Exemplo n.º 1
0
	def testDataExists(self):
		"""
		Test that count of  ALL_Cre_Cache is non-zero
			and is equal to or greater than the count
			of recombinase results in GXD_Expression.
			(The reason the count is likely higher is because
			  the cre cache duplicates rows with multiple 
			  systems)
		"""

		creCacheCountQuery = """select count(*) cnt from all_cre_cache"""
                creCacheCount = runQuery(creCacheCountQuery)[0]['cnt']

		# assert cache is non-empty
		self.assertDataTrue(creCacheCount, "ALL_Cre_Cache should not be empty")

		creExpressionCountQuery = """select count(*) cnt
			from gxd_expression 
			where isrecombinase = 1
		"""
		creExpressionCount = runQuery(creExpressionCountQuery)[0]['cnt']

		# assert cache has appropriate count
                failMsg = "Count of results in ALL_Cre_Cache should be greater " + \
			"than or equal to count of recombinase results in GXD_Expression"
                self.assertDataTrue(creCacheCount >= creExpressionCount, failMsg)
	def testMarkerCreationDate(self):
		"""
		Test that no MP-annotated markers are newer
			than the latest Derived MP annotations
		"""

		derivedDateQuery = """select creation_date 
			from voc_annot va
			where va._annottype_key = %d
			limit 1
		""" % MP_MARKER_DERIVED_TYPE_KEY
		derivedCreationDate = runQuery(derivedDateQuery)[0]['creation_date']
		
		newMarkerDateQuery = """select max(m.creation_date) as creation_date
			from mrk_marker m
			join gxd_allelegenotype gag on
				gag._marker_key = m._marker_key
			join voc_annot va on
				va._object_key = gag._genotype_key
			where va._annottype_key = %d
		""" % MP_GENO_TYPE_KEY
		markerCreationDate = runQuery(newMarkerDateQuery)[0]['creation_date']

		failMsg = "Derived MP annotations older than latest marker with MP annotations"
		self.assertDataTrue(derivedCreationDate >= markerCreationDate, failMsg)
	def testDerivedCreationDate(self):
		"""
		Test that no source OMIM annotations are newer
			than the latest Derived OMIM annotations
		"""

		derivedDateQuery = """select creation_date 
			from voc_annot va
			where va._annottype_key = %d
			limit 1
		""" % OMIM_MARKER_DERIVED_TYPE_KEY
		derivedCreationDate = runQuery(derivedDateQuery)[0]['creation_date']
		
		sourceAnnotDateQuery = """select max(modification_date) as modification_date
			from voc_annot va
			where va._annottype_key = %d
		""" % OMIM_GENO_TYPE_KEY
		sourceModificationDate = runQuery(sourceAnnotDateQuery)[0]['modification_date']

		failMsg = "Derived OMIM annotations older than the latest source OMIM annotations"
		self.assertDataTrue(derivedCreationDate >= sourceModificationDate, failMsg)