def initialize_table_defaults(g: Graph, opts: Namespace) -> None:
"""
Initialize all of the table defaults
:param g: Graph containing fhir.ttl
:param opts: input options
"""
# TODO: This is kind of messy -- we've refactored so we should be able to consolidate this
CommonDimension.graph = g
ConceptDimension._clear()
ConceptDimension.sourcesystem_cd = opts.sourcesystem
ConceptDimension.update_date = opts.updatedate
ConceptDimensionRoot._clear()
ConceptDimensionRoot.sourcesystem_cd = opts.sourcesystem
ConceptDimensionRoot.update_date = opts.updatedate
ModifierDimension._clear()
ModifierDimension.sourcesystem_cd = opts.sourcesystem
ModifierDimension.update_date = opts.updatedate
OntologyEntry._clear()
OntologyEntry.sourcesystem_cd = opts.sourcesystem
OntologyEntry.update_date = opts.updatedate
OntologyRoot._clear()
OntologyRoot.sourcesystem_cd = opts.sourcesystem
OntologyRoot.update_date = opts.updatedate
def test_ontology_root(self):
from i2fhirb2.i2b2model.metadata.i2b2ontology import OntologyRoot, OntologyEntry
OntologyRoot._clear()
OntologyEntry._clear()
o = OntologyRoot("FHIR")
OntologyRoot.update_date = datetime.datetime(2017, 5, 25, 13, 0)
self.assertEqual(('0\t\\FHIR\\\tFHIR\tN\tCA \t\tFHIR:\t\t\t\t'
'\tT\t\t\t\t\t@\t2017-05-25 13:00:00\t2017-05-25 '
'13:00:00\t2017-05-25 13:00:00\tFHIR\t\t\t\t'),
repr(o))
def test_modifier_ontology_entry(self):
from i2fhirb2.fhir.fhirspecific import FHIR
from i2fhirb2.i2b2model.metadata.i2b2ontology import OntologyEntry, ModifierOntologyEntry
OntologyEntry._clear()
navigational_path = '\\FHIR\\administrative\\individual\\Patient\\'
modifier_path = "\\FHIRMod\\Patient\\active\\"
OntologyEntry.graph = shared_graph
OntologyEntry.sourcesystem_cd = "STU3"
OntologyEntry.update_date = datetime.datetime(2017, 5, 25, 13, 0)
subj = FHIR.Patient
mod = FHIR.Patient.active
o = ModifierOntologyEntry(1, subj, mod, modifier_path,
navigational_path, True, mod, FHIR.boolean)
self.assertEqual(
OrderedDict([
('c_hlevel', 1),
('c_fullname', '\\FHIRMod\\Patient\\active\\'),
('c_name', 'active'), ('c_synonym_cd', 'N'),
('c_visualattributes', 'RA '), ('c_totalnum', None),
('c_basecode', 'FHIR:Patient.active'),
('c_metadataxml', '<?xml version="1.0"?>\n'
'<ValueMetadata>\n'
' <Version>3.02</Version>\n'
' <CreationDateTime>2017-05-25 13:00:00</CreationDateTime>\n'
' <TestID>FHIR:Patient.active</TestID>\n'
' <TestName>active</TestName>\n'
' <DataType>Enum</DataType>\n'
' <Flagstouse/>\n'
' <Oktousevalues>Y</Oktousevalues>\n'
' <EnumValues>\n'
' <Val description="True value">True</Val>\n'
' <Val description="False value">False</Val>\n'
' </EnumValues>\n'
' <UnitValues/>\n'
'</ValueMetadata>'), ('c_facttablecolumn', 'modifier_cd'),
('c_tablename', 'modifier_dimension'),
('c_columnname', 'modifier_path'), ('c_columndatatype', 'T'),
('c_operator', 'like'),
('c_dimcode', '\\FHIR\\Patient\\active\\'),
('c_comment', 'Whether this patient record is in active use.'),
('c_tooltip',
"Whether this patient's record is in active use"),
('m_applied_path',
'\\FHIR\\administrative\\individual\\Patient\\'),
('update_date', datetime.datetime(2017, 5, 25, 13, 0)),
('download_date', datetime.datetime(2017, 5, 25, 13, 0)),
('import_date', datetime.datetime(2017, 5, 25, 13, 0)),
('sourcesystem_cd', 'STU3'), ('valuetype_cd', None),
('m_exclusion_cd', None), ('c_path', None), ('c_symbol', None)
]), o._freeze())
def test_patient_query(self):
from i2fhirb2.i2b2model.metadata.i2b2ontologyquery import PatientQuery
from i2fhirb2.i2b2model.metadata.i2b2ontology import OntologyEntry
q = PatientQuery('patient_num', '=', 12345)
self.assertEqual(
"SELECT patient_num\nFROM patient_dimension\nWHERE patient_num = 12345",
str(q))
pq = PatientQuery(
'birth_date', 'BETWEEN',
"(CURRENT_DATE - INTERVAL '731.5 day') AND"
" (CURRENT_DATE - INTERVAL '366.25 day')")
self.assertEqual(
"SELECT patient_num\nFROM patient_dimension\n"
"WHERE birth_date BETWEEN "
"(CURRENT_DATE - INTERVAL '731.5 day') AND "
"(CURRENT_DATE - INTERVAL '366.25 day')", str(pq))
o = OntologyEntry("\\PATH\\subpath\\", pq, None, "Q117.3")
self.assertEqual(o.c_facttablecolumn, 'patient_num')
self.assertEqual(o.c_tablename, 'patient_dimension')
self.assertEqual(o.c_columndatatype, 'N')
self.assertEqual(o.c_columnname, 'birth_date')
self.assertEqual(o.c_operator, 'BETWEEN')
self.assertEqual(
o.c_dimcode, "(CURRENT_DATE - INTERVAL '731.5 day') "
"AND (CURRENT_DATE - INTERVAL '366.25 day')")
def setUp(self):
super().setUp()
from i2fhirb2.i2b2model.metadata import dimensionmetadata
ref_datetime = datetime(2017, 5, 25, 13, 0)
dimensionmetadata.creation_date = ref_datetime
from i2fhirb2.i2b2model.metadata.i2b2ontology import OntologyEntry
OntologyEntry._clear()
OntologyEntry.update_date = OntologyRoot.update_date = ref_datetime
from i2fhirb2.i2b2model.metadata.i2b2modifierdimension import ModifierDimension
ModifierDimension._clear()
ModifierDimension.update_date = ref_datetime
ModifierDimension.graph = shared_graph
from i2fhirb2.i2b2model.metadata.i2b2conceptdimension import ConceptDimension
ConceptDimension._clear()
ConceptDimension.update_date = ConceptDimension.import_date = ConceptDimension.download_date = \
ref_datetime
ConceptDimension.graph = shared_graph
def tst_output(self, dimensions: Tuple[List[OntologyEntry], List[ConceptDimension], List[ModifierDimension]],
resource_name: str) -> None:
"""
Test the output of FHIROntologyTable.dimension_list as generated against resource
:param dimensions: ontology, concept and modifier dimension entries
:param resource_name: name of specific test file (e.g. 'observation', 'domain_resource', etc.)
"""
self.set_sourcesystem_cds()
self.tst_dimension(OntologyEntry._header(), dimensions[0], 'fhir_ontology_' + resource_name)
self.tst_dimension(ConceptDimension._header(), dimensions[1], 'fhir_concept_dimension_' + resource_name)
self.tst_dimension(ModifierDimension._header(), dimensions[2], 'fhir_modifier_dimension_' + resource_name)
def test_empty_query(self):
from i2fhirb2.i2b2model.metadata.i2b2ontologyquery import EmptyQuery
from i2fhirb2.i2b2model.metadata.i2b2ontology import OntologyEntry
q = EmptyQuery()
self.assertEqual("NO QUERY", str(q))
o = OntologyEntry("\\PATH\\subpath\\", EmptyQuery(), None, "74400008")
self.assertEqual(o.c_facttablecolumn, '')
self.assertEqual(o.c_tablename, '')
self.assertEqual(o.c_columndatatype, 'T')
self.assertEqual(o.c_columnname, '')
self.assertEqual(o.c_operator, '')
self.assertEqual(o.c_dimcode, '')
def test_basics(self):
from i2fhirb2.i2b2model.metadata.i2b2ontology import OntologyEntry
from i2fhirb2.i2b2model.metadata.i2b2ontologyquery import ConceptQuery
OntologyEntry.download_date = datetime.datetime(2017, 5, 25)
OntologyEntry.sourcesystem_cd = "FHIR"
OntologyEntry.import_date = datetime.datetime(2017, 5, 25)
OntologyEntry.update_date = datetime.datetime(2001, 12, 1)
ontrec = OntologyEntry('\\X\\Y\\Z\\', ConceptQuery('\\X\\Y\\Z\\'),
None, "17400008")
self.assertEqual(
'c_hlevel\tc_fullname\tc_name\tc_synonym_cd\tc_visualattributes\t'
'c_totalnum\tc_basecode\tc_metadataxml\tc_facttablecolumn\tc_tablename\t'
'c_columnname\tc_columndatatype\tc_operator\tc_dimcode\tc_comment\t'
'c_tooltip\tm_applied_path\tupdate_date\tdownload_date\t'
'import_date\tsourcesystem_cd\tvaluetype_cd\tm_exclusion_cd\tc_path\tc_symbol',
ontrec._header())
# Note that hierarchy level is zero based
self.assertEqual(
OrderedDict([('c_hlevel', 2), ('c_fullname', '\\X\\Y\\Z\\'),
('c_name', 'Z'), ('c_synonym_cd', 'N'),
('c_visualattributes', 'FAE'), ('c_totalnum', None),
('c_basecode', '17400008'), ('c_metadataxml', None),
('c_facttablecolumn', 'concept_cd'),
('c_tablename', 'concept_dimension'),
('c_columnname', 'concept_path'),
('c_columndatatype', 'T'), ('c_operator', '='),
('c_dimcode', '\\X\\Y\\Z\\'), ('c_comment', None),
('c_tooltip', None), ('m_applied_path', '@'),
('update_date', datetime.datetime(2001, 12, 1, 0, 0)),
('download_date',
datetime.datetime(2017, 5, 25, 0, 0)),
('import_date', datetime.datetime(2017, 5, 25, 0, 0)),
('sourcesystem_cd', 'FHIR'), ('valuetype_cd', None),
('m_exclusion_cd', None), ('c_path', None),
('c_symbol', None)]), ontrec._freeze())
def test_visit_query(self):
from i2fhirb2.i2b2model.metadata.i2b2ontologyquery import VisitQuery
from i2fhirb2.i2b2model.metadata.i2b2ontology import OntologyEntry
vq = VisitQuery('length_of_stay', '>', 10)
self.assertEqual(
"SELECT encounter_num\nFROM visit_dimension\nWHERE length_of_stay > 10",
str(vq))
o = OntologyEntry("\\PATH\\subpath\\", vq, None, "Q117.3")
self.assertEqual(o.c_facttablecolumn, 'encounter_num')
self.assertEqual(o.c_tablename, 'visit_dimension')
self.assertEqual(o.c_columndatatype, 'N')
self.assertEqual(o.c_columnname, 'length_of_stay')
self.assertEqual(o.c_operator, '>')
self.assertEqual(o.c_dimcode, 10)
def test_modifier_query(self):
from i2fhirb2.i2b2model.metadata.i2b2ontologyquery import ModifierQuery
from i2fhirb2.i2b2model.metadata.i2b2ontology import OntologyEntry
q = ModifierQuery("foo")
self.assertEqual(
"SELECT modifier_cd\nFROM modifier_dimension\nWHERE modifier_path like 'foo'",
str(q))
o = OntologyEntry("\\PATH\\subpath\\",
ModifierQuery('\\PATH\\subpath\\'), None, "74400008")
self.assertEqual(o.c_facttablecolumn, 'modifier_cd')
self.assertEqual(o.c_tablename, 'modifier_dimension')
self.assertEqual(o.c_columndatatype, 'T')
self.assertEqual(o.c_columnname, 'modifier_path')
self.assertEqual(o.c_operator, 'like')
self.assertEqual(o.c_dimcode, '\\PATH\\subpath\\')
def test_concept_query(self):
from i2fhirb2.i2b2model.metadata.i2b2ontologyquery import ConceptQuery
from i2fhirb2.i2b2model.metadata.i2b2ontology import OntologyEntry
q = ConceptQuery("foo")
self.assertEqual(
"SELECT concept_cd\nFROM concept_dimension\nWHERE concept_path = 'foo'",
str(q))
q.where_obj = '\\path\\%'
self.assertEqual(
"SELECT concept_cd\nFROM concept_dimension\nWHERE concept_path = '\\path\\%'",
str(q))
o = OntologyEntry("\\PATH\\subpath\\",
ConceptQuery('\\PATH\\subpath\\'), None, "74400008")
self.assertEqual(o.c_facttablecolumn, 'concept_cd')
self.assertEqual(o.c_tablename, 'concept_dimension')
self.assertEqual(o.c_columndatatype, 'T')
self.assertEqual(o.c_columnname, 'concept_path')
self.assertEqual(o.c_operator, '=')
self.assertEqual(o.c_dimcode, '\\PATH\\subpath\\')
def output_ontology(opts: Namespace, output: List[OntologyEntry]) -> bool:
"""
Generate the i2b2 ontology output if required
:param opts: input options
:param output: set of ontology entries
:return: success indicator
"""
table_name = i2b2tablenames.ontology_table
if not opts.table or opts.table == table_name:
if opts.outdir:
return write_tsv(opts.outdir, table_name, OntologyEntry._header(),
output)
else:
table = opts.tables.ontology_table
change_column_length(table, table.c.c_basecode, 200,
opts.tables.ont_engine)
# MedicationStatement is 1547 long
change_column_length(table, table.c.c_tooltip, 1600,
opts.tables.ont_engine)
return update_dimension_table(
output, opts, table, 'c_basecode',
[opts.base.replace('\\', '') + ':', 'W5'])
else:
return True
def test_concept_ontology_entry(self):
from i2fhirb2.fhir.fhirspecific import FHIR
from i2fhirb2.i2b2model.metadata.i2b2ontology import ConceptOntologyEntry, OntologyEntry
OntologyEntry._clear()
navigational_path = '\\FHIR\\administrative\\individual\\Patient\\'
ontology_path = "\\FHIR\\Patient\\"
OntologyEntry.graph = shared_graph
OntologyEntry.sourcesystem_cd = "STU3"
OntologyEntry.update_date = datetime.datetime(2017, 5, 25, 13, 0)
subj = FHIR.Patient
o = ConceptOntologyEntry(subj, navigational_path, ontology_path, True)
self.assertEqual(
OrderedDict([
('c_hlevel', 3),
('c_fullname',
'\\FHIR\\administrative\\individual\\Patient\\'),
('c_name', 'Patient'), ('c_synonym_cd', 'N'),
('c_visualattributes', 'LA '), ('c_totalnum', None),
('c_basecode', 'FHIR:Patient'), ('c_metadataxml', None),
('c_facttablecolumn', 'concept_cd'),
('c_tablename', 'concept_dimension'),
('c_columnname', 'concept_path'), ('c_columndatatype', 'T'),
('c_operator', '='), ('c_dimcode', '\\FHIR\\Patient\\'),
('c_comment',
'Demographics and other administrative information about an '
'individual or animal receiving care or other health-related '
'services.'),
('c_tooltip',
'Demographics and other administrative information about an '
'individual or animal receiving care or other health-related '
'services.'), ('m_applied_path', '@'),
('update_date', datetime.datetime(2017, 5, 25, 13, 0)),
('download_date', datetime.datetime(2017, 5, 25, 13, 0)),
('import_date', datetime.datetime(2017, 5, 25, 13, 0)),
('sourcesystem_cd', 'STU3'), ('valuetype_cd', None),
('m_exclusion_cd', None), ('c_path', None), ('c_symbol', None)
]), o._freeze())
o = ConceptOntologyEntry(subj, navigational_path, ontology_path, False)
self.assertEqual(
OrderedDict([
('c_hlevel', 3),
('c_fullname',
'\\FHIR\\administrative\\individual\\Patient\\'),
('c_name', 'Patient'), ('c_synonym_cd', 'N'),
('c_visualattributes', 'FA '), ('c_totalnum', None),
('c_basecode', 'FHIR:Patient'), ('c_metadataxml', None),
('c_facttablecolumn', 'concept_cd'),
('c_tablename', 'concept_dimension'),
('c_columnname', 'concept_path'), ('c_columndatatype', 'T'),
('c_operator', '='), ('c_dimcode', '\\FHIR\\Patient\\'),
('c_comment',
'Demographics and other administrative information about an '
'individual or animal receiving care or other health-related '
'services.'),
('c_tooltip',
'Demographics and other administrative information about an '
'individual or animal receiving care or other health-related '
'services.'), ('m_applied_path', '@'),
('update_date', datetime.datetime(2017, 5, 25, 13, 0)),
('download_date', datetime.datetime(2017, 5, 25, 13, 0)),
('import_date', datetime.datetime(2017, 5, 25, 13, 0)),
('sourcesystem_cd', 'STU3'), ('valuetype_cd', None),
('m_exclusion_cd', None), ('c_path', None), ('c_symbol', None)
]), o._freeze())