本文整理汇总了Python中ngi_pipeline.database.classes.CharonSession.post方法的典型用法代码示例。如果您正苦于以下问题:Python CharonSession.post方法的具体用法?Python CharonSession.post怎么用?Python CharonSession.post使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类ngi_pipeline.database.classes.CharonSession
的用法示例。
在下文中一共展示了CharonSession.post方法的2个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: TestCommunicate
# 需要导入模块: from ngi_pipeline.database.classes import CharonSession [as 别名]
# 或者: from ngi_pipeline.database.classes.CharonSession import post [as 别名]
class TestCommunicate(unittest.TestCase):
def setUp(self):
# Create the test project
self.project_id = "P100000"
self.project_name = "P.Mayhem_14_01"
self.project_data = dict(projectid=self.project_id, name=self.project_name, status=None)
self.session = CharonSession()
response = self.session.post(self.session.construct_charon_url('project'),
data=json.dumps(self.project_data))
assert response.status_code == 201, "Could not create test project in Charon: {}".format(response.reason)
project = response.json()
assert project['projectid'] == self.project_id, "Test project ID is incorrect"
def tearDown(self):
# Remove the test project
response = self.session.delete(self.session.construct_charon_url('project', self.project_id))
assert response.status_code == 204, "Could not delete test project from Charon: {}".format(response.reason)
def test_get_project_id_from_name(self):
# Check that it matches
self.assertEqual(self.project_id, get_project_id_from_name(self.project_name))
def test_rebuild_project_obj_from_charon(self):
# Create fake project / sample / libprep / seqrun
pass
示例2: main
# 需要导入模块: from ngi_pipeline.database.classes import CharonSession [as 别名]
# 或者: from ngi_pipeline.database.classes.CharonSession import post [as 别名]
def main(args):
originalProject = {}
originalProject["fc_dir"] = "/proj/a2010002/INBOX/140702_D00415_0052_AC41A2ANXX/"
originalProject["fc_name"] = "140702_D00415_0052_AC41A2ANXX"
originalProject["fc_id"] = "C41A2ANXX"
originalProject["project_name"] = "M.Kaller_14_06"
originalProject["project_name_ill"] = "M__Kaller_14_06"
originalProject["project_id"] = "P1171"
originalProject["samples_id"] = ["102", "104", "106", "108"]
##create random
rnd_fc_id_noplate = id_generator_digits_chars(9)
rnd_fc_id = "A{}".format(rnd_fc_id_noplate)
rnd_instrument = id_generator_digits_chars(6)
rnd_date = id_generator_digits(6)
rnd_fc_name = "{}_{}_{}_{}".format(rnd_date, rnd_instrument, id_generator_digits(4), rnd_fc_id)
rnd_fc_path = os.path.join(data_folder, rnd_fc_name)
if os.path.isdir(rnd_fc_path):
print "flowcell name already exists: bad luck!!!! Abort"
return 1
rnd_project_name = args.rnd_project_name
if args.rnd_project_name is "":
print "error project-name must be specified (something like M.Kaller_14_06)"
return 1
charon_session = CharonSession()
rndProject = {}
try:
rnd_project_id = get_project_id_from_name(rnd_project_name)
rndProject["project_id"] = rnd_project_id
rndProject["project_name"] = rnd_project_name
except (RuntimeError, ValueError) as e:
print " project does not exits on Charon, creating it"
rnd_project_id = "P{}".format(id_generator_digits(4))
rndProject["project_id"] = rnd_project_id
rndProject["project_name"] = rnd_project_name
base_url = charon_session.construct_charon_url("project")
project_dict = {
"projectid": rndProject["project_id"],
"name": rndProject["project_name"],
"status": "SEQUENCED",
"pipeline": "NGI",
"best_practice_analysis": "IGN",
"sequencing_facility": "NGI-S",
}
# create the project on charon
charon_session.post(base_url, json.dumps(project_dict))
rndProject["fc_dir"] = rnd_fc_path
rndProject["fc_name"] = rnd_fc_name
rndProject["fc_id"] = rnd_fc_id
rndProject["project_name_ill"] = rnd_project_name.replace(".", "__")
rndProject["samples_id"] = [
"{}".format(id_generator_digits(3)),
"{}".format(id_generator_digits(3)),
"{}".format(id_generator_digits(3)),
"{}".format(id_generator_digits(3)),
]
if args.restrict_to_sample is not "":
originalProject["samples_id"] = [args.restrict_to_sample]
rndProject["samples_id"] = ["{}".format(id_generator_digits(3))]
# TODO: check that this project does not already exists on charon
os.mkdir(rnd_fc_path)
# parse SampleSheet_16bp.csv
parse_sample_sheet("SampleSheet_16bp.csv", originalProject, rndProject)
# parse SampleSheet.csv
parse_sample_sheet("SampleSheet.csv", originalProject, rndProject)
createDir(rndProject["fc_dir"], "Data")
createDir(rndProject["fc_dir"], "InterOp")
# Unaligned
createDir(rndProject["fc_dir"], "Unaligned")
Unaligned_dir = os.path.join(rndProject["fc_dir"], "Unaligned")
BaseCall_stats_dir = "Basecall_Stats_{}".format(rndProject["fc_id"])
createDir(Unaligned_dir, BaseCall_stats_dir)
# I do not need to copy the file... I hope as it is madness parse them
# Unaligned_16bp
createDir(rndProject["fc_dir"], "Unaligned_16bp")
Unaligned_path = os.path.join(rndProject["fc_dir"], "Unaligned_16bp")
BaseCall_stats_dir = "Basecall_Stats_{}".format(rndProject["fc_id"])
createDir(Unaligned_path, BaseCall_stats_dir)
Project_dir = "Project_{}".format(rndProject["project_name_ill"])
createDir(Unaligned_path, Project_dir)
# need to create samples now
Project_path = os.path.join(Unaligned_path, Project_dir)
rndSamplePos = 0
for originalSample in originalProject["samples_id"]:
rndSample = rndProject["samples_id"][rndSamplePos]
sample_dir = "Sample_{}_{}".format(rndProject["project_id"], rndSample)
createDir(Project_path, sample_dir)
Sample_path = os.path.join(Project_path, sample_dir)
#.........这里部分代码省略.........