History of mangal
The changes to the source code of this entry in the repository, newest first, each with the differences it made to the entry's files. They are also listed on GitLab.
[entries] New entry: mangal 477f0fd
diff --git a/entries/mangal/__init__.py b/entries/mangal/__init__.py
new file mode 100644
index 0000000..ef3a357
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+++ b/entries/mangal/__init__.py
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+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# Copyright (C) 2020-2026 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 collections import defaultdict
+
+title = "Mangal ecological interaction networks"
+description = """A collection of ecological interaction networks from Mangal, a database and web service of ecological networks developed by Poisot, Gravel and colleagues (Poisot et al. 2016). Mangal gathers published networks of interactions between organisms, such as food webs (predation, herbivory, detritivory, scavenging), plant-pollinator and seed-dispersal networks (mutualism), and host-parasite networks, from many sources (most of them digitized from the literature, some of them from other collections such as the Interaction Web Database), and describes them in a common format, with the taxa of the nodes matched to taxonomic databases. Each Mangal network is a network of this entry (1,481 networks), named as in Mangal; they come from 175 data sets, and a data set can contain many networks, e.g. one per site or sampling date (e.g. the 783 small host-parasitoid networks of `kolpelke_2007`).
+
+Nodes are taxa (species or higher taxonomic groups), populations or individuals, as given by the authors, and edges are interactions between them. An interaction can be directed (with the direction recorded in Mangal), undirected, or of unknown direction; a network is directed if any of its interactions is directed. Interactions have a type (e.g. `predation`, `mutualism`, `herbivory`, `parasitism`) and a value with an attribute that says what the value measures: most are `presence/absence` (value 1), and the others are, e.g., numbers of visits of pollinators, frequencies or diet fractions (some networks are therefore weighted). The 180 interactions recorded as absent (`presence/absence` with value 0, in four networks of `rejmanek_stary_1979`) are left out, as are the six networks of `kolpelke_2007` that have no interactions at all. The data were retrieved from the Mangal web service (API version 2) in October 2026; the latest records of the database date from November 2021.
+
+Many of these networks are also part of the entries `iwdb` and `web_of_life`, from other collections.
+
+The networks have the following properties:
+
+- `name`: the name of the node as given by the original authors; `node_id`: the Mangal node id; `node_level`: whether the node is a `taxon`, a `population` or an `individual`; `taxon`: the name of the taxon matched in Mangal (empty if not matched); `rank`: its taxonomic rank (e.g. `species`, `genus`); `ncbi`, `tsn`, `gbif`, `eol`, `bold`: its identifiers in the NCBI Taxonomy, ITIS, GBIF, the Encyclopedia of Life and BOLD (-1 if unknown); `col`: its identifier in the Catalogue of Life.
+- Edge `interaction_id`: the Mangal interaction id; `type`: the type of interaction; `method`: the method by which the interaction was recorded (e.g. `field observations`, `gut content`, `literature`); `direction`: `directed`, `undirected` or `unknown`; `attribute`: what the value measures (e.g. `presence/absence`, `number of visit by a pollinator`); `value`: the value of the interaction (NaN if not given); `date`: the date of the observation (as given in Mangal; often the date of the whole network).
+- Network properties: `network_id`, `network_description` and `network_date`: the id, description and date of the Mangal network; `geometry`: its location, as a GeoJSON point or polygon (longitude, latitude), if known; `all_interactions`: whether absences of interactions were recorded as well; `dataset` and `dataset_description`: the Mangal data set it belongs to; `reference_doi`, `reference_bibtex`: the reference of the original publication; `data_url`: the address of the original data, if any."""
+tags = ['Biological', 'Food web', 'Unweighted', 'Weighted', 'Metadata']
+url = 'https://mangal.io/'
+citation = [('T. Poisot, B. Baiser, J. A. Dunne, S. Kéfi, F. Massol, N. Mouquet, T. N. Romanuk, D. B. Stouffer, S. A. Wood, D. Gravel, "mangal - making ecological network analysis simple." Ecography 39, 384-390 (2016)',
+ 'https://doi.org/10.1111/ecog.00976')]
+icon_hash = None
+upstream_license = None
+
+# The data are served by the REST API of Mangal, read in pages of 5000
+# records sorted by id; the numbers of records (as of October 2026) are
+# pinned, and checked when parsing.
+api = 'https://mangal.io/api/v2'
+page_size = 5000
+totals = {'network': 1487, 'dataset': 175, 'reference': 175, 'node': 39939,
+ 'interaction': 145989}
+
+def _pages(kind):
+ return [(f'{kind}_{p:03d}.json',
+ f'{api}/{kind}?count={page_size}&page={p}&sort=id&order=asc')
+ for p in range((totals[kind] + page_size - 1) // page_size)]
+
+upstream_urls = dict(p for kind in totals for p in _pages(kind))
+
+# The names of the networks, sorted by their Mangal ids
+networks = [
+ 'howking_1968_19680601_12', 'witt_1998_19980101_13',
+ 'silva_2002_20000301_15', 'mosquin_martin_1967_19650731_18',
+ 'roberson_1929_18990701_19', 'kaehler_et_al_2005_20020401_23',
+ 'woodwell_1967_19670101_26', 'barret_helenurm_1987_19870101_27',
+ 'copeland_1974_19740101_28', 'kemp_1977_19770101_80',
+ 'bradstreet_1982_19780101_81', 'patten_1979_19780101_82',
+ 'clarke_1967_19650831_83', 'van_es_1967_19750101_84',
+ 'macginitie_1935_19260601_85', 'zetina_2003_20030101_86',
+ 'cruz_2007_20070101_87', 'lancraft_1991_19880620_88',
+ 'lin_2006_20060101_89', 'torres_2013_20130101_91',
+ 'yodzis_1998_19980101_92', 'kremer_1978_19780101_93',
+ 'rosenthal_1974_19670901_94', 'peterson_1979_19721001_95',
+ 'gontikaki_2011_20070501_96', 'christian_1999_19940101_97',
+ 'hiatt_1960_19601001_98', 'landry_1977_19770101_99',
+ 'mackintosh_1967_19450101_100', 'qazim_1970_19700101_101',
+ 'knox_1970_19700101_102', 'parin_1970_19700101_103',
+ 'hogetsu_1979_19790101_889', 'hatanaka_1977_19770101_890',
+ 'thompson_2004_20040101_893', 'petipa_1970_19700101_906',
+ 'petipa_1970_19700101_907', 'lundgren_olesen_2005_20020804_908',
+ 'elberling_olesen_1999_19940823_909', 'brodeur_1992_19810501_918',
+ 'brodeur_1992_19820501_919', 'brodeur_1992_19830501_920',
+ 'brodeur_1992_19840601_921', 'saldanha_1980_19800101_922',
+ 'day_1967_19670101_924', 'yanez_1978_19730901_926',
+ 'yanez_1978_19730901_927', 'varassin_sazima_2012_20010601_928',
+ 'bezerra_2009_20061201_929', 'smith_2007_20070101_930',
+ 'frost_1980_19800101_931', 'olesen_al_2002_19990601_934',
+ 'olesen_al_2002_20000701_935', 'percival_1974_19740101_938',
+ 'fautin_1993_19930101_939', 'mccullen_1993_19930101_940',
+ 'milne_1972_19720101_942', 'milne_1972_19720101_943',
+ 'wheelwringht_1984_19780101_944', 'motten_1982_19820101_945',
+ 'elberling_olesen__946', 'johnston_1956_19560101_947',
+ 'kato_1993_19910901_948', 'arroyo_1982_19810301_949',
+ 'arroyo_1982_19810301_950', 'arroyo_1982_19810301_951',
+ 'kohler_2011_20110101_952', 'kohler_2011_20110101_953',
+ 'kohler_2011_20110101_954', 'olesen__955', 'hadfield_2014_20140201_1007',
+ 'hadfield_2014_20140201_1008', 'hadfield_2014_20140201_1009',
+ 'hadfield_2014_20140201_1010', 'hadfield_2014_20140201_1011',
+ 'hadfield_2014_20140201_1012', 'hadfield_2014_20140201_1013',
+ 'hadfield_2014_20140201_1014', 'hadfield_2014_20140201_1015',
+ 'hadfield_2014_20140201_1016', 'hadfield_2014_20140201_1017',
+ 'hadfield_2014_20140201_1018', 'hadfield_2014_20140201_1019',
+ 'hadfield_2014_20140201_1020', 'dunbar_1953_19530101_1021',
+ 'hadfield_2014_20140201_1022', 'hadfield_2014_20140201_1023',
+ 'hadfield_2014_20140201_1024', 'hadfield_2014_20140201_1025',
+ 'hadfield_2014_20140201_1026', 'hadfield_2014_20140201_1027',
+ 'hadfield_2014_20140201_1028', 'hadfield_2014_20140201_1029',
+ 'hadfield_2014_20140201_1030', 'hadfield_2014_20140201_1031',
+ 'hadfield_2014_20140201_1032', 'hadfield_2014_20140201_1033',
+ 'hadfield_2014_20140201_1034', 'hadfield_2014_20140201_1035',
+ 'hadfield_2014_20140201_1036', 'hadfield_2014_20140201_1037',
+ 'hadfield_2014_20140201_1038', 'hadfield_2014_20140201_1044',
+ 'hadfield_2014_20140201_1045', 'hadfield_2014_20140201_1046',
+ 'hadfield_2014_20140201_1047', 'hadfield_2014_20140201_1048',
+ 'hadfield_2014_20140201_1049', 'hadfield_2014_20140201_1050',
+ 'hadfield_2014_20140201_1051', 'hadfield_2014_20140201_1052',
+ 'hadfield_2014_20140201_1053', 'hadfield_2014_20140201_1054',
+ 'hadfield_2014_20140201_1055', 'hadfield_2014_20140201_1056',
+ 'hadfield_2014_20140201_1057', 'hadfield_2014_20140201_1058',
+ 'hadfield_2014_20140201_1059', 'hadfield_2014_20140201_1060',
+ 'hadfield_2014_20140201_1061', 'hadfield_2014_20140201_1062',
+ 'hadfield_2014_20140201_1063', 'baeta_2011_19930101_1064',
+ 'baeta_2011_19990101_1065', 'baeta_2011_20010101_1066',
+ 'baeta_2011_19930101_1067', 'baeta_2011_19990101_1068',
+ 'baeta_2011_20010101_1069', 'ricciardi_2010_20060701_1070',
+ 'ricciardi_2010_20060701_1071', 'ricciardi_2010_20060701_1072',
+ 'ricciardi_2010_20060701_1073', 'ricciardi_2010_20060701_1074',
+ 'ricciardi_2010_20060701_1075', 'ricciardi_2010_20060701_1076',
+ 'ricciardi_2010_20060701_1077', 'ricciardi_2010_20060701_1078',
+ 'ricciardi_2010_20060701_1079', 'ricciardi_2010_20060701_1080',
+ 'ricciardi_2010_20060701_1081', 'ricciardi_2010_20060701_1082',
+ 'ricciardi_2010_20060701_1083', 'ricciardi_2010_20060701_1084',
+ 'ricciardi_2010_20060701_1085', 'closs_1994_19850501_1089',
+ 'closs_1994_19850501_1090', 'closs_1994_19850501_1091',
+ 'closs_1994_19850901_1092', 'closs_1994_19850901_1093',
+ 'closs_1994_19850901_1094', 'closs_1994_19851201_1095',
+ 'closs_1994_19851201_1096', 'closs_1994_19851201_1097',
+ 'closs_1994_19860301_1098', 'closs_1994_19860301_1099',
+ 'closs_1994_19860301_1100', 'angelini_2010_20100601_1101',
+ 'bulman_2001_19930701_1102', 'cornejo-donoso_2008_20080101_1103',
+ 'dexter_1947_19330601_1104', 'dexter_1947_19330601_1105',
+ 'dexter_1947_19330601_1106', 'dexter_1947_19330601_1107',
+ 'dexter_1947_19330601_1108', 'douglas_2011_20050421_1112',
+ 'douglas_2011_20060519_1113', 'douglas_2011_20060821_1114',
+ 'filgueira_2011_20000201_1115', 'havens_1992_19840601_1216',
+ 'havens_1992_19840601_1217', 'havens_1992_19840601_1218',
+ 'havens_1992_19840601_1219', 'havens_1992_19840601_1220',
+ 'havens_1992_19840601_1221', 'havens_1992_19840601_1222',
+ 'havens_1992_19840601_1223', 'havens_1992_19840601_1224',
+ 'havens_1992_19840601_1225', 'havens_1992_19840601_1226',
+ 'havens_1992_19840601_1227', 'havens_1992_19840601_1228',
+ 'havens_1992_19840601_1229', 'havens_1992_19840601_1230',
+ 'havens_1992_19840601_1231', 'havens_1992_19840601_1232',
+ 'havens_1992_19840601_1233', 'havens_1992_19840601_1234',
+ 'havens_1992_19840601_1235', 'havens_1992_19840601_1236',
+ 'havens_1992_19840601_1237', 'havens_1992_19840601_1238',
+ 'havens_1992_19840601_1239', 'havens_1992_19840601_1240',
+ 'havens_1992_19840601_1241', 'havens_1992_19840601_1242',
+ 'havens_1992_19840601_1243', 'havens_1992_19840601_1244',
+ 'havens_1992_19840601_1245', 'havens_1992_19840601_1246',
+ 'havens_1992_19840601_1247', 'havens_1992_19840601_1248',
+ 'havens_1992_19840601_1249', 'havens_1992_19840601_1250',
+ 'havens_1992_19840601_1251', 'havens_1992_19840601_1252',
+ 'havens_1992_19840601_1253', 'havens_1992_19840601_1254',
+ 'havens_1992_19840601_1255', 'havens_1992_19840601_1256',
+ 'havens_1992_19840601_1257', 'havens_1992_19840601_1258',
+ 'havens_1992_19840601_1259', 'havens_1992_19840601_1260',
+ 'havens_1992_19840601_1261', 'havens_1992_19840601_1262',
+ 'havens_1992_19840601_1263', 'havens_1992_19840601_1264',
+ 'havens_1992_19840601_1265', 'odum_1975_19750101_1268',
+ 'shushkina_1979_19790101_1280', 'simenstad_1978_19690101_1281',
+ 'simenstad_1978_19690101_1282', 'vinogradov_1978_19740114_1284',
+ 'ponisio_2017_20060101_1285', 'ponisio_2017_20070101_1286',
+ 'ponisio_2017_20080101_1287', 'ponisio_2017_20090101_1288',
+ 'ponisio_2017_20110101_1289', 'ponisio_2017_20120101_1290',
+ 'ponisio_2017_20130101_1291', 'ponisio_2017_20140101_1292',
+ 'ponisio_2017_20090101_1293', 'ponisio_2017_20100101_1294',
+ 'ponisio_2017_20120101_1295', 'ponisio_2017_20130101_1296',
+ 'ponisio_2017_20140101_1297', 'ponisio_2017_20070101_1298',
+ 'ponisio_2017_20080101_1299', 'ponisio_2017_20090101_1300',
+ 'ponisio_2017_20110101_1301', 'ponisio_2017_20120101_1302',
+ 'ponisio_2017_20130101_1303', 'ponisio_2017_20140101_1304',
+ 'ponisio_2017_20060101_1305', 'ponisio_2017_20070101_1306',
+ 'ponisio_2017_20080101_1307', 'ponisio_2017_20090101_1308',
+ 'ponisio_2017_20110101_1309', 'ponisio_2017_20120101_1310',
+ 'ponisio_2017_20130101_1311', 'ponisio_2017_20140101_1312',
+ 'ponisio_2017_20070101_1313', 'ponisio_2017_20080101_1314',
+ 'ponisio_2017_20090101_1315', 'ponisio_2017_20110101_1316',
+ 'ponisio_2017_20120101_1317', 'ponisio_2017_20130101_1318',
+ 'ponisio_2017_20140101_1319', 'ponisio_2017_20060101_1320',
+ 'ponisio_2017_20070101_1321', 'ponisio_2017_20080101_1322',
+ 'ponisio_2017_20090101_1323', 'ponisio_2017_20110101_1324',
+ 'ponisio_2017_20120101_1325', 'ponisio_2017_20130101_1326',
+ 'ponisio_2017_20140101_1327', 'ponisio_2017_20080101_1328',
+ 'ponisio_2017_20090101_1329', 'ponisio_2017_20100101_1330',
+ 'ponisio_2017_20110101_1331', 'ponisio_2017_20120101_1332',
+ 'ponisio_2017_20130101_1333', 'ponisio_2017_20140101_1334',
+ 'ponisio_2017_20070101_1335', 'ponisio_2017_20080101_1336',
+ 'ponisio_2017_20090101_1337', 'ponisio_2017_20110101_1338',
+ 'ponisio_2017_20120101_1339', 'ponisio_2017_20130101_1340',
+ 'ponisio_2017_20140101_1341', 'ponisio_2017_20060101_1342',
+ 'ponisio_2017_20070101_1343', 'ponisio_2017_20080101_1344',
+ 'ponisio_2017_20090101_1345', 'ponisio_2017_20110101_1346',
+ 'ponisio_2017_20130101_1347', 'ponisio_2017_20140101_1348',
+ 'ponisio_2017_20090101_1349', 'ponisio_2017_20110101_1350',
+ 'ponisio_2017_20120101_1351', 'ponisio_2017_20130101_1352',
+ 'ponisio_2017_20140101_1353', 'ponisio_2017_20070101_1354',
+ 'ponisio_2017_20080101_1355', 'ponisio_2017_20090101_1356',
+ 'ponisio_2017_20110101_1357', 'ponisio_2017_20120101_1358',
+ 'ponisio_2017_20130101_1359', 'ponisio_2017_20140101_1360',
+ 'ponisio_2017_20090101_1361', 'ponisio_2017_20100101_1362',
+ 'ponisio_2017_20120101_1363', 'ponisio_2017_20130101_1364',
+ 'ponisio_2017_20140101_1365', 'ponisio_2017_20070101_1366',
+ 'ponisio_2017_20080101_1367', 'ponisio_2017_20090101_1368',
+ 'ponisio_2017_20110101_1369', 'ponisio_2017_20120101_1370',
+ 'ponisio_2017_20130101_1371', 'ponisio_2017_20060101_1372',
+ 'ponisio_2017_20070101_1373', 'ponisio_2017_20080101_1374',
+ 'ponisio_2017_20090101_1375', 'ponisio_2017_20110101_1376',
+ 'ponisio_2017_20120101_1377', 'ponisio_2017_20130101_1378',
+ 'ponisio_2017_20140101_1379', 'ponisio_2017_20100101_1380',
+ 'ponisio_2017_20110101_1381', 'ponisio_2017_20120101_1382',
+ 'ponisio_2017_20130101_1383', 'ponisio_2017_20140101_1384',
+ 'ponisio_2017_20090101_1385', 'ponisio_2017_20100101_1386',
+ 'ponisio_2017_20110101_1387', 'ponisio_2017_20120101_1388',
+ 'ponisio_2017_20130101_1389', 'ponisio_2017_20140101_1390',
+ 'ponisio_2017_20070101_1391', 'ponisio_2017_20080101_1392',
+ 'ponisio_2017_20090101_1393', 'ponisio_2017_20110101_1394',
+ 'ponisio_2017_20120101_1395', 'ponisio_2017_20130101_1396',
+ 'ponisio_2017_20140101_1402', 'ponisio_2017_20070101_1403',
+ 'ponisio_2017_20080101_1404', 'ponisio_2017_20090101_1405',
+ 'ponisio_2017_20110101_1406', 'ponisio_2017_20120101_1407',
+ 'ponisio_2017_20130101_1408', 'ponisio_2017_20140101_1409',
+ 'ponisio_2017_20090101_1410', 'ponisio_2017_20110101_1411',
+ 'ponisio_2017_20120101_1412', 'ponisio_2017_20130101_1413',
+ 'ponisio_2017_20140101_1414', 'ponisio_2017_20060101_1415',
+ 'ponisio_2017_20070101_1416', 'ponisio_2017_20080101_1417',
+ 'ponisio_2017_20090101_1418', 'ponisio_2017_20110101_1419',
+ 'ponisio_2017_20120101_1420', 'ponisio_2017_20130101_1421',
+ 'ponisio_2017_20140101_1422', 'ponisio_2017_20060101_1423',
+ 'ponisio_2017_20070101_1424', 'ponisio_2017_20080101_1425',
+ 'ponisio_2017_20090101_1426', 'ponisio_2017_20110101_1427',
+ 'ponisio_2017_20120101_1428', 'ponisio_2017_20130101_1429',
+ 'ponisio_2017_20140101_1430', 'alcorlo_et_al_2001_19941101_1439',
+ 'alcorlo_et_al_2001_19941101_1440', 'alcorlo_et_al_2001_19960101_1441',
+ 'alcorlo_et_al_2001_19960101_1442', 'allan_1982_19750708_1443',
+ 'angelini_agostinho_2005_19920101_1444',
+ 'angelini_et_al_2006_19880101_1446', 'angelini_et_al_2006_19830101_1447',
+ 'angelini_et_al_2010_20030501_1448', 'beaver_1985__1449',
+ 'beaver_1985__1450', 'beaver_1985__1451', 'beaver_1985__1452',
+ 'beaver_1985__1453', 'bird_1930_19280101_1454', 'bird_1930_19280101_1455',
+ 'bird_1930_19280101_1456', 'bird_1930_19280101_1457',
+ 'carlson_1968_19600614_1458', 'collins_et_al_1976_19720711_1459',
+ 'cornaby_1974_19680208_1460', 'cornaby_1974_19680229_1461',
+ 'cruz_escalona_et_al_2007_19910101_1462', 'edwards_1982_19780501_1463',
+ 'fetahi_et_al_2011_20071001_1464', 'fryer_1959_19550101_1465',
+ 'fryer_1959_19550101_1466', 'fryer_1959_19550101_1467',
+ 'gaedke_straile_1994_19870323_1468', 'hampton_et_al_2011_20040601_1469',
+ 'hildrew_et_al_1985_19740401_1470', 'jiron_cartin_1981_19770101_1471',
+ 'jones_1949_19480324_1472', 'liu_et_al_2007_20040101_1473',
+ 'hopkins_et_al_1993_19830101_1474', 'massana_et_al_1996_19900101_1475',
+ 'menge_et_al_1986_19770101_1476', 'menge_sutherland_1976_19730311_1477',
+ 'menge_sutherland_1976_19730311_1478',
+ 'menge_sutherland_1976_19730311_1479',
+ 'menge_sutherland_1976_19730311_1480', 'mninshall_1967_19630401_1481',
+ 'mohr_1943_19301001_1482', 'morgan_mclusky_1972_19710101_1483',
+ 'niering_1963_19540622_1484', 'nybakken_2001__1485', 'paine_19630601_1486',
+ 'paine_19630601_1487', 'rayner_et_al_2010_20040401_1488',
+ 'rejmanek_stary_1979_19790726_1489', 'rejmanek_stary_1979_19790726_1490',
+ 'rejmanek_stary_1979_19790726_1491', 'rejmanek_stary_1979_19790726_1492',
+ 'robinson_1953_19480101_1493', 'savely_1939_19360901_1494',
+ 'savely_1939_19360901_1495', 'savely_1939_19360901_1496',
+ 'savely_1939_19360901_1497', 'schneider_1997_19850101_1498',
+ 'schoenly_1983_19810601_1499', 'seifert_1976a_19700701_1500',
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+ 'kolpelke_2007_731', 'kolpelke_2007_745', 'kolpelke_2007_574',
+ 'kolpelke_2007_754', 'kolpelke_2007_703', 'kolpelke_2007_722',
+ 'kolpelke_2007_753', 'kolpelke_2007_576', 'kolpelke_2007_577',
+ 'kolpelke_2007_7', 'kolpelke_2007_8', 'kolpelke_2007_637',
+ 'kolpelke_2007_643', 'kolpelke_2007_644', 'kolpelke_2007_661',
+ 'kolpelke_2007_6', 'kolpelke_2007_221', 'kolpelke_2007_308',
+ 'kolpelke_2007_582', 'kolpelke_2007_591', 'kolpelke_2007_601',
+ 'kolpelke_2007_607', 'kolpelke_2007_704', 'kolpelke_2007_752',
+ 'kolpelke_2007_636', 'kolpelke_2007_665', 'kolpelke_2007_667',
+ 'kolpelke_2007_758', 'kolpelke_2007_759', 'kolpelke_2007_642',
+ 'kolpelke_2007_662', 'kolpelke_2007_664', 'kolpelke_2007_666',
+ 'kolpelke_2007_669', 'kolpelke_2007_757', 'kolpelke_2007_668',
+ 'kolpelke_2007_670', 'kolpelke_2007_663', 'kolpelke_2007_677',
+ 'kolpelke_2007_692', 'kolpelke_2007_659', 'kolpelke_2007_693',
+ 'kolpelke_2007_676', 'kolpelke_2007_658', 'kolpelke_2007_694',
+ 'kolpelke_2007_657', 'kolpelke_2007_764', 'kolpelke_2007_765',
+ 'kolpelke_2007_698', 'kolpelke_2007_691', 'kolpelke_2007_760',
+ 'kolpelke_2007_10', 'kolpelke_2007_312', 'kolpelke_2007_679',
+ 'kolpelke_2007_762', 'kolpelke_2007_9', 'kolpelke_2007_531',
+ 'kolpelke_2007_678', 'kolpelke_2007_700', 'kolpelke_2007_732',
+ 'kolpelke_2007_744', 'kolpelke_2007_763', 'kolpelke_2007_697',
+ 'kolpelke_2007_699', 'kolpelke_2007_675', 'kolpelke_2007_272',
+ 'kolpelke_2007_701', 'kolpelke_2007_776', 'kolpelke_2007_634',
+ 'kolpelke_2007_773', 'kolpelke_2007_740', 'kolpelke_2007_771',
+ 'kolpelke_2007_74', 'kolpelke_2007_303', 'kolpelke_2007_783',
+ 'kolpelke_2007_437', 'kolpelke_2007_433', 'kolpelke_2007_741',
+ 'kolpelke_2007_73', 'kolpelke_2007_726', 'kolpelke_2007_533',
+ 'kolpelke_2007_18', 'kolpelke_2007_138', 'kolpelke_2007_434',
+ 'kolpelke_2007_623', 'kolpelke_2007_728', 'kolpelke_2007_416',
+ 'kolpelke_2007_137', 'kolpelke_2007_411', 'kolpelke_2007_413',
+ 'kolpelke_2007_739', 'kolpelke_2007_772', 'kolpelke_2007_54',
+ 'kolpelke_2007_56', 'kolpelke_2007_99', 'kolpelke_2007_630',
+ 'kolpelke_2007_635', 'kolpelke_2007_738', 'kolpelke_2007_767',
+ 'kolpelke_2007_633', 'kolpelke_2007_736', 'kolpelke_2007_768',
+ 'kolpelke_2007_136', 'kolpelke_2007_775', 'kolpelke_2007_55',
+ 'kolpelke_2007_632', 'kolpelke_2007_725', 'kolpelke_2007_730',
+ 'kolpelke_2007_766', 'kolpelke_2007_53', 'kolpelke_2007_100',
+ 'kolpelke_2007_631', 'kolpelke_2007_770', 'kolpelke_2007_302',
+ 'kolpelke_2007_278', 'kolpelke_2007_727', 'kolpelke_2007_72',
+ 'kolpelke_2007_17', 'kolpelke_2007_135', 'kolpelke_2007_277',
+ 'kolpelke_2007_735', 'kolpelke_2007_742', 'kolpelke_2007_103',
+ 'kolpelke_2007_534', 'kolpelke_2007_71', 'kolpelke_2007_16',
+ 'kolpelke_2007_418', 'kolpelke_2007_774', 'kolpelke_2007_629',
+ 'kolpelke_2007_628', 'kolpelke_2007_69', 'kolpelke_2007_729',
+ 'kolpelke_2007_724', 'kolpelke_2007_627', 'kolpelke_2007_737',
+ 'kolpelke_2007_734', 'kolpelke_2007_769', 'kolpelke_2007_611',
+ 'kolpelke_2007_301', 'kolpelke_2007_626', 'kolpelke_2007_299',
+ 'kolpelke_2007_298', 'kolpelke_2007_535', 'kolpelke_2007_279',
+ 'kolpelke_2007_280', 'kolpelke_2007_625', 'kolpelke_2007_536',
+ 'kolpelke_2007_300', 'kolpelke_2007_57', 'kolpelke_2007_101',
+ 'kolpelke_2007_386', 'kolpelke_2007_624', 'kolpelke_2007_266',
+ 'kolpelke_2007_134', 'kolpelke_2007_259', 'kolpelke_2007_612',
+ 'kolpelke_2007_297', 'kolpelke_2007_613', 'kolpelke_2007_282',
+ 'kolpelke_2007_537', 'kolpelke_2007_552', 'kolpelke_2007_58',
+ 'kolpelke_2007_70', 'kolpelke_2007_113', 'kolpelke_2007_132',
+ 'kolpelke_2007_258', 'kolpelke_2007_281', 'kolpelke_2007_621',
+ 'kolpelke_2007_112', 'kolpelke_2007_130', 'kolpelke_2007_296',
+ 'kolpelke_2007_133', 'kolpelke_2007_551', 'kolpelke_2007_59',
+ 'kolpelke_2007_68', 'kolpelke_2007_778', 'kolpelke_2007_265',
+ 'kolpelke_2007_275', 'kolpelke_2007_410', 'kolpelke_2007_615',
+ 'kolpelke_2007_761', 'kolpelke_2007_276', 'kolpelke_2007_620',
+ 'kolpelke_2007_131', 'kolpelke_2007_619', 'kolpelke_2007_273',
+ 'kolpelke_2007_614', 'kolpelke_2007_432', 'kolpelke_2007_415',
+ 'kolpelke_2007_435', 'kolpelke_2007_618', 'kolpelke_2007_622',
+ 'kolpelke_2007_67', 'kolpelke_2007_111', 'kolpelke_2007_128',
+ 'kolpelke_2007_293', 'kolpelke_2007_60', 'kolpelke_2007_129',
+ 'kolpelke_2007_782', 'kolpelke_2007_270', 'kolpelke_2007_429',
+ 'kolpelke_2007_538', 'kolpelke_2007_271', 'kolpelke_2007_428',
+ 'kolpelke_2007_616', 'kolpelke_2007_617', 'kolpelke_2007_295',
+ 'kolpelke_2007_66', 'kolpelke_2007_431', 'kolpelke_2007_405',
+ 'kolpelke_2007_102', 'kolpelke_2007_121', 'kolpelke_2007_294',
+ 'kolpelke_2007_414', 'kolpelke_2007_61', 'kolpelke_2007_65',
+ 'kolpelke_2007_110', 'kolpelke_2007_263', 'kolpelke_2007_408',
+ 'kolpelke_2007_547', 'kolpelke_2007_261', 'kolpelke_2007_403',
+ 'kolpelke_2007_546', 'kolpelke_2007_406', 'kolpelke_2007_290',
+ 'kolpelke_2007_427', 'kolpelke_2007_540', 'kolpelke_2007_542',
+ 'kolpelke_2007_543', 'kolpelke_2007_544', 'kolpelke_2007_545',
+ 'kolpelke_2007_563', 'kolpelke_2007_548', 'kolpelke_2007_564',
+ 'kolpelke_2007_260', 'kolpelke_2007_409', 'kolpelke_2007_123',
+ 'kolpelke_2007_262', 'kolpelke_2007_561', 'kolpelke_2007_539',
+ 'kolpelke_2007_421', 'kolpelke_2007_549', 'kolpelke_2007_291',
+ 'kolpelke_2007_105', 'kolpelke_2007_550', 'kolpelke_2007_62',
+ 'kolpelke_2007_269', 'kolpelke_2007_426', 'kolpelke_2007_425',
+ 'kolpelke_2007_64', 'kolpelke_2007_104', 'kolpelke_2007_127',
+ 'kolpelke_2007_122', 'kolpelke_2007_562', 'kolpelke_2007_541',
+ 'kolpelke_2007_63', 'kolpelke_2007_292', 'kolpelke_2007_423',
+ 'kolpelke_2007_424', 'kolpelke_2007_422', 'kolpelke_2007_267',
+ 'kolpelke_2007_106', 'kolpelke_2007_125', 'kolpelke_2007_288',
+ 'kolpelke_2007_289', 'kolpelke_2007_412', 'kolpelke_2007_264',
+ 'kolpelke_2007_430', 'kolpelke_2007_436', 'kolpelke_2007_109',
+ 'kolpelke_2007_124', 'kolpelke_2007_407', 'kolpelke_2007_126',
+ 'kolpelke_2007_107', 'kolpelke_2007_108', 'kolpelke_2007_268',
+ 'kolpelke_2007_420', 'kolpelke_2007_402', 'kolpelke_2007_404',
+ 'hines_et_al_2019', 'bartomeus_2005_BAT1CA', 'bartomeus_2005_BAT2CA',
+ 'bartomeus_2005_FRA1OP', 'bartomeus_2005_FRA2OP', 'bartomeus_2005_MED1CA',
+ 'bartomeus_2005_MED2CA', 'bartomeus_2005_MED3CA', 'bartomeus_2005_MED4CA',
+ 'bartomeus_2005_MIQ1OP', 'bartomeus_2005_MIQ2OP', 'bartomeus_2005_SEL1OP',
+ 'bartomeus_2005_SEL2OP', 'roopnarine_2013_Cuba', 'roopnarine_2013_Jamaica',
+ 'roopnarine_2013_Cayman', 'RMBL_pollination_2013_week1_shady_point',
+ 'RMBL_pollination_2013_week2_shady_point',
+ 'RMBL_pollination_2013_week3_shady_point',
+ 'RMBL_pollination_2013_week4_shady_point',
+ 'RMBL_pollination_2013_week5_shady_point',
+ 'RMBL_pollination_2013_week6_shady_point',
+ 'RMBL_pollination_2013_week7_shady_point',
+ 'RMBL_pollination_2013_week8_shady_point',
+ 'RMBL_pollination_2013_week9_shady_point',
+ 'RMBL_pollination_2013_week10_shady_point',
+ 'RMBL_pollination_2013_week11_shady_point',
+ 'RMBL_pollination_2013_week13_shady_point',
+ 'RMBL_pollination_2013_week1_twin_meadows',
+ 'RMBL_pollination_2013_week2_twin_meadows',
+ 'RMBL_pollination_2013_week3_twin_meadows',
+ 'RMBL_pollination_2013_week4_twin_meadows',
+ 'RMBL_pollination_2013_week5_twin_meadows',
+ 'RMBL_pollination_2013_week6_twin_meadows',
+ 'RMBL_pollination_2013_week7_twin_meadows',
+ 'RMBL_pollination_2013_week8_twin_meadows',
+ 'RMBL_pollination_2013_week9_twin_meadows',
+ 'RMBL_pollination_2013_week10_twin_meadows',
+ 'RMBL_pollination_2013_week11_twin_meadows',
+ 'RMBL_pollination_2013_week13_twin_meadows',
+ 'RMBL_pollination_2014_week1_shady_point',
+ 'RMBL_pollination_2014_week2_shady_point',
+ 'RMBL_pollination_2014_week3_shady_point',
+ 'RMBL_pollination_2014_week4_shady_point',
+ 'RMBL_pollination_2014_week5_shady_point',
+ 'RMBL_pollination_2014_week6_shady_point',
+ 'RMBL_pollination_2014_week7_shady_point',
+ 'RMBL_pollination_2014_week8_shady_point',
+ 'RMBL_pollination_2014_week9_shady_point',
+ 'RMBL_pollination_2014_week10_shady_point',
+ 'RMBL_pollination_2014_week11_shady_point',
+ 'RMBL_pollination_2014_week12_shady_point',
+ 'RMBL_pollination_2014_week13_shady_point',
+ 'RMBL_pollination_2014_week14_shady_point',
+ 'RMBL_pollination_2014_week15_shady_point',
+ 'RMBL_pollination_2014_week1_twin_meadows',
+ 'RMBL_pollination_2014_week2_twin_meadows',
+ 'RMBL_pollination_2014_week3_twin_meadows',
+ 'RMBL_pollination_2014_week4_twin_meadows',
+ 'RMBL_pollination_2014_week5_twin_meadows',
+ 'RMBL_pollination_2014_week6_twin_meadows',
+ 'RMBL_pollination_2014_week7_twin_meadows',
+ 'RMBL_pollination_2014_week8_twin_meadows',
+ 'RMBL_pollination_2014_week9_twin_meadows',
+ 'RMBL_pollination_2014_week10_twin_meadows',
+ 'RMBL_pollination_2014_week11_twin_meadows',
+ 'RMBL_pollination_2014_week12_twin_meadows',
+ 'RMBL_pollination_2014_week13_twin_meadows',
+ 'RMBL_pollination_2014_week14_twin_meadows',
+ 'RMBL_pollination_2014_week15_twin_meadows',
+ 'RMBL_pollination_2015_week1_shady_point',
+ 'RMBL_pollination_2015_week2_shady_point',
+ 'RMBL_pollination_2015_week3_shady_point',
+ 'RMBL_pollination_2015_week4_shady_point',
+ 'RMBL_pollination_2015_week5_shady_point',
+ 'RMBL_pollination_2015_week6_shady_point',
+ 'RMBL_pollination_2015_week7_shady_point',
+ 'RMBL_pollination_2015_week8_shady_point',
+ 'RMBL_pollination_2015_week9_shady_point',
+ 'RMBL_pollination_2015_week10_shady_point',
+ 'RMBL_pollination_2015_week11_shady_point',
+ 'RMBL_pollination_2015_week12_shady_point',
+ 'RMBL_pollination_2015_week13_shady_point',
+ 'RMBL_pollination_2015_week14_shady_point',
+ 'RMBL_pollination_2015_week15_shady_point',
+ 'RMBL_pollination_2015_week16_shady_point',
+ 'RMBL_pollination_2015_week1_twin_meadows',
+ 'RMBL_pollination_2015_week2_twin_meadows',
+ 'RMBL_pollination_2015_week3_twin_meadows',
+ 'RMBL_pollination_2015_week4_twin_meadows',
+ 'RMBL_pollination_2015_week5_twin_meadows',
+ 'RMBL_pollination_2015_week6_twin_meadows',
+ 'RMBL_pollination_2015_week7_twin_meadows',
+ 'RMBL_pollination_2015_week8_twin_meadows',
+ 'RMBL_pollination_2015_week9_twin_meadows',
+ 'RMBL_pollination_2015_week10_twin_meadows',
+ 'RMBL_pollination_2015_week11_twin_meadows',
+ 'RMBL_pollination_2015_week12_twin_meadows',
+ 'RMBL_pollination_2015_week13_twin_meadows',
+ 'RMBL_pollination_2015_week14_twin_meadows',
+ 'RMBL_pollination_2015_week15_twin_meadows',
+ 'RMBL_pollination_2015_week16_twin_meadows']
+
+# Networks without any interaction, left out
+empty = ['kolpelke_2007_13', 'kolpelke_2007_145', 'kolpelke_2007_202',
+ 'kolpelke_2007_553', 'kolpelke_2007_560', 'kolpelke_2007_579']
+
+files = [(tuple(upstream_urls.keys()), alt, None) for alt in networks
+ if alt not in empty]
+
+def fetch_upstream(force=False):
+ return fetch_archived_files(__name__.split(".")[-1], upstream_urls, force,
+ tries=3, timeout=600)
+
+_data = None
+
+def _load(name):
+ """Load the records of all the pages (once per process, since parse() is
+ called for each network in turn), keeping only the fields used."""
+ global _data
+ if _data is not None:
+ return _data
+ recs = {}
+ for kind in totals:
+ recs[kind] = []
+ for fname, url in _pages(kind):
+ with open_upstream_file(name, fname, "rb") as f:
+ page = json.load(f)
+ assert isinstance(page, list), (fname, str(page)[:200])
+ if kind == 'interaction':
+ page = [dict(id=x['id'], node_from=x['node_from'],
+ node_to=x['node_to'], date=x['date'],
+ direction=x['direction'], type=x['type'],
+ method=x['method'], value=x['value'],
+ attribute=(x.get('attribute') or {}).get('name'),
+ unit=(x.get('attribute') or {}).get('unit'),
+ network_id=x['network_id'])
+ for x in page]
+ recs[kind].extend(page)
+ ids = [x['id'] for x in recs[kind]]
+ assert len(ids) == len(set(ids)) == totals[kind], \
+ (kind, len(ids), len(set(ids)), totals[kind])
+ assert sorted(x['name'] for x in recs['network']) == sorted(networks)
+ recs['datasets'] = {x['id']: x for x in recs['dataset']}
+ recs['refs'] = {x['id']: x for x in recs['reference']}
+ recs['nodes'] = defaultdict(list)
+ for x in recs['node']:
+ recs['nodes'][x['network_id']].append(x)
+ recs['inters'] = defaultdict(list)
+ for x in recs['interaction']:
+ recs['inters'][x['network_id']].append(x)
+ _data = recs
+ return _data
+
+def _int(x):
+ return -1 if x is None else int(x)
+
+@cache_network()
+@coerce_props(vforce={'name': 'string', 'taxon': 'string', 'rank': 'string',
+ 'col': 'string', 'node_level': 'string'},
+ eforce={'type': 'string', 'method': 'string',
+ 'direction': 'string', 'attribute': 'string',
+ 'date': 'string', 'value': 'double'})
+@annotate()
+def parse(alts=None):
+ name = __name__.split(".")[-1]
+ d = _load(name)
+ datasets, refs, nodes, inters = (d['datasets'], d['refs'], d['nodes'],
+ d['inters'])
+
+ for net in sorted(d['network'], key=lambda x: x['id']):
+ alt = net['name']
+ if alts is not None and alt not in alts:
+ continue
+ if alt in empty:
+ assert len(inters[net['id']]) == 0
+ continue
+ ns = sorted(nodes[net['id']], key=lambda x: x['id'])
+ # recorded absences of interactions are left out
+ es = sorted((e for e in inters[net['id']]
+ if not (e['attribute'] == 'presence/absence' and
+ e['value'] == 0)),
+ key=lambda x: x['id'])
+ directed = any(e['direction'] == 'directed' for e in es)
+ g = Graph(directed=directed)
+ vidx = {x['id']: i for i, x in enumerate(ns)}
+ g.add_vertex(len(ns))
+ g.add_edge_list([(vidx[e['node_from']], vidx[e['node_to']]) for e in es])
+ tax = [x.get('taxonomy') or {} for x in ns]
+ g.vp.name = g.new_vp("string", vals=[x['original_name'] or "" for x in ns])
+ g.vp.node_id = g.new_vp("int64_t", vals=[x['id'] for x in ns])
+ g.vp.node_level = g.new_vp("string", vals=[x['node_level'] or "" for x in ns])
+ g.vp.taxon = g.new_vp("string", vals=[t.get('name') or "" for t in tax])
+ g.vp.rank = g.new_vp("string", vals=[t.get('rank') or "" for t in tax])
+ for k in ['ncbi', 'tsn', 'gbif', 'eol', 'bold']:
+ g.vp[k] = g.new_vp("int64_t", vals=[_int(t.get(k)) for t in tax])
+ g.vp.col = g.new_vp("string", vals=[t.get('col') or "" for t in tax])
+
+ g.ep.interaction_id = g.new_ep("int64_t", vals=[e['id'] for e in es])
+ g.ep.type = g.new_ep("string", vals=[e['type'] or "" for e in es])
+ g.ep.method = g.new_ep("string", vals=[e['method'] or "" for e in es])
+ g.ep.direction = g.new_ep("string", vals=[e['direction'] or "" for e in es])
+ g.ep.attribute = g.new_ep("string", vals=[e['attribute'] or "" for e in es])
+ g.ep.value = g.new_ep("double", vals=[numpy.nan if e['value'] is None
+ else float(e['value']) for e in es])
+ g.ep.date = g.new_ep("string", vals=[(e['date'] or "")[:10] for e in es])
+
+ ds = datasets.get(net['dataset_id'], {})
+ ref = refs.get(ds.get('ref_id'), {})
+ g.gp.network_id = g.new_gp("int64_t", val=net['id'])
+ g.gp.network_description = g.new_gp("string", val=net['description'] or "")
+ g.gp.network_date = g.new_gp("string", val=(net['date'] or "")[:10])
+ g.gp.geometry = g.new_gp("string", val=json.dumps(net['geom'])
+ if net['geom'] else "")
+ g.gp.all_interactions = g.new_gp("bool", val=bool(net['all_interactions']))
+ g.gp.dataset = g.new_gp("string", val=ds.get('name') or "")
+ g.gp.dataset_description = g.new_gp("string", val=ds.get('description') or "")
+ g.gp.reference_doi = g.new_gp("string", val=ref.get('doi') or "")
+ g.gp.reference_bibtex = g.new_gp("string", val=ref.get('bibtex') or "")
+ g.gp.data_url = g.new_gp("string", val=ref.get('data_url') or "")
+ yield alt, g