def test_list_annotations2(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
res = epidb.add_genome("GRCh38", "GRCh38",
"chr1 1000000\nchr2 2000000", self.admin_key)
self.assertSuccess(res)
status, anns = epidb.list_annotations("GRCh38", self.admin_key)
self.assertEqual(anns, [['a1', 'Chromosomes size for GRCh38']])
def test_list_annotations(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
genome_info = None
with open("data/genomes/hg19", 'r') as f:
genome_info = f.read().replace(",", "")
file_data = None
with open("data/cpgIslandExt.txt", 'r') as f:
file_data = f.read()
res = epidb.add_genome("hg19", "Human genome 19", genome_info,
self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res = epidb.add_genome("hg19a", "Human genome 19a", genome_info,
self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19a", "CpG islands are associated ...",
file_data, "", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res = epidb.add_genome("hg19b", "Human genome 19b", genome_info,
self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19b", "CpG islands are associated ...",
file_data, "", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
expected = [
'okay',
[['a1', 'Chromosomes size for hg19'], ['a2', 'Cpg Islands'],
['a3', 'Chromosomes size for hg19a'], ['a4', 'Cpg Islands'],
['a5', 'Chromosomes size for hg19b'], ['a6', 'Cpg Islands']]
]
result = epidb.list_annotations("", self.admin_key)
self.assertEqual(expected, result)
def test_remove_genome(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init(epidb)
genome_info = None
with open("data/genomes/hg19", 'r') as f:
genome_info = f.read().replace(",", "")
res = epidb.add_genome("A1", "ANGELICA", genome_info, self.admin_key)
self.assertSuccess(res)
genome_id = res[1]
res, user = epidb.add_user("user1", "*****@*****.**", "test",
self.admin_key)
self.assertSuccess(res, user)
res = epidb.remove(genome_id, user[1])
self.assertFailure(res)
res = epidb.add_genome("A1", "XUXA", genome_info, self.admin_key)
self.assertFailure(res)
(res, genomes) = epidb.list_genomes(self.admin_key)
self.assertEqual(len(genomes), 1)
self.assertEqual(genomes[0][0], genome_id)
self.assertEqual(genomes[0][1], "A1")
res = epidb.remove(genome_id, self.admin_key)
self.assertSuccess(res)
res = epidb.add_genome("A1", "XUXA", genome_info, self.admin_key)
self.assertSuccess(res)
status, found = epidb.search("XUXA", "", self.admin_key)
self.assertEqual(len(found), 2)
status, found = epidb.search("ANGELICA", "", self.admin_key)
self.assertEqual(len(found), 0)
status, genomes = epidb.list_genomes(self.admin_key)
self.assertSuccess(status, genomes)
for genome in genomes:
res = epidb.remove(genome[0], self.admin_key)
self.assertSuccess(res)
res, anns = epidb.list_annotations(genome[1], self.admin_key)
self.assertEqual(len(anns), 0)
def test_annotation(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
file_data = None
with open("data/cpgIslandExt.txt", 'r') as f:
file_data = f.read()
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res, annotations = epidb.list_annotations("hg19", self.admin_key)
self.assertSuccess(res, annotations)
self.assertEqual(len(annotations), 2)
self.assertEqual(annotations[0][1], "Chromosomes size for hg19")
self.assertEqual(annotations[1][1], "Cpg Islands")
size = len(file_data.split("\n"))
res, qid = epidb.select_annotations("Cpg Islands", "hg19", None, None,
None, self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.count_regions(qid, self.admin_key)
self.assertSuccess(res, req)
count = self.count_request(req)
self.assertEqual(size, count)
res, req = epidb.get_regions(qid, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
self.assertEqual(regions, file_data)
def test_remove_annotation(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
file_data = None
with open("data/cpgIslandExt.txt", 'r') as f:
file_data = f.read()
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
annotation_id = res[1]
res, user = epidb.add_user("user1", "*****@*****.**", "test",
self.admin_key)
self.assertSuccess(res, user)
res = epidb.remove(annotation_id, user[1])
self.assertFailure(res)
res = epidb.remove(annotation_id, self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
annotation_id = res[1]
res, genomes = epidb.search("hg19", "genomes", self.admin_key)
res, anns = epidb.remove(genomes[0][0], self.admin_key)
self.assertFailure(res, anns)
self.assertEqual(anns, "This genome is being used by annotations.")
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertFailure(res)
res = epidb.remove(annotation_id, self.admin_key)
self.assertSuccess(res)
res = epidb.add_annotation(
"Cpg Islands", "hg19", "CpG islands are associated ...", file_data,
"", {
"url":
"genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=regulation&hgta_track=cpgIslandExt&hgta_table=cpgIslandExt&hgta_doSchema=describe+table+schema"
}, self.admin_key)
self.assertSuccess(res)
res = epidb.remove(res[1], self.admin_key)
self.assertSuccess(res)
res, genomes = epidb.list_genomes(self.admin_key)
for genome in genomes:
res = epidb.remove(genome[0], self.admin_key)
self.assertSuccess(res)
res, anns = epidb.list_annotations("hg18", self.admin_key)
self.assertSuccess(res, anns)
self.assertEqual(len(anns), 0)
res, anns = epidb.list_annotations("hg19", self.admin_key)
self.assertSuccess(res, anns)
self.assertEqual(len(anns), 0)
