Python Output.getMessages方法代码示例

# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getMessages [as 别名]
def syntax_checker():
    """
    Parse the given variant and render the syntax checker HTML form.
    """
    # Backwards compatibility.
    if 'variant' in request.args:
        return redirect(url_for('.syntax_checker',
                                description=request.args['variant']),
                        code=301)

    description = request.args.get('description')

    if not description:
        return render_template('syntax-checker.html')

    output = Output(__file__)
    output.addMessage(__file__, -1, 'INFO',
                      'Received request syntaxCheck(%s) from %s'
                      % (description, request.remote_addr))
    stats.increment_counter('syntax-checker/website')

    grammar = Grammar(output)
    grammar.parse(description)

    parse_error = output.getOutput('parseError')
    messages = map(util.message_info, output.getMessages())

    output.addMessage(__file__, -1, 'INFO',
                      'Finished request syntaxCheck(%s)' % description)

    return render_template('syntax-checker.html',
                           description=description,
                           messages=messages,
                           parse_error=parse_error)

# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getMessages [as 别名]
def snp_converter():
    """
    SNP converter.

    Convert a dbSNP rs number to HGVS description(s) of the SNP specified on
    the reference sequence(s) used by dbSNP.
    """
    # Backwards compatibility.
    if 'rsId' in request.args:
        return redirect(url_for('.snp_converter',
                                rs_id=request.args['rsId']),
                        code=301)

    rs_id = request.args.get('rs_id')

    if not rs_id:
        return render_template('snp-converter.html')

    output = Output(__file__)
    output.addMessage(__file__, -1, 'INFO',
                      'Received request snpConvert(%s) from %s'
                      % (rs_id, request.remote_addr))
    stats.increment_counter('snp-converter/website')

    try:
        descriptions = ncbi.rsid_to_descriptions(rs_id)
    except ncbi.ServiceError:
        output.addMessage(__file__, 4, 'EENTREZ',
                          'An error occured while communicating with dbSNP.')

    messages = map(util.message_info, output.getMessages())

    output.addMessage(__file__, -1, 'INFO',
                      'Finished request snpConvert(%s)' % rs_id)

    return render_template('snp-converter.html',
                           rs_id=rs_id,
                           descriptions=descriptions,
                           messages=messages,
                           summary=output.Summary()[2])

# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getMessages [as 别名]
def snp_converter():
    """
    SNP converter.

    Convert a dbSNP rs number to HGVS description(s) of the SNP specified on
    the reference sequence(s) used by dbSNP.
    """
    # Backwards compatibility.
    if 'rsId' in request.args:
        return redirect(url_for('.snp_converter',
                                rs_id=request.args['rsId']),
                        code=301)

    rs_id = request.args.get('rs_id')

    if not rs_id:
        return render_template('snp-converter.html')

    output = Output(__file__)
    output.addMessage(__file__, -1, 'INFO',
                      'Received request snpConvert(%s) from %s'
                      % (rs_id, request.remote_addr))
    stats.increment_counter('snp-converter/website')

    retriever = Retriever.Retriever(output)
    descriptions = retriever.snpConvert(rs_id)

    messages = map(util.message_info, output.getMessages())

    output.addMessage(__file__, -1, 'INFO',
                      'Finished request snpConvert(%s)' % rs_id)

    return render_template('snp-converter.html',
                           rs_id=rs_id,
                           descriptions=descriptions,
                           messages=messages,
                           summary=output.Summary()[2])

# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getMessages [as 别名]
def back_translator():
    """
    Back translator.
    """
    output = Output(__file__)
    output.addMessage(
        __file__, -1, 'INFO',
        'Received Back Translate request from {}'.format(request.remote_addr))
    stats.increment_counter('back-translator/website')

    description = request.args.get('description')

    variants = []
    if description:
        variants = backtranslator.backtranslate(output, description)

    errors, warnings, summary = output.Summary()
    messages = map(util.message_info, output.getMessages())

    output.addMessage(__file__, -1, 'INFO', 'Finished Back Translate request')

    return render_template(
        'back-translator.html', errors=errors, summary=summary,
        description=description or '', messages=messages, variants=variants)

# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getMessages [as 别名]
def batch_jobs_submit():
    """
    Run batch jobs and render batch checker HTML form. The batch jobs are
    added to the database by the scheduler and ran by the BatchChecker
    daemon.
    """
    job_type = request.form.get('job_type')
    email = request.form.get('email')

    # Note that this is always a seekable binary file object.
    batch_file = request.files.get('file')

    assemblies = Assembly.query \
        .order_by(*Assembly.order_by_criteria) \
        .all()
    assembly_name_or_alias = request.form.get('assembly_name_or_alias',
                                              settings.DEFAULT_ASSEMBLY)

    errors = []

    if not email:
        errors.append('Please provide an email address.')

    if job_type not in BATCH_JOB_TYPES:
        errors.append('Invalid batch job type.')

    if not file:
        errors.append('Please select a local file for upload.')

    if job_type == 'position-converter':
        try:
            Assembly.by_name_or_alias(assembly_name_or_alias)
        except NoResultFound:
            errors.append('Not a valid assembly.')
        argument = assembly_name_or_alias
    else:
        argument = None

    output = Output(__file__)

    if not errors:
        stats.increment_counter('batch-job/website')

        scheduler = Scheduler.Scheduler()
        file_instance = File.File(output)
        job, columns = file_instance.parseBatchFile(batch_file)

        if job is None:
            errors.append('Could not parse input file, please check your '
                          'file format.')
        else:
            # Creates the result download URL from a job result_id.
            def create_download_url(result_id):
                return url_for('.batch_job_result',
                               result_id=result_id,
                               _external=True)

            result_id = scheduler.addJob(
                email, job, columns, job_type, argument=argument,
                create_download_url=create_download_url)

            # Todo: We now assume that the job was not scheduled if there are
            #   messages, which is probably not correct.
            if not output.getMessages():
                return redirect(url_for('.batch_job_progress',
                                        result_id=result_id))

    for error in errors:
        output.addMessage(__file__, 3, 'EBATCHJOB', error)

    messages = map(util.message_info, output.getMessages())

    return render_template('batch-jobs.html',
                           assemblies=assemblies,
                           assembly_name_or_alias=assembly_name_or_alias,
                           job_type=job_type,
                           max_file_size=settings.MAX_FILE_SIZE // 1048576,
                           messages=messages)

# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getMessages [as 别名]

#.........这里部分代码省略.........
        sequence.
    """
    output = Output(__file__)
    output.addMessage(__file__, -1, 'INFO',
                      'Received Description Extract request from %s'
                      % request.remote_addr)
    stats.increment_counter('description-extractor/website')

    r = s = ''
    reference_method = request.form.get('reference_method')
    sample_method = request.form.get('sample_method')
    reference_sequence = request.form.get('reference_sequence')
    sample_sequence = request.form.get('sample_sequence')
    reference_file = request.files.get('reference_file')
    sample_file = request.files.get('sample_file')
    reference_filename = ''
    sample_filename = ''
    reference_accession_number = request.form.get('reference_accession_number')
    sample_accession_number = request.form.get('sample_accession_number')

    if reference_method == 'refseq_method':
        if reference_accession_number:
            retriever = Retriever.GenBankRetriever(output)
            genbank_record = retriever.loadrecord(reference_accession_number)
            if genbank_record:
                r = unicode(genbank_record.seq)
        else:
            output.addMessage(__file__, 3, 'EEMPTYFIELD',
                'Reference accession number input fields is empty.')
    elif reference_method == 'file_method':
        if reference_file:
            reference_filename = reference_file.filename
            r = util.read_dna(reference_file)
        else:
            output.addMessage(__file__, 3, 'EEMPTYFIELD',
                'No reference file provided.')
    else: # raw_method
        if reference_sequence:
            r = util.read_dna(StringIO.StringIO(reference_sequence))
        else:
            output.addMessage(__file__, 3, 'EEMPTYFIELD',
                'Reference sequence number input fields is empty.')

    if sample_method == 'refseq_method':
        if sample_accession_number:
            retriever = Retriever.GenBankRetriever(output)
            genbank_record = retriever.loadrecord(sample_accession_number)
            if genbank_record:
                s = unicode(genbank_record.seq)
        else:
            output.addMessage(__file__, 3, 'EEMPTYFIELD',
                'Sample accession number input fields is empty.')
    elif sample_method == 'file_method':
        if sample_file:
            sample_filename = sample_file.filename
            s = util.read_dna(sample_file)
        else:
            output.addMessage(__file__, 3, 'EEMPTYFIELD',
                'No sample file provided.')
    else: # raw_method
        if sample_sequence:
            s = util.read_dna(StringIO.StringIO(sample_sequence))
        else:
            output.addMessage(__file__, 3, 'EEMPTYFIELD',
                'Sample sequence number input fields is empty.')

    # Todo: Move this to the describe module.
    if not r or not util.is_dna(r):
        output.addMessage(__file__, 3, 'ENODNA',
                          'Reference sequence is not DNA.')
    if not s or not util.is_dna(s):
        output.addMessage(__file__, 3, 'ENODNA',
                          'Sample sequence is not DNA.')

    raw_vars = None
    if r and s:
        if (len(r) > settings.EXTRACTOR_MAX_INPUT_LENGTH or
            len(s) > settings.EXTRACTOR_MAX_INPUT_LENGTH):
            output.addMessage(__file__, 3, 'EMAXSIZE',
                              'Input sequences are restricted to {:,} bp.'
                              .format(settings.EXTRACTOR_MAX_INPUT_LENGTH))
        else:
            raw_vars = extractor.describe_dna(r, s)

    errors, warnings, summary = output.Summary()
    messages = map(util.message_info, output.getMessages())

    output.addMessage(__file__, -1, 'INFO',
                      'Finished Description Extract request')

    return render_template('description-extractor.html',
        extractor_max_input_length=settings.EXTRACTOR_MAX_INPUT_LENGTH,
        reference_sequence=reference_sequence or '',
        sample_sequence=sample_sequence or '',
        reference_accession_number=reference_accession_number or '',
        sample_accession_number=sample_accession_number or '',
        reference_filename=reference_filename or '',
        sample_filename=sample_filename or '',
        raw_vars=raw_vars, errors=errors, summary=summary, messages=messages,
        reference_method=reference_method, sample_method=sample_method)

# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getMessages [as 别名]
def position_converter():
    """
    Position converter.
    """
    # Backwards compatibility.
    if 'variant' in request.args:
        return redirect(url_for('.position_converter',
                                description=request.args['variant']),
                        code=301)

    assemblies = Assembly.query \
        .order_by(*Assembly.order_by_criteria) \
        .all()

    assembly_name_or_alias = request.args.get('assembly_name_or_alias',
                                              settings.DEFAULT_ASSEMBLY)
    description = request.args.get('description')

    if not description:
        return render_template('position-converter.html',
                               assemblies=assemblies,
                               assembly_name_or_alias=assembly_name_or_alias)

    output = Output(__file__)
    output.addMessage(__file__, -1, 'INFO',
                      'Received request positionConverter(%s, %s) from %s'
                      % (assembly_name_or_alias, description,
                         request.remote_addr))
    stats.increment_counter('position-converter/website')

    chromosomal_description = None
    transcript_descriptions = None

    try:
        assembly = Assembly.by_name_or_alias(assembly_name_or_alias)
    except NoResultFound:
        output.addMessage(__file__, 3, 'ENOASSEMBLY',
                          'Not a valid assembly.')
    else:
        converter = Converter(assembly, output)

        # Convert chromosome name to accession number.
        corrected_description = converter.correctChrVariant(description)

        if corrected_description:
            # Now we're ready to actually do position conversion.
            if not(':c.' in corrected_description or
                   ':n.' in corrected_description or
                   ':g.' in corrected_description or
                   ':m.' in corrected_description):
                grammar = Grammar(output)
                grammar.parse(corrected_description)

            if (':c.' in corrected_description or
                ':n.' in corrected_description):
                corrected_description = converter.c2chrom(
                        corrected_description)

            chromosomal_description = corrected_description

            if corrected_description and (':g.' in corrected_description or
                                          ':m.' in corrected_description):
                descriptions = converter.chrom2c(corrected_description, 'dict')
                if descriptions is None:
                    chromosomal_description = None
                elif descriptions:
                    transcript_descriptions = [
                        '%-10s:\t%s' % (key[:10], '\n\t\t'.join(value))
                        for key, value in descriptions.items()]

    messages = map(util.message_info, output.getMessages())

    output.addMessage(__file__, -1, 'INFO',
                      'Finished request positionConverter(%s, %s)'
                      % (assembly_name_or_alias, description))

    return render_template('position-converter.html',
                           assemblies=assemblies,
                           assembly_name_or_alias=assembly_name_or_alias,
                           description=description,
                           chromosomal_description=chromosomal_description,
                           transcript_descriptions=transcript_descriptions,
                           messages=messages)

# 需要导入模块: from mutalyzer.output import Output [as 别名]
# 或者: from mutalyzer.output.Output import getMessages [as 别名]
def name_checker():
    """
    Name checker.
    """
    # For backwards compatibility with older LOVD versions, we support the
    # `mutationName` argument. If present, we redirect and add `standalone=1`.
    #
    # Also for backwards compatibility, we support the `name` argument as an
    # alias for `description`.
    if 'name' in request.args:
        return redirect(url_for('.name_checker',
                                description=request.args['name'],
                                standalone=request.args.get('standalone')),
                        code=301)
    if 'mutationName' in request.args:
        return redirect(url_for('.name_checker',
                                description=request.args['mutationName'],
                                standalone=1),
                        code=301)

    description = request.args.get('description')

    if not description:
        return render_template('name-checker.html')

    output = Output(__file__)
    output.addMessage(__file__, -1, 'INFO', 'Received variant %s from %s'
                      % (description, request.remote_addr))
    stats.increment_counter('name-checker/website')

    variantchecker.check_variant(description, output)

    errors, warnings, summary = output.Summary()
    parse_error = output.getOutput('parseError')

    record_type = output.getIndexedOutput('recordType', 0, '')
    reference = output.getIndexedOutput('reference', 0, '')
    if reference:
        if record_type == 'LRG':
            reference_filename = reference + '.xml'
        else :
            reference_filename = reference + '.gb'
    else:
        reference_filename = None

    genomic_dna = output.getIndexedOutput('molType', 0) != 'n'
    genomic_description = output.getIndexedOutput('genomicDescription', 0, '')

    # Create a link to the UCSC Genome Browser.
    browser_link = None
    raw_variants = output.getIndexedOutput('rawVariantsChromosomal', 0)
    if raw_variants:
        positions = [pos
                     for descr, (first, last) in raw_variants[2]
                     for pos in (first, last)]
        bed_url = url_for('.bed', description=description, _external=True)
        browser_link = ('http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&'
                        'position={chromosome}:{start}-{stop}&hgt.customText='
                        '{bed_file}'.format(chromosome=raw_variants[0],
                                            start=min(positions) - 10,
                                            stop=max(positions) + 10,
                                            bed_file=urllib.quote(bed_url)))

    # Experimental description extractor.
    if (output.getIndexedOutput('original', 0) and
        output.getIndexedOutput('mutated', 0)):
        allele = extractor.describe_dna(output.getIndexedOutput('original', 0),
                                        output.getIndexedOutput('mutated', 0))
        extracted = '(skipped)'
        if allele:
            extracted = unicode(allele)

    else:
        extracted = ''

    # Todo: Generate the fancy HTML views for the proteins here instead of in
    #   `mutalyzer.variantchecker`.
    arguments = {
        'description'         : description,
        'messages'            : map(util.message_info, output.getMessages()),
        'summary'             : summary,
        'parse_error'         : parse_error,
        'errors'              : errors,
        'genomicDescription'  : genomic_description,
        'chromDescription'    : output.getIndexedOutput(
                                  'genomicChromDescription', 0),
        'genomicDNA'          : genomic_dna,
        'visualisation'       : output.getOutput('visualisation'),
        'descriptions'        : output.getOutput('descriptions'),
        'protDescriptions'    : output.getOutput('protDescriptions'),
        'oldProtein'          : output.getOutput('oldProteinFancy'),
        'altStart'            : output.getIndexedOutput('altStart', 0),
        'altProtein'          : output.getOutput('altProteinFancy'),
        'newProtein'          : output.getOutput('newProteinFancy'),
        'transcriptInfo'      : output.getIndexedOutput('hasTranscriptInfo',
                                                        0, False),
        'transcriptCoding'    : output.getIndexedOutput('transcriptCoding', 0,
                                                        False),
        'exonInfo'            : output.getOutput('exonInfo'),
        'cdsStart_g'          : output.getIndexedOutput('cdsStart_g', 0),
#.........这里部分代码省略.........