import os
import logging
import logging.handlers
import math
import json
from metadata.MetaDataElement import MetaDataElement
from cx.aspects.NodeAttributesElement import NodeAttributesElement
from cx.aspects.EdgeAttributesElement import EdgeAttributesElement
from cx.aspects.NetworkAttributesElement import NetworkAttributesElement
from cx.aspects.AspectElement import AspectElement
from cx import CX_CONSTANTS
from cx.aspects import ATTRIBUTE_DATA_TYPE
from cx import known_aspects_min

root = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
log_path = os.path.join(root, 'logs')
# solr_url = 'http://localhost:8983/solr/'
# solr_url = 'http://dev2.ndexbio.org:8983/solr/'
# deprecation_message = 'This function is now deprecated. use NiceCX'


def get_logger(name, level=logging.DEBUG):
    logger = logging.getLogger(name)
    logger.setLevel(level)

    logger.handlers = []

    formatter = logging.Formatter('%(asctime)s.%(msecs)d ' + 
                                  name + ' %(levelname)s: %(message)s', '%Y-%m-%d %H:%M:%S')

    handler = logging.handlers.TimedRotatingFileHandler(os.path.join(log_path, 'app.log'), 
                                                        when='midnight', backupCount=28)
    handler.setFormatter(formatter)
    logger.addHandler(handler)

    handler = logging.StreamHandler()
    handler.setFormatter(formatter)
    logger.addHandler(handler)

    return logger


def create_empty_nice_cx():
    my_nicecx = NiceCXNetwork()
    return my_nicecx


def _create_cartesian_coordinates_aspect_from_networkx(G):
    return [
        {'node': n, 'x': float(G.pos[n][0]), 'y': float(G.pos[n][1])} for n in G.pos
    ]


def create_nice_cx_from_networkx(G):
    """
    Create a NiceCXNetwork based on a networkx graph. The resulting NiceCXNetwork
    contains the nodes edges and their attributes from the networkx graph and also
    preserves the graph 'pos' attribute as a CX cartesian coordinates aspect.

    :param G: networkx graph
    :type G: networkx graph
    :return: NiceCXNetwork
    :rtype: NiceCXNetwork
    """
    if G is None:
        raise Exception('Networkx input is empty')

    my_nicecx = NiceCXNetwork()

    if G.graph.get('name'):
        my_nicecx.set_name(G.graph.get('name'))
    else:
        my_nicecx.set_name('created from networkx')

    my_nicecx.add_metadata_stub('networkAttributes')
    for n, d in G.nodes_iter(data=True):
        # =============
        # ADD NODES
        # =============
        if d and d.get('name'):
            my_nicecx.create_node(id=n, node_name=d.get('name'), node_represents=d.get('name'))
        else:
            my_nicecx.create_node(id=n, node_name=n, node_represents=n)

        # ======================
        # ADD NODE ATTRIBUTES
        # ======================
        for k, v in d.items():
            attr_type = None
            if isinstance(v, float):
                attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
            elif isinstance(v, int):
                attr_type = ATTRIBUTE_DATA_TYPE.INTEGER

            my_nicecx.set_node_attribute(n, k, v, type=attr_type)

    index = 0
    for u, v, d in G.edges_iter(data=True):
        # =============
        # ADD EDGES
        # =============
        my_nicecx.create_edge(id=index, edge_source=u, edge_target=v, edge_interaction=d.get('interaction'))

        # ==============================
        # ADD EDGE ATTRIBUTES
        # ==============================
        for k, val in d.items():
            if k != 'interaction':
                attr_type = None
                if isinstance(val, float):
                    attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
                elif isinstance(val, int):
                    attr_type = ATTRIBUTE_DATA_TYPE.INTEGER
                my_nicecx.set_edge_attribute(index, k, val, type=attr_type)

        index += 1

    my_nicecx.add_metadata_stub('nodes')
    my_nicecx.add_metadata_stub('edges')
    if my_nicecx.nodeAttributes:
        my_nicecx.add_metadata_stub('nodeAttributes')
    if my_nicecx.edgeAttributes:
        my_nicecx.add_metadata_stub('edgeAttributes')

    if hasattr(G, 'pos'):
        aspect = _create_cartesian_coordinates_aspect_from_networkx(G)
        my_nicecx.add_opaque_aspect('cartesianLayout', aspect)
        my_nicecx.add_metadata_stub('cartesianLayout')

    return my_nicecx


def create_nice_cx_from_cx(cx):
    """
    Create a NiceCXNetwork from a CX list.

    :param cx: a list in CX format
    :return: NiceCXNetwork
    """
    my_nicecx = NiceCXNetwork()

    if cx:
        # ===================
        # METADATA
        # ===================
        available_aspects = []
        for ae in (o for o in my_nicecx.get_frag_from_list_by_key(cx, 'metaData')):
            available_aspects.append(ae.get(CX_CONSTANTS.METADATA_NAME))
            mde = MetaDataElement(cx_fragment=ae)
            my_nicecx.add_metadata(mde)

        opaque_aspects = set(available_aspects).difference(known_aspects_min)

        # ====================
        # NETWORK ATTRIBUTES
        # ====================
        if 'networkAttributes' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'networkAttributes')
            for network_item in objects:
                add_this_network_attribute = NetworkAttributesElement(cx_fragment=network_item)

                my_nicecx.add_network_attribute(network_attribute_element=add_this_network_attribute)
            my_nicecx.add_metadata_stub('networkAttributes')

        # ===================
        # NODES
        # ===================
        if 'nodes' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'nodes')
            for node_item in objects:
                my_nicecx.create_node(cx_fragment=node_item)
            my_nicecx.add_metadata_stub('nodes')

        # ===================
        # EDGES
        # ===================
        if 'edges' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'edges')
            for edge_item in objects:
                my_nicecx.create_edge(cx_fragment=edge_item)
            my_nicecx.add_metadata_stub('edges')

        # ===================
        # NODE ATTRIBUTES
        # ===================
        if 'nodeAttributes' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'nodeAttributes')
            for att in objects:
                # my_nicecx.set_node_attribute(None, None, None, cx_fragment=att)
                node_attribute_element = NodeAttributesElement(cx_fragment=att)
                my_nicecx.nodeAttributeHeader.add(node_attribute_element.get_name())
                nodeAttrs = my_nicecx.nodeAttributes.get(node_attribute_element.get_property_of())
                if nodeAttrs is None:
                    nodeAttrs = []
                    my_nicecx.nodeAttributes[node_attribute_element.get_property_of()] = nodeAttrs

                nodeAttrs.append(node_attribute_element)
            my_nicecx.add_metadata_stub('nodeAttributes')

        # ===================
        # EDGE ATTRIBUTES
        # ===================
        if 'edgeAttributes' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'edgeAttributes')
            for att in objects:
                #my_nicecx.set_edge_attribute(None, None, None, cx_fragment=att)
                edge_attribute_element = EdgeAttributesElement(cx_fragment=att)

                my_nicecx.edgeAttributeHeader.add(edge_attribute_element.get_name())
                edge_attrs = my_nicecx.edgeAttributes.get(att.get('po'))
                if edge_attrs is None:
                    edge_attrs = []
                    my_nicecx.edgeAttributes[edge_attribute_element.get_property_of()] = edge_attrs

                edge_attrs.append(edge_attribute_element)

            my_nicecx.add_metadata_stub('edgeAttributes')

        # ===================
        # CITATIONS
        # ===================
        if 'citations' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'citations')
            for cit in objects:
                aspect_element = AspectElement(cit, 'citations')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('citations')

        # ===================
        # SUPPORTS
        # ===================
        if 'supports' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'supports')
            for sup in objects:
                aspect_element = AspectElement(sup, 'supports')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('supports')

        # ===================
        # EDGE SUPPORTS
        # ===================
        if 'edgeSupports' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'edgeSupports')
            for add_this_edge_sup in objects:
                aspect_element = AspectElement(add_this_edge_sup, 'edgeSupports')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('edgeSupports')

        # ===================
        # NODE CITATIONS
        # ===================
        if 'nodeCitations' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'nodeCitations')
            for node_cit in objects:
                aspect_element = AspectElement(node_cit, 'nodeCitations')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('nodeCitations')

        # ===================
        # EDGE CITATIONS
        # ===================
        if 'edgeCitations' in available_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, 'edgeCitations')
            for edge_cit in objects:
                aspect_element = AspectElement(edge_cit, 'edgeCitations')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('edgeCitations')

        # ===================
        # OPAQUE ASPECTS
        # ===================
        for oa in opaque_aspects:
            objects = my_nicecx.get_frag_from_list_by_key(cx, oa)
            for oa_item in objects:
                aspect_element = AspectElement(oa_item, oa)
                my_nicecx.add_opaque_aspect_element(aspect_element)
                my_nicecx.add_metadata_stub(oa)

        return my_nicecx
    else:
        raise Exception('CX is empty')


def create_nice_cx_from_pandas(df, source_field=None, target_field=None,
                               source_node_attr=[], target_node_attr=[],
                               edge_attr=[], edge_interaction=None):
    """
    Create a NiceCXNetwork from a pandas dataframe in which each row
    specifies one edge in the network.

    If only the df argument is provided the dataframe is treated as 'SIF' format,
    where the first two columns specify the source and target node ids of the edge
    and all other columns are ignored. The edge interaction is defaulted to "interacts-with"

    If both the source_field and target_field arguments are provided, the those and any other
    arguments refer to headers in the dataframe, controlling the mapping of columns to
    the attributes of nodes, and edges in the resulting NiceCXNetwork. If a header is not
    mapped the corresponding column is ignored. If the edge_interaction is not specified it
    defaults to "interacts-with"

    :param df: pandas dataframe to process
    :param source_field: header name specifying the name of the source node.
    :param target_field: header name specifying the name of the target node.
    :param source_node_attr: list of header names specifying attributes of the source node.
    :param target_node_attr: list of header names specifying attributes of the target node.
    :param edge_attr: list of header names specifying attributes of the edge.
    :param edge_interaction: the relationship between the source node and the target node, defaulting to "interacts-with"
    :return: NiceCXNetwork
    """

    my_nicecx = NiceCXNetwork()

    # ====================================================
    # IF NODE FIELD NAME (SOURCE AND TARGET) IS PROVIDED
    # THEN USE THOSE FIELDS OTHERWISE USE INDEX 0 & 1
    # ====================================================
    my_nicecx.set_name('Pandas Upload')
    my_nicecx.add_metadata_stub('networkAttributes')
    count = 0
    if source_field and target_field:
        for index, row in df.iterrows():
            if count % 10000 == 0:
                print(count)
            count += 1
            # =============
            # ADD NODES
            # =============
            my_nicecx.create_node(id=row[source_field], node_name=row[source_field], node_represents=row[source_field])
            my_nicecx.create_node(id=row[target_field], node_name=row[target_field], node_represents=row[target_field])

            # =============
            # ADD EDGES
            # =============
            if edge_interaction:
                if row.get(edge_interaction):
                    my_nicecx.create_edge(id=index, edge_source=row[source_field],
                                          edge_target=row[target_field],
                                          edge_interaction=row[edge_interaction])
                else:
                    my_nicecx.create_edge(id=index, edge_source=row[source_field],
                                          edge_target=row[target_field],
                                          edge_interaction=edge_interaction)
            else:
                my_nicecx.create_edge(id=index, edge_source=row[source_field],
                                      edge_target=row[target_field],
                                      edge_interaction='interacts-with')

            # ==============================
            # ADD SOURCE NODE ATTRIBUTES
            # ==============================
            for sp in source_node_attr:
                attr_type = None
                if type(row[sp]) is float and math.isnan(row[sp]):
                    row[sp] = ''
                    attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
                elif type(row[sp]) is float and math.isinf(row[sp]):
                    row[sp] = 'Inf'
                    attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
                elif type(row[sp]) is float:
                    attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
                elif isinstance(row[sp], int):
                    attr_type = ATTRIBUTE_DATA_TYPE.INTEGER
                my_nicecx.set_node_attribute(row[source_field], sp, row[sp], type=attr_type)

            # ==============================
            # ADD TARGET NODE ATTRIBUTES
            # ==============================
            for tp in target_node_attr:
                attr_type = None
                if type(row[tp]) is float and math.isnan(row[tp]):
                    row[tp] = ''
                    attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
                elif type(row[tp]) is float and math.isinf(row[tp]):
                    row[tp] = 'Inf'
                    attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
                elif type(row[tp]) is float:
                    attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
                elif isinstance(row[tp], int):
                    attr_type = ATTRIBUTE_DATA_TYPE.INTEGER
                my_nicecx.set_node_attribute(row[target_field], tp, row[tp], type=attr_type)

            # ==============================
            # ADD EDGE ATTRIBUTES
            # ==============================
            for ep in edge_attr:
                attr_type = None
                if type(row[ep]) is float and math.isnan(row[ep]):
                    row[ep] = ''
                    attr_type = ATTRIBUTE_DATA_TYPE.FLOAT
                elif type(row[ep]) is float and math.isinf(row[ep]):
                    row[ep] = 'INFINITY'
                    attr_type = ATTRIBUTE_DATA_TYPE.FLOAT

                my_nicecx.set_edge_attribute(index, ep, row[ep], type=attr_type)

    else:
        for index, row in df.iterrows():
            # =============
            # ADD NODES
            # =============
            my_nicecx.create_node(id=row[0], node_name=row[0], node_represents=row[0])
            my_nicecx.create_node(id=row[1], node_name=row[1], node_represents=row[1])

            # =============
            # ADD EDGES
            # =============
            if len(row) > 2:
                my_nicecx.create_edge(id=index, edge_source=row[0],
                                      edge_target=row[1], edge_interaction=row[2])
            else:
                my_nicecx.create_edge(id=index, edge_source=row[0],
                                      edge_target=row[1], edge_interaction='interacts-with')

    my_nicecx.add_metadata_stub('nodes')
    my_nicecx.add_metadata_stub('edges')
    if source_node_attr or target_node_attr:
        my_nicecx.add_metadata_stub('nodeAttributes')
    if edge_attr:
        my_nicecx.add_metadata_stub('edgeAttributes')

    return my_nicecx


def create_nice_cx_from_server(server=None, username=None, password=None, uuid=None):
    """
    Create a NiceCXNetwork based on a network retrieved from NDEx, specified by its UUID.
    If the network is not public, then username and password arguments for an account on
    the server with permission to access the network must be supplied.

    :param server: the URL of the NDEx server hosting the network.
    :param username: the user name of an account with permission to access the network.
    :param password: the password of an account with permission to access the network.
    :param uuid: the UUID of the network.
    :return: NiceCXNetwork
    """
    if server and uuid:
        my_nicecx = NiceCXNetwork()

        # ===================
        # METADATA
        # ===================
        available_aspects = []
        md_aspect_iter = my_nicecx.get_aspect(uuid, 'metaData', server, username, password)
        if md_aspect_iter:
            for ae in (o for o in md_aspect_iter):
                available_aspects.append(ae.get(CX_CONSTANTS.METADATA_NAME))
                mde = MetaDataElement(cx_fragment=ae)
                my_nicecx.add_metadata(mde)
        else:
            if not username or not password:
                raise Exception('Network is not available.  Username and/or password not supplied')
            else:
                raise Exception('Network not available')

        opaque_aspects = set(available_aspects).difference(known_aspects_min)

        # ====================
        # NETWORK ATTRIBUTES
        # ====================
        if 'networkAttributes' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'networkAttributes', server, username, password)
            for network_item in objects:
                my_nicecx.add_network_attribute(json_obj=network_item)
            my_nicecx.add_metadata_stub('networkAttributes')

        # ===================
        # @CONTEXT
        # ===================
        if '@context' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, '@context', server, username, password)
            my_nicecx.set_context(objects)
            if(my_nicecx.metadata.get('@context') is None):
                my_nicecx.add_metadata_stub('@context')
            else:
                my_nicecx.metadata.get('@context').set_element_count(1)

        # ===================
        # NODES
        # ===================
        if 'nodes' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'nodes', server, username, password)
            for node_item in objects:
                my_nicecx.create_node(cx_fragment=node_item)
            my_nicecx.add_metadata_stub('nodes')

        # ===================
        # EDGES
        # ===================
        if 'edges' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'edges', server, username, password)
            for edge_item in objects:
                my_nicecx.create_edge(cx_fragment=edge_item)
            my_nicecx.add_metadata_stub('edges')

        # ===================
        # NODE ATTRIBUTES
        # ===================
        if 'nodeAttributes' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'nodeAttributes', server, username, password)
            for att in objects:
                # my_nicecx.set_node_attribute(att.get('po'), att.get('n'), att.get('v'), type=att.get('d'))

                node_attribute_element = NodeAttributesElement(cx_fragment=att)
                my_nicecx.nodeAttributeHeader.add(node_attribute_element.get_name())
                nodeAttrs = my_nicecx.nodeAttributes.get(node_attribute_element.get_property_of())
                if nodeAttrs is None:
                    nodeAttrs = []
                    my_nicecx.nodeAttributes[node_attribute_element.get_property_of()] = nodeAttrs

                nodeAttrs.append(node_attribute_element)

            my_nicecx.add_metadata_stub('nodeAttributes')

        # ===================
        # EDGE ATTRIBUTES
        # ===================
        if 'edgeAttributes' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'edgeAttributes', server, username, password)
            for att in objects:
                edge_attribute_element = EdgeAttributesElement(cx_fragment=att)

                my_nicecx.edgeAttributeHeader.add(edge_attribute_element.get_name())
                edge_attrs = my_nicecx.edgeAttributes.get(att.get('po'))
                if edge_attrs is None:
                    edge_attrs = []
                    my_nicecx.edgeAttributes[edge_attribute_element.get_property_of()] = edge_attrs

                edge_attrs.append(edge_attribute_element)

            my_nicecx.add_metadata_stub('edgeAttributes')

        # ===================
        # CITATIONS
        # ===================
        if 'citations' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'citations', server, username, password)
            for cit in objects:
                aspect_element = AspectElement(cit, 'citations')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('citations')

        # ===================
        # SUPPORTS
        # ===================
        if 'supports' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'supports', server, username, password)
            for sup in objects:
                aspect_element = AspectElement(sup, 'supports')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('supports')

        # ===================
        # EDGE SUPPORTS
        # ===================
        if 'edgeSupports' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'edgeSupports', server, username, password)
            for add_this_edge_sup in objects:
                aspect_element = AspectElement(add_this_edge_sup, 'edgeSupports')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('edgeSupports')

        # ===================
        # NODE CITATIONS
        # ===================
        if 'nodeCitations' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'nodeCitations', server, username, password)
            for node_cit in objects:
                aspect_element = AspectElement(node_cit, 'nodeCitations')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('nodeCitations')

        # ===================
        # EDGE CITATIONS
        # ===================
        if 'edgeCitations' in available_aspects:
            objects = my_nicecx.get_aspect(uuid, 'edgeCitations', server, username, password)
            for edge_cit in objects:
                aspect_element = AspectElement(edge_cit, 'edgeCitations')
                my_nicecx.add_opaque_aspect_element(aspect_element)

            my_nicecx.add_metadata_stub('edgeCitations')

        # ===================
        # OPAQUE ASPECTS
        # ===================
        for oa in opaque_aspects:
            objects = my_nicecx.get_aspect(uuid, oa, server, username, password)
            for oa_item in objects:
                aspect_element = AspectElement(oa_item, oa)
                my_nicecx.add_opaque_aspect_element(aspect_element)
                my_nicecx.add_metadata_stub(oa)
    else:
        raise Exception('Server and uuid not specified')

    return my_nicecx


def create_nice_cx_from_file(path):
    """
    Create a NiceCXNetwork based on CX JSON from a file.

    :param path: the path from which the CX will be loaded
    :return: NiceCXNetwork
    """
    if os.path.isfile(path):
        my_nicecx = NiceCXNetwork()
        with open(path, 'rU') as file_cx:
            # ====================================
            # BUILD NICECX FROM FILE
            # ====================================
            my_nicecx.create_from_cx(json.load(file_cx))
            return my_nicecx
    else:
        raise Exception('The file ' + path + '  does not exist.')


from ndex2.niceCXNetwork import NiceCXNetwork
