# Copyright (C) 2013 by Ben Morris (ben@bendmorris.com)
# Based on Bio.Nexus, copyright 2005-2008 by Frank Kauff & Cymon J. Cox
# and Bio.Phylo.Newick, copyright 2009 by Eric Talevich.
# All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""I/O function wrappers for the RDF/CDAO file format.
This is an RDF format that conforms to the Comparative Data Analysis Ontology (CDAO).
See: http://www.evolutionaryontology.org/cdao
This module requires the librdf Python bindings (http://www.librdf.org)
The CDAOIO.Parser, in addition to parsing text files, can also parse directly
from a triple store that implements the Redland storage interface; similarly,
the CDAOIO.Writer can store triples in a triple store instead of serializing
them to a file.
__docformat__ = "restructuredtext en"
from Bio._py3k import StringIO
from Bio.Phylo import CDAO
from ._cdao_owl import cdao_elements, cdao_namespaces, resolve_uri
import os
class CDAOError(Exception):
    """Exception raised when CDAO object construction cannot continue."""
    import rdflib
    rdfver = rdflib.__version__
    if rdfver[0] in ["1", "2"] or (rdfver in ["3.0.0", "3.1.0", "3.2.0"]):
        raise CDAOError('Support for CDAO tree format requires RDFlib v3.2.1 or later.')
except ImportError:
    raise CDAOError('Support for CDAO tree format requires RDFlib.')
                  'owl':  'http://www.w3.org/2002/07/owl#',
                  'rdf':  'http://www.w3.org/1999/02/22-rdf-syntax-ns#',
                  'rdfs': 'http://www.w3.org/2000/01/rdf-schema#',
# pad node ids with zeroes until they're at least this length
def qUri(x):
    return resolve_uri(x, namespaces=RDF_NAMESPACES)
def format_label(x):
    return x.replace('_', ' ')
# ---------------------------------------------------------
# Public API
def parse(handle, **kwargs):
    """Iterate over the trees in a CDAO file handle.
    :returns: generator of Bio.Phylo.CDAO.Tree objects.
    return Parser(handle).parse(**kwargs)
def write(trees, handle, plain=False, **kwargs):
    """Write a trees in CDAO format to the given file handle.
    :returns: number of trees written.
    return Writer(trees).write(handle, plain=plain, **kwargs)
# ---------------------------------------------------------
# Input
class Parser(object):
    """Parse a CDAO tree given a file handle.
    def __init__(self, handle=None):
        self.handle = handle
        self.graph = None
        self.node_info = None
        self.children = {}
        self.rooted = False
    def from_string(cls, treetext):
        handle = StringIO(treetext)
        return cls(handle)
    def parse(self, **kwargs):
        """Parse the text stream this object was initialized with."""
        return self.parse_graph()
    def parse_handle_to_graph(self, rooted=False,
                              parse_format='turtle', context=None, **kwargs):
        '''Parse self.handle into RDF model self.model.'''
        if self.graph is None:
            self.graph = rdflib.Graph()
        graph = self.graph
        for k, v in RDF_NAMESPACES.items():
            graph.bind(k, v)
        self.rooted = rooted
        if 'base_uri' in kwargs:
            base_uri = kwargs['base_uri']
            base_uri = "file://"+os.path.abspath(self.handle.name)
        graph.parse(file=self.handle, publicID=base_uri, format=parse_format)
        return self.parse_graph(graph, context=context)
    def parse_graph(self, graph=None, context=None):
        '''Generator that yields CDAO.Tree instances from an RDF model.'''
        if graph is None:
            graph = self.graph
        # look up branch lengths/TUs for all nodes
        self.get_node_info(graph, context=context)
        for root_node in self.tree_roots:
            clade = self.parse_children(root_node)
            yield CDAO.Tree(root=clade, rooted=self.rooted)
    def new_clade(self, node):
        '''Returns a CDAO.Clade object for a given named node.'''
        result = self.node_info[node]
        kwargs = {}
        if 'branch_length' in result:
            kwargs['branch_length'] = result['branch_length']
        if 'label' in result:
            kwargs['name'] = result['label'].replace('_', ' ')
        if 'confidence' in result:
            kwargs['confidence'] = result['confidence']
        clade = CDAO.Clade(**kwargs)
        return clade
    def get_node_info(self, graph, context=None):
        '''Creates a dictionary containing information about all nodes in the tree.'''
        self.node_info = {}
        self.obj_info = {}
        self.children = {}
        self.nodes = set()
        self.tree_roots = set()
        assignments = {
                       qUri('cdao:has_Parent'): 'parent',
                       qUri('cdao:belongs_to_Edge_as_Child'): 'edge',
                       qUri('cdao:has_Annotation'): 'annotation',
                       qUri('cdao:has_Value'): 'value',
                       qUri('cdao:represents_TU'): 'tu',
                       qUri('rdfs:label'): 'label',
                       qUri('cdao:has_Support_Value'): 'confidence',
        for s, v, o in graph:
            # process each RDF triple in the graph sequentially
            s, v, o = str(s), str(v), str(o)
            if not s in self.obj_info: self.obj_info[s] = {}
            this = self.obj_info[s]
                # if the predicate is one we care about, store information for later
                this[assignments[v]] = o
            except KeyError:
            if v == qUri('rdf:type'):
                if o in (qUri('cdao:AncestralNode'), qUri('cdao:TerminalNode')):
                    # this is a tree node; store it in set of all nodes
            if v == qUri('cdao:has_Root'):
                # this is a tree; store its root in set of all tree roots
        for node in self.nodes:
            # for each node, look up all information needed to create a CDAO.Clade
            self.node_info[node] = {}
            node_info = self.node_info[node]
            obj = self.obj_info[node]
            if 'edge' in obj:
                # if this object points to an edge, we need a branch length from
                # the annotation on that edge
                edge = self.obj_info[obj['edge']]
                if 'annotation' in edge:
                    annotation = self.obj_info[edge['annotation']]
                    if 'value' in annotation:
                        node_info['branch_length'] = float(annotation['value'])
            if 'tu' in obj:
                # if this object points to a TU, we need the label of that TU
                tu = self.obj_info[obj['tu']]
                if 'label' in tu:
                    node_info['label'] = tu['label']
            if 'parent' in obj:
                # store this node as a child of its parent, if it has one,
                # so that the tree can be traversed from parent to children
                parent = obj['parent']
                if not parent in self.children:
                    self.children[parent] = []
    def parse_children(self, node):
        '''Return a CDAO.Clade, and calls itself recursively for each child,
        traversing the  entire tree and creating a nested structure of CDAO.Clade
        clade = self.new_clade(node)
        children = self.children[node] if node in self.children else []
        clade.clades = [self.parse_children(child_node) for child_node in children]
        return clade
# ---------------------------------------------------------
# Output
class Writer(object):
    """Based on the writer in Bio.Nexus.Trees (str, to_string)."""
    prefixes = RDF_NAMESPACES
    def __init__(self, trees):
        self.trees = trees
        self.node_counter = 0
        self.edge_counter = 0
        self.tu_counter = 0
        self.tree_counter = 0
    def write(self, handle, tree_uri='', record_complete_ancestry=False,
              rooted=False, **kwargs):
        """Write this instance's trees to a file handle."""
        self.rooted = rooted
        self.record_complete_ancestry = record_complete_ancestry
        if tree_uri and not tree_uri.endswith('/'): tree_uri += '/'
        trees = self.trees
        if tree_uri: handle.write('@base <%s>\n' % tree_uri)
        for k, v in self.prefixes.items():
            handle.write('@prefix %s: <%s> .\n' % (k, v))
        handle.write('<%s> a owl:Ontology .\n' % self.prefixes['cdao'])
        for tree in trees:
            self.tree_counter += 1
            self.tree_uri = 'tree%s'
            first_clade = tree.clade
            statements = self.process_clade(first_clade, root=tree)
            for stmt in statements:
                self.add_stmt_to_handle(handle, stmt)
    def add_stmt_to_handle(self, handle, stmt):
        # apply URI prefixes
        stmt_strings = []
        for n, part in enumerate(stmt):
            if isinstance(part, rdflib.URIRef):
                node_uri = str(part)
                changed = False
                for prefix, uri in self.prefixes.items():
                    if node_uri.startswith(uri):
                        node_uri = node_uri.replace(uri, '%s:'%prefix, 1)
                        if node_uri == 'rdf:type': node_uri = 'a'
                        changed = True
                if changed or ':' in node_uri: stmt_strings.append(node_uri)
                else: stmt_strings.append('<%s>' % node_uri)
            elif isinstance(part, rdflib.Literal):
        handle.write('%s .\n' % ' '.join(stmt_strings))
    def process_clade(self, clade, parent=None, root=False):
        '''recursively generate triples describing a tree of clades'''
        self.node_counter += 1
        clade.uri = 'node%s' % str(self.node_counter).zfill(ZEROES)
        if parent: clade.ancestors = parent.ancestors + [parent.uri]
        else: clade.ancestors = []
        nUri = lambda s: rdflib.URIRef(s)#':%s' % s
        pUri = lambda s: rdflib.URIRef(qUri(s))
        tree_id = nUri('')
        statements = []
        if not root is False:
            # create a cdao:RootedTree with reference to the tree root
            tree_type = pUri('cdao:RootedTree') if self.rooted else pUri('cdao:UnrootedTree')
            statements += [
                           (tree_id, pUri('rdf:type'), tree_type),
                           (tree_id, pUri('cdao:has_Root'), nUri(clade.uri)),
            try: tree_attributes = root.attributes
            except AttributeError: tree_attributes = []
            for predicate, obj in tree_attributes:
                statements.append((tree_id, predicate, obj))
        if clade.name:
            # create TU
            self.tu_counter += 1
            tu_uri = 'tu%s' % str(self.tu_counter).zfill(ZEROES)
            statements += [
                           (nUri(tu_uri), pUri('rdf:type'), pUri('cdao:TU')),
                           (nUri(clade.uri), pUri('cdao:represents_TU'), nUri(tu_uri)),
                           (nUri(tu_uri), pUri('rdfs:label'), rdflib.Literal(format_label(clade.name))),
            try: tu_attributes = clade.tu_attributes
            except AttributeError: tu_attributes = []
            for predicate, obj in tu_attributes:
                yield (nUri(tu_uri), predicate, obj)
        # create this node
        node_type = 'cdao:TerminalNode' if clade.is_terminal() else 'cdao:AncestralNode'
        statements += [
                       (nUri(clade.uri), pUri('rdf:type'), pUri(node_type)),
                       (nUri(clade.uri), pUri('cdao:belongs_to_Tree'), tree_id),
        if not parent is None:
            # create edge from the parent node to this node
            self.edge_counter += 1
            edge_uri = 'edge%s' % str(self.edge_counter).zfill(ZEROES)
            statements += [
                           (nUri(edge_uri), pUri('rdf:type'), pUri('cdao:DirectedEdge')),
                           (nUri(edge_uri), pUri('cdao:belongs_to_Tree'), tree_id),
                           (nUri(edge_uri), pUri('cdao:has_Parent_Node'), nUri(parent.uri)),
                           (nUri(edge_uri), pUri('cdao:has_Child_Node'), nUri(clade.uri)),
                           (nUri(clade.uri), pUri('cdao:belongs_to_Edge_as_Child'), nUri(edge_uri)),
                           (nUri(clade.uri), pUri('cdao:has_Parent'), nUri(parent.uri)),
                           (nUri(parent.uri), pUri('cdao:belongs_to_Edge_as_Parent'), nUri(edge_uri)),
            if hasattr(clade, 'confidence') and not clade.confidence is None:
                confidence = rdflib.Literal(clade.confidence, datatype='http://www.w3.org/2001/XMLSchema#decimal')
                statements += [(nUri(clade.uri), pUri('cdao:has_Support_Value'), confidence)]
            if self.record_complete_ancestry and len(clade.ancestors) > 0:
                statements += [(nUri(clade.uri), pUri('cdao:has_Ancestor'), nUri(ancestor))
                               for ancestor in clade.ancestors]
            if not clade.branch_length is None:
                # add branch length
                edge_ann_uri = 'edge_annotation%s' % str(self.edge_counter).zfill(ZEROES)
                branch_length = rdflib.Literal(clade.branch_length, datatype=rdflib.URIRef('http://www.w3.org/2001/XMLSchema#decimal'))
                statements += [
                               (nUri(edge_ann_uri), pUri('rdf:type'), pUri('cdao:EdgeLength')),
                               (nUri(edge_uri), pUri('cdao:has_Annotation'), nUri(edge_ann_uri)),
                               (nUri(edge_ann_uri), pUri('cdao:has_Value'), branch_length),
            try: edge_attributes = clade.edge_attributes
            except AttributeError: edge_attributes = []
            for predicate, obj in edge_attributes:
                yield (nUri(edge_uri), predicate, obj)
        for stmt in statements:
            yield stmt
        try: clade_attributes = clade.attributes
        except AttributeError: clade_attributes = []
        for predicate, obj in clade_attributes:
            yield (nUri(clade.uri), predicate, obj)
        if not clade.is_terminal():
            for new_clade in clade.clades:
                for stmt in self.process_clade(new_clade, parent=clade, root=False):
                    yield stmt