--- a/lexmapr/ontology_reasoner.py	Wed Aug 31 14:32:14 2022 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,449 +0,0 @@
-"""Ontology finder and visualizer"""
-
-import copy, json, logging, requests, time
-import pygraphviz as pgv
-
-logging.getLogger('urllib3').setLevel(logging.WARNING)
-
-
-# TODO: figure out what to do with root Thing:Thing
-class Ontology_accession:
-    '''Base class for defining attributes and behavior of single ontology accesions;
-       Assume format definition (whitespace and punctuation okay):ontology_id'''
-    existing_ontologies = {}
-
-    @staticmethod
-    def make_instance(acc):
-      '''Use instead of default __init__ to enforce one instance per ontology'''
-      try:
-          return(Ontology_accession.existing_ontologies[acc])
-      except(KeyError):
-          Ontology_accession.existing_ontologies[acc] = Ontology_accession(acc)
-          return(Ontology_accession.existing_ontologies[acc])
-
-    def __init__(self, acc):
-        '''If ontology is not recognized, just use short form, ex THING'''
-        def_split = acc.split(':')
-        self.label = ':'.join(def_split[:-1])
-        self.id = def_split[-1].replace('_',':')
-        self.parents = 'not assigned yet'
-        self.children = 'not assigned yet'
-        self.ancestors = 'not assigned yet'
-        self.descendants = 'not assigned yet'
-        self.graph_nodes = 'not assigned yet'
-        self.graph_fill = False
-        self.ontology = def_split[1].split('_')[0]
-        if self.label == '':
-            self._get_label()
-
-    def _api_results(self, input_list, return_list):
-        '''Ignore obsolete terms, not currently checking for \'term_replaced_by\''''
-        for x_term in input_list:
-            if x_term['is_obsolete']:
-                continue
-            new_term = x_term['label'] + ':' + x_term['short_form']
-            return_list.append(Ontology_accession.make_instance(new_term))
-        return(return_list)
-
-    def _add_edges(self, family_member, family_list, edge_set, round_num):
-        '''Add edges to graph'''
-        if edge_set == []:
-            return(edge_set)
-        elif round_num > 0:
-            for x in family_list:
-                x.get_family(family_member)
-                if family_member == 'parents': # TODO: how get x.family_member to collapse code
-                    if x.parents == ['none found']:
-                        continue
-                    if len(x.parents) > 5:
-                        time.sleep(0.05)
-                    new_edges = [(y._graph_label(),x._graph_label()) for y in x.parents]
-                    edge_set = edge_set + [z for z in new_edges if z not in edge_set]
-                    edge_set = x._add_edges(family_member, x.parents, edge_set, round_num-1)
-                elif family_member == 'children':
-                    if x.children == ['none found']:
-                        continue
-                    if len(x.children) > 5:
-                        time.sleep(0.05)
-                    new_edges = [(x._graph_label(),y._graph_label()) for y in x.children]
-                    edge_set = edge_set + [z for z in new_edges if z not in edge_set]
-                    edge_set = x._add_edges(family_member, x.children, edge_set, round_num-1)
-        return(edge_set)
-
-    def _draw_graph(self, o_file, node_color, edge_color):
-        '''Draw and save the graph'''
-        ontol_graph = pgv.AGraph(name='ontology_graph')
-        ontol_graph.add_node(self._graph_label())
-        for x in self.graph_nodes:
-            ontol_graph.add_edge(x[0], x[1])
-        ontol_graph.node_attr.update(shape='box',
-                                     style='rounded,filled',
-                                     fillcolor='lightgrey',
-                                     color=node_color)
-        ontol_graph.edge_attr.update(shape='normal',
-                                     color=edge_color,
-                                     dir='back')
-        ontol_graph.get_node(self._graph_label()).attr.update(fillcolor='lightblue')
-        # TODO: determine best algorithm: neato, fdp, nop, twopi; tried circo; not dot, sfdp
-        ontol_graph.draw(o_file, prog='twopi')
-
-    def _expand_edge(self, family_member, family_list, edge_set, old_set='', stop_terms=False):
-        '''Add edges to graph'''
-        while old_set != edge_set:
-            old_set = copy.deepcopy(edge_set)
-        for x in family_list:
-            if x == 'none found':
-                break
-            if type(stop_terms) == list:
-                if x in stop_terms:
-                    break
-            x.get_family(family_member)
-            if family_member == 'parents': # TODO: how get x.family_member to collapse code
-                if x.parents == ['none found']:
-                    continue
-                if len(x.parents) > 5:
-                    time.sleep(0.05)
-                new_edges = [(y._graph_label(),x._graph_label()) for y in x.parents]
-                edge_set = edge_set + [z for z in new_edges if z not in edge_set]
-                edge_set = x._expand_edge(family_member,x.parents,edge_set,old_set,stop_terms)
-            elif family_member == 'children':
-                if x.children == ['none found']:
-                    continue
-                if len(x.children) > 5:
-                    time.sleep(0.05)
-                new_edges = [(x._graph_label(),y._graph_label()) for y in x.children]
-                edge_set = edge_set + [z for z in new_edges if z not in edge_set]
-                edge_set = x._expand_edge(family_member,x.children,edge_set,old_set,stop_terms)
-        return(edge_set)
-
-    def _get_label(self):
-        '''Retrieve definition is correct for an id; updates instance'''
-        query_url = 'http://www.ebi.ac.uk/ols/api/terms?obo_id={}'.format(self.id)
-        ols_resp = self._get_request(query_url)
-        if ols_resp is None:
-            logging.warning(f'Did not retrieve PURL for {self.id}')
-            self.label = 'unk'
-            return
-        try:
-            self.label = ols_resp.json()['_embedded']['terms'][0]['label']
-        except(KeyError):
-            logging.warning(f'Did not find label for {self.id} in OLS')
-            self.label = 'unk'
-        except json.decoder.JSONDecodeError as err:
-            time.sleep(0.05)
-            self._get_label()
-
-    def _get_request(self, request_url, max_retries=5):
-        '''Retrieve URL'''
-        while max_retries > 0:
-            try:
-                return(requests.get(request_url))
-            except:
-                time.sleep(0.05)
-            max_retries -= 1
-        return(None)
-
-    def _graph_label(self):
-        '''Format a graph label'''
-        return(self.id+'\\n'+self.label)
-
-    def _next_page(self, url_link, return_list):
-        '''Get next page of search results'''
-        next_resp = self._get_request(url_link)
-        if next_resp is None:
-            logging.warning(f'Did not retrieve URL for {url_link} during API search')
-            return(False, return_list)
-        else:
-            try:
-                next_link = next_resp.json()['_links']['next']['href']
-            except(KeyError):
-                next_link = False
-            return_list = self._api_results(next_resp.json()['_embedded']['terms'], return_list)
-        return(next_link, return_list)
-
-    def check_label(self):
-        '''Check if given definition is correct for an id; returns Boolean or str `unk`'''
-        self._get_label()
-        if self.label != 'unk':
-            return(ols_resp.json()['_embedded']['terms'][0]['label'] == self.label)
-        else:
-            return(self.label)
-
-    def get_family(self, family_member):
-        '''Returns list of parents, ancestors, children or descendants'''
-        if family_member == 'parents' and self.parents != 'not assigned yet':
-            return(self.parents)
-        elif family_member == 'children' and self.children != 'not assigned yet': 
-            return(self.children)
-        elif family_member == 'ancestors' and self.ancestors != 'not assigned yet': 
-            return(self.ancestors)
-        elif family_member == 'descendants' and self.descendants != 'not assigned yet': 
-            return(self.descendants)
-
-        if self.id.split(':')[0].lower() == 'gaz':
-            query_url = 'https://www.ebi.ac.uk/ols/api/ontologies/gaz/terms?iri='
-            query_url += 'http://purl.obolibrary.org/obo/' + self.id.replace(':','_')
-            ols_resp = self._get_request(query_url)
-            qry_url = ols_resp.json()['_embedded']['terms'][0]['_links']\
-                                     ['hierarchical'+family_member.title()]['href']
-        else:
-            query_url = 'http://www.ebi.ac.uk/ols/api/ontologies/{}/{}?id={}'
-            qry_url = query_url.format(self.id.split(':')[0].lower(),family_member,self.id)
-
-        ols_resp = self._get_request(qry_url)
-        if ols_resp is None:
-            logging.warning(f'Did not get URL for {url_link} during search for {family_member}')
-            result_list = ['none found']
-        elif ols_resp.status_code > 200:
-            result_list = ['none found']
-        elif ols_resp.json()['page']['totalElements'] > 0:
-            result_list = self._api_results(ols_resp.json()['_embedded']['terms'], [])
-            if ols_resp.json()['page']['totalPages'] > 1:
-                next_url = ols_resp.json()['_links']['next']['href']
-                while next_url:
-                    next_url,result_list = self._next_page(next_url,result_list)
-        else:
-            result_list = ['none found']
-
-        if family_member == 'parents':
-            self.parents = list(set(result_list))
-        elif family_member == 'children':
-            self.children = list(set(result_list))
-        elif family_member == 'ancestors':
-            self.ancestors = list(set(result_list))
-        elif family_member == 'descendants':
-            self.descendants = list(set(result_list))
-        return(result_list)
-
-    def bin_term(self, bin_package):
-        '''Categorize term into given bins as Ontology_package'''
-        term_bins = []
-        self.get_family('ancestors')
-        if self.ancestors == ['none found']:
-            ancestor_labels = [x.label + ':' + x.id.replace(':','_') for x in [self]]
-        else:
-            ancestor_labels = [x.label+':'+x.id.replace(':','_') for x in [self]+self.ancestors]
-        return([x for x in ancestor_labels if x in bin_package.ontologies])
-
-    def visualize_term(self, o_file, node_color='black', edge_color='black',
-                       fill_out=False, stop_terms=False, draw_graph=True):
-        '''Visualize one term'''
-        if self.graph_nodes!='not assigned yet' and self.graph_fill==fill_out:
-            if draw_graph:
-                self._draw_graph(o_file, node_color, edge_color)
-        else:
-            self.get_family('parents')
-            self.get_family('children')
-            edge_set1,edge_set2 = [],[]
-            if self.parents != ['none found']:
-                edge_set1 = [(x._graph_label(),self._graph_label()) for x in self.parents]
-            if self.children != ['none found']:
-                edge_set2 = [(self._graph_label(),x._graph_label()) for x in self.children]
-            if type(fill_out) == int:
-                edge_set1 = self._add_edges('parents', self.parents, edge_set1, fill_out-1)
-                edge_set2 = self._add_edges('children', self.children, edge_set2, fill_out-1)
-            elif fill_out==True:
-                edge_set1 = self._expand_edge('parents',self.parents,edge_set1,'',stop_terms)
-                edge_set2 = self._expand_edge('children',self.children,edge_set2,'',stop_terms)
-            self.graph_nodes = list(set(edge_set1+edge_set2))
-            if draw_graph:
-                self._draw_graph(o_file, node_color, edge_color)
-
-
-class Ontology_package:
-    '''Associate or package Ontology_accession objects together'''
-    def __init__(self, package_label, ontol_list):
-        self.label = package_label
-        self.ontologies = ontol_list
-        self.bins = []
-        self.lcp = 'not assigned yet'
-        self.hcc = 'not assigned yet'
-        self._lcp_state = (True,[])
-        self._hcc_state = (True,[])
-        self._bin_state = []
-        self.graph_nodes = 'not assigned yet'
-        self.graph_state = False
-
-    def _common_family(self,family_member,incl_terms,excl_terms):
-        '''Find common family members'''
-        family_candidates = {}
-        for ontol_term in [x for x in self.ontologies if x.id not in excl_terms]:
-            family_candidates[ontol_term] = ontol_term.get_family(family_member)
-        common_members = self._common_list(family_candidates, incl_terms)
-        while common_members == []:
-            for ontol_term in [x for x in self.ontologies if x.id not in excl_terms]:
-                if len(self.ontologies) > 30:
-                    time.sleep(0.05)
-                original_list = list(family_candidates[ontol_term])
-                for family_ontol in original_list:
-                    if len(original_list) > 30:
-                        time.sleep(0.05)
-                    try:
-                        family_candidates[ontol_term].extend(\
-                                                      family_ontol.get_family(family_member))
-                    except(AttributeError):
-                        family_candidates[ontol_term].extend(['none found'])
-        return(common_members)
-
-    def _common_list(self, input_dic, incl_terms):
-        '''Compare input dictionary keys and list'''
-        term_lists = []
-        for ontol_key in input_dic:
-            append_list = [ontol_key]
-            for ontol_val in input_dic[ontol_key]:
-                append_list.append(ontol_val)
-            term_lists.append(append_list)
-        common_set = set.intersection(*map(set, term_lists))
-        if incl_terms:
-          common_keys = []
-          for ontol_acc in common_set:
-              if ontol_acc in input_dic.keys():
-                  common_keys.append(ontol_acc)
-              if common_keys != []:
-                  return(common_keys)
-        return(list(common_set - set(input_dic.keys())))
-
-    def _draw_graph(self, o_file, node_color, edge_color, show_lcp, show_hcc):
-        '''Draw and save graph'''
-        ontol_graph = pgv.AGraph(name='ontology_graph')
-        for x in self.ontologies:
-            ontol_graph.add_node(x._graph_label())
-        for x in self.graph_nodes:
-            ontol_graph.add_edge(x[0], x[1])
-        ontol_graph.node_attr.update(shape='box', style='rounded,filled',
-                                     fillcolor='lightgrey', color=node_color)
-        ontol_graph.edge_attr.update(shape='normal', color=edge_color, dir='back')
-        if show_lcp:
-            for x in self.lcp:
-                ontol_graph.get_node(x._graph_label()).attr.update(fillcolor='beige')
-        if show_hcc:
-            for x in self.hcc:
-                ontol_graph.get_node(x._graph_label()).attr.update(fillcolor='beige')
-        for x in self.ontologies:
-            ontol_graph.get_node(x._graph_label()).attr.update(fillcolor='lightblue')
-        ontol_graph.draw(o_file,prog='dot')
-
-    def _list_hierarchy(self, input_list, input_position):
-        '''Get lowest or highest terms'''
-        if input_list == ['none found']:
-            return(input_list)
-        family_lists = {}
-        for input_term in input_list:
-            if len(input_list) > 30: time.sleep(0.05)
-            if input_position == 'lowest':
-                if input_term == 'none found':
-                    family_list = 'none found'
-                else:
-                    family_list = input_term.get_family('ancestors')
-            elif input_position == 'highest':
-                if input_term == 'none found':
-                    family_list = 'none found'
-                else:
-                    family_list = input_term.get_family('descendants')
-            family_lists[input_term] = family_list
-        while True:
-            remove_terms = []
-            for input_term in input_list:
-                if [True for f_l in family_lists if input_term in family_lists[f_l]] != []:
-                    del family_lists[input_term]
-                    remove_terms.append(input_term)
-            if remove_terms != []:
-                for x_term in remove_terms:
-                    input_list.remove(x_term)
-            else:
-                break
-        return(input_list)
-
-    def _trim_tips(self):
-        '''Remove descendants of self.ontologies and parents of self.lcp'''
-        tip_nodes = [x._graph_label() for x in self.ontologies] +\
-                    [x._graph_label() for x in self.lcp]
-        old_nodes = []
-        while old_nodes != self.graph_nodes:
-            old_nodes = self.graph_nodes
-            right_nodes = set()
-            left_nodes = set()
-            for x in self.graph_nodes:
-                left_nodes.add(x[0])
-                right_nodes.add(x[1])
-            top_nodes = [x for x in left_nodes.difference(right_nodes) if x not in tip_nodes]
-            bot_nodes = [x for x in right_nodes.difference(left_nodes) if x not in tip_nodes]
-            self.graph_nodes = [x for x in self.graph_nodes if x[0] not in top_nodes]
-            self.graph_nodes = [x for x in self.graph_nodes if x[1] not in bot_nodes]
-
-    def get_lcp(self, incl_terms=True, excl_terms=[]): # TODO: missing excl_terms
-        '''Find lowest common parent(s); can include input terms as lcp,
-           exclude terms by obo id; saves results in lcp attribute'''
-        if self._lcp_state == (incl_terms, excl_terms):
-            if self.lcp != 'not assigned yet':
-                return
-        common_members = self._common_family('parents',incl_terms, excl_terms)
-        common_members = self._list_hierarchy(common_members, 'lowest')
-        if common_members != []:
-            self.lcp = common_members
-            self._lcp_state = (incl_terms, excl_terms)
-
-    def get_hcc(self, incl_terms=True, excl_terms=[]):
-        '''Get highest common child(ren); can include input terms as hcc;
-           exclude terms by obo id; saves results in hcc attribute'''
-        if self._hcc_state == (incl_terms, excl_terms):
-            if self.hcc != 'not assigned yet':
-                return
-        common_members = self._common_family('children', incl_terms, excl_terms)
-        common_members = self._list_hierarchy(common_members, 'highest')
-        if common_members != []:
-            self.hcc = common_members
-            self._hcc_state = (incl_terms, excl_terms)
-
-    def set_lcp(self, lcp_acc, incl_terms=True, excl_terms=[]):
-        self.lcp = lcp_acc
-        self._lcp_state = (incl_terms, excl_terms)
-
-    def set_hcc(self, hcc_acc, incl_terms=True, excl_terms=[]):
-        self.hcc = hcc_acc
-        self._hcc_state = (incl_terms, excl_terms)
-
-    def bin_terms(self, bin_package):
-        '''Categorize terms by those in Ontology_package; saves results in bins attribute'''
-        if self._bin_state == bin_package:
-            return
-        package_bins = []
-        for x in self.ontologies:
-            package_bins.extend(x.bin_term(bin_package))
-        self.bins = list(set(package_bins))
-
-    def visualize_terms(self, o_file, fill_out=False, show_lcp=False, show_hcc=False,
-                                      node_color='black', edge_color='black',
-                                      lcp_stop=False, hcc_stop=False, trim_nodes=False):
-        '''Visualize terms'''
-        if self.graph_nodes=='not assigned yet' or self.graph_fill!=fill_out:
-            self.graph_nodes = []
-        for x in self.ontologies:
-            if lcp_stop and not hcc_stop:
-                if x in self.lcp:
-                    continue
-                x.visualize_term(o_file, fill_out=fill_out,
-                                 stop_terms=self.lcp, draw_graph=False)
-            elif hcc_stop and not lcp_stop:
-                if x in self.hcc:
-                    continue
-                x.visualize_term(o_file, fill_out=fill_out, 
-                                 stop_terms=self.hcc, draw_graph=False)
-            elif hcc_stop and lcp_stop:
-                if x in self.lcp+self.hcc:
-                    continue
-                x.visualize_term(o_file, fill_out=fill_out,
-                                 stop_terms=self.lcp+self.hcc, draw_graph=False)
-            else:
-                x.visualize_term(o_file, fill_out=fill_out, draw_graph=False)
-            self.graph_nodes.extend([z for z in x.graph_nodes if z not in self.graph_nodes])
-        if trim_nodes:
-            self._trim_tips()
-        if len(self.graph_nodes) > 150:
-            edge_string = 'Parent node\tChild node'
-            for edge_tuple in self.graph_nodes:
-                edge_string += '\n'+'\t'.join(edge_tuple)
-            logging.info(f'Not drawing graph with {len(self.graph_nodes)} edges:\
-                           \n\n{edge_string}\n')
-        else:
-            self._draw_graph(o_file,node_color,edge_color,show_lcp,show_hcc)