class WormbaseTextMatchCSVDataSource(DSMixin, CSVDataSource):
class_context = CONTEXT
initial_cell_column = Informational(
'Initial Cell Column',
description='The index of the first column with a cell name',
multiple=False)
cell_type = Informational('Cell Type',
description='The type of cell to be produced',
multiple=False)
class NeuronCSVDataSource(DSMixin, CSVDataSource):
class_context = CONTEXT
bibtex_files = Informational(
display_name='BibTeX files',
description=
'List of BibTeX files that are referenced in the csv file by entry ID')
class EvidenceDataSource(DSMixin, DataSource):
class_context = SCI_CTX
context_property = Informational(display_name='Context',
property_name='evidence_context',
property_type='ObjectProperty',
description='The context')
def __init__(self, *args, **kwargs):
super(EvidenceDataSource, self).__init__(*args, **kwargs)
self.context = _EvidenceContext.contextualize(self.context)(maker=self,
imported=(CONTEXT,))
self.context_property(self.evidence_context.rdf_object)
def commit_augment(self):
saved_contexts = set([])
self.data_context.save_context(inline_imports=True, saved_contexts=saved_contexts)
self.context.save_context(inline_imports=True, saved_contexts=saved_contexts)
self.context.save_imports()
class ModelDBDataSource(ModelDB, DataSource):
'''
A data source of a single ModelDB record
'''
class_context = CONTEXT
accession_id = Informational(display_name='Accession ID',
description='Accession ID within ModelDB',
multiple=False)
download_url = Informational(display_name='Download URL',
description='URL for downloading',
multiple=False)
base_directory = Informational(
display_name='Base Model Directory',
Description='Base directory of the downloaded model archive')
key_property = 'accession_id'
def __getattr__(self, name):
# Tries to load the property from the graph
if name.startswith(DATAOBJECT_PROPERTY_NAME_PREFIX):
# Skip attributes that we *really* shouldn't be able to resolve
return super().__getattr__(name)
cd_type = ModelDBPropertyClassDescription.contextualize(
self.context).query
try:
pclass = cd_type(local_id=name).resolve_class()
return self.attach_property(pclass)
except ClassResolutionFailed:
raise AttributeError(name)
def download(self,
dest,
base_url='https://senselab.med.yale.edu',
session=None):
'''
Download model files. Note that if the destination file already exists, it will be
overwritten without warning if the operating system permits that.
Parameters
----------
dest : str
Destination file for the download.
base_url : str, optional
Base URL for the download
session : requests.session.Session, optional
Session to use for the download. If not provided, a new session will be
created
'''
if session is None:
session = requests.Session()
response = session.get(base_url + self.download_url(), stream=True)
with open(dest, 'wb') as out:
copyfileobj(response.raw, out)
@classmethod
def scrape_to_datasource(cls, accession, session=None, init_params=None):
'''
Scrape a ModelDB page into a `owmeta_core.datasource.DataSource`
Parameters
----------
accession : str or int
Accession number or URL for the model
session : requests.Session
Session to use for getting the document. Optional.
init_params : dict, optional
Additional parameters to the DataSource created
Returns
-------
ModelDBDataSource
The datasource created from the indicated ModelDB page
See Also
--------
`scrape` shares some parameters
'''
data = scrape(accession, session)
if init_params is None:
init_params = dict()
res = cls(**init_params)
for d in data:
if d['id'] == 'accession_id':
for v in d['values']:
res.accession_id(v)
continue
elif d['id'] == 'download_url':
for v in d['values']:
res.download_url(v)
continue
prop_class = create_property_class(d['id'], d['display_name'])
prop = res.attach_property(prop_class)
for v in d['values']:
prop(v)
return res
class C(self.DS1):
q = Informational(also=self.DS1.a)
p = Informational(also=self.DS1.a)
def test_default_property_type(self):
inf = Informational()
self.assertEqual(inf.property_type, 'DatatypeProperty')
class C(self.DS1):
q = Informational(also=self.DS1.a, default_value='Q')
p = Informational(also=self.DS1.a)
class DS1(DataSource):
a = Informational(default_value='A')
class DS2(DS1):
b = Informational()
a = 'D'
class C(DataSource):
q = Informational()
def test_default_display_name(self):
inf = Informational(name='test')
self.assertEqual(inf.display_name, 'test')
class C(self.DS1):
q = Informational(also=self.DS1.a, default_value='R')
a = 'M'
def test_default_multiple(self):
inf = Informational()
self.assertTrue(inf.multiple)
class DataWithEvidenceDataSource(DSMixin, DataSource):
'''
A data source that has an "evidence context" containing statements which support those
in its "data context". The data source also has a combined context which imports both
the data and evidence contexts.
'''
class_context = SCI_CTX
evidence_context_property = Informational(
display_name='Evidence context',
property_name='evidence_context',
property_type='ObjectProperty',
multiple=False,
description='The context in which evidence'
' for the "Data context" is defined')
data_context_property = Informational(
display_name='Data context',
property_name='data_context',
property_type='ObjectProperty',
multiple=False,
description='The context in which primary data'
' for this data source is defined')
combined_context_property = Informational(
display_name='Combined context',
property_name='combined_context',
property_type='ObjectProperty',
multiple=False,
description='Context importing both the data and evidence contexts')
def __init__(self, *args, **kwargs):
super(DataWithEvidenceDataSource, self).__init__(*args, **kwargs)
self.__ad_hoc_contexts = dict()
self.data_context = _DataContext.contextualize(self.context)(
maker=self, imported=(CONTEXT, ))
self.evidence_context = _EvidenceContext.contextualize(self.context)(
maker=self, imported=(CONTEXT, ))
self.combined_context = _CombinedContext.contextualize(self.context)(
maker=self, imported=(self.data_context, self.evidence_context))
if not type(self).query_mode:
if not self.data_context_property.has_defined_value():
self.data_context_property(self.data_context.rdf_object)
if not self.evidence_context_property.has_defined_value():
self.evidence_context_property(
self.evidence_context.rdf_object)
if not self.combined_context_property.has_defined_value():
self.combined_context_property(
self.combined_context.rdf_object)
def data_context_for(self, **kwargs):
ctx = self.context_for(**kwargs)
self.data_context.add_import(ctx)
return ctx
def context_for(self, ident=None, **kwargs):
key = "&".join(k + "=" +
getattr(kwargs[k], 'identifier', str(kwargs[k]))
for k in sorted(kwargs.keys()))
res = self.__ad_hoc_contexts.get(key)
if res is None:
if ident:
ctxid = ident
else:
ctxid = self.identifier + '/context_for?' + key
self.__ad_hoc_contexts[key] = Context.contextualize(
self.context)(ident=ctxid)
res = self.__ad_hoc_contexts[key]
return res
def commit_augment(self):
for ctx in self.__ad_hoc_contexts.values():
ctx.save()
self.evidence_context.save()
self.data_context.save()
self.combined_context.save()
for ctx in self.__ad_hoc_contexts.values():
ctx.save_imports(transitive=False)
self.evidence_context.save_imports(transitive=False)
self.data_context.save_imports(transitive=False)
self.combined_context.save_imports(transitive=False)