def test_mdoc(self):
jordan = odml.Document(author="Michael Jordan",
date=dt.date(1991, 9, 1),
version=0.01)
mjordan = odml.Document(author="Michael Jordan",
date=dt.date(1991, 9, 1),
version=0.01)
section_bulls = odml.Section(
name="Chicago_Bulls",
definition="NBA team based in Chicago, IL",
type="team")
section_nc = odml.Section(
name="North_Caroline",
definition="NCAA team based in Wilmington, NC",
type="team")
jordan.append(section_bulls)
jordan.append(section_nc)
mjordan.append(
section_bulls,
section_nc,
)
self.assertTrue(jordan.sections[0].name == mjordan.sections[0].name)
self.assertTrue(jordan.sections[1].name == mjordan.sections[1].name)
def save_metadata(self):
trial_name = 'trial_{0:04d}'.format(self.trial_counter)
file_list = [f for f in os.listdir(self.data_dir) if f.startswith(trial_name)]
""" create a document """
doc = odml.Document()
""" create dataset section """
ds = odml.Section('datasets', 'dataset')
p = odml.Property('files', None)
ds.append(p)
for f in file_list:
p.append('{0:s}/{1:s}'.format(self.data_dir, f))
doc.append(ds)
for t in list(self.metadata_tabs.values()):
m = t.metadata()
if m.type == 'recording':
v = odml.Value(self.record_timestamp, dtype='datetime')
m.append(odml.Property('StartTime', v))
doc.append(m)
for cam_name, cam in list(self.cameras.items()):
s = odml.Section(cam_name,'hardware/camera')
if not cam.is_raspicam():
v = odml.Value(frames_per_second, unit="Hz")
s.append(odml.Property('Framerate', v))
for p, v in list(cam.get_properties().items()):
prop = odml.Property(p, v)
s.append(prop)
doc.append(s)
doc.append(self.event_list)
print(self.event_list)
from odml.tools.xmlparser import XMLWriter
writer = XMLWriter(doc)
writer.write_file('{0}/{1}.xml'.format(self.data_dir, trial_name))
def create_odmltable_example():
"""
"""
species = ''
gender = ''
weight = 0.0
start_date = datetime.date(1, 2, 3)
end_date = datetime.date(1, 2, 3)
duration = 1
doc = odml.Document()
doc.append(odml.Section(name='Subject',
definition='Information on the investigated '
'experimental subject (animal or '
'person)'))
parent = doc['Subject']
parent.append(odml.Section(name='Training',
definition='Information on the training given '
'to subject'))
parent.append(odml.Property(name='Species',
definition='Binomial species name',
values=species,
dtype=odml.DType.string))
parent.append(odml.Property(name='Gender',
definition='Gender (male or female)',
values=gender,
dtype=odml.DType.string))
parent.append(odml.Property(name='Weight',
values=weight,
dtype=odml.DType.float,
unit='kg',
uncertainty=5))
parent = doc['Subject']['Training']
parent.append(odml.Property(name='PeriodStart',
definition='start date of training',
values=start_date,
dtype=odml.DType.date))
parent.append(odml.Property(name='PeriodEnd',
definition='end date of training',
values=end_date,
dtype=odml.DType.date))
parent.append(odml.Property(name='Duration',
definition='Duration of the training',
values=duration,
dtype=odml.DType.int,
unit='work days'))
return doc
def create_showall_test_odml():
"""
creates a test-odml-document specifically to test the 'showall'-attributes
(showall_sections, showall_properties, showall_value_information) to test
if the right cells are left free
"""
doc = odml.Document()
doc.append(odml.Section(name='section1', definition='sec1'))
doc.append(odml.Section(name='section2', definition='sec2'))
doc.append(odml.Section(name='section3', definition='sec3'))
parent = doc['section1']
parent.append(
odml.Property(name='property1',
definition='prop1',
value=['value1', 'value2', 'value3'],
dtype=odml.DType.string,
unit='g',
uncertainty=1))
parent.append(
odml.Property(name='property2',
definition='prop2',
value='value1',
dtype=odml.DType.text,
unit='g',
uncertainty=1))
parent.append(
odml.Property(name='property3',
definition='prop3',
value='value1',
dtype=odml.DType.text,
unit='g',
uncertainty=1))
parent = doc['section2']
parent.append(
odml.Property(name='property1',
definition='prop1',
value='value1',
dtype=odml.DType.string,
unit='g',
uncertainty=1))
parent = doc['section3']
parent.append(
odml.Property(name='property1',
definition='prop1',
value=['value1', 'value2'],
dtype=odml.DType.string,
unit='g',
uncertainty=1))
return doc
def test_msec(self):
# Test case for odml_msec
section_bulls = odml.Section(
name="Chicago_Bulls",
definition="NBA team based in Chicago, IL",
type="team"
)
section_bulls0 = odml.Section(
name="Chicago_Bulls",
definition="NBA team based in Chicago, IL",
type="team"
)
section_bulls2 = odml.Section(
name="Chicago_City_Pub",
definition="NBA team pub",
type="pub"
)
section_bull3 = odml.Section(
name="Bill_Clinton",
definition="President supporter",
type="fan"
)
prop1 = odml.Property(
name="Coach",
value="Phil Jackson",
definition="Run the team."
)
prop2 = odml.Property(
name="Euro_player",
value="Tony Kukoc",
definition="European Player"
)
section_bulls.append(
section_bulls2,
section_bull3,
prop1,
prop2
)
section_bulls0.append(section_bulls2)
section_bulls0.append(section_bull3)
section_bulls0.append(prop1)
section_bulls0.append(prop2)
self.assertTrue(section_bulls.sections[0].name == section_bulls0.sections[0].name)
self.assertTrue(section_bulls.sections[1].name == section_bulls0.sections[1].name)
self.assertTrue(section_bulls.properties[0].name == section_bulls0.properties[0].name)
self.assertTrue(section_bulls.properties[1].name == section_bulls0.properties[1].name)
def test_property_unique_ids(self):
"""
Test if identical ids in properties raise a validation error
"""
doc = odml.Document()
sec_one = odml.Section("sec1", parent=doc)
sec_two = odml.Section("sec2", parent=doc)
prop = odml.Property("prop", parent=sec_one)
cprop = prop.clone(keep_id=True)
sec_two.append(cprop)
res = validate(doc)
self.assertError(res, "Duplicate id in Property")
def test_section_events(self):
s = odml.Section("sec1")
p = odml.Property(name="p", value="1")
s.append(p)
event_log = []
def record(context):
event_log.append((context.obj, context.action, context.val))
s.add_change_handler(record)
p.value = "2"
p.value = "1"
log1 = event_log
event_log = []
s.remove_change_handler(record)
ps = proxy.NonexistantSection("psec")
pp = proxy.PropertyProxy(p)
ps.append(pp)
ps.add_change_handler(record)
p.value = "2"
p.value = "1"
self.assertEqual(log1, event_log)
def test_nix_to_odml_none(self):
file_name = 'tmp'
nix_path = os.path.join(self.test_dir, file_name + '.nix')
odml_path = os.path.join(self.test_dir, file_name + '.xml')
odml.Section(name=None,
oid=None,
definition=None,
parent=self.odml_doc,
type="MustBeSet",
reference=None,
repository=None,
link=None,
include=None)
convert.nixwrite(self.odml_doc, nix_path, nix.FileMode.Overwrite)
nix_file_r = nix.File.open(nix_path, nix.FileMode.ReadOnly)
convert.odmlwrite(nix_file_r, odml_path)
odml_doc = odml.load(odml_path)
self.assertEqual(len(odml_doc.sections), 1)
odml_sec = odml_doc.sections[0]
self.assertGreater(len(getattr(odml_sec, "id")), 0)
self.assertEqual(getattr(odml_sec, "name"), getattr(odml_sec, "id"))
self.assertEqual(getattr(odml_sec, "type"), "MustBeSet")
self.assertEqual(getattr(odml_sec, "definition"), None)
self.assertEqual(getattr(odml_sec, "reference"), None)
self.assertEqual(getattr(odml_sec, "repository"), None)
self.assertEqual(getattr(odml_sec, "link"), None)
self.assertEqual(getattr(odml_sec, "include"), None)
nix_file_r.close()
def setUp(self):
self.odml_doc = odml.Document(author='me',
date=datetime.date.today(),
version='0.0.1',
repository='unknown')
odml.Section(name='first section',
definition='arbitrary definiton',
type='testsection',
parent=self.odml_doc,
reference='reference 1',
repository='also unknown',
link='???',
include=False)
odml.Property(name='first property',
value=[1, 2, 3],
parent=self.odml_doc.sections[0],
unit='Volt',
uncertainty=3,
reference='still unknown',
definition='first property recorded',
dependency='unknown',
dependency_value='also unknown',
dtype='int',
value_origin='ref 2')
def nix_to_odml_recurse(nix_section_list, odml_section):
for nix_sec in nix_section_list:
info["sections read"] += 1
# extract and convert section attributes from nix
# TODO: add 'include' here as soon as available in nix
attributes = ['name', 'type', 'definition', 'reference', 'repository', 'link', 'id']
nix_attributes = {attr: getattr(nix_sec, attr) for attr in attributes if
hasattr(nix_sec, attr)}
nix_attributes['parent'] = odml_section
if 'id' in nix_attributes:
nix_attributes['oid'] = nix_attributes.pop('id')
odml_sec = odml.Section(**nix_attributes)
info["sections written"] += 1
for nixprop in nix_sec.props:
info["properties read"] += 1
# extract and convert property attributes from nix
prop_attributes = ['name', 'values', 'unit', 'uncertainty', 'reference', 'definition',
'dependency', 'dependency_value', 'odml_type', 'value_origin', 'id']
nix_prop_attributes = {attr: getattr(nixprop, attr) for attr in prop_attributes if
hasattr(nixprop, attr)}
if 'id' in nix_prop_attributes:
nix_prop_attributes['oid'] = nix_prop_attributes.pop('id')
if 'odml_type' in nix_prop_attributes:
nix_prop_attributes['dtype'] = nix_prop_attributes.pop('odml_type').value
nix_prop_attributes['parent'] = odml_sec
nix_prop_attributes['value'] = list(nix_prop_attributes.pop('values'))
odml.Property(**nix_prop_attributes)
info["properties written"] += 1
nix_to_odml_recurse(nix_sec.sections, odml_sec)
def test_odml_to_nix_none(self):
file_name = 'tmp'
nix_path = os.path.join(self.test_dir, file_name + '.nix')
odml.Section(name=None,
oid=None,
definition=None,
parent=self.odml_doc,
type="MustBeSet",
reference=None,
repository=None,
link=None,
include=None)
convert.nixwrite(self.odml_doc, nix_path, 'overwrite')
nix_file = nix.File.open(nix_path)
self.assertEqual(len(nix_file.sections[0].sections), 1)
nix_sec = nix_file.sections[0].sections[0]
self.assertGreater(len(getattr(nix_sec, "id")), 0)
self.assertEqual(getattr(nix_sec, "name"), getattr(nix_sec, "id"))
self.assertEqual(getattr(nix_sec, "type"), "MustBeSet")
self.assertEqual(getattr(nix_sec, "definition"), None)
self.assertEqual(getattr(nix_sec, "reference"), None)
self.assertEqual(getattr(nix_sec, "repository"), None)
self.assertEqual(getattr(nix_sec, "link"), None)
#self.assertEqual(getattr(nix_sec, "include"), None)
nix_file.close()
def create_compare_test(sections=3, properties=3, levels=1):
"""
"""
doc = odml.Document()
def append_children(sec, level):
if level < levels:
for i in list(range(sections)):
sec.append(odml.Section(name='Section' + str(i + 1)))
parent = sec['Section' + str(i + 1)]
append_children(parent, level + 1)
if (i != 2):
for j in list(range(properties)):
parent.append(
odml.Property(name='Property' + str(j + 1),
values=[i + j]))
else:
for j in list(range(properties - 2)):
parent.append(
odml.Property(name='Property' + str(j + 1),
values=[i + j]))
parent.append(
odml.Property(name='Property' + str(properties),
values=[i + properties - 1]))
append_children(doc, 0)
doc.append(odml.Section(name='One more Section'))
parent = doc['One more Section']
parent.append(odml.Property(name='Property2', values=[11]))
return doc
def add_section(self, widget, obj_section_pair):
"""
popup menu action: add section
add a section to the selected section (or document if None selected)
"""
(obj, section) = obj_section_pair
if section is None:
name = self.get_new_obj_name(obj.sections,
prefix='Unnamed Section')
section = odml.Section(name=name)
else:
prefix = section.name
name = self.get_new_obj_name(obj.sections, prefix=prefix)
section = section.clone()
section.name = name
# It is a terminology section. By default, pull in all its properties.
section.merge()
cmd = commands.AppendValue(obj=obj, val=section)
self.execute(cmd)
# Expand tree if the parent object is a section
if isinstance(obj, odml.section.Section):
tv = self._treeview
(model, tree_iter) = tv.get_selection().get_selected()
tv.expand_row(model.get_path(tree_iter), False)
def test_paths(self):
sec = odml.Section("bar")
self.assertEqual(sec._get_relative_path("/a", "/b"), "/b")
self.assertEqual(sec._get_relative_path("/a", "/a/b"), "b")
self.assertEqual(sec._get_relative_path("/a/b", "/a/c"), "../c")
self.assertEqual(sec._get_relative_path("/a/b/c", "/a"), "../..")
self.assertEqual(sec._get_relative_path("/a/b", "/a"), "..")
def clicked_record(self):
self.record_timestamp = str(datetime.now()).split('.')[0]
self.create_and_start_new_videorecordings()
self.button_record.setDisabled(True)
self.button_cancel.setEnabled(True)
self.button_tag.setEnabled(True)
self.button_stop.setDisabled(False)
self.event_list = odml.Section('events', 'event_list')
def create_2samerows_test_odml():
"""
creates an odml-document in which there is a property with two same values
to create a table with two rows that are the same
"""
doc = odml.Document()
doc.append(odml.Section(name='section1'))
doc.append(odml.Section(name='section2'))
parent = doc['section1']
parent.append(odml.Property(name='property1', value=[1, 2, 2]))
parent = doc['section2']
parent.append(odml.Property(name='property1', value=2))
return doc
def test_merge_overwrite_values_true(self):
doc1 = odml.Document()
doc1.append(odml.Section('first sec'))
doc1.sections[0].append(
odml.Property('first prop', values='first value'))
doc2 = odml.Document()
doc2.append(odml.Section('first sec'))
doc2.sections[0].append(
odml.Property('first prop', values='second value'))
self.test_table.load_from_odmldoc(doc1)
self.test_table.merge(doc2, overwrite_values=True)
self.assertEqual(len(self.test_table._odmldict[0]['Value']), 1)
self.assertEqual(self.test_table._odmldict[0]['Value'][0],
doc2.sections[0].properties[0].values[0])
def test_rdf_subclassing_definitions(self):
"""
Test that RDF Subclass definitions are written to the resulting graph.
"""
# -- Test default subclassing
doc = odml.Document()
_ = odml.Section(name="test_subclassing", type="cell", parent=doc)
rdf_writer = RDFWriter([doc])
curr_str = " ".join(rdf_writer.get_rdf_str().split())
self.assertIn("odml:Cell a rdfs:Class ; rdfs:subClassOf odml:Section",
curr_str)
self.assertIn("odml:Section a rdfs:Class", curr_str)
# -- Test multiple entries; a definition should only occur once in an RDF document
doc = odml.Document()
sec = odml.Section(name="test_subclassing", type="cell", parent=doc)
sub_sec = odml.Section(name="test_subclassing",
type="cell",
parent=sec)
_ = odml.Section(name="test_subclassing", type="cell", parent=sub_sec)
rdf_writer = RDFWriter([doc])
curr_str = " ".join(rdf_writer.get_rdf_str().split())
self.assertIn("odml:Cell a rdfs:Class ; rdfs:subClassOf odml:Section",
curr_str)
self.assertIs(
curr_str.count(
"odml:Cell a rdfs:Class ; rdfs:subClassOf odml:Section"), 1)
self.assertIn("odml:Section a rdfs:Class", curr_str)
self.assertIs(curr_str.count("odml:Section a rdfs:Class"), 1)
# -- Test custom subclassing
type_custom_class = "species"
custom_class_dict = {type_custom_class: "Species"}
doc = odml.Document()
_ = odml.Section(name="test_subclassing", type="cell", parent=doc)
_ = odml.Section(name="test_custom_subclassing",
type=type_custom_class,
parent=doc)
rdf_writer = RDFWriter([doc], custom_subclasses=custom_class_dict)
curr_str = " ".join(rdf_writer.get_rdf_str().split())
self.assertIn("odml:Cell a rdfs:Class ; rdfs:subClassOf odml:Section",
curr_str)
self.assertIn(
"odml:Species a rdfs:Class ; rdfs:subClassOf odml:Section",
curr_str)
self.assertIn("odml:Section a rdfs:Class", curr_str)
# -- Test inactive subclassing
doc = odml.Document()
_ = odml.Section(name="test_subclassing", type="cell", parent=doc)
rdf_writer = RDFWriter([doc], rdf_subclassing=False)
curr_str = " ".join(rdf_writer.get_rdf_str().split())
self.assertNotIn("odml:Section a rdfs:Class", curr_str)
self.assertNotIn(
"odml:Cell a rdfs:Class ; rdfs:subClassOf odml:Section", curr_str)
def create_ui_doc(author=""):
doc = odml.Document(author=author)
sec = odml.Section(name="sec", parent=doc)
_ = odml.Property(name="prop", parent=sec)
for sec in doc.sections:
handle_section_import(sec)
return doc
def test_section_name_readable(self):
"""
Test if section name is not uuid and thus more readable.
"""
doc = odml.Document()
sec = odml.Section("sec", parent=doc)
sec.name = sec.id
res = Validate(doc)
self.assertError(res, "Name not assigned")
def test_standalone_section(self):
"""
Test if standalone section does not return errors if required attributes are correct.
If type is not specified, check error message.
"""
sec_one = odml.Section("sec1")
res = Validate(sec_one)
self.assertError(res, "Section type not specified")
def test_proxy_equality(self):
p = odml.Property(name="p", value="1")
pp = proxy.PropertyProxy(p)
self.assertTrue(p == pp)
s = odml.Section(name="sec1")
ps = proxy.MappedSection(s)
s.append(p)
self.assertEqual(s, ps)
def setUp(self):
self.test_dir = tempfile.mkdtemp("_odmlnix", "test_",
tempfile.gettempdir())
self.odml_doc = odml.Document(author='me',
date=datetime.date.today(),
version='0.0.1',
repository='unknown')
odml.Section(name='first section', parent=self.odml_doc)
def create_electrode_example():
"""
"""
electrode_type = 'Utah Array'
count = 10
electrode_id = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
impedance = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] # 40-50
length = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] # 2mm-2cm
suaids = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] # between 1 and 4
doc = odml.Document()
doc.append(odml.Section(name='Multielectrode Array'))
parent = doc['Multielectrode Array']
parent.append(odml.Property(name='Type', value=electrode_type))
parent.append(odml.Section(name='Electrodes'))
parent = doc['Multielectrode Array']['Electrodes']
parent.append(odml.Property(name='count', value=count))
for i in list(range(count)):
parent = doc['Multielectrode Array']
sec_name = 'Electrode' + str(i + 1)
parent.append(odml.Section(name=sec_name))
parent = doc['Multielectrode Array'][sec_name]
parent.append(
odml.Property(name='ID',
definition='Electrode ID',
value=electrode_id[i]))
parent.append(
odml.Property(name='Impedance',
definition='Pre-implantation impedance',
value=impedance[i]))
parent.append(
odml.Property(name='Length', definition='Length', value=length[i]))
parent.append(
odml.Property(name='SUAIDs',
definition='ID of single units',
value=suaids[i]))
return doc
def test_property_name_readable(self):
"""
Test if property name is not uuid and thus more readable.
"""
doc = odml.Document()
sec = odml.Section("sec", parent=doc)
prop = odml.Property("prop", parent=sec)
prop.name = prop.id
res = Validate(doc)
self.assertError(res, "Name not assigned")
def clicked_tag(self):
ts = str(datetime.now()).split('.')[0]
text, ok = QtGui.QInputDialog.getText(self, 'Tag data with Event',
'Enter tag comment:')
if ok:
tag_name = 'event_{0:02d}'.format(len(self.tags) + 1)
e = odml.Section(tag_name, 'event')
e.append(odml.Property('timestamp', ts, dtype='datetime'))
e.append(odml.Property('comment', text, dtype='string'))
self.event_list.append(e)
def test_event_passing(self):
s = odml.Section(name="section")
v = odml.Value(1)
p = odml.Property(name="prop", value=v)
s.append(p)
v.data = 4
self.assertEqual(v._modified, [v])
self.assertEqual(p._modified, [v, p])
self.assertEqual(s._modified, [v, p, s])
self.assertEqual(v.data, 4)
def create_section(self, name, depth=0):
s = odml.Section(name=name, type=name.replace("sec", "type"))
if depth < 1:
for i in range(2):
s.append(self.create_section("%s,%d" % (name, i), depth=depth+1))
if name.endswith("1"):
for i in range(3):
s.append(self.create_property("%s:%d" % (name, i)))
return s
def test_sec_cardinality(self):
"""
Test saving and loading of Section sections cardinality variants to
and from all supported file formats.
"""
doc = odml.Document()
sec_empty = "card_empty"
sec_max = "card_max"
sec_min = "card_min"
sec_full = "card_full"
card_dict = {
sec_empty: None,
sec_max: (None, 10),
sec_min: (2, None),
sec_full: (1, 5)
}
_ = odml.Section(name=sec_empty, type="test", parent=doc)
_ = odml.Section(name=sec_max, sec_cardinality=card_dict[sec_max], type="test", parent=doc)
_ = odml.Section(name=sec_min, sec_cardinality=card_dict[sec_min], type="test", parent=doc)
_ = odml.Section(name=sec_full, sec_cardinality=card_dict[sec_full],
type="test", parent=doc)
# Test saving to and loading from an XML file
odml.save(doc, self.xml_file)
xml_doc = odml.load(self.xml_file)
self._test_cardinality_load("sec_cardinality", xml_doc, card_dict,
sec_empty, sec_max, sec_min, sec_full)
# Test saving to and loading from a JSON file
odml.save(doc, self.json_file, "JSON")
json_doc = odml.load(self.json_file, "JSON")
self._test_cardinality_load("sec_cardinality", json_doc, card_dict,
sec_empty, sec_max, sec_min, sec_full)
# Test saving to and loading from a YAML file
odml.save(doc, self.yaml_file, "YAML")
yaml_doc = odml.load(self.yaml_file, "YAML")
self._test_cardinality_load("sec_cardinality", yaml_doc, card_dict,
sec_empty, sec_max, sec_min, sec_full)
def setUp(self):
# Set up test environment
self.tmp_dir = create_test_dir(__file__)
self.json_file = os.path.join(self.tmp_dir, "test.json")
self.xml_file = os.path.join(self.tmp_dir, "test.xml")
self.yaml_file = os.path.join(self.tmp_dir, "test.yaml")
# Set up odML document stub
doc = odml.Document()
_ = odml.Section(name="properties", type="test", parent=doc)
self.doc = doc
