本文整理汇总了Python中qiita_db.software.Parameters.from_default_params方法的典型用法代码示例。如果您正苦于以下问题:Python Parameters.from_default_params方法的具体用法?Python Parameters.from_default_params怎么用?Python Parameters.from_default_params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qiita_db.software.Parameters
的用法示例。
在下文中一共展示了Parameters.from_default_params方法的6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: write_demux_files
# 需要导入模块: from qiita_db.software import Parameters [as 别名]
# 或者: from qiita_db.software.Parameters import from_default_params [as 别名]
def write_demux_files(self, prep_template, generate_hdf5=True):
"""Writes a demux test file to avoid duplication of code"""
fna_fp = join(self.temp_dir, 'seqs.fna')
demux_fp = join(self.temp_dir, 'demux.seqs')
if generate_hdf5:
with open(fna_fp, 'w') as f:
f.write(FASTA_EXAMPLE)
with File(demux_fp, "w") as f:
to_hdf5(fna_fp, f)
else:
with open(demux_fp, 'w') as f:
f.write('')
if prep_template.artifact is None:
ppd = Artifact.create(
[(demux_fp, 6)], "Demultiplexed", prep_template=prep_template,
can_be_submitted_to_ebi=True, can_be_submitted_to_vamps=True)
else:
params = Parameters.from_default_params(
DefaultParameters(1),
{'input_data': prep_template.artifact.id})
ppd = Artifact.create(
[(demux_fp, 6)], "Demultiplexed",
parents=[prep_template.artifact], processing_parameters=params,
can_be_submitted_to_ebi=True, can_be_submitted_to_vamps=True)
return ppd
示例2: post
# 需要导入模块: from qiita_db.software import Parameters [as 别名]
# 或者: from qiita_db.software.Parameters import from_default_params [as 别名]
def post(self):
study_id = int(self.get_argument('study_id'))
preprocessed_data_id = int(self.get_argument('preprocessed_data_id'))
param_id = self.get_argument('parameter-set-%s' % preprocessed_data_id)
parameters = Parameters.from_default_params(
DefaultParameters(param_id), {'input_data': preprocessed_data_id})
job_id = plugin_submit(self.current_user, parameters)
self.render('compute_wait.html',
job_id=job_id, title='Processing',
completion_redirect='/study/description/%d?top_tab='
'preprocessed_data_tab&sub_tab=%s'
% (study_id, preprocessed_data_id))
示例3: post
# 需要导入模块: from qiita_db.software import Parameters [as 别名]
# 或者: from qiita_db.software.Parameters import from_default_params [as 别名]
def post(self):
study_id = int(self.get_argument("study_id"))
prep_template_id = int(self.get_argument("prep_template_id"))
raw_data = PrepTemplate(prep_template_id).artifact
param_id = int(self.get_argument("preprocessing_parameters_id"))
parameters = Parameters.from_default_params(DefaultParameters(param_id), {"input_data": raw_data.id})
job_id = plugin_submit(self.current_user, parameters)
self.render(
"compute_wait.html",
job_id=job_id,
title="Preprocessing",
completion_redirect="/study/description/%d?top_tab="
"prep_template_tab&sub_tab=%s" % (study_id, prep_template_id),
)
示例4: test_submit_to_EBI
# 需要导入模块: from qiita_db.software import Parameters [as 别名]
# 或者: from qiita_db.software.Parameters import from_default_params [as 别名]
def test_submit_to_EBI(self):
# setting up test
fna_fp = join(self.temp_dir, 'seqs.fna')
demux_fp = join(self.temp_dir, 'demux.seqs')
with open(fna_fp, 'w') as f:
f.write(FASTA_EXAMPLE)
with File(demux_fp, "w") as f:
to_hdf5(fna_fp, f)
pt = PrepTemplate(1)
params = Parameters.from_default_params(
DefaultParameters(1), {'input_data': pt.artifact.id})
artifact = Artifact.create(
[(demux_fp, 6)], "Demultiplexed", parents=[pt.artifact],
processing_parameters=params)
# submit job
job = self._create_job('submit_to_EBI', {
'artifact': artifact.id, 'submission_type': 'VALIDATE'})
job._set_status('in_construction')
job.submit()
# wait for the job to fail, and check that the status is submitting
checked_submitting = True
while job.status != 'error':
if checked_submitting:
self.assertEqual('submitting',
artifact.study.ebi_submission_status)
checked_submitting = False
# once it fails wait for a few to check status again
sleep(5)
exp = 'Some artifact submissions failed: %d' % artifact.id
obs = artifact.study.ebi_submission_status
self.assertEqual(obs, exp)
# make sure that the error is correct, we have 2 options
if environ.get('ASPERA_SCP_PASS', '') != '':
self.assertIn('1.SKM2.640199', job.log.msg)
else:
self.assertIn('ASCP Error:', job.log.msg)
# wait for everything to finish to avoid DB deadlocks
sleep(5)
示例5: test_download_study
# 需要导入模块: from qiita_db.software import Parameters [as 别名]
# 或者: from qiita_db.software.Parameters import from_default_params [as 别名]
def test_download_study(self):
tmp_dir = mkdtemp()
self._clean_up_files.append(tmp_dir)
biom_fp = join(tmp_dir, 'otu_table.biom')
smr_dir = join(tmp_dir, 'sortmerna_picked_otus')
log_dir = join(smr_dir, 'seqs_otus.log')
tgz = join(tmp_dir, 'sortmerna_picked_otus.tgz')
with biom_open(biom_fp, 'w') as f:
et.to_hdf5(f, "test")
makedirs(smr_dir)
with open(log_dir, 'w') as f:
f.write('\n')
with open(tgz, 'w') as f:
f.write('\n')
files_biom = [(biom_fp, 'biom'), (smr_dir, 'directory'), (tgz, 'tgz')]
params = Parameters.from_default_params(
Command(3).default_parameter_sets.next(), {'input_data': 1})
a = Artifact.create(files_biom, "BIOM", parents=[Artifact(2)],
processing_parameters=params)
for _, fp, _ in a.filepaths:
self._clean_up_files.append(fp)
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'- 1256812 /protected/processed_data/1_study_1001_closed_'
'reference_otu_table.biom processed_data/1_study_1001_closed_'
'reference_otu_table.biom\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/4_mapping_file.txt\n'
'- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table.biom processed_data/'
'1_study_1001_closed_reference_otu_table.biom\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/5_mapping_file.txt\n'
'- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table_Silva.biom processed_data'
'/1_study_1001_closed_reference_otu_table_Silva.biom\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/6_mapping_file.txt\n'
'- 36615 /protected/templates/1_prep_2_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/7_mapping_file.txt\n'
'- [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
self.assertRegexpMatches(response.body, exp)
response = self.get('/download_study_bioms/200')
self.assertEqual(response.code, 405)
# changing user so we can test the failures
BaseHandler.get_current_user = Mock(
return_value=User("[email protected]"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
a.visibility = 'public'
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'- [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
'- 36615 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
self.assertRegexpMatches(response.body, exp)
示例6: test_download_study
# 需要导入模块: from qiita_db.software import Parameters [as 别名]
# 或者: from qiita_db.software.Parameters import from_default_params [as 别名]
def test_download_study(self):
tmp_dir = mkdtemp()
self._clean_up_files.append(tmp_dir)
biom_fp = join(tmp_dir, 'otu_table.biom')
smr_dir = join(tmp_dir, 'sortmerna_picked_otus')
log_dir = join(smr_dir, 'seqs_otus.log')
tgz = join(tmp_dir, 'sortmerna_picked_otus.tgz')
with biom_open(biom_fp, 'w') as f:
et.to_hdf5(f, "test")
makedirs(smr_dir)
with open(log_dir, 'w') as f:
f.write('\n')
with open(tgz, 'w') as f:
f.write('\n')
files_biom = [(biom_fp, 'biom'), (smr_dir, 'directory'), (tgz, 'tgz')]
params = Parameters.from_default_params(
next(Command(3).default_parameter_sets), {'input_data': 1})
a = Artifact.create(files_biom, "BIOM", parents=[Artifact(2)],
processing_parameters=params)
for x in a.filepaths:
self._clean_up_files.append(x['fp'])
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'1579715020 1256812 /protected/processed_data/1_study_1001_closed_'
'reference_otu_table.biom processed_data/1_study_1001_closed_'
'reference_otu_table.biom\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/4_mapping_file.txt\n'
'1579715020 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table.biom processed_data/'
'1_study_1001_closed_reference_otu_table.biom\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/5_mapping_file.txt\n'
'1579715020 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table_Silva.biom processed_data'
'/1_study_1001_closed_reference_otu_table_Silva.biom\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/6_mapping_file.txt\n'
'1756512010 1093210 /protected/BIOM/7/biom_table.biom '
'BIOM/7/biom_table.biom\n'
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/7_mapping_file.txt\n'
'[0-9]* [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.'
'txt mapping_files/{0}_mapping_file.txt\n'.format(a.id))
self.assertRegex(response.body.decode('ascii'), exp)
response = self.get('/download_study_bioms/200')
self.assertEqual(response.code, 405)
# changing user so we can test the failures
BaseHandler.get_current_user = Mock(
return_value=User("[email protected]"))
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 405)
a.visibility = 'public'
response = self.get('/download_study_bioms/1')
# returning visibility
a.visibility = 'private'
self.assertEqual(response.code, 200)
# we should have the same files than the previous test, except artifact
# and mapping file 7: position 6 and 7; thus removing 6 twice
exp = exp.split('\n')
exp.pop(6)
exp.pop(6)
exp = '\n'.join(exp)
self.assertRegex(response.body.decode('ascii'), exp)