def count_request(self, req):
if req[0] is not 'r':
print "Invalid request " + req
return
epidb = DeepBlueClient(address="localhost", port=31415)
sleep = 0.1
(s, ss) = epidb.info(req, self.admin_key)
while ss[0]["state"] != "done":
time.sleep(sleep)
(s, ss) = epidb.info(req, self.admin_key)
sleep += sleep
(s, data) = epidb.get_request_data(req, self.admin_key)
self.assertSuccess(s, data)
return data["count"]
def __get_regions_request(self, req, status=["done"]):
if req[0] is not 'r':
print "Invalid request " + req
return
epidb = DeepBlueClient(address="localhost", port=31415)
sleep = 0.1
count = 0
(s, ss) = epidb.info(req, self.admin_key)
while ss[0]["state"] not in status:
time.sleep(sleep)
(s, ss) = epidb.info(req, self.admin_key)
sleep += 0.5
count += 1
if count > 5:
print ss
(s, data) = epidb.get_request_data(req, self.admin_key)
return (s, data)
def test_gene_expression(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
(s, project) = epidb.add_project("DEEP", "Deutsche Epigenom",
self.admin_key)
self.assertSuccess(s, project)
data = gzip.open("data/fpkm/small_1.fpkm_tracking.gz").read()
(s, gene_expression) = epidb.add_expression("gene", "s2", 1, data,
"cufflinks", "DEEP", None,
self.admin_key)
self.assertSuccess(s, gene_expression)
data = gzip.open("data/fpkm/small_2.fpkm_tracking.gz").read()
(s, gene_expression) = epidb.add_expression("gene", "s2", 2, data,
"cufflinks", "DEEP", None,
self.admin_key)
self.assertSuccess(s, gene_expression)
data = gzip.open("data/fpkm/small_3.fpkm_tracking.gz").read()
(s, gene_expression) = epidb.add_expression("gene", "s2", 44, data,
"cufflinks", "DEEP", None,
self.admin_key)
self.assertSuccess(s, gene_expression)
(s, gex) = epidb.list_expressions("gene", "s1", None, None,
self.admin_key)
self.assertEquals(gex, [])
(s, gex) = epidb.list_expressions("gene", "s2", None, None,
self.admin_key)
self.assertEquals(gex, [['gx1', ''], ['gx2', ''], ['gx3', '']])
(s, gex) = epidb.list_expressions("gene", "s2", [1, 2], None,
self.admin_key)
self.assertEquals(gex, [['gx1', ''], ['gx2', '']])
(s, gex) = epidb.list_expressions("gene", "s2", 44, None,
self.admin_key)
self.assertEquals(gex, [['gx3', '']])
(s, gex) = epidb.list_expressions("gene", None, 1, "DEEP",
self.admin_key)
self.assertEquals(gex, [['gx1', '']])
data = gzip.open(
"data/fpkm/51_Hf03_BlTN_Ct_mRNA_M_1.LXPv1.20150708_genes.fpkm_tracking.gz"
).read()
(s, gene_expression) = epidb.add_expression("gene", "s1", 1, data,
"cufflinks", "ENCODE",
None, self.admin_key)
self.assertSuccess(s, gene_expression)
(s, gex) = epidb.list_expressions("gene", None, None, None,
self.admin_key)
self.assertEquals(gex,
[['gx1', ''], ['gx2', ''], ['gx3', ''], ['gx4', '']])
(s, gex) = epidb.list_expressions("gene", "s1", 1, None,
self.admin_key)
self.assertEquals(gex, [['gx4', '']])
(s, gex) = epidb.list_expressions("gene", None, None, "ENCODE",
self.admin_key)
self.assertEquals(gex, [['gx4', '']])
(s, gex) = epidb.list_expressions("gene", ["s1", "s2"], 1, None,
self.admin_key)
self.assertEquals(gex, [['gx1', ''], ['gx4', '']])
(s, gex) = epidb.list_expressions("gene", ["s1", "s2"], 2, None,
self.admin_key)
self.assertEquals(gex, [['gx2', '']])
(s, gex) = epidb.list_expressions("gene", None, 1, "ENCODE",
self.admin_key)
self.assertEquals(gex, [['gx4', '']])
s, user = epidb.add_user("user", "email", "institution",
self.admin_key)
(user_id, user_key) = user
self.assertSuccess(s)
(s, ss) = epidb.modify_user_admin(user_id, "permission_level",
"GET_DATA", self.admin_key)
self.assertSuccess(s, ss)
(s, gex) = epidb.list_expressions("gene", None, None, None, user_key)
self.assertEquals(gex, [])
(s, gex) = epidb.list_expressions("gene", "s1", 1, None, user_key)
self.assertEquals(gex, [])
(s, gex) = epidb.list_expressions("gene", None, None, "ENCODE",
user_key)
self.assertEquals(gex, "107000:Project 'ENCODE' does not exist.")
(s, info) = epidb.info(gene_expression, self.admin_key)
self.assertEquals(
info[0], {
'format':
'TRACKING_ID,GENE_ID,GENE_SHORT_NAME,FPKM,FPKM_CONF_LO,FPKM_CONF_HI,FPKM_STATUS',
'sample_info': {
'biosource_name': 'K562',
'karyotype': 'cancer',
'sex': 'F'
},
'content_format':
'cufflinks',
'total_genes':
57910,
'replica':
1,
'sample_id':
's1',
'_id':
'gx4',
'extra_metadata': {},
'columns': [{
'name': 'TRACKING_ID',
'column_type': 'string'
}, {
'name': 'GENE_ID',
'column_type': 'string'
}, {
'name': 'GENE_SHORT_NAME',
'column_type': 'string'
}, {
'name': 'FPKM',
'column_type': 'double'
}, {
'name': 'FPKM_CONF_LO',
'column_type': 'double'
}, {
'name': 'FPKM_CONF_HI',
'column_type': 'double'
}, {
'name': 'FPKM_STATUS',
'column_type': 'string'
}]
})
data = gzip.open(
"data/grape2/SP8-TH91.gene_quantification.rsem_grape2_crg.GRCh38.20150622.results.txt.gz"
).read()
(s, gene_expression) = epidb.add_expression("gene", "s1", 1, data,
"grape2", "ENCODE", None,
self.admin_key)
self.assertEquals(
gene_expression,
"131001:A Expression of the type 'gene' with sample_id 's1' and replica '1' already exists."
)
(s, gene_expression) = epidb.add_expression("gene", "s1", 2, data,
"grape2", "ENCODE", None,
self.admin_key)
self.assertSuccess(s, gene_expression)
data = gzip.open(
"data/gtf/gencode.v19.annotation.ONLY_GENES.gtf.gz").read()
(s, ss) = epidb.add_gene_model("gencode v19", "hg19",
"Test One Description", data, "GTF", {},
self.admin_key)
self.assertSuccess(s, ss)
(status, gx_query) = epidb.select_expressions("gene", "s1", 2,
"ENSG00000000003.13",
"ENCODE", "gencode v19",
self.admin_key)
self.assertSuccess(status, gx_query)
status, info = epidb.info(gx_query, user_key)
(status, r_id) = epidb.get_regions(
gx_query,
"CHROMOSOME,START,END,@STRAND,GENE_ID,TRANSCRIPT_IDS,LENGTH,EFFECTIVE_LENGTH,EXPECTED_COUNT,TPM,FPKM,POSTERIOR_MEAN_COUNT,POSTERIOR_STANDARD_DEVIATION_OF_COUNT,PME_TPM,PME_FPKM,TPM_CI_LOWER_BOUND,TPM_CI_UPPER_BOUND,FPKM_CI_LOWER_BOUND,FPKM_CI_UPPER_BOUND",
self.admin_key)
self.assertSuccess(status, r_id)
regions = self.get_regions_request(r_id)
self.assertEquals(
regions,
"chrX\t99883667\t99894988\t-\tENSG00000000003.13\tENSG00000000003.13\t2025\t1855.4301\t161.0000\t1.0000\t2.1300\t161.0000\t0.0000\t1.0500\t2.2700\t0.8742\t1.2451\t1.8882\t2.6879"
)
(status, gx_query) = epidb.select_expressions("gene", "s1", 2,
"ENSG00000000003.13",
"ENCODE", "gencode v19",
self.admin_key)
self.assertSuccess(status, gx_query)
status, info = epidb.info(gx_query, user_key)
(status, r_id) = epidb.get_regions(
gx_query,
"GENE_ID,TRANSCRIPT_IDS,LENGTH,EFFECTIVE_LENGTH,EXPECTED_COUNT,TPM,FPKM,POSTERIOR_MEAN_COUNT,POSTERIOR_STANDARD_DEVIATION_OF_COUNT,PME_TPM,PME_FPKM,TPM_CI_LOWER_BOUND,TPM_CI_UPPER_BOUND,FPKM_CI_LOWER_BOUND,FPKM_CI_UPPER_BOUND",
self.admin_key)
self.assertSuccess(status, r_id)
regions = self.get_regions_request(r_id)
self.assertEquals(
regions,
"ENSG00000000003.13\tENSG00000000003.13\t2025\t1855.4301\t161.0000\t1.0000\t2.1300\t161.0000\t0.0000\t1.0500\t2.2700\t0.8742\t1.2451\t1.8882\t2.6879"
)
(status, gx_query) = epidb.select_expressions("gene", "s1", 1,
"OR4G11P", "ENCODE",
"gencode v19",
self.admin_key)
self.assertSuccess(status, gx_query)
status, info = epidb.info("gx1", user_key)
(status, r_id) = epidb.get_regions(gx_query, info[0]["format"],
self.admin_key)
self.assertSuccess(status, r_id)
regions = self.get_regions_request(r_id)
self.assertEquals(
regions,
"ENSG00000240361.1\tENSG00000240361.1\tOR4G11P\t0.0000\t0.0000\t0.0000\tOK"
)
(status, gx_query) = epidb.select_expressions(
"gene", "s1", 1,
['CCR1', 'CD164', 'CD1D', 'CD2', 'CD34', 'CD3G', 'CD44'], "ENCODE",
"gencode v19", self.admin_key)
self.assertSuccess(status, gx_query)
status, info = epidb.info("gx1", user_key)
(status, r_id) = epidb.get_regions(gx_query, info[0]["format"],
self.admin_key)
self.assertSuccess(status, r_id)
regions_a = self.get_regions_request(r_id)
excepted = "ENSG00000135535.10\tENSG00000135535.10\tCD164\t101.3820\t98.8947\t103.8680\tOK\nENSG00000026508.12\tENSG00000026508.12\tCD44\t193.4920\t189.4020\t197.5830\tOK\nENSG00000160654.5\tENSG00000160654.5\tCD3G\t53.0051\t51.4405\t54.5696\tOK\nENSG00000163823.3\tENSG00000163823.3\tCCR1\t0.0201\t0.0000\t0.0433\tOK\nENSG00000116824.4\tENSG00000116824.4\tCD2\t90.0146\t87.9630\t92.0661\tOK\nENSG00000158473.6\tENSG00000158473.6\tCD1D\t0.0241\t0.0000\t0.0519\tOK\nENSG00000174059.12\tENSG00000174059.12\tCD34\t0.0000\t0.0000\t0.0000\tOK"
lexp = excepted.split("\n")
lresult = regions_a.split("\n")
self.assertEquals(len(lresult), len(lexp))
for l in lresult:
self.assertTrue(l in lexp)
(status, gx_query) = epidb.select_expressions("gene", "s1", 1, 'CCR1',
"ENCODE", "gencode v19",
self.admin_key)
self.assertSuccess(status, gx_query)
status, info = epidb.info("gx1", user_key)
(status, r_id) = epidb.get_regions(gx_query, info[0]["format"],
self.admin_key)
self.assertSuccess(status, r_id)
regions = self.get_regions_request(r_id)
self.assertEquals(
regions,
"ENSG00000163823.3\tENSG00000163823.3\tCCR1\t0.0201\t0.0000\t0.0433\tOK"
)
q1 = gx_query
(status, gx_query) = epidb.select_expressions("gene", "s1", 1, 'CD164',
"ENCODE", "gencode v19",
self.admin_key)
self.assertSuccess(status, gx_query)
status, info = epidb.info("gx1", user_key)
(status, r_id) = epidb.get_regions(gx_query, info[0]["format"],
self.admin_key)
self.assertSuccess(status, r_id)
regions = self.get_regions_request(r_id)
self.assertEquals(
regions,
"ENSG00000135535.10\tENSG00000135535.10\tCD164\t101.3820\t98.8947\t103.8680\tOK"
)
self.assertTrue(q1 != gx_query)
(s, info) = epidb.info(ss, self.admin_key)
self.assertEquals(
info[0], {
'total_genes': 57820,
'_id': 'gs1',
'genome': 'hg19',
'description': 'Test One Description',
'format': 'GTF',
'name': 'gencode v19'
})
(status, gene_info) = epidb.info("gn1", self.admin_key)
self.assertEquals(
gene_info[0], {
'transcript_status': 'KNOWN',
'gene_name': 'DDX11L1',
'gene_type': 'pseudogene',
'end': 14412,
'source': 'HAVANA',
'frame': '.',
'level': '2',
'gene_id': 'ENSG00000223972.4',
'start': 11869,
'transcript_id': 'ENSG00000223972.4',
'score': 0.0,
'strand': '+',
'havana_gene': 'OTTHUMG00000000961.2',
'transcript_name': 'DDX11L1',
'_id': 'gn1',
'gene_status': 'KNOWN',
'transcript_type': 'pseudogene',
'chromosome': 'chr1'
})
(status, query) = epidb.select_expressions("gene", "s1",
[1, 5, 10, 122], None,
"ENCODE", "gencode v19",
self.admin_key)
query_one = query
self.assertSuccess(status, query)
(status, filtered) = epidb.filter_regions(query, "FPKM_STATUS", "!=",
"OK", "string",
self.admin_key)
self.assertSuccess(status, filtered)
(status, filtered_chr) = epidb.filter_regions(filtered, "CHROMOSOME",
"==", "chr21", "string",
self.admin_key)
self.assertSuccess(status, filtered_chr)
(status, r_id) = epidb.get_regions(
filtered_chr, "GENE_ID,FPKM_STATUS,@SAMPLE_ID,@BIOSOURCE",
self.admin_key)
self.assertSuccess(status, r_id)
regions = self.get_regions_request(r_id)
self.assertEquals(
regions,
"ENSG00000240755.1\tLOWDATA\ts1\tK562\nENSG00000256386.1\tLOWDATA\ts1\tK562\nENSG00000198743.5\tLOWDATA\ts1\tK562\nENSG00000267937.1\tLOWDATA\ts1\tK562\nENSG00000238556.1\tLOWDATA\ts1\tK562\nENSG00000255902.1\tLOWDATA\ts1\tK562\nENSG00000266692.1\tLOWDATA\ts1\tK562"
)
(status, query) = epidb.select_expressions("gene", "s1",
[1, 5, 10, 122], None, "",
"gencode v19", user_key)
self.assertSuccess(status, query)
(status, filtered) = epidb.filter_regions(query, "FPKM_STATUS", "!=",
"OK", "string", user_key)
self.assertSuccess(status, filtered)
(status, filtered_chr) = epidb.filter_regions(filtered, "CHROMOSOME",
"==", "chr21", "string",
user_key)
self.assertSuccess(status, filtered_chr)
(status,
req) = epidb.get_regions(filtered_chr,
"GENE_ID,FPKM_STATUS,@SAMPLE_ID,@BIOSOURCE",
user_key)
self.assertSuccess(status, r_id)
(s, ss) = epidb.info(req, user_key)
while ss[0]["state"] != "done":
time.sleep(1)
(s, ss) = epidb.info(req, user_key)
s, regions = epidb.get_request_data(req, user_key)
self.assertEquals(
regions,
"ENSG00000240755.1\tLOWDATA\ts1\tK562\nENSG00000256386.1\tLOWDATA\ts1\tK562\nENSG00000198743.5\tLOWDATA\ts1\tK562\nENSG00000267937.1\tLOWDATA\ts1\tK562\nENSG00000238556.1\tLOWDATA\ts1\tK562\nENSG00000255902.1\tLOWDATA\ts1\tK562\nENSG00000266692.1\tLOWDATA\ts1\tK562"
)
def test_janitor(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base()
# Test parameters
s, v = epidb.modify_user_admin(None, "old_request_age_in_sec", None,
self.admin_key)
self.assertEqual(v, ['old_request_age_in_sec', '2592000'])
s, v = epidb.modify_user_admin(None, "old_request_age_in_sec", "-1",
self.admin_key)
self.assertEqual(v, ['old_request_age_in_sec', '2592000'])
s, v = epidb.modify_user_admin(None, "janitor_periodicity", None,
self.admin_key)
self.assertEqual(v, ['janitor_periodicity', '60'])
s, v = epidb.modify_user_admin(None, "janitor_periodicity", "-1",
self.admin_key)
self.assertEqual(v, ['janitor_periodicity', '60'])
# Do a simple request
res, qid = epidb.tiling_regions(1000000, "hg19",
["chr15", "chrX", "chr3"],
self.admin_key)
self.assertSuccess(res, qid)
res, req = epidb.get_regions(qid, "CHROMOSOME,START,END",
self.admin_key)
self.assertSuccess(res, req)
regions = self.get_regions_request(req)
chr3_tiles = 198022430 / 1000000
chr15_tiles = 102531392 / 1000000
chrX_tiles = 155270560 / 1000000
self.assertEqual(len(regions.strip().split('\n')),
chr3_tiles + chr15_tiles + chrX_tiles)
# Check removal
s, m = epidb.modify_user_admin(None, "janitor_periodicity", "1",
self.admin_key)
s, v = epidb.modify_user_admin(None, "janitor_periodicity", None,
self.admin_key)
self.assertEqual(v, ['janitor_periodicity', '1'])
s, m = epidb.modify_user_admin(None, "old_request_age_in_sec", "3",
self.admin_key)
s, v = epidb.modify_user_admin(None, "old_request_age_in_sec", None,
self.admin_key)
self.assertEqual(v, ['old_request_age_in_sec', '3'])
time.sleep(4)
s, info = epidb.info(req, self.admin_key)
self.assertEqual(info[0]["state"], "cleared")
# Check reprocessing by re-requesting the data
s, m = epidb.get_request_data(req, self.admin_key)
self.assertFailure(s, m)
self.assertEqual(
m,
'Request ID r1 was cleared. We are going to reprocess this request. Please, check its status.'
)
s, info = epidb.info(req, self.admin_key)
self.assertEqual(info[0]["state"], "reprocess")
regions = self.get_regions_request(req)
chr3_tiles = 198022430 / 1000000
chr15_tiles = 102531392 / 1000000
chrX_tiles = 155270560 / 1000000
self.assertEqual(len(regions.strip().split('\n')),
chr3_tiles + chr15_tiles + chrX_tiles)
# Check reprocessing by making performing the request again
s, m = epidb.modify_user_admin(None, "janitor_periodicity", "1",
self.admin_key)
time.sleep(1)
s, info = epidb.info(req, self.admin_key)
self.assertEqual(info[0]["state"], "done")
time.sleep(3)
s, info = epidb.info(req, self.admin_key)
self.assertEqual(info[0]["state"], "cleared")
s, m = epidb.modify_user_admin(None, "janitor_periodicity", "10",
self.admin_key)
res, req = epidb.get_regions(qid, "CHROMOSOME,START,END",
self.admin_key)
s, info = epidb.info(req, self.admin_key)
self.assertEqual(info[0]["state"], "reprocess")
regions = self.get_regions_request(req)
chr3_tiles = 198022430 / 1000000
chr15_tiles = 102531392 / 1000000
chrX_tiles = 155270560 / 1000000
def test_cancel_aggregation(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_big_2", sample_id)
cpg_island = ",".join([
"CHROMOSOME", "START", "END", "NAME", "LENGTH", "NUM_CPG",
"NUM_GC", "PER_CPG", "PER_CG", "OBS_EXP"
])
with open("data/cpgIslandExtFull.txt", 'r') as f:
file_data = f.read()
(res, a_1) = epidb.add_annotation("Cpg Islands", "hg19",
"Complete CpG islands",
file_data, cpg_island, None,
self.admin_key)
self.assertSuccess(res, a_1)
res, q_cgi = epidb.select_annotations("Cpg Islands", "hg19", None,
None, None, self.admin_key)
self.assertSuccess(res, q_cgi)
res, qid_2 = epidb.tiling_regions(1000000, "hg19", None,
self.admin_key)
self.assertSuccess(res, qid_2)
res, req_count = epidb.count_regions(qid_2, self.admin_key)
self.assertSuccess(res, req_count)
count = self.count_request(req_count)
self.assertEquals(count, 3118)
res, qid_3 = epidb.aggregate(q_cgi, qid_2, "@LENGTH", self.admin_key)
self.assertSuccess(res, qid_3)
res, qid_4 = epidb.filter_regions(qid_3, "@AGG.COUNT", ">=", "100",
"number", self.admin_key)
(res, req_regions) = epidb.get_regions(
qid_4,
"CHROMOSOME,START,END,@AGG.MIN,@AGG.MAX,@AGG.MEDIAN,@AGG.MEAN,@AGG.VAR,@AGG.SD,@AGG.COUNT",
self.admin_key)
self.assertSuccess(res, req_regions)
(s, user_two) = epidb.add_user("ANOTHER NAME", "ANOTHER EMAIL",
"INSTITUTE", self.admin_key)
s, tmp_user = epidb.modify_user_admin(user_two[0], "permission_level",
"GET_DATA", self.admin_key)
s, msg = epidb.cancel_request(req_regions, user_two[1])
self.assertEquals(msg, "130003:The request ID 'r2' is invalid.")
s, msg = epidb.cancel_request(req_count, user_two[1])
self.assertEquals(msg, "130003:The request ID 'r1' is invalid.")
(s, m) = epidb.cancel_request(req_regions, self.admin_key)
self.assertSuccess(s, m)
(s, m) = epidb.cancel_request(req_count, self.admin_key)
self.assertSuccess(s, m)
(s, user_ass) = epidb.add_user("ASS NAME", "ASS EMAIL", "INSTITUTE",
self.admin_key)
s, tmp_user = epidb.modify_user_admin(user_ass[0], "permission_level",
"GET_DATA", self.admin_key)
res, q_cgi_other = epidb.select_annotations("Cpg Islands", "hg19",
None, None, None,
user_two[1])
self.assertSuccess(res, q_cgi)
(res, req_other) = epidb.get_regions(q_cgi_other,
"CHROMOSOME,START,END",
user_two[1])
self.assertSuccess(res, req_regions)
(s, msg) = epidb.cancel_request(req_other, user_ass[1])
self.assertEquals(msg, "130003:The request ID 'r3' is invalid.")
(s, m) = epidb.cancel_request(req_other, self.admin_key)
self.assertSuccess(s, m)
(s, ss) = epidb.info(req_other, self.admin_key)
self.assertEquals(ss[0]['state'], 'canceled')
(s, ss_count) = epidb.info(req_count, self.admin_key)
self.assertEquals(ss_count[0]["state"], "removed")
(s, ss_regions) = epidb.info(req_regions, self.admin_key)
self.assertEquals(ss_regions[0]["state"], "canceled")
s, e1 = epidb.get_request_data(req_count, self.admin_key)
self.assertEqual(
e1, "Request ID r1 was not finished. Please, check its status.")
s, e2 = epidb.get_request_data(req_regions, self.admin_key)
self.assertEqual(
e2, "Request ID r2 was not finished. Please, check its status.")
def test_basic_binning(self):
epidb = DeepBlueClient(address="localhost", port=31415)
self.init_base(epidb)
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_big_2", sample_id)
res, qid = epidb.select_regions("hg19_big_2", "hg19", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid)
status, req = epidb.binning(qid, "P_VALUE", 5, self.admin_key)
self.assertSuccess(status, req)
binning = self.get_regions_request(req)
self.assertEquals(
binning, {
'binning': {
'ranges':
[2.0006, 37.8473, 73.6939, 109.5406, 145.3873, 181.234],
'counts': [63506, 2632, 3111, 6626, 1668]
}
})
sample_id = self.sample_ids[0]
self.insert_experiment(epidb, "hg19_big_1", sample_id)
res, qid = epidb.select_regions("hg19_big_1", "hg19", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid)
status, req = epidb.binning(qid, "P_VALUE", 5, self.admin_key)
self.assertSuccess(status, req)
binning = self.get_regions_request(req)
self.assertEquals(
binning, {
'binning': {
'ranges':
[2.0017, 41.3178, 80.6338, 119.9499, 159.2659, 198.582],
'counts': [39349, 2824, 2510, 5325, 4299]
}
})
status, req = epidb.binning(qid, "P_VALUE", 0, self.admin_key)
self.assertFailure(status, req)
status, req = epidb.binning(qid, "P_VALUE", -1, self.admin_key)
self.assertFailure(status, req)
status, req = epidb.binning(qid, "P_VALUE", 66666, self.admin_key)
self.assertFailure(status, req)
res, qid = epidb.select_regions("hg19_big_1", "hg19", None, None, None,
None, None, None, None, self.admin_key)
self.assertSuccess(res, qid)
status, req = epidb.binning(qid, "QEERR", 5, self.admin_key)
self.assertSuccess(status, req)
msg = self.get_regions_request_error(req)
status, msg = epidb.get_request_data(req, self.admin_key)
self.assertEqual(
msg,
"101007:The experiment 'hg19_big_1' does not have the column 'QEERR'."
)
