNOTATION_START_ROW]
ann_rows.extend(
ANNOTATION_ROW_TEMPLATE % (
attr.uri, escape(six.text_type(attr)),
' href=\"%s\"' % value.uri if isinstance(value, Identifier)
else '',
escape(six.text_type(value)
if not isinstance(value, datetime) else
six.text_type(value.isoformat())))
for attr, value in attributes
)
ann_rows.append(ANNOTATION_END_ROW)
count[3] += 1
annotations = pydot.Node(
'ann%d' % count[3], label='\n'.join(ann_rows),
**ANNOTATION_STYLE
)
dot.add_node(annotations)
dot.add_edge(pydot.Edge(annotations, node, **ANNOTATION_LINK_STYLE))
def _attach_attribute_annotation(node, record):
# Adding a node to show all attributes
attributes = list((attr_name, value)
for attr_name, value in record.attributes
if attr_name not in PROV_ATTRIBUTE_QNAMES)
if not attributes:
return # No attribute to display
# Sort the attributes.
attributes = sorted_attributes(record.get_type(), attributes)
ann_rows = [ANNOTATION_START_ROW]
ann_rows.extend(
ANNOTATION_ROW_TEMPLATE %
(attr.uri, escape(six.text_type(attr)), ' href=\"%s\"' %
value.uri if isinstance(value, Identifier) else '',
escape(
six.text_type(value) if not isinstance(value, datetime)
else six.text_type(value.isoformat())))
for attr, value in attributes)
ann_rows.append(ANNOTATION_END_ROW)
count[3] += 1
annotations = pydot.Node('ann%d' % count[3],
label='\n'.join(ann_rows),
**ANNOTATION_STYLE)
dot.add_node(annotations)
dot.add_edge(pydot.Edge(annotations, node,
**ANNOTATION_LINK_STYLE))
def serialize_bundle(self, bundle, element=None, force_types=False):
"""
Serializes a bundle or document to PROV XML.
:param bundle: The bundle or document.
:param element: The XML element to write to. Will be created if None.
:type force_types: boolean, optional
:param force_types: Will force xsd:types to be written for most
attributes mainly PROV-"attributes", e.g. tags not in the
PROV namespace. Off by default meaning xsd:type attributes will
only be set for prov:type, prov:location, and prov:value as is
done in the official PROV-XML specification. Furthermore the
types will always be set if the Python type requires it. False
is a good default and it should rarely require changing.
"""
# Build the namespace map for lxml and attach it to the root XML
# element.
nsmap = {
ns.prefix: ns.uri
for ns in self.document._namespaces.get_registered_namespaces()
}
if self.document._namespaces._default:
nsmap[None] = self.document._namespaces._default.uri
for namespace in bundle.namespaces:
if namespace not in nsmap:
nsmap[namespace.prefix] = namespace.uri
for key, value in DEFAULT_NAMESPACES.items():
uri = value.uri
if value.prefix == "xsd":
# The XSD namespace for some reason has no hash at the end
# for PROV XML, but for all other serializations it does.
uri = uri.rstrip("#")
nsmap[value.prefix] = uri
if element is not None:
xml_bundle_root = etree.SubElement(element,
_ns_prov("bundleContent"),
nsmap=nsmap)
else:
xml_bundle_root = etree.Element(_ns_prov("document"), nsmap=nsmap)
if bundle.identifier:
xml_bundle_root.attrib[_ns_prov("id")] = str(bundle.identifier)
for record in bundle._records:
rec_type = record.get_type()
identifier = str(
record._identifier) if record._identifier else None
if identifier:
attrs = {_ns_prov("id"): identifier}
else:
attrs = None
# Derive the record label from its attributes which is sometimes
# needed.
attributes = list(record.attributes)
rec_label = self._derive_record_label(rec_type, attributes)
elem = etree.SubElement(xml_bundle_root, _ns_prov(rec_label),
attrs)
for attr, value in sorted_attributes(rec_type, attributes):
subelem = etree.SubElement(
elem, _ns(attr.namespace.uri, attr.localpart))
if isinstance(value, prov.model.Literal):
if value.datatype not in [
None, PROV["InternationalizedString"]
]:
subelem.attrib[_ns_xsi("type")] = "%s:%s" % (
value.datatype.namespace.prefix,
value.datatype.localpart,
)
if value.langtag is not None:
subelem.attrib[_ns_xml("lang")] = value.langtag
v = value.value
elif isinstance(value, prov.model.QualifiedName):
if attr not in PROV_ATTRIBUTE_QNAMES:
subelem.attrib[_ns_xsi("type")] = "xsd:QName"
v = str(value)
elif isinstance(value, datetime.datetime):
v = value.isoformat()
else:
v = str(value)
# xsd type inference.
#
# This is a bit messy and there are all kinds of special
# rules but it appears to get the job done.
#
# If it is a type element and does not yet have an
# associated xsi type, try to infer it from the value.
# The not startswith("prov:") check is a little bit hacky to
# avoid type interference when the type is a standard prov
# type.
#
# To enable a mapping of Python types to XML and back,
# the XSD type must be written for these types.
ALWAYS_CHECK = [
bool,
datetime.datetime,
float,
int,
prov.identifier.Identifier,
]
ALWAYS_CHECK = tuple(ALWAYS_CHECK)
if ((force_types or type(value) in ALWAYS_CHECK
or attr in [PROV_TYPE, PROV_LOCATION, PROV_VALUE])
and _ns_xsi("type") not in subelem.attrib
and not str(value).startswith("prov:")
and not (attr in PROV_ATTRIBUTE_QNAMES and v)
and attr not in [PROV_ATTR_TIME, PROV_LABEL]):
xsd_type = None
if isinstance(value, bool):
xsd_type = XSD_BOOLEAN
v = v.lower()
elif isinstance(value, str):
xsd_type = XSD_STRING
elif isinstance(value, float):
xsd_type = XSD_DOUBLE
elif isinstance(value, int):
xsd_type = XSD_INT
elif isinstance(value, datetime.datetime):
# Exception of the exception, while technically
# still correct, do not write XSD dateTime type for
# attributes in the PROV namespaces as the type is
# already declared in the XSD and PROV XML also does
# not specify it in the docs.
if (attr.namespace.prefix != "prov"
or "time" not in attr.localpart.lower()):
xsd_type = XSD_DATETIME
elif isinstance(value, prov.identifier.Identifier):
xsd_type = XSD_ANYURI
if xsd_type is not None:
subelem.attrib[_ns_xsi("type")] = str(xsd_type)
if attr in PROV_ATTRIBUTE_QNAMES and v:
subelem.attrib[_ns_prov("ref")] = v
else:
subelem.text = v
return xml_bundle_root
def serialize_bundle(self, bundle, element=None, force_types=False):
"""
Serializes a bundle or document to PROV XML.
:param bundle: The bundle or document.
:param element: The XML element to write to. Will be created if None.
:type force_types: boolean, optional
:param force_types: Will force xsd:types to be written for most
attributes mainly PROV-"attributes", e.g. tags not in the
PROV namespace. Off by default meaning xsd:type attributes will
only be set for prov:type, prov:location, and prov:value as is
done in the official PROV-XML specification. Furthermore the
types will always be set if the Python type requires it. False
is a good default and it should rarely require changing.
"""
# Build the namespace map for lxml and attach it to the root XML
# element. No dictionary comprehension in Python 2.6!
nsmap = dict((ns.prefix, ns.uri) for ns in
self.document._namespaces.get_registered_namespaces())
if self.document._namespaces._default:
nsmap[None] = self.document._namespaces._default.uri
for namespace in bundle.namespaces:
if namespace not in nsmap:
nsmap[namespace.prefix] = namespace.uri
for key, value in DEFAULT_NAMESPACES.items():
uri = value.uri
if value.prefix == "xsd":
# The XSD namespace for some reason has no hash at the end
# for PROV XML, but for all other serializations it does.
uri = uri.rstrip("#")
nsmap[value.prefix] = uri
if element is not None:
xml_bundle_root = etree.SubElement(
element, _ns_prov("bundleContent"), nsmap=nsmap)
else:
xml_bundle_root = etree.Element(_ns_prov("document"), nsmap=nsmap)
if bundle.identifier:
xml_bundle_root.attrib[_ns_prov("id")] = six.text_type(bundle.identifier)
for record in bundle._records:
rec_type = record.get_type()
identifier = six.text_type(record._identifier) \
if record._identifier else None
if identifier:
attrs = {_ns_prov("id"): identifier}
else:
attrs = None
# Derive the record label from its attributes which is sometimes
# needed.
attributes = list(record.attributes)
rec_label = self._derive_record_label(rec_type, attributes)
elem = etree.SubElement(xml_bundle_root,
_ns_prov(rec_label), attrs)
for attr, value in sorted_attributes(rec_type, attributes):
subelem = etree.SubElement(
elem, _ns(attr.namespace.uri, attr.localpart))
if isinstance(value, prov.model.Literal):
if value.datatype not in \
[None, PROV["InternationalizedString"]]:
subelem.attrib[_ns_xsi("type")] = "%s:%s" % (
value.datatype.namespace.prefix,
value.datatype.localpart)
if value.langtag is not None:
subelem.attrib[_ns_xml("lang")] = value.langtag
v = value.value
elif isinstance(value, prov.model.QualifiedName):
if attr not in PROV_ATTRIBUTE_QNAMES:
subelem.attrib[_ns_xsi("type")] = "xsd:QName"
v = six.text_type(value)
elif isinstance(value, datetime.datetime):
v = value.isoformat()
else:
v = six.text_type(value)
# xsd type inference.
#
# This is a bit messy and there are all kinds of special
# rules but it appears to get the job done.
#
# If it is a type element and does not yet have an
# associated xsi type, try to infer it from the value.
# The not startswith("prov:") check is a little bit hacky to
# avoid type interference when the type is a standard prov
# type.
#
# To enable a mapping of Python types to XML and back,
# the XSD type must be written for these types.
ALWAYS_CHECK = [bool, datetime.datetime, float,
prov.identifier.Identifier]
# Add long and int on Python 2, only int on Python 3.
ALWAYS_CHECK.extend(six.integer_types)
ALWAYS_CHECK = tuple(ALWAYS_CHECK)
if (force_types or
type(value) in ALWAYS_CHECK or
attr in [PROV_TYPE, PROV_LOCATION, PROV_VALUE]) and \
_ns_xsi("type") not in subelem.attrib and \
not six.text_type(value).startswith("prov:") and \
not (attr in PROV_ATTRIBUTE_QNAMES and v) and \
attr not in [PROV_ATTR_TIME, PROV_LABEL]:
xsd_type = None
if isinstance(value, bool):
xsd_type = XSD_BOOLEAN
v = v.lower()
elif isinstance(value, six.string_types):
xsd_type = XSD_STRING
elif isinstance(value, float):
xsd_type = XSD_DOUBLE
elif isinstance(value, six.integer_types):
xsd_type = XSD_INT
elif isinstance(value, datetime.datetime):
# Exception of the exception, while technically
# still correct, do not write XSD dateTime type for
# attributes in the PROV namespaces as the type is
# already declared in the XSD and PROV XML also does
# not specify it in the docs.
if attr.namespace.prefix != "prov" \
or "time" not in attr.localpart.lower():
xsd_type = XSD_DATETIME
elif isinstance(value, prov.identifier.Identifier):
xsd_type = XSD_ANYURI
if xsd_type is not None:
subelem.attrib[_ns_xsi("type")] = six.text_type(xsd_type)
if attr in PROV_ATTRIBUTE_QNAMES and v:
subelem.attrib[_ns_prov("ref")] = v
else:
subelem.text = v
return xml_bundle_root
