Source code for allensdk.internal.api.queries.grid_data_api_prerelease

import os
import six

from allensdk.config.manifest import Manifest
from allensdk.api.warehouse_cache.cache import Cache, cacheable
from allensdk.api.queries.grid_data_api import GridDataApi
from allensdk.core import json_utilities

from ..api_prerelease import ApiPrerelease
from ...core import lims_utilities as lu


_STORAGE_DIRECTORY_QUERY = '''
select     iser.id,
           iser.storage_directory
from       image_series as iser
where      iser.storage_directory is not null
'''


@cacheable()
def _get_grid_storage_directories(grid_data_directory):
    query_result = lu.query(_STORAGE_DIRECTORY_QUERY)

    storage_directories = dict()
    for row in query_result:
        path = lu.safe_system_path(row[b'storage_directory'])

        # NOTE: hacky, but grid directory contains files without having
        #       injection_density_*.nrrd, projection_density_*.nrrd, ...
        grid_example = os.path.join(path, grid_data_directory, 'data_mask_100.nrrd')

        if os.path.exists(grid_example):
            storage_directories[str(row[b'id'])] = path

    return storage_directories

class GridDataApiPrerelease(GridDataApi):
    '''Client for retrieving prereleased mouse connectivity data from lims.

    Parameters
    ----------
    base_uri : string, optional
        Does not affect pulling from lims.
    file_name : string, optional
        File name to save/read storage_directories dict. Passed to
        GridDataApiPrerelease constructor.
    '''
    GRID_DATA_DIRECTORY = 'grid'

    @classmethod
    def from_file_name(cls, file_name, cache=True, **kwargs):
        '''Alternative constructor using cache path file_name.

        Parameters
        ----------
        file_name : string
            Path where storage_directories will be saved.
        **kwargs
            Keyword arguments to be supplied to __init__

        Returns
        -------
        cls : instance of GridDataApiPrerelease
        '''
        if os.path.exists(file_name):
            storage_directories = json_utilities.read(file_name)
        else:
            storage_directories = _get_grid_storage_directories(cls.GRID_DATA_DIRECTORY)

            if cache:
                Manifest.safe_make_parent_dirs(file_name)
                json_utilities.write(file_name, storage_directories)

        return cls(storage_directories, **kwargs)

    def __init__(self, storage_directories, resolution=None, base_uri=None):
        super(GridDataApiPrerelease, self).__init__(resolution=resolution,
                                                    base_uri=base_uri)
        self.storage_directories = storage_directories
        self.api = ApiPrerelease()

    def download_projection_grid_data(self, path, experiment_id, file_name):
        '''Copy data from path to file_name.

        Parameters
        ----------
        path : string
            path to file in shared directory (copy source)
        experiment_id : int
            image series id.
        file_name : string
            path to file destination (copy target)
        '''
        try:
            storage_path = self.storage_directories[str(experiment_id)]
        except KeyError as e:
            error = '''
            experiment %s is not in the storage_directories dictionary
            this can be a result of one or more of:
                * an invalid experiment id
                * a valid experiment id whose grid data has not yet been computed
            try either removing the storage_directories_prerelease.json manifest
            from you manifest directory, or passing an updated storage_directories
            dict to the GridDataApiPrerelase constructor.
            ''' % experiment_id

            self._file_download_log.error(error)
            self.cleanup_truncated_file(path)
            raise six.raise_from(ValueError(error), e)

        storage_path = os.path.join(
            storage_path, self.GRID_DATA_DIRECTORY, file_name)

        self.api.retrieve_file_from_storage(storage_path, path)