Add plant_pol_kato

entries/plant_pol_kato/__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 *
+from openpyxl import load_workbook
+import pandas
+import shutil
+import subprocess
+import tempfile
+
+title = "Kato plant-pollinator web"
+description = """A bipartite network of plants and pollinators from Kyoto University Forest of Ashu, Japan, from 1984 to 1987. Edge weights represent frequency of interactions[^icon]
+[^icon]: Description obtained from the [ICON](https://icon.colorado.edu) project."""
+tags = ['Biological', 'Food web', 'Weighted']
+url = 'https://iwdb.nceas.ucsb.edu/html/kato_1990.html'
+citation = [('M. Kato et al., "Insect-flower relationship in the primary beech forest of Ashu, Kyoto: an overview of the flowering phenology and seasonal pattern of insect visits." Contr. Biol. Lab. Kyoto Univ. 27, 309-375 (1990)', 'http://www.researchgate.net/publication/236969168_Insect-flower_relationship_in_the_primary_beech_forest_of_Ashu_Kyoto_an_overview_of_the_flowering_phenology_and_the_seasonal_pattern_of_insect_visits')]
+icon_hash = '56a85c8e26855e083a2f7900'
+ustream_license = None
+upstream_prefix = 'https://iwdb.nceas.ucsb.edu/data/plant_pollinator/excel'
+files = [('kato_et_al_1990.xls', None, None)]
+
+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, "rb")) for fn in fnames]
+            with tempfile.TemporaryDirectory(dir="./cache/temp") as tdir:
+                with open(f"{tdir}/dump.xls", "wb") as fw:
+                    shutil.copyfileobj(fs[0], fw)
+                subprocess.run(["localc", "--convert-to", "xlsx",
+                                f"dump.xls"], cwd=tdir, check=True)
+                wb = load_workbook(f"{tdir}/dump.xlsx", read_only=True)
+
+            g = Graph(directed=False)
+            g.vp.idx = g.new_vp("int")
+            g.vp.pollinator = g.new_vp("bool")
+            g.ep.count = g.new_ep("int")
+
+            def add_bip_edges(m):
+                plts = {}
+                pols = {}
+                for i in range(1, m.shape[0]):
+                    v = g.add_vertex()
+                    g.vp.pollinator[v] = True
+                    pols[m[i,0]] = v
+                    g.vp.idx[v] = m[i,0]
+
+                    for j in range(1, m.shape[1]):
+                        u = plts.get(m[0, j], None)
+                        if u is None:
+                            u = g.add_vertex()
+                            g.vp.pollinator[u] = False
+                            plts[m[0, j]] = u
+                            g.vp.idx[u] = m[0, j]
+
+                        if m[i,j] is None:
+                            continue
+                        if numpy.isnan(float(m[i,j])):
+                            continue
+                        x = int(m[i, j])
+                        if x > 0:
+                            e = g.add_edge(v, u)
+                            g.ep.count[e] = x
+                return plts, pols
+
+            m = pandas.DataFrame(wb["matr"].values).values
+            plts, pols = add_bip_edges(m[2:,1:])
+
+            for ti, (idxs, vals) in enumerate([(m[2:,1], m[2:,0]),
+                                               (m[2,1:].T, m[0,1:].T),
+                                               (m[2,1:].T, m[1,1:].T)]):
+                vs = pols if ti == 0 else plts
+                p = vals[0]
+                if p not in g.vp:
+                    g.vp[p] = g.new_vp("string")
+                for i in range(1, len(vals)):
+                    idx = idxs[i]
+                    if idx is None:
+                        continue
+                    g.vp[p][vs[idx]] = vals[i]
+        yield alt, g