示例#1
0
def sample_template_handler_post_request(study_id,
                                         user,
                                         filepath,
                                         data_type=None):
    """Creates a new sample template

    Parameters
    ----------
    study_id: int
        The study to add the sample information
    user: qiita_db.user import User
        The user performing the request
    filepath: str
        The path to the sample template file
    data_type: str, optional
        If filepath is a QIIME mapping file, the data type of the prep
        information file

    Returns
    -------
    dict of {'job': str}
        job: the id of the job adding the sample information to the study

    Raises
    ------
    HTTPError
        404 if the filepath doesn't exist
    """
    # Check if the current user has access to the study
    sample_template_checks(study_id, user)

    # Check if the file exists
    fp_rsp = check_fp(study_id, filepath)
    if fp_rsp['status'] != 'success':
        raise HTTPError(404, 'Filepath not found')
    filepath = fp_rsp['file']

    is_mapping_file = looks_like_qiime_mapping_file(filepath)
    if is_mapping_file and not data_type:
        raise HTTPError(
            400, 'Please, choose a data type if uploading a '
            'QIIME mapping file')

    qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
    cmd = qiita_plugin.get_command('create_sample_template')
    params = Parameters.load(cmd,
                             values_dict={
                                 'fp': filepath,
                                 'study_id': study_id,
                                 'is_mapping_file': is_mapping_file,
                                 'data_type': data_type
                             })
    job = ProcessingJob.create(user, params, True)
    r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
                 dumps({'job_id': job.id}))
    job.submit()
    return {'job': job.id}
示例#2
0
def sample_template_handler_post_request(study_id, user, filepath,
                                         data_type=None, direct_upload=False):
    """Creates a new sample template

    Parameters
    ----------
    study_id: int
        The study to add the sample information
    user: qiita_db.user import User
        The user performing the request
    filepath: str
        The path to the sample template file
    data_type: str, optional
        If filepath is a QIIME mapping file, the data type of the prep
        information file
    direct_upload: boolean, optional
        If filepath is a direct upload; if False we need to process the
        filepath as part of the study upload folder

    Returns
    -------
    dict of {'job': str}
        job: the id of the job adding the sample information to the study

    Raises
    ------
    HTTPError
        404 if the filepath doesn't exist
    """
    # Check if the current user has access to the study
    sample_template_checks(study_id, user)

    # Check if the file exists
    if not direct_upload:
        fp_rsp = check_fp(study_id, filepath)
        if fp_rsp['status'] != 'success':
            raise HTTPError(404, reason='Filepath not found')
        filepath = fp_rsp['file']

    is_mapping_file = looks_like_qiime_mapping_file(filepath)
    if is_mapping_file and not data_type:
        raise HTTPError(400, reason='Please, choose a data type if uploading '
                        'a QIIME mapping file')

    qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
    cmd = qiita_plugin.get_command('create_sample_template')
    params = Parameters.load(
        cmd, values_dict={'fp': filepath, 'study_id': study_id,
                          'is_mapping_file': is_mapping_file,
                          'data_type': data_type})
    job = ProcessingJob.create(user, params, True)
    r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
                 dumps({'job_id': job.id}))
    job.submit()
    return {'job': job.id}
示例#3
0
def sample_template_handler_patch_request(user,
                                          req_op,
                                          req_path,
                                          req_value=None,
                                          req_from=None,
                                          direct_upload=False):
    """Patches the sample template

    Parameters
    ----------
    user: qiita_db.user.User
        The user performing the request
    req_op : str
        The operation to perform on the sample template
    req_path : str
        The path to the attribute to patch
    req_value : str, optional
        The new value
    req_from : str, optional
        The original path of the element
    direct_upload : boolean, optional
        If the file being uploaded comes from a direct upload (True)

    Returns
    -------

    Raises
    ------
    HTTPError
        400 If the path parameter doens't follow the expected format
        400 If the given operation is not supported
    """
    req_path = [v for v in req_path.split('/') if v]
    # At this point we know the path should be at least length 2
    if len(req_path) < 2:
        raise HTTPError(400, reason='Incorrect path parameter')

    study_id = int(req_path[0])
    # Check if the current user has access to the study and if the sample
    # template exists
    sample_template_checks(study_id, user, check_exists=True)

    if req_op == 'remove':
        # Path format
        # column: study_id/columns/column_name
        # sample: study_id/samples/sample_id
        if len(req_path) != 3:
            raise HTTPError(400, reason='Incorrect path parameter')

        attribute = req_path[1]
        attr_id = req_path[2]

        qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
        cmd = qiita_plugin.get_command('delete_sample_or_column')
        params = Parameters.load(cmd,
                                 values_dict={
                                     'obj_class': 'SampleTemplate',
                                     'obj_id': study_id,
                                     'sample_or_col': attribute,
                                     'name': attr_id
                                 })
        job = ProcessingJob.create(user, params, True)
        # Store the job id attaching it to the sample template id
        r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
                     dumps({'job_id': job.id}))
        job.submit()
        return {'job': job.id}
    elif req_op == 'replace':
        # WARNING: Although the patch operation is a replace, is not a full
        # true replace. A replace is in theory equivalent to a remove + add.
        # In this case, the replace operation doesn't necessarily removes
        # anything (e.g. when only new columns/samples are being added to the)
        # sample information.
        # Path format: study_id/data
        # Forcing to specify data for extensibility. In the future we may want
        # to use this function to replace other elements of the sample
        # information
        if len(req_path) != 2:
            raise HTTPError(400, reason='Incorrect path parameter')

        attribute = req_path[1]

        if attribute == 'data':
            # Update the sample information
            if req_value is None:
                raise HTTPError(400,
                                reason="Value is required when updating "
                                "sample information")

            if direct_upload:
                # We can assume that the file exist as it was generated by
                # the system
                filepath = req_value
                if not exists(filepath):
                    reason = ('Upload file not found (%s), please report to '
                              '*****@*****.**' % filepath)
                    raise HTTPError(404, reason=reason)
            else:
                # Check if the file exists
                fp_rsp = check_fp(study_id, req_value)
                if fp_rsp['status'] != 'success':
                    raise HTTPError(404, reason='Filepath not found')
                filepath = fp_rsp['file']

            qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
            cmd = qiita_plugin.get_command('update_sample_template')
            params = Parameters.load(cmd,
                                     values_dict={
                                         'study': study_id,
                                         'template_fp': filepath
                                     })
            job = ProcessingJob.create(user, params, True)

            # Store the job id attaching it to the sample template id
            r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
                         dumps({'job_id': job.id}))

            job.submit()
            return {'job': job.id}
        else:
            raise HTTPError(404, reason='Attribute %s not found' % attribute)

    else:
        raise HTTPError(400,
                        reason='Operation %s not supported. Current '
                        'supported operations: remove, replace' % req_op)
示例#4
0
def sample_template_handler_patch_request(user, req_op, req_path,
                                          req_value=None, req_from=None):
    """Patches the sample template

    Parameters
    ----------
    user: qiita_db.user.User
        The user performing the request
    req_op : str
        The operation to perform on the sample template
    req_path : str
        The path to the attribute to patch
    req_value : str, optional
        The new value
    req_from : str, optional
        The original path of the element

    Returns
    -------

    Raises
    ------
    HTTPError
        400 If the path parameter doens't follow the expected format
        400 If the given operation is not supported
    """
    req_path = [v for v in req_path.split('/') if v]
    # At this point we know the path should be at least length 2
    if len(req_path) < 2:
        raise HTTPError(400, reason='Incorrect path parameter')

    study_id = int(req_path[0])
    # Check if the current user has access to the study and if the sample
    # template exists
    sample_template_checks(study_id, user, check_exists=True)

    if req_op == 'remove':
        # Path format
        # column: study_id/columns/column_name
        # sample: study_id/samples/sample_id
        if len(req_path) != 3:
            raise HTTPError(400, reason='Incorrect path parameter')

        attribute = req_path[1]
        attr_id = req_path[2]

        qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
        cmd = qiita_plugin.get_command('delete_sample_or_column')
        params = Parameters.load(
            cmd, values_dict={'obj_class': 'SampleTemplate',
                              'obj_id': study_id,
                              'sample_or_col': attribute,
                              'name': attr_id})
        job = ProcessingJob.create(user, params, True)
        # Store the job id attaching it to the sample template id
        r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
                     dumps({'job_id': job.id}))
        job.submit()
        return {'job': job.id}
    elif req_op == 'replace':
        # WARNING: Although the patch operation is a replace, is not a full
        # true replace. A replace is in theory equivalent to a remove + add.
        # In this case, the replace operation doesn't necessarily removes
        # anything (e.g. when only new columns/samples are being added to the)
        # sample information.
        # Path format: study_id/data
        # Forcing to specify data for extensibility. In the future we may want
        # to use this function to replace other elements of the sample
        # information
        if len(req_path) != 2:
            raise HTTPError(400, reason='Incorrect path parameter')

        attribute = req_path[1]

        if attribute == 'data':
            # Update the sample information
            if req_value is None:
                raise HTTPError(400, reason="Value is required when updating "
                                "sample information")

            # Check if the file exists
            fp_rsp = check_fp(study_id, req_value)
            if fp_rsp['status'] != 'success':
                raise HTTPError(404, reason='Filepath not found')
            filepath = fp_rsp['file']

            qiita_plugin = Software.from_name_and_version('Qiita', 'alpha')
            cmd = qiita_plugin.get_command('update_sample_template')
            params = Parameters.load(
                cmd, values_dict={'study': study_id,
                                  'template_fp': filepath})
            job = ProcessingJob.create(user, params, True)

            # Store the job id attaching it to the sample template id
            r_client.set(SAMPLE_TEMPLATE_KEY_FORMAT % study_id,
                         dumps({'job_id': job.id}))

            job.submit()
            return {'job': job.id}
        else:
            raise HTTPError(404, reason='Attribute %s not found' % attribute)

    else:
        raise HTTPError(400, reason='Operation %s not supported. Current '
                        'supported operations: remove, replace' % req_op)