Пример #1
0
 def test_generate_param_str(self):
     params = DefaultParameters(10)
     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<br/>"
            "<b>sortmerna_max_pos:</b> 10000<br/>"
            "<b>threads:</b> 1<br/>"
            "<b>sortmerna_coverage:</b> 0.97")
     self.assertEqual(obs, exp)
Пример #2
0
 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)
Пример #3
0
 def test_generate_param_str(self):
     params = DefaultParameters(10)
     obs = generate_param_str(params)
     exp = ('<b>Reference:</b> Greengenes 13_8<br/>'
            '<b>sortmerna_e_value:</b> 1<br/>'
            '<b>sortmerna_max_pos:</b> 10000<br/>'
            '<b>similarity:</b> 0.97<br/>'
            '<b>sortmerna_coverage:</b> 0.97<br/>'
            '<b>threads:</b> 1')
     self.assertEqual(obs, exp)
Пример #4
0
    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)
Пример #5
0
    def render(self, study_id, preprocessed_data):
        user = self.current_user
        ppd_id = preprocessed_data.id
        vamps_status = preprocessed_data.is_submitted_to_vamps
        filepaths = preprocessed_data.filepaths
        is_local_request = is_localhost(self.request.headers['host'])
        show_ebi_btn = user.level == "admin"
        processing_status, processing_status_msg = \
            get_artifact_processing_status(preprocessed_data)
        processed_data = sorted([pd.id for pd in preprocessed_data.children])

        # 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']

        # ppd can only have 1 prep template
        prep_template = preprocessed_data.prep_templates[0]
        # this block might seem wrong but is here due to a possible
        # pathological case that we used to have in the system: preprocessed
        # data without valid prep_templates
        prep_templates = preprocessed_data.prep_templates
        if len(prep_templates) == 1:
            prep_template_id = prep_template.id
            raw_data_id = prep_template.artifact.id
            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 Command(3).default_parameter_sets
        }
        # We just need to provide an ID for the default parameters,
        # so we can initialize the interface
        default_params = min(process_params.keys())

        ebi_link = None
        if preprocessed_data.is_submitted_to_ebi:
            ebi_link = EBI_LINKIFIER.format(
                Study(study_id).ebi_study_accession)

        return self.render_string(
            "study_description_templates/preprocessed_data_info_tab.html",
            ppd_id=ppd_id,
            show_ebi_btn=show_ebi_btn,
            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.id,
            processing_status=processing_status,
            processing_status_msg=processing_status_msg,
            processed_data=processed_data,
            ebi_link=ebi_link)
    def render(self, study_id, preprocessed_data):
        user = self.current_user
        ppd_id = preprocessed_data.id
        vamps_status = preprocessed_data.is_submitted_to_vamps
        filepaths = preprocessed_data.filepaths
        is_local_request = is_localhost(self.request.headers['host'])
        show_ebi_btn = user.level == "admin"
        processing_status, processing_status_msg = \
            get_artifact_processing_status(preprocessed_data)
        processed_data = sorted([pd.id for pd in preprocessed_data.children])

        # 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']

        # ppd can only have 1 prep template
        prep_template = preprocessed_data.prep_templates[0]
        # this block might seem wrong but is here due to a possible
        # pathological case that we used to have in the system: preprocessed
        # data without valid prep_templates
        prep_templates = preprocessed_data.prep_templates
        if len(prep_templates) == 1:
            prep_template_id = prep_template.id
            raw_data_id = prep_template.artifact.id
            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 Command(3).default_parameter_sets}
        # We just need to provide an ID for the default parameters,
        # so we can initialize the interface
        default_params = min(process_params.keys())

        ebi_link = None
        if preprocessed_data.is_submitted_to_ebi:
            ebi_link = EBI_LINKIFIER.format(
                Study(study_id).ebi_study_accession)

        return self.render_string(
            "study_description_templates/preprocessed_data_info_tab.html",
            ppd_id=ppd_id,
            show_ebi_btn=show_ebi_btn,
            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.id,
            processing_status=processing_status,
            processing_status_msg=processing_status_msg,
            processed_data=processed_data,
            ebi_link=ebi_link)