Beispiel #1
0
def audit_item_status(value, system):
    if 'status' not in value:
        return

    level = STATUS_LEVEL.get(value['status'], 50)
    if level == 0:
        return

    context = system['context']
    request = system['request']
    linked = set()
    for schema_path in context.type_info.schema_links:
        if schema_path in ['supercedes', 'step_run']:
            continue
        linked.update(simple_path_ids(value, schema_path))

    for path in linked:
        linked_value = request.embed(path + '@@object')
        if 'status' not in linked_value:
            continue
        if linked_value['status'] == 'disabled':
            continue
        if (  # Special case: A revoked file can have a deleted replicate ticket #2938
            'file' in value['@type'] and
            value['status'] == 'revoked' and
            'replicate' in linked_value['@type'] and
            linked_value['status'] == 'deleted'
        ):
            continue
        linked_level = STATUS_LEVEL.get(linked_value['status'], 50)
        if linked_level == 0:
            detail = '{} {} has {} subobject {}'.format(
                value['status'], value['@id'], linked_value['status'], linked_value['@id'])
            yield AuditFailure('mismatched status', detail, level='ERROR')
        elif linked_level < level:
            detail = '{} {} has {} subobject {}'.format(
                value['status'], value['@id'], linked_value['status'], linked_value['@id'])
            yield AuditFailure('mismatched status', detail, level='DCC_ACTION')
Beispiel #2
0
def metadata_tsv(context, request):

    param_list = parse_qs(request.matchdict['search_params'])
    param_list['field'] = []
    header = []
    file_attributes = []
    for prop in _tsv_mapping:
        header.append(prop)
        param_list['field'] = param_list['field'] + _tsv_mapping[prop]
        if _tsv_mapping[prop][0].startswith('files'):
            file_attributes = file_attributes + [_tsv_mapping[prop][0]]
    param_list['limit'] = ['all']
    path = '/search/?%s' % urlencode(param_list, True)
    results = request.embed(path, as_user=True)
    rows = []
    for row in results['@graph']:
        if row['files']:
            exp_data_row = []
            for column in header:
                if not _tsv_mapping[column][0].startswith('files'):
                    temp = []
                    for c in _tsv_mapping[column]:
                        c_value = []
                        for value in simple_path_ids(row, c):
                            if str(value) not in c_value:
                                c_value.append(str(value))
                        if c == 'replicates.library.biosample.post_synchronization_time' and len(temp):
                            if len(c_value):
                                temp[0] = temp[0] + ' + ' + c_value[0]
                        elif len(temp):
                            if len(c_value):
                                temp = [x + ' ' + c_value[0] for x in temp]
                        else:
                            temp = c_value
                    exp_data_row.append(', '.join(list(set(temp))))
            f_attributes = ['files.title', 'files.file_type',
                            'files.output_type']
            for f in row['files']:
                if 'files.file_type' in param_list:
                    if f['file_type'] not in param_list['files.file_type']:
                        continue
                f['href'] = request.host_url + f['href']
                f_row = []
                for attr in f_attributes:
                    f_row.append(f[attr[6:]])
                data_row = f_row + exp_data_row
                internal_prop = True
                for prop in file_attributes:
                    if prop in f_attributes:
                        continue
                    if prop == 'files.replicate.library':
                        if not internal_prop:
                            continue
                        internal_prop = False
                        libraries = []
                        for l in simple_path_ids(f, prop[6:]):
                            libraries.append(l)
                        if len(libraries):
                            library = request.embed(libraries[0])
                            data_row.append(library.get('fragmentation_method', ''))
                            data_row.append(library.get('size_range', ''))
                            if 'biosample' in library:
                                data_row.append(library['biosample'].get('age_display', ''))
                            else:
                                data_row.append('')
                            continue
                        else:
                            data_row = data_row + [''] * 3
                            continue
                    path = prop[6:]
                    temp = []
                    for value in simple_path_ids(f, path):
                        temp.append(str(value))
                    if prop == 'files.replicate.rbns_protein_concentration':
                        if 'replicate' in f and 'rbns_protein_concentration_units' in f['replicate']:
                            temp[0] = temp[0] + ' ' + f['replicate']['rbns_protein_concentration_units']
                    data_row.append(', '.join(list(set(temp))))
                rows.append(data_row)
    fout = io.StringIO()
    writer = csv.writer(fout, delimiter='\t')
    writer.writerow(header)
    writer.writerows(rows)
    return Response(
        content_type='text/tsv',
        body=fout.getvalue(),
        content_disposition='attachment;filename="%s"' % 'metadata.tsv'
    )