def test_annotation(self):
sbol3.set_namespace('https://github.com/synbiodex/pysbol3')
# Create custom annotation
annotation_uri = 'http://example.org/boolean_property'
annotation_value = 'foo'
c = sbol3.Component('c1', sbol3.SBO_DNA)
c.annotation = sbol3.TextProperty(c, annotation_uri,
0, 1, [])
c.annotation = annotation_value
self.assertEqual(annotation_value, c.annotation)
doc = sbol3.Document()
doc.add(c)
doc2 = sbol3.Document()
with tempfile.TemporaryDirectory() as tmpdirname:
test_file = os.path.join(tmpdirname, 'annotation.xml')
doc.write(test_file, sbol3.RDF_XML)
# Roundtrip
doc2.read(test_file, sbol3.RDF_XML)
# Recover annotation
c = doc2.find('c1')
c.annotation = sbol3.TextProperty(c, annotation_uri,
0, 1, [])
self.assertEqual(annotation_value, c.annotation)
def dataSource(self):
self.obj.wasDerivedFrom = self.cell_val
if "pubmed.ncbi.nlm.nih.gov/" in self.cell_val:
if 'obo' not in self.doc_pref_terms:
self.doc.addNamespace('http://purl.obolibrary.org/obo/', 'obo')
self.doc_pref_terms.append('obo')
self.obj.OBI_0001617 = sbol3.TextProperty(
self.obj, 'http://purl.obolibrary.org/obo/OBI_0001617', 0, 1,
[])
self.obj.OBI_0001617 = self.cell_val.split(".gov/")[1].replace(
"/", "")
def __init__(self, identity,
*, information: Optional[str, list[str]] = None,
namespace: str = None,
attachments: list[str] = None,
name: str = None, description: str = None,
derived_from: list[str] = None,
generated_by: list[str] = None,
measures: list[sbol3.SBOLObject] = None) -> None:
super().__init__(identity=identity,
type_uri=TextPropertyExtension.TYPE_URI,
namespace=namespace,
attachments=attachments, name=name,
description=description, derived_from=derived_from,
generated_by=generated_by, measures=measures)
self.information = sbol3.TextProperty(self,
TextPropertyExtension.TPE_INFO_URI,
0, math.inf,
initial_value=information)
def __init__(self, *args, **kwargs):
base_kwargs = {
kw: val
for kw, val in kwargs.items() if kw not in property_names
}
if 'type_uri' not in base_kwargs:
base_kwargs['type_uri'] = CLASS_URI
Super.__init__(self, *args, **base_kwargs)
if 'http://sbols.org/v3#' in superclass_uri and not superclass_uri == SBOL_TOP_LEVEL and not superclass_uri == SBOL_IDENTIFIED:
if class_is_top_level:
self._rdf_types.append(SBOL_TOP_LEVEL)
else:
self._rdf_types.append(SBOL_IDENTIFIED)
# Initialize associative properties
for property_uri in associative_properties:
property_name = property_uri_to_name[property_uri]
lower_bound, upper_bound = property_cardinalities[property_uri]
self.__dict__[property_name] = sbol.ReferencedObject(
self, property_uri, lower_bound, upper_bound)
# Initialize compositional properties
for property_uri in compositional_properties:
property_name = property_uri_to_name[property_uri]
lower_bound, upper_bound = property_cardinalities[property_uri]
self.__dict__[property_name] = sbol.OwnedObject(
self, property_uri, lower_bound, upper_bound)
# Initialize datatype properties
for property_uri in datatype_properties:
# TODO: Cache query information outside of constructor
property_name = property_uri_to_name[property_uri]
# Get the datatype of this property
datatypes = property_datatypes[property_uri]
if len(datatypes) == 0:
continue
if len(datatypes
) > 1: # This might indicate an error in the ontology
raise
# Get the cardinality of this datatype property
lower_bound, upper_bound = property_cardinalities[property_uri]
if datatypes[0] == 'http://www.w3.org/2001/XMLSchema#string':
self.__dict__[property_name] = sbol.TextProperty(
self, property_uri, lower_bound, upper_bound)
elif datatypes[
0] == 'http://www.w3.org/2001/XMLSchema#integer':
self.__dict__[property_name] = sbol.IntProperty(
self, property_uri, lower_bound, upper_bound)
elif datatypes[
0] == 'http://www.w3.org/2001/XMLSchema#boolean':
self.__dict__[property_name] = sbol.BooleanProperty(
self, property_uri, lower_bound, upper_bound)
elif datatypes[0] == 'http://www.w3.org/2001/XMLSchema#anyURI':
self.__dict__[property_name] = sbol.URIProperty(
self, property_uri, lower_bound, upper_bound)
elif datatypes[
0] == 'http://www.w3.org/2001/XMLSchema#dateTime':
self.__dict__[property_name] = sbol.DateTimeProperty(
self, property_uri, lower_bound, upper_bound)
for kw, val in kwargs.items():
if kw == 'type_uri':
continue
if kw in self.__dict__:
try:
self.__dict__[kw].set(val)
except:
pass
def switch(self, sbol_term):
"""Switch statement that calls a different method based on the
sbol_term. For example if the sbol_term is sbh_alteredSequence
then the function sbh_alteredSequence() will be run. If there is
no function with a name equal to the sbol_term then the add_new method
is run.
Args:
sbol_term (str): String indicating the method of processing
required by the cell_value
Returns:
Nothing is returned but the componentDefinition and sbol doc
are updated according to the sbol_term and cell_value
"""
self.sbol_term_pref = sbol_term.split("_", 1)[0]
try:
self.sbol_term_suf = sbol_term.split("_", 1)[1]
except IndexError:
raise ValueError(
f"The SBOL Term '{sbol_term}' (sheet name: {self.sheet}) does not appear to have an underscore"
)
if self.parental_lookup:
# switches the object being worked on
self.obj = self.obj_dict[self.cell_val]['object']
self.cell_val = self.obj_uri
# if not applicable then do nothing
if sbol_term == "Not_applicable":
pass
# if a special function has been defined below then do something
elif hasattr(self, self.sbol_term_suf):
return getattr(self, self.sbol_term_suf)()
# if it is an sbol term use standard pySBOL implementation
# unless it is a top level object in which case the standard
# implementations don't work
elif self.sbol_term_pref == "sbol":
if hasattr(self.obj, self.sbol_term_suf):
# if the attribute is a list append the new value
if isinstance(getattr(self.obj, self.sbol_term_suf), list):
current = getattr(self.obj, self.sbol_term_suf)
# if the cell_val is a list append the whole list
if isinstance(self.cell_val, list):
setattr(self.obj, self.sbol_term_suf,
current + self.cell_val)
else:
setattr(self.obj, self.sbol_term_suf,
current + [self.cell_val])
elif isinstance(getattr(self.obj, self.sbol_term_suf),
sbol3.refobj_property.ReferencedObjectList):
getattr(getattr(self.obj, self.sbol_term_suf),
'append')(self.cell_val)
else:
# no iteration over list as else suggests that the property
# can't have multiple values
setattr(self.obj, self.sbol_term_suf, self.cell_val)
else:
raise ValueError(
f'This SBOL object ({type(self.obj)}) has no attribute {self.sbol_term_suf} (sheet:{self.sheet}, row:{self.sht_row}, col:{self.sht_col})'
)
else:
# logging.warning(f'This sbol term ({self.sbol_term}) has not yet been implemented so it has been added via the default method')
# define a new namespace if needed
if self.sbol_term_pref not in self.doc_pref_terms:
self.doc.addNamespace(self.namespace_url, self.sbol_term_pref)
self.doc_pref_terms.append(self.sbol_term_pref)
# if type is uri make it a uri property
if self.col_type == "URI":
# * allows multiple instance of this property
if not hasattr(self.obj, self.sbol_term_suf):
setattr(
self.obj, self.sbol_term_suf,
sbol3.URIProperty(
self.obj,
f'{self.namespace_url}{self.sbol_term_suf}',
'0',
'*',
initial_value=[self.cell_val]))
else:
if not isinstance(self.cell_val, list):
self.cell_val = [self.cell_val]
current = getattr(self.obj, self.sbol_term_suf)
setattr(self.obj, self.sbol_term_suf,
list(current) + self.cell_val)
# otherwise implement as text property
else:
# * allows multiple instance of this property
if not hasattr(self.obj, self.sbol_term_suf):
setattr(
self.obj, self.sbol_term_suf,
sbol3.TextProperty(
self.obj,
f'{self.namespace_url}{self.sbol_term_suf}',
'0',
'*',
initial_value=str(self.cell_val)))
else:
if not isinstance(self.cell_val, list):
self.cell_val = [self.cell_val]
current = getattr(self.obj, self.sbol_term_suf)
setattr(self.obj, self.sbol_term_suf,
list(current) + self.cell_val)
def switch(self, rowobj, sbol_term, sbol_version):
if sbol_version == 2:
self.func_list = self.func_list2
exutil = exutil2
elif sbol_version == 3:
self.func_list = self.func_list3
exutil = exutil3
else:
raise ValueError(
f"SBOL Version ({sbol_version}) given to switch has not been implemented yet"
)
# split sbol term into prefix and suffix
self.sbol_term = sbol_term
self.sbol_term_pref = sbol_term.split("_", 1)[0]
try:
self.sbol_term_suf = sbol_term.split("_", 1)[1]
except IndexError:
raise ValueError(
f"The SBOL Term '{sbol_term}' (sheet name: {self.sheet}) does not appear to have an underscore"
)
# if not applicable then do nothing
if sbol_term == "Not_applicable":
pass
# if a special function has been defined in excel-sbol-utils then use that
elif self.sbol_term_suf in self.func_list:
return getattr(exutil, self.sbol_term_suf)(rowobj)
# if it is an sbol term use standard pySBOL implementation
# unless it is a top level object in which case the standard
# implementations don't work
elif self.sbol_term_pref == "sbol":
for col in rowobj.col_cell_dict:
cell_val = rowobj.col_cell_dict[col]
parental_lookup = rowobj.term_coldef_df[
rowobj.term_coldef_df['Column Name'] ==
col]['Parent Lookup']
if parental_lookup.values[0]:
# switches the object being worked on
rowobj.obj = rowobj.obj_dict[cell_val]['object']
cell_val = rowobj.obj_uri
if hasattr(rowobj.obj, self.sbol_term_suf):
# if the attribute is a list append the new value
if isinstance(getattr(rowobj.obj, self.sbol_term_suf),
list):
current = getattr(rowobj.obj, self.sbol_term_suf)
# if the col_cell_dict has multiple columns append each
# if cell_val is a dict then mcol must have been given
if isinstance(cell_val, dict):
raise TypeError(
f"A multicolumn value was unexpectedly given for sheet:{rowobj.sheet}, row:{rowobj.sht_row}, sbol term :{self.sbol_term}, sbol term dict: {rowobj.col_cell_dict}"
)
# if the cell_val is a list append the whole list
elif isinstance(cell_val, list):
setattr(rowobj.obj, self.sbol_term_suf,
current + cell_val)
# otherwise append as a list object
else:
setattr(rowobj.obj, self.sbol_term_suf,
current + [cell_val])
# if type sbol list then add by special append
# rather than regular list append
elif isinstance(
getattr(rowobj.obj, self.sbol_term_suf),
sbol3.refobj_property.ReferencedObjectList):
# if cell_val is a dict then mcol must have been given
if isinstance(cell_val, dict):
raise TypeError(
f"A multicolumn value was unexpectedly given for sheet:{rowobj.sheet}, row:{rowobj.sht_row}, sbol term :{self.sbol_term}, sbol term dict: {rowobj.col_cell_dict}"
)
# else should be fine to append
else:
getattr(getattr(rowobj.obj, self.sbol_term_suf),
'append')(cell_val)
else:
# no iteration over list as else suggests that the property
# can't have multiple values
setattr(rowobj.obj, self.sbol_term_suf, cell_val)
else:
raise ValueError(
f'This SBOL object ({type(rowobj.obj)}) has no attribute {self.sbol_term_suf} (sheet:{rowobj.sheet}, row:{rowobj.sht_row}, sbol term dict:{rowobj.col_cell_dict})'
)
else:
# logging.warning(f'This sbol term ({self.sbol_term}) has not yet been implemented so it has been added via the default method')
# define a new namespace if needed
for col in rowobj.col_cell_dict:
cell_val = rowobj.col_cell_dict[col]
col_coldef_df = rowobj.term_coldef_df[
rowobj.term_coldef_df['Column Name'] == col]
if len(col_coldef_df) == 0:
raise TypeError(
f"A multicolumn value was unexpectedly given for sheet:{rowobj.sheet}, row:{rowobj.sht_row}, sbol term :{self.sbol_term}, sbol term dict: {rowobj.col_cell_dict}"
)
parental_lookup = col_coldef_df['Parent Lookup'].values[0]
if parental_lookup:
# switches the object being worked on
rowobj.obj = rowobj.obj_dict[cell_val]['object']
cell_val = rowobj.obj_uri
namespace_url = col_coldef_df['Namespace URL'].values[0]
if self.sbol_term_pref not in rowobj.doc_pref_terms:
rowobj.doc.addNamespace(namespace_url, self.sbol_term_pref)
rowobj.doc_pref_terms.append(self.sbol_term_pref)
col_type = col_coldef_df['Type'].values[0]
# if type is uri make it a uri property
if col_type == "URI":
# * allows multiple instance of this property
if not hasattr(rowobj.obj, self.sbol_term_suf):
if sbol_version == 2:
setattr(
rowobj.obj, self.sbol_term_suf,
sbol2.URIProperty(
rowobj.obj,
f'{namespace_url}{self.sbol_term_suf}',
'0', '*', []))
setattr(rowobj.obj, self.sbol_term_suf, cell_val)
elif sbol_version == 3:
setattr(
rowobj.obj, self.sbol_term_suf,
sbol3.URIProperty(
rowobj.obj,
f'{namespace_url}{self.sbol_term_suf}',
'0',
'*',
initial_value=[cell_val]))
else:
if not isinstance(cell_val, list):
cell_val = [cell_val]
current = getattr(rowobj.obj, self.sbol_term_suf)
setattr(rowobj.obj, self.sbol_term_suf,
list(current) + cell_val)
# otherwise implement as text property
else:
# * allows multiple instance of this property
if not hasattr(rowobj.obj, self.sbol_term_suf):
if sbol_version == 2:
setattr(
rowobj.obj, self.sbol_term_suf,
sbol2.TextProperty(
rowobj.obj,
f'{namespace_url}{self.sbol_term_suf}',
'0', '*'))
setattr(rowobj.obj, self.sbol_term_suf,
str(cell_val))
elif sbol_version == 3:
setattr(
rowobj.obj, self.sbol_term_suf,
sbol3.TextProperty(
rowobj.obj,
f'{namespace_url}{self.sbol_term_suf}',
'0',
'*',
initial_value=str(cell_val)))
else:
if not isinstance(cell_val, list):
cell_val = [cell_val]
current = getattr(rowobj.obj, self.sbol_term_suf)
setattr(rowobj.obj, self.sbol_term_suf,
list(current) + cell_val)