code stringlengths 3 6.57k |
|---|
print(e) |
get_nMaxBioReps_experimentIDAndSampleNameAbbreviationAndExpType_sampleDescription(self,experiment_id_I,sample_name_abbreviation_I,exp_type_I) |
self.session.query(sample_description.sample_replicate) |
experiment.id.like(experiment_id_I) |
experiment.sample_name.like(sample.sample_name) |
sample.sample_id.like(sample_description.sample_id) |
sample_description.sample_name_abbreviation.like(sample_name_abbreviation_I) |
sample_description.sample_desc.like('Broth') |
sample_description.sample_replicate.desc() |
all() |
max(bioReps[0]) |
print('no biological replicates found for experiment ' + experiment_id_I) |
exit(-1) |
print(e) |
get_sampleIDs_experimentID_experiment(self,experiment_id_I) |
self.session.query(sample.sample_id) |
experiment.id.like(experiment_id_I) |
experiment.sample_name.like(sample.sample_name) |
sample.sample_id.asc() |
all() |
sample_names_O.append(sn.sample_id) |
print(e) |
get_sampleNameAbbreviation_experimentIDAndSampleID(self,experiment_id_I,sample_id_I) |
self.session.query(sample_description.sample_name_abbreviation) |
sample.sample_id.like(sample_id_I) |
experiment.id.like(experiment_id_I) |
experiment.sample_name.like(sample.sample_name) |
sample.sample_id.like(sample_description.sample_id) |
sample_description.sample_name_abbreviation.asc() |
all() |
print(e) |
get_sampleNameAbbreviation_experimentIDAndSampleName(self,experiment_id_I,sample_name_I) |
self.session.query(sample_description.sample_name_abbreviation) |
sample.sample_name.like(sample_name_I) |
experiment.id.like(experiment_id_I) |
experiment.sample_name.like(sample.sample_name) |
sample.sample_id.like(sample_description.sample_id) |
sample_description.sample_name_abbreviation.asc() |
all() |
print(e) |
get_sampleLabelAndBoxAndPos_experimentIDAndExperimentTypeID_sampleStorage(self,experiment_id_I,exp_type_id_I) |
experiment.id.like(experiment_id_I) |
experiment.sample_name.like(sample.sample_name) |
sample.sample_id.like(sample_storage.sample_id) |
sample_storage.sample_id.asc() |
all() |
print(e) |
os.path.join(tempfile.gettempdir() |
threading.Semaphore(1) |
logging.getLogger(__name__) |
threading.RLock() |
CustomEncoder(json.JSONEncoder) |
default(self, o) |
isinstance(o, decimal.Decimal) |
float(o) |
int(o) |
isinstance(o, datetime) |
str(o) |
isinstance(o, six.binary_type) |
to_str(o) |
super(CustomEncoder, self) |
default(o) |
ShellCommandThread(FuncThread) |
FuncThread.__init__(self, self.run_cmd, params, quiet=quiet) |
run_cmd(self, params) |
convert_line(line) |
to_str(line or '') |
line.strip() |
filter_line(line) |
iter(instream.readline, None) |
not (line and line.strip() |
self.is_killed() |
convert_line(line) |
filter_line(line) |
outstream.write(line) |
outstream.flush() |
self.process.wait() |
self.process.communicate() |
LOG.warning('Shell command error "%s": %s' % (e, self.cmd) |
LOG.warning('Shell command exit code "%s": %s' % (self.process.returncode, self.cmd) |
is_killed(self) |
psutil.pid_exists(self.process.pid) |
stop(self, quiet=False) |
LOG.warning("No process found for command '%s'" % self.cmd) |
psutil.Process(parent_pid) |
parent.children(recursive=True) |
child.kill() |
parent.kill() |
LOG.warning('Unable to kill process with pid %s' % parent_pid) |
JsonObject(object) |
to_json(self, indent=None) |
float(o) |
int(o) |
isinstance(o, decimal.Decimal) |
apply_json(self, j) |
isinstance(j, str) |
json.loads(j) |
self.__dict__.update(j) |
to_dict(self) |
json.loads(self.to_json() |
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