コード例 #1
0
ファイル: test_parameters.py プロジェクト: jwdebelius/qiita
    def test_to_file(self):
        params = ProcessedSortmernaParams(1)
        fd, fp = mkstemp()
        close(fd)
        with open(fp, 'w') as f:
            params.to_file(f)
        with open(fp, 'U') as f:
            obs = f.read()

        self.assertEqual(obs, EXP_SMR_PARAMS_FILE)
コード例 #2
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    def test_get_process_target_gene_cmd(self):
        preprocessed_data = PreprocessedData(1)
        params = ProcessedSortmernaParams(1)

        obs_cmd, obs_output_dir = _get_process_target_gene_cmd(
            preprocessed_data, params)

        _, ref_dir = get_mountpoint('reference')[0]
        _, preprocessed_dir = get_mountpoint('preprocessed_data')[0]

        exp_cmd = ("pick_closed_reference_otus.py -i {}1_seqs.fna -r "
                   "{}GreenGenes_13_8_97_otus.fasta -o {} -p placeholder -t "
                   "{}GreenGenes_13_8_97_otu_taxonomy.txt".format(
                       preprocessed_dir, ref_dir, obs_output_dir, ref_dir))

        obs_tokens = obs_cmd.split()[::-1]
        exp_tokens = exp_cmd.split()[::-1]
        self.assertEqual(len(obs_tokens), len(exp_tokens))
        while obs_tokens:
            o_t = obs_tokens.pop()
            e_t = exp_tokens.pop()
            if o_t == '-p':
                # skip parameters file
                obs_tokens.pop()
                exp_tokens.pop()
            else:
                self.assertEqual(o_t, e_t)
コード例 #3
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 def test_generate_param_str(self):
     params = ProcessedSortmernaParams(1)
     obs = generate_param_str(params)
     exp = ("<b>Reference:</b> Greengenes 13_8<br/>"
            "<b>similarity:</b> 0.97<br/>"
            "<b>sortmerna_e_value:</b> 1.0<br/>"
            "<b>sortmerna_max_pos:</b> 10000<br/>"
            "<b>threads:</b> 1<br/>"
            "<b>sortmerna_coverage:</b> 0.97")
     self.assertEqual(obs, exp)
コード例 #4
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    def test_insert_processed_data_target_gene(self):
        fd, fna_fp = mkstemp(suffix='_seqs.fna')
        close(fd)
        fd, qual_fp = mkstemp(suffix='_seqs.qual')
        close(fd)
        filepaths = [
            (fna_fp, convert_to_id('preprocessed_fasta', 'filepath_type')),
            (qual_fp, convert_to_id('preprocessed_fastq', 'filepath_type'))
        ]

        preprocessed_data = PreprocessedData.create(
            Study(1),
            "preprocessed_sequence_illumina_params",
            1,
            filepaths,
            data_type="18S")

        params = ProcessedSortmernaParams(1)
        pick_dir = mkdtemp()
        path_builder = partial(join, pick_dir)
        db_path_builder = partial(join, get_mountpoint('processed_data')[0][1])

        # Create a placeholder for the otu table
        with open(path_builder('otu_table.biom'), 'w') as f:
            f.write('\n')

        # Create a placeholder for the directory
        mkdir(path_builder('sortmerna_picked_otus'))

        # Create the log file
        fd, fp = mkstemp(dir=pick_dir, prefix='log_', suffix='.txt')
        close(fd)
        with open(fp, 'w') as f:
            f.write('\n')

        _insert_processed_data_target_gene(preprocessed_data, params, pick_dir)

        new_id = get_count('qiita.processed_data')

        # Check that the files have been copied
        db_files = [
            db_path_builder("%s_otu_table.biom" % new_id),
            db_path_builder("%s_sortmerna_picked_otus" % new_id),
            db_path_builder("%s_%s" % (new_id, basename(fp)))
        ]
        for fp in db_files:
            self.assertTrue(exists(fp))

        # Check that a new preprocessed data has been created
        self.assertTrue(
            self.conn_handler.execute_fetchone(
                "SELECT EXISTS(SELECT * FROM qiita.processed_data WHERE "
                "processed_data_id=%s)", (new_id, ))[0])
コード例 #5
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    def render(self, study_id, preprocessed_data):
        user = self.current_user
        ppd_id = preprocessed_data.id
        ebi_status = preprocessed_data.submitted_to_insdc_status()
        ebi_study_accession = preprocessed_data.ebi_study_accession
        ebi_submission_accession = preprocessed_data.ebi_submission_accession
        vamps_status = preprocessed_data.submitted_to_vamps_status()
        filepaths = preprocessed_data.get_filepaths()
        is_local_request = self._is_local()
        show_ebi_btn = user.level == "admin"
        processing_status = preprocessed_data.processing_status
        processed_data = preprocessed_data.processed_data

        # Get all the ENA terms for the investigation type
        ontology = Ontology(convert_to_id('ENA', 'ontology'))
        # make "Other" show at the bottom of the drop down menu
        ena_terms = []
        for v in sorted(ontology.terms):
            if v != 'Other':
                ena_terms.append('<option value="%s">%s</option>' % (v, v))
        ena_terms.append('<option value="Other">Other</option>')

        # New Type is for users to add a new user-defined investigation type
        user_defined_terms = ontology.user_defined_terms + ['New Type']

        if PrepTemplate.exists(preprocessed_data.prep_template):
            prep_template_id = preprocessed_data.prep_template
            prep_template = PrepTemplate(prep_template_id)
            raw_data_id = prep_template.raw_data
            inv_type = prep_template.investigation_type or "None Selected"
        else:
            prep_template_id = None
            raw_data_id = None
            inv_type = "None Selected"

        process_params = {param.id: (generate_param_str(param), param.name)
                          for param in ProcessedSortmernaParams.iter()}
        # We just need to provide an ID for the default parameters,
        # so we can initialize the interface
        default_params = 1

        return self.render_string(
            "study_description_templates/preprocessed_data_info_tab.html",
            ppd_id=ppd_id,
            show_ebi_btn=show_ebi_btn,
            ebi_status=ebi_status,
            ebi_study_accession=ebi_study_accession,
            ebi_submission_accession=ebi_submission_accession,
            filepaths=filepaths,
            is_local_request=is_local_request,
            prep_template_id=prep_template_id,
            raw_data_id=raw_data_id,
            inv_type=inv_type,
            ena_terms=ena_terms,
            vamps_status=vamps_status,
            user_defined_terms=user_defined_terms,
            process_params=process_params,
            default_params=default_params,
            study_id=preprocessed_data.study,
            processing_status=processing_status,
            processed_data=processed_data)
コード例 #6
0
ファイル: test_parameters.py プロジェクト: jwdebelius/qiita
 def test_to_str(self):
     params = ProcessedSortmernaParams(1)
     obs = params.to_str()
     exp = ("--similarity 0.97 --sortmerna_coverage 0.97 "
            "--sortmerna_e_value 1.0 --sortmerna_max_pos 10000 --threads 1")
     self.assertEqual(obs, exp)