added phylogeny

grambank/__init__.py

@@ -52,6 +52,7 @@ def main(global_config, **settings):
     config = Configurator(settings=settings)
     config.include('clldmpg')
     config.include('clld_glottologfamily_plugin')
+    config.include('clld_phylogeny_plugin')
 
     config.registry.settings['home_comp'].append('coverage')
     config.add_route('coverage', pattern='/coverage')

grambank/adapters.py

@@ -4,6 +4,14 @@
 from clld.web.adapters.geojson import GeoJsonParameter
 from clld.db.meta import DBSession
 from clld.db.models.common import ValueSet, Value, DomainElement
+from clld_phylogeny_plugin.interfaces import ITree
+from clld_phylogeny_plugin.tree import Tree
+
+
+class GrambankTree(Tree):
+    def get_marker(self, valueset):
+        res = valueset.values[0].domainelement.jsondata['icon']
+        return res[0], '#' + res[1:]
 
 
 class GrambankGeoJsonParameter(GeoJsonParameter):
@@ -21,6 +29,7 @@ def feature_iterator(self, ctx, req):
 
 
 def includeme(config):
+    config.registry.registerUtility(GrambankTree, ITree)
     config.register_adapter(
         GrambankGeoJsonParameter,
         interfaces.IParameter,

grambank/scripts/global_tree.py

@@ -0,0 +1,53 @@
+# coding: utf8
+"""
+Recreate glottolog data files from the current version published at http://glottolog.org
+"""
+from __future__ import unicode_literals
+import re
+
+from ete3 import Tree
+from pyglottolog.api import Glottolog
+
+
+def tree(glottocodes, gl_repos):
+    label_pattern = re.compile("'[^\[]+\[([a-z0-9]{4}[0-9]{4})[^']*'")
+
+    def rename(n):
+        n.name = label_pattern.match(n.name).groups()[0]
+        n.length = 1
+
+    glottocodes = set(glottocodes)
+    glottocodes_in_global_tree = set()
+    languoids = {}
+    families = []
+    for lang in Glottolog(gl_repos).languoids():
+        if not lang.lineage:  # a top-level node
+            if not lang.category.startswith('Pseudo '):
+                families.append(lang)
+        languoids[lang.id] = lang
+
+    glob = Tree()
+    glob.name = 'glottolog_global'
+
+    for family in sorted(families):
+        node = family.newick_node(nodes=languoids)
+        node.visit(rename)
+        langs_in_tree = set(n.name for n in node.walk())
+        langs_selected = glottocodes.intersection(langs_in_tree)
+        if not langs_selected:
+            continue
+
+        tree = Tree("({0});".format(node.newick), format=3)
+        tree.name = 'glottolog_{0}'.format(family.id)
+        if family.level.name == 'family':
+            tree.prune([n.encode('ascii') for n in langs_selected])
+            glottocodes_in_global_tree = glottocodes_in_global_tree.union(
+                set(n.name for n in tree.traverse()))
+        else:
+            glottocodes_in_global_tree = glottocodes_in_global_tree.union(langs_in_tree)
+        glob.add_child(tree)
+
+    # global
+    nodes = glottocodes_in_global_tree.intersection(glottocodes)
+    glob.prune([n.encode('ascii') for n in nodes])
+    return glob.write(format=9), nodes

grambank/scripts/initializedb.py

@@ -6,15 +6,18 @@
 from clld.db.meta import DBSession
 from clld.db.models import common
 from clld.db.util import compute_language_sources
+from clldutils.path import read_text, Path
 from clld_glottologfamily_plugin.models import Family
 from clld_glottologfamily_plugin.util import load_families
+from clld_phylogeny_plugin.models import Phylogeny, LanguageTreeLabel, TreeLabel
 from pyglottolog.api import Glottolog
 
 import grambank
 from grambank.scripts.util import (
     import_gb20_features, import_cldf, get_clf_paths, get_names,
     GLOTTOLOG_REPOS, GRAMBANK_REPOS,
 )
+from grambank.scripts.global_tree import tree
 
 from stats_util import grp, grp2, feature_stability, feature_incidence, feature_dependencies, feature_diachronic_dependencies, dependencies_graph #, havdist, deep_families
 from grambank.models import Dependency, Transition, Stability, Feature, GrambankLanguage #, DeepFamily, Support, HasSupport
@@ -99,6 +102,15 @@ def checkpoint(s, msg=None):
         print(n - s, msg or '')
         return n
 
+    newick, _ = tree([l.id for l in DBSession.query(common.Language)], GLOTTOLOG_REPOS)
+    phylo = Phylogeny(
+        id='p',
+        name='glottolog global tree',
+        newick=newick)
+    for l in DBSession.query(common.Language):
+        LanguageTreeLabel(
+            language=l, treelabel=TreeLabel(id=l.id, name=l.id, phylogeny=phylo))
+    DBSession.add(phylo)
 
     dump()
 

grambank/templates/phylogeny/detail_html.mako

@@ -0,0 +1,76 @@
+<%inherit file="../${context.get('request').registry.settings.get('clld.app_template', 'app.mako')}"/>
+<%namespace name="util" file="../util.mako"/>
+<%! active_menu_item = "phylogenys" %>
+<%block name="title">Phylogeny ${ctx.name}</%block>
+<%! from clld_phylogeny_plugin.tree import Tree %>
+<%! from clld_phylogeny_plugin.interfaces import ITree %>
+<% tree = req.registry.queryUtility(ITree)(ctx, req) %>
+
+<%block name="head">
+    ${Tree.head(req)|n}
+    <link href="${request.static_url('clld:web/static/css/select2.css')}"
+          rel="stylesheet">
+    <script src="${request.static_url('clld:web/static/js/select2.js')}"></script>
+</%block>
+
+<div class="row-fluid">
+    <div class="span8">
+        <h2>${title()}</h2>
+
+        % if ctx.description:
+            <div class="alert alert-info">${ctx.description}</div>
+        % endif
+        % if tree.parameters:
+            <div class="alert alert-success">
+                The tree has been pruned to only contain leaf nodes with values for
+                the selected variables. For the full tree click
+                <a href="${req.resource_url(ctx)}">here</a>.
+            </div>
+        % endif
+        <div>
+            <form action="${req.resource_url(ctx)}">
+                <fieldset>
+                    <p>
+                        You may combine these ${_('Parameters').lower()} with another
+                        one.
+                        Start typing the ${_('Parameter').lower()} name or number in
+                        the field below.
+                    </p>
+                    ${ms(request, combination=tree).render()|n}
+                    <button class="btn" type="submit">Submit</button>
+                </fieldset>
+            </form>
+        </div>
+        ${tree.render()}
+    </div>
+
+    <div class="span4">
+        <% ca = h.get_adapter(h.interfaces.IRepresentation, ctx, req, ext='description.html') %>
+        % if ca:
+            <div class="well well-small">
+                ${ca.render(ctx, req)|n}
+            </div>
+        % endif
+        % if tree.parameters:
+            <div class="accordion" id="values-acc" data-spy="affix" data-offset-top="0"
+                 style="margin-right: 10px;">
+                % for parameter in tree.parameters:
+                    <div class="accordion-group">
+                        <div class="accordion-heading">
+                            <a class="accordion-toggle" data-toggle="collapse"
+                               data-parent="#values-acc" href="#acc-${parameter.id}">
+                                ${parameter.name}
+                            </a>
+                        </div>
+                        <div id="acc-${parameter.id}"
+                             class="accordion-body collapse${' in' if loop.first else ''}">
+                            <div class="accordion-inner">
+                                ${h.get_adapter(h.interfaces.IRepresentation, parameter, req, ext='valuetable.html').render(parameter, req)|n}
+                            </div>
+                        </div>
+                    </div>
+                % endfor
+            </div>
+        % endif
+    </div>
+</div>

grambank/util.py

@@ -20,6 +20,7 @@
 from clld_glottologfamily_plugin.models import Family
 from clld.web.icon import SHAPES
 from clld.interfaces import IIcon
+from clld.web.util.multiselect import CombinationMultiSelect
 
 from grambank.maps import DeepFamilyMap
 from grambank.models import Dependency, Transition, GrambankLanguage
@@ -30,6 +31,12 @@
 ]
 
 
+def phylogeny_detail_html(request=None, context=None, **kw):
+    return {
+        'ms': CombinationMultiSelect,
+    }
+
+
 def table_incidence(*ds):
     values = set([x for d in ds for x in d.keys()])
     totals = [sum(d.values()) for d in ds]

setup.py

@@ -23,6 +23,7 @@
         'clld~=4.0',
         'clldmpg~=3.1.0',
         'clld-glottologfamily-plugin>=2.0.0',
+        'clld-phylogeny-plugin>=1.1.0',
         'pyglottolog>=0.3.1',
         'sqlalchemy',
         'waitress',