def set_item_properties(self, entity, item_type, item_name,
item_definition_uri, item_lab_ids, lab_id_select):
sbol.TextProperty(entity, 'http://purl.org/dc/terms/title', '0', '1',
item_name)
time_stamp = datetime.utcnow().strftime('%Y-%m-%dT%H:%M:%S-00')
sbol.TextProperty(entity, 'http://purl.org/dc/terms/created', '0', '1',
time_stamp)
sbol.TextProperty(entity, 'http://purl.org/dc/terms/modified', '0',
'1', time_stamp)
if item_type in intent_parser_constants.ITEM_TYPES['collection']:
return
if len(item_definition_uri) > 0:
if item_type == 'CHEBI':
if not item_definition_uri.startswith(
'http://identifiers.org/chebi/CHEBI'):
item_definition_uri = 'http://identifiers.org/chebi/CHEBI:' + item_definition_uri
else:
sbol.URIProperty(entity,
'http://www.w3.org/ns/prov#wasDerivedFrom',
'0', '1', item_definition_uri)
if len(item_lab_ids) > 0:
lab_id_tag = lab_id_select.replace(' ', '_')
tp = None
for item_lab_id in item_lab_ids.split(','):
if tp is None:
tp = sbol.TextProperty(entity,
'http://sd2e.org#' + lab_id_tag,
'0', '1', item_lab_id)
else:
tp.add(item_lab_id)
def test_validation_rules(self):
md = sbol2.ModuleDefinition()
with self.assertRaises(TypeError):
# No validation rules, so `'AND'` is interpreted
# as validation rules.
tp = sbol2.TextProperty(md, 'http://example.com#logic', '0', '1',
'AND', 'initial_value')
# Use an empty list to specify no validation rules
tp = sbol2.TextProperty(md, 'http://example.com#logic', '0', '1', [],
'AND')
def create_synbiohub_entry(self, sbol_type, sbol_type_map, display_id,
item_type, item_name, item_definition_uri,
item_lab_ids, item_lab_id_tag):
document = sbol.Document()
document.addNamespace('http://sd2e.org#', 'sd2')
document.addNamespace('http://purl.org/dc/terms/', 'dcterms')
document.addNamespace('http://www.w3.org/ns/prov#', 'prov')
document.displayId = 'foo'
document.version = '1'
if sbol_type == 'component':
if item_type == 'CHEBI':
item_sbol_type = item_definition_uri
else:
item_sbol_type = sbol_type_map[item_type]
component = sbol.ComponentDefinition(display_id, item_sbol_type)
sbol.TextProperty(component, 'http://sd2e.org#stub_object', '0',
'1', 'true')
self.set_item_properties(component, item_type, item_name,
item_definition_uri, item_lab_ids,
item_lab_id_tag)
document.addComponentDefinition(component)
elif sbol_type == 'module':
module = sbol.ModuleDefinition(display_id)
sbol.TextProperty(module, 'http://sd2e.org#stub_object', '0', '1',
'true')
module.roles = sbol_type_map[item_type]
self.set_item_properties(module, item_type, item_name,
item_definition_uri, item_lab_ids,
item_lab_id_tag)
document.addModuleDefinition(module)
elif sbol_type == 'external':
top_level = sbol.TopLevel('http://sd2e.org/types/#attribute',
display_id)
self.set_item_properties(top_level, item_type, item_name,
item_definition_uri, item_lab_ids,
item_lab_id_tag)
document.add(top_level)
elif sbol_type == 'collection':
collection = sbol.Collection(display_id)
self.set_item_properties(collection, item_type, item_name,
item_definition_uri, item_lab_ids,
item_lab_id_tag)
document.addCollection(collection)
else:
raise IntentParserException(
'Failed to create a SynBioHub entry: %s as a supported sbol type in Intent Parser'
% sbol_type)
return document
def test_text_property_constructor(self):
# Test None as parent object
with self.assertRaises(AttributeError):
sbol.TextProperty(None, sbol.SBOL_NAME, '0', '*', [], 'foo')
# Test string as parent object
with self.assertRaises(AttributeError):
sbol.TextProperty('foo', sbol.SBOL_NAME, '0', '*', [], 'foo')
# Test with object whose properties attribute is not a dict
with self.assertRaises(TypeError):
md = sbol.ModuleDefinition()
md.properties = []
sbol.TextProperty(md, sbol.SBOL_NAME, '0', '*', [], 'foo')
def test_six_arg_constructor_none(self):
cd = sbol2.ComponentDefinition()
type_uri = 'http://example.com/test#testText'
initial_value = 'omega'
prop = sbol2.TextProperty(cd, type_uri, '0', '1', None, initial_value)
self.assertEqual(initial_value, prop.value)
self.assertEqual([], prop._validation_rules)
def test_five_arg_constructor_values(self):
cd = sbol2.ComponentDefinition()
type_uri = 'http://example.com/test#testText'
initial_value = ['alpha', 'bravo', 'charlie']
prop = sbol2.TextProperty(cd, type_uri, '0', '*', initial_value)
self.assertEqual(initial_value, prop.value)
self.assertEqual([], prop._validation_rules)
def test_five_arg_constructor_validators(self):
cd = sbol2.ComponentDefinition()
type_uri = 'http://example.com/test#testText'
validation_rules = [print]
prop = sbol2.TextProperty(cd, type_uri, '0', '*', validation_rules)
self.assertEqual([], prop.value)
self.assertEqual(validation_rules, prop._validation_rules)
def test_init_store(self):
# Ensure that property constructors initialize the parent
# object's value store
obj = sbol2.SBOLObject()
type_uri = 'http://example.com#thing'
obj.thing = sbol2.TextProperty(obj, type_uri, '0', '*')
self.assertIn(type_uri, obj.properties)
self.assertEqual([], obj.properties[type_uri])
self.assertEqual([], obj.thing)
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 = sbol2.TextProperty(
self.obj, 'http://purl.obolibrary.org/obo/OBI_0001617', 0, 1,
[])
self.obj.OBI_0001617 = self.cell_val.split(".gov/")[1].replace(
"/", "")
def test_text_property_setting_single(self):
md = sbol.ModuleDefinition()
testing_uri = rdflib.URIRef(sbol.SBOL_URI + "#Testing")
tp = sbol.TextProperty(md, testing_uri, '0', '1', [])
# Test setting to string
expected = 'foo'
tp.value = expected
self.assertEqual(tp.value, expected)
# Test setting to None
tp.value = None
self.assertIsNone(tp.value)
# Test integer
with self.assertRaises(TypeError):
tp.value = 3
# Test setting to list
with self.assertRaises(TypeError):
tp.value = ['foo', 'bar']
def test_text_property_setting_list(self):
md = sbol.ModuleDefinition()
testing_uri = rdflib.URIRef(sbol.SBOL_URI + "#Testing")
tp = sbol.TextProperty(md, testing_uri, '0', '*', [])
# Test setting to string
expected = 'foo'
tp.value = expected
self.assertEqual(tp.value, [expected])
# Test setting to None
with self.assertRaises(TypeError):
tp.value = None
# Test setting to list
expected = ['foo', 'bar']
tp.value = expected
self.assertEqual(tp.value, expected)
# Test setting to list of integers
with self.assertRaises(TypeError):
tp.value = [1, 2, 3]
# Test setting to empty list
expected = []
tp.value = expected
self.assertEqual(tp.value, [])
def create_sbh_stub(self, data):
# Extract some fields from the form
try:
item_type = data['itemType']
item_name = data['commonName']
item_definition_uri = data['definitionURI']
item_display_id = data['displayId']
except Exception as e:
return intent_parser_view.operation_failed(
'Form submission missing key: ' + str(e))
# Make sure Common Name was specified
if len(item_name) == 0:
return intent_parser_view.operation_failed(
'Common Name must be specified')
# Sanitize the display id
if len(item_display_id) > 0:
display_id = self.sanitize_name_to_display_id(item_display_id)
if display_id != item_display_id:
return intent_parser_view.operation_failed(
'Illegal display_id')
else:
display_id = self.sanitize_name_to_display_id(item_name)
# Derive document URL
document_url = self.sbh_uri_prefix + display_id + '/1'
# Make sure document does not already exist
try:
if self.sbh.exists(document_url):
return intent_parser_view.operation_failed(
'"' + display_id + '" already exists in SynBioHub')
except:
return intent_parser_view.operation_failed(
'Failed to access SynBioHub')
# Look up sbol type uri
sbol_type = None
for sbol_type_key in intent_parser_constants.ITEM_TYPES:
sbol_type_map = intent_parser_constants.ITEM_TYPES[sbol_type_key]
if item_type in sbol_type_map:
sbol_type = sbol_type_key
break
# Fix CHEBI URI
if item_type == 'CHEBI':
if len(item_definition_uri) == 0:
item_definition_uri = sbol_type_map[item_type]
else:
if not item_definition_uri.startswith(
'http://identifiers.org/chebi/CHEBI'):
item_definition_uri = 'http://identifiers.org/chebi/CHEBI:' + \
item_definition_uri
# Create a dictionary entry for the item
try:
self.create_dictionary_entry(data, document_url,
item_definition_uri)
except Exception as e:
return intent_parser_view.operation_failed(str(e))
# Create an entry in SynBioHub
try:
document = sbol.Document()
document.addNamespace('http://sd2e.org#', 'sd2')
document.addNamespace('http://purl.org/dc/terms/', 'dcterms')
document.addNamespace('http://www.w3.org/ns/prov#', 'prov')
if sbol_type == 'component':
if item_type == 'CHEBI':
item_sbol_type = item_definition_uri
else:
item_sbol_type = sbol_type_map[item_type]
component = sbol.ComponentDefinition(display_id,
item_sbol_type)
sbol.TextProperty(component, 'http://sd2e.org#stub_object',
'0', '1', 'true')
self.set_item_properties(component, data)
document.addComponentDefinition(component)
elif sbol_type == 'module':
module = sbol.ModuleDefinition(display_id)
sbol.TextProperty(module, 'http://sd2e.org#stub_object', '0',
'1', 'true')
module.roles = sbol_type_map[item_type]
self.set_item_properties(module, data)
document.addModuleDefinition(module)
elif sbol_type == 'external':
top_level = sbol.TopLevel('http://sd2e.org/types/#attribute',
display_id)
self.set_item_properties(top_level, data)
document.addTopLevel(top_level)
elif sbol_type == 'collection':
collection = sbol.Collection(display_id)
self.set_item_properties(collection, data)
document.addCollection(collection)
else:
raise Exception()
self.sbh.submit(document, self.sbh_collection_uri, 3)
paragraph_index = data['selectionStartParagraph']
offset = data['selectionStartOffset']
end_offset = data['selectionEndOffset']
action = intent_parser_view.link_text(paragraph_index, offset,
end_offset, document_url)
except Exception as e:
self.logger.error(''.join(
traceback.format_exception(etype=type(e),
value=e,
tb=e.__traceback__)))
message = 'Failed to add "' + display_id + '" to SynBioHub'
return intent_parser_view.operation_failed(message)
return_info = {
'actions': [action],
'results': {
'operationSucceeded': True
}
}
return return_info
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])
else:
# no iteration over list as else suggests that the property
# can't have multiple values
try:
current = getattr(self.obj, self.sbol_term_suf)
if isinstance(current, type(None)):
setattr(self.obj, self.sbol_term_suf,
self.cell_val)
else:
if isinstance(self.cell_val, str) and isinstance(
current, str):
value = current + "\n" + self.cell_val
logging.warning(
f'The SBOL term {self.sbol_term_suf} for sheet:{self.sheet}, col: {self.sht_col}, row: {self.sht_row} is being concatenated {current} with {self.cell_val}'
)
setattr(self.obj, self.sbol_term_suf, value)
except AttributeError:
raise ValueError(
f"Can't set attribute {self.sbol_term_pref}_{self.sbol_term_suf} for sheet:{self.sheet}, col: {self.sht_col}, row: {self.sht_row}. It is likely an issue with plural e.g. not sbol_type but sbol_types"
)
else:
raise ValueError(
f'This SBOL object ({type(self.obj)}) has no attribute {self.sbol_term_suf}. The column definitions sheet SBOL Term needs to be updated. (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,
sbol2.URIProperty(
self.obj,
f'{self.namespace_url}{self.sbol_term_suf}', '0',
'*', []))
setattr(self.obj, self.sbol_term_suf, 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,
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,
sbol2.TextProperty(
self.obj,
f'{self.namespace_url}{self.sbol_term_suf}', '0',
'*'))
setattr(self.obj, self.sbol_term_suf, 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,
current + self.cell_val)
def test_four_arg_constructor(self):
cd = sbol2.ComponentDefinition()
type_uri = 'http://example.com/test#testText'
prop = sbol2.TextProperty(cd, type_uri, '0', '1')
self.assertEqual(None, prop.value)
self.assertEqual([], prop._validation_rules)
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)
