class BusinessTests(unittest.TestCase):
def setUp(self):
self.queries = Queries(connectionFactory)
def testGetRegionSequence(self):
data = self.queries.getFeatureLocs(1, 1, 100000, [42, 69])
print Formatter(data).formatJSON()
def testGetTopLevel(self):
data = self.queries.getTopLevel(14)
print Formatter(data).formatJSON()
class FeatureLengthTest(unittest.TestCase):
def setUp(self):
self.queries = Queries(connectionFactory)
def test1(self):
result = self.queries.getFeatureLength("Pf3D7_01")
print Formatter(result).formatJSON()
class GeneTests(unittest.TestCase):
def setUp(self):
self.queries = Queries(connectionFactory)
def test1(self):
# print dir(self.queries)
gene_results = self.queries.getCDSs(22)
print Formatter(gene_results).formatJSON()[1:10000]
genes = []
for gene_result in gene_results:
genes.append(gene_result["gene"])
mrnas = self.queries.getMRNAs(genes)
print Formatter(mrnas).formatJSON()[1:10000]
peps = self.queries.getPEPs(genes)
print Formatter(peps).formatJSON()[1:10000]
class BoundaryTest(unittest.TestCase):
def setUp(self):
self.queries = Queries(connectionFactory)
def testGetOrganismProp(self):
# eurkaryotes and prokaryotes have different translation tables, so choose both a eukaryote and a prokaryote for this test
organism_ids = [22, 71]
cvterm_name = 'translationTable'
cv_name = 'genedb_misc'
translation_tables = self.queries.getOrganismProp(organism_ids, cvterm_name, cv_name)
print Formatter(translation_tables).formatJSON()
self.assertNotEqual(translation_tables[0]["value"], translation_tables[1]["value"])
def testGetFeatureCoordinates(self):
coords = self.queries.getFeatureCoordinates( ["PFA0170c", "PFA0170c:mRNA", "PFA0170c:exon:1", "PFA0170c:pep", "PFA0315w", "PFA0315w:mRNA", "PFA0315w:exon:1", "PFA0315w:exon:2", "PFA0315w:exon:3", "PFA0315w:exon:4"], "Pf3D7_01" )
print Formatter(coords).formatJSON()
def testGetExonCoordinates(self):
coords = self.queries.getExons( "Pf3D7_01", ["PFA0170c", "PFA0315w"] )
print Formatter(coords).formatJSON()
def setUp(self):
self.queries = Queries(connectionFactory)
class BusinessTests2(unittest.TestCase):
def setUp(self):
self.queries = Queries(connectionFactory)
def testAllChanged(self):
since = "2009-06-01"
organism_id = 14
changed_features = self.queries.getAllChangedFeaturesForOrganism(since, organism_id)
data = {
"response" : {
"name" : "genome/changes",
"taxonID" : "420245",
"count" : len(changed_features),
"since" : since,
"results" : changed_features
}
}
formatter = Formatter(data, os.path.dirname(__file__) + "/../tpl/")
formatter.formatJSON()
formatter.formatXML("changes.xml.tpl")
def testGetOrganismFromTaxon(self):
taxonID = self.queries.getOrganismFromTaxon('420245')
self.assertEquals(taxonID, 14)
def testGetGenesWithPrivateAnnotationChanges(self):
since = "2009-06-01"
rows = self.queries.getGenesWithPrivateAnnotationChanges(14, since)
data = {
"response" : {
"name" : "genome/recorded_annotation_changes",
"taxonID" : "420245",
"count" : len(rows),
"results" : rows
}
}
formatter = Formatter(data, os.path.dirname(__file__) + "/../tpl/")
formatter.formatXML('private_annotations.xml.tpl')
formatter.formatJSON()
def testAllOrganisms(self):
since = "2009-06-01"
organism_list = self.queries.getAllOrganismsAndTaxonIDs()
organismIDs = []
organismHash = {}
for organism_details in organism_list:
organism_details["count"] = 0
organismIDs.append(organism_details["organism_id"])
organismHash [organism_details["organism_id"]] = organism_details
counts = self.queries.countAllChangedFeaturesForOrganisms(since, organismIDs)
for count in counts:
organismID = str(count[0])
print organismID
org = organismHash[organismID]
org["count"] = count[1]
data = {
"response" : {
"name" : "genomes/changes",
"since" : since,
"results" : organismHash.values()
}
}
formatter = Formatter(data, os.path.dirname(__file__) + "/../tpl/")
print formatter.formatXML('genomes_changed.xml.tpl')
def testCountAllOrganisms(self):
since = "2009-06-01"
organismIDs = [12, 14, 15, 20]
result = self.queries.countAllChangedFeaturesForOrganisms(since, organismIDs)
print result
def testGetRegionSequence(self):
rows = self.queries.getRegionSequence("Pf3D7_01")
row = rows[0]
length = row["length"]
start = 1
end = 10
dna = row["dna"]
dna = dna[start-1:end-1]
data = {
"response" : {
"name" : "region/sequence",
"sequence" : {
"start" : start,
"end" : end,
"length" : length,
"dna" : dna
}
}
}
formatter = Formatter(data, os.path.dirname(__file__) + "/../tpl/")
print formatter.formatJSON()
def testGetFeatureLocs(self):
json_data = self.queries.getFeatureLocs(1, 1, 10000, [42, 69])
print json.dumps(json_data, sort_keys=True, indent=4)
def testGetID(self):
print self.queries.getFeatureID("Pf3D7_01")
