ALLEN INSTITUTE

# Source code for bmtk.utils.sonata.file

    # Copyright 2017. Allen Institute. All rights reserved
    #
    # Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
    # following conditions are met:
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    # 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following
    # disclaimer.
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    # 2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following
    # disclaimer in the documentation and/or other materials provided with the distribution.
    #
    # 3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote
    # products derived from this software without specific prior written permission.
    #
    # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
    # INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
    # DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
    # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
    # SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
    # WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
    # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
    #
    from . import utils
    from .file_root import NodesRoot, EdgesRoot

    class File(object):
        def __init__(self, data_files, data_type_files, mode='r', gid_table=None, require_magic=True):
            if mode != 'r':
                raise Exception('Currently only read mode is supported.')

            self._data_files = utils.listify(data_files)
            self._data_type_files = utils.listify(data_type_files)

            # Open and check HDF5 file(s)
            self._h5_file_handles = [utils.load_h5(f, mode) for f in self._data_files]
            if require_magic:
                map(utils.check_magic, self._h5_file_handles)  # Check magic attribute in h5 files

            # Check version number
            avail_versions = set(map(utils.get_version, self._h5_file_handles))
            if len(avail_versions) == 1:
                self._version = list(avail_versions)[0]
            elif len(avail_versions) > 1:
                # TODO: log as warning
                print('Warning: Passing in multiple hdf5 files of different version')
                self._version = ','.join(avail_versions)
            else:
                self._version = utils.VERSION_NA

            self._csv_file_handles = [(f, utils.load_csv(f)) for f in self._data_type_files]

            self._has_nodes = False
            self._nodes = None  # /nodes object
            self._nodes_groups = []  # list of all hdf5 /nodes group
            self._node_types_dataframes = []  # list of all csv node-types dataframe

            self._has_edges = False
            self._edges = None  # /edges object
            self._edges_groups = []  # list of all hdf5 /edges group
            self._edge_types_dataframes = []  # list of csv edge-types dataframes

            # for multiple inputs sort into edge files and node files
            self._sort_types_file()
            self._sort_h5_files()

            if not (self._has_nodes or self._has_edges):
                raise Exception('Could not find neither nodes nor edges for the given file(s).')

            if self._has_nodes:
                self._nodes = NodesRoot(nodes=self._nodes_groups, node_types=self._node_types_dataframes, gid_table=gid_table)

            if self._has_edges:
                self._edges = EdgesRoot(edges=self._edges_groups, edge_types=self._edge_types_dataframes)

        @property
        def nodes(self):
            return self._nodes

        @property
        def has_nodes(self):
            return self._has_nodes

        @property
        def edges(self):
            return self._edges

        @property
        def has_edges(self):
            return self._has_edges

        @property
        def version(self):
            return self._version

        def _sort_types_file(self):
            # TODO: node/edge type_id columnn names should not be hardcoded
            for filename, df in self._csv_file_handles:
                has_node_type_id = 'node_type_id' in df.columns
                has_edge_type_id = 'edge_type_id' in df.columns
                if has_node_type_id and has_edge_type_id:
                    # TODO: users may be creating their own dataframe and thus not have a filename
                    raise Exception('types file {} has both node_types_id and edge_types_id column.'.format(filename))
                elif has_node_type_id:
                    self._node_types_dataframes.append(df)
                elif has_edge_type_id:
                    self._edge_types_dataframes.append(df)
                else:
                    # TODO: if strict this should fail immedietely
                    print('Warning: Could not determine if file {} was an edge-types or node-types file. Ignoring'.format(filename))

        def _sort_h5_files(self):
            for h5 in self._h5_file_handles:
                has_nodes = '/nodes' in h5
                has_edges = '/edges' in h5
                if not (has_nodes or has_edges):
                    print('File {} contains neither nodes nor edges. Ignoring'.format(h5.filename))
                else:
                    if has_nodes:
                        self._nodes_groups.append(h5)
                        self._has_nodes = True
                    if has_edges:
                        self._edges_groups.append(h5)
                        self._has_edges = True