Python Parameters.from_default_params方法代码示例

# 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

# 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))

# 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),
        )

# 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)

# 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)

# 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)