from __future__ import absolute_import
# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE).  http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE.  If not, see <http://www.gnu.org/licenses/>.
#
#
#                     ABOUT THE ETE PACKAGE
#                     =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
from .common import dump, src_tree_iterator
from six.moves import map

DESC = ""
def populate_args(annotate_args_p):
    annotate_args = annotate_args_p.add_argument_group("TREE ANNOTATE OPTIONS")
    annotate_args.add_argument("--ncbi", dest="ncbi", action="store_true",
                               help="annotate tree nodes using ncbi taxonomy database.")
    annotate_args.add_argument("--taxid_attr", dest="taxid_attr", default='name',
                               help="attribute used as NCBI taxid number")
    annotate_args.add_argument("--feature", dest="feature", nargs="+", action='append', default=[],
                               help="")
def run(args):
    from .. import Tree, PhyloTree

    features = set()
    for nw in src_tree_iterator(args):
        if args.ncbi:
            tree = PhyloTree(nw)
            features.update(["taxid", "name", "rank", "bgcolor", "sci_name",
                             "collapse_subspecies", "named_lineage", "lineage"])
            tree.annotate_ncbi_taxa(args.taxid_attr)
        else:
            tree = Tree(nw)

        type2cast = {"str":str, "int":int, "float":float, "set":set, "list":list}

        for annotation in args.feature:
            aname, asource, amultiple, acast = None, None, False, str
            for field in annotation:
                try:
                    key, value = [_f.strip() for _f in field.split(":")]
                except Exception:
                    raise ValueError("Invalid feature option [%s]" %field )

                if key == "name":
                    aname = value
                elif key == "source":
                    asource = value
                elif key == "multiple":
                    #append
                    amultiple = value
                elif key == "type":
                    try:
                        acast = type2cast[value]
                    except KeyError:
                        raise ValueError("Invalid feature type [%s]" %field)
                else:
                    raise ValueError("Unknown feature option [%s]" %field)

            if not aname and not asource:
                ValueError('name and source are required when annotating a new feature [%s]'
                           % annotation)

            features.add(aname)
            for line in open(asource, 'rU'):
                line = line.strip()
                if not line or line.startswith('#'):
                    continue
                nodenames, attr_value = [_ln.strip() for _ln in line.split('\t')]
                nodenames = list(map(str.strip, nodenames.split(',')))
                relaxed_grouping = True
                if nodenames[0].startswith('!'):
                    relaxed_grouping = False
                    nodenames[0] = nodenames[0][1:]

                if len(nodenames) > 1:
                    target_node = tree.get_common_ancestor(nodenames)
                    if not relaxed_grouping:
                        pass
                        # do something
                else:
                    target_node = tree & nodenames[0]

                if hasattr(target_node, aname):
                    log.warning('Overwriting annotation for node" [%s]"' %nodenames)
                else:
                    target_node.add_feature(aname, acast(attr_value))

        dump(tree, features=features)
