Add nematode_mammal

entries/nematode_mammal/__init__.py

+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2020 Tiago de Paula Peixoto <tiago@skewed.de>
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU Affero General Public License as published by the Free
+# Software Foundation, either version 3 of the License, or (at your option) any
+# later version.
+#
+# This program 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 Affero General Public License for more
+# details.
+#
+# You should have received a copy of the GNU Affero General Public License along
+# with this program.  If not, see <http://www.gnu.org/licenses/>.
+
+from .. import *
+
+title = "Global nematode–mammal interactions (2018)"
+description = """A global interaction web of interactions between nematodes and their host mammal species, extracted from the helminthR package and dataset. Nodes are annotated with species-level information.[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+tags = ['Biological', 'Food web', 'Unweighted', 'Metadata']
+url = 'https://github.com/cjcarlson/brevity/tree/master/Figure%201%20Demo%20Networks'
+citation = [('T. Dallas et al. "Gauging support for macroecological patterns in helminth parasites." Glob. Ecol. Biogeogr. 27, 1437–1447 (2018)', 'https://onlinelibrary.wiley.com/doi/full/10.1111/geb.12819')]
+icon_hash = '5d0d28f751da6551647736a8'
+ustream_license = None
+upstream_prefix = 'https://raw.githubusercontent.com/cjcarlson/brevity/master/Figure%201%20Demo%20Networks'
+files = [('helminths.csv', None, 'csv')]
+
+def fetch_upstream(force=False):
+    return fetch_upstream_files(__name__.split(".")[-1], upstream_prefix, files,
+                                force)
+
+@cache_network()
+@coerce_props()
+@annotate()
+def parse(alts=None):
+    global files
+    name = __name__.split(".")[-1]
+    for fnames, alt, fmt in files:
+        if alts is not None and alt not in alts:
+            continue
+        if isinstance(fnames, str):
+            fnames = [fnames]
+        with ExitStack() as stack:
+            fs = [stack.enter_context(open_upstream_file(name, fn, "r", encoding="ISO-8859-1")) for fn in fnames]
+
+            g = Graph(directed=False)
+
+            g.vp.name = g.new_vp("string")
+            g.vp.full_name = g.new_vp("string")
+            g.vp.locality = g.new_vp("string")
+            g.vp.group = g.new_vp("string")
+            g.vp.is_host = g.new_vp("bool")
+
+            hs = {}
+            ps = {}
+            reader = csv.reader(fs[0])
+
+            next(reader)
+            for row in reader:
+                s = hs.get(row[1], None)
+                if s is None:
+                    s = hs[row[1]] = g.add_vertex()
+                    g.vp.name[s] = row[1]
+                t = ps.get(row[2], None)
+                if t is None:
+                    t = ps[row[2]] = g.add_vertex()
+                    g.vp.name[t] = row[2]
+                g.add_edge(s, t)
+                g.vp.is_host[s] = True
+                g.vp.full_name[s] = row[3]
+                g.vp.group[s] = row[4]
+                g.vp.locality[s] = row[5]
+                g.vp.group[t] = row[6]
+
+        yield alt, g