-
Notifications
You must be signed in to change notification settings - Fork 25
/
search.py
410 lines (361 loc) · 20.4 KB
/
search.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
import re
from pygbif.gbifutils import gbif_baseurl, bool2str, requests_argset, gbif_GET
def search(
taxonKey=None,
repatriated=None,
kingdomKey=None,
phylumKey=None,
classKey=None,
orderKey=None,
familyKey=None,
genusKey=None,
subgenusKey=None,
scientificName=None,
country=None,
publishingCountry=None,
hasCoordinate=None,
typeStatus=None,
recordNumber=None,
lastInterpreted=None,
continent=None,
geometry=None,
recordedBy=None,
recordedByID=None,
identifiedByID=None,
basisOfRecord=None,
datasetKey=None,
eventDate=None,
catalogNumber=None,
year=None,
month=None,
decimalLatitude=None,
decimalLongitude=None,
elevation=None,
depth=None,
institutionCode=None,
collectionCode=None,
hasGeospatialIssue=None,
issue=None,
q=None,
spellCheck=None,
mediatype=None,
limit=300,
offset=0,
establishmentMeans=None,
facet=None,
facetMincount=None,
facetMultiselect=None,
**kwargs
):
"""
Search GBIF occurrences
:param taxonKey: [int] A GBIF occurrence identifier
:param q: [str] Simple search parameter. The value for this parameter can be a simple word or a phrase.
:param spellCheck: [bool] If ``True`` ask GBIF to check your spelling of the value passed to the ``search`` parameter.
IMPORTANT: This only checks the input to the ``search`` parameter, and no others. Default: ``False``
:param repatriated: [str] Searches for records whose publishing country is different to the country where the record was recorded in
:param kingdomKey: [int] Kingdom classification key
:param phylumKey: [int] Phylum classification key
:param classKey: [int] Class classification key
:param orderKey: [int] Order classification key
:param familyKey: [int] Family classification key
:param genusKey: [int] Genus classification key
:param subgenusKey: [int] Subgenus classification key
:param scientificName: [str] A scientific name from the GBIF backbone. All included and synonym taxa are included in the search.
:param datasetKey: [str] The occurrence dataset key (a uuid)
:param catalogNumber: [str] An identifier of any form assigned by the source within a physical collection or digital dataset for the record which may not unique, but should be fairly unique in combination with the institution and collection code.
:param recordedBy: [str] The person who recorded the occurrence.
:param recordedByID: [str] Identifier (e.g. ORCID) for the person who recorded the occurrence
:param identifiedByID: [str] Identifier (e.g. ORCID) for the person who provided the taxonomic identification of the occurrence.
:param collectionCode: [str] An identifier of any form assigned by the source to identify the physical collection or digital dataset uniquely within the text of an institution.
:param institutionCode: [str] An identifier of any form assigned by the source to identify the institution the record belongs to. Not guaranteed to be que.
:param country: [str] The 2-letter country code (as per ISO-3166-1) of the country in which the occurrence was recorded. See here http://en.wikipedia.org/wiki/ISO_3166-1_alpha-2
:param basisOfRecord: [str] Basis of record, as defined in our BasisOfRecord enum here http://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/BasisOfRecord.html Acceptable values are:
- ``FOSSIL_SPECIMEN`` An occurrence record describing a fossilized specimen.
- ``HUMAN_OBSERVATION`` An occurrence record describing an observation made by one or more people.
- ``LITERATURE`` An occurrence record based on literature alone.
- ``LIVING_SPECIMEN`` An occurrence record describing a living specimen, e.g.
- ``MACHINE_OBSERVATION`` An occurrence record describing an observation made by a machine.
- ``OBSERVATION`` An occurrence record describing an observation.
- ``PRESERVED_SPECIMEN`` An occurrence record describing a preserved specimen.
- ``UNKNOWN`` Unknown basis for the record.
:param eventDate: [date] Occurrence date in ISO 8601 format: yyyy, yyyy-MM, yyyy-MM-dd, or
MM-dd. Supports range queries, smaller,larger (e.g., ``1990,1991``, whereas ``1991,1990``
wouldn't work)
:param year: [int] The 4 digit year. A year of 98 will be interpreted as AD 98. Supports range queries,
smaller,larger (e.g., ``1990,1991``, whereas ``1991,1990`` wouldn't work)
:param month: [int] The month of the year, starting with 1 for January. Supports range queries,
smaller,larger (e.g., ``1,2``, whereas ``2,1`` wouldn't work)
:param q: [str] Query terms. The value for this parameter can be a simple word or a phrase.
:param decimalLatitude: [float] Latitude in decimals between -90 and 90 based on WGS 84.
Supports range queries, smaller,larger (e.g., ``25,30``, whereas ``30,25`` wouldn't work)
:param decimalLongitude: [float] Longitude in decimals between -180 and 180 based on WGS 84.
Supports range queries (e.g., ``-0.4,-0.2``, whereas ``-0.2,-0.4`` wouldn't work).
:param publishingCountry: [str] The 2-letter country code (as per ISO-3166-1) of the
country in which the occurrence was recorded.
:param elevation: [int/str] Elevation in meters above sea level. Supports range queries, smaller,larger
(e.g., ``5,30``, whereas ``30,5`` wouldn't work)
:param depth: [int/str] Depth in meters relative to elevation. For example 10 meters below a
lake surface with given elevation. Supports range queries, smaller,larger (e.g., ``5,30``,
whereas ``30,5`` wouldn't work)
:param geometry: [str] Searches for occurrences inside a polygon described in Well Known
Text (WKT) format. A WKT shape written as either POINT, LINESTRING, LINEARRING
POLYGON, or MULTIPOLYGON. Example of a polygon: ``((30.1 10.1, 20, 20 40, 40 40, 30.1 10.1))`` would be queried as http://bit.ly/1BzNwDq.
Polygons must have counter-clockwise ordering of points.
:param hasGeospatialIssue: [bool] Includes/excludes occurrence records which contain spatial
issues (as determined in our record interpretation), i.e. ``hasGeospatialIssue=TRUE``
returns only those records with spatial issues while ``hasGeospatialIssue=FALSE`` includes
only records without spatial issues. The absence of this parameter returns any
record with or without spatial issues.
:param issue: [str] One or more of many possible issues with each occurrence record. See
Details. Issues passed to this parameter filter results by the issue.
:param hasCoordinate: [bool] Return only occurence records with lat/long data (``True``) or
all records (``False``, default).
:param typeStatus: [str] Type status of the specimen. One of many options. See ?typestatus
:param recordNumber: [int] Number recorded by collector of the data, different from GBIF record
number. See http://rs.tdwg.org/dwc/terms/#recordNumber} for more info
:param lastInterpreted: [date] Date the record was last modified in GBIF, in ISO 8601 format:
yyyy, yyyy-MM, yyyy-MM-dd, or MM-dd. Supports range queries, smaller,larger (e.g.,
``1990,1991``, whereas ``1991,1990`` wouldn't work)
:param continent: [str] Continent. One of ``africa``, ``antarctica``, ``asia``, ``europe``, ``north_america``
(North America includes the Caribbean and reachies down and includes Panama), ``oceania``,
or ``south_america``
:param fields: [str] Default (``all``) returns all fields. ``minimal`` returns just taxon name,
key, latitude, and longitude. Or specify each field you want returned by name, e.g.
``fields = c('name','latitude','elevation')``.
:param mediatype: [str] Media type. Default is ``NULL``, so no filtering on mediatype. Options:
``NULL``, ``MovingImage``, ``Sound``, and ``StillImage``
:param limit: [int] Number of results to return. Default: ``300``
:param offset: [int] Record to start at. Default: ``0``
:param facet: [str] a character vector of length 1 or greater
:param establishmentMeans: [str] EstablishmentMeans, possible values include: INTRODUCED,
INVASIVE, MANAGED, NATIVE, NATURALISED, UNCERTAIN
:param facetMincount: [int] minimum number of records to be included in the faceting results
:param facetMultiselect: [bool] Set to ``True`` to still return counts for values that are not currently
filtered. See examples. Default: ``False``
:return: A dictionary
Usage::
from pygbif import occurrences
occurrences.search(taxonKey = 3329049)
# Return 2 results, this is the default by the way
occurrences.search(taxonKey=3329049, limit=2)
# Instead of getting a taxon key first, you can search for a name directly
# However, note that using this approach (with `scientificName="..."`)
# you are getting synonyms too. The results for using `scientifcName` and
# `taxonKey` parameters are the same in this case, but I wouldn't be surprised if for some
# names they return different results
occurrences.search(scientificName = 'Ursus americanus')
from pygbif import species
key = species.name_backbone(name = 'Ursus americanus', rank='species')['usageKey']
occurrences.search(taxonKey = key)
# Search by dataset key
occurrences.search(datasetKey='7b5d6a48-f762-11e1-a439-00145eb45e9a', limit=20)
# Search by catalog number
occurrences.search(catalogNumber="49366", limit=20)
# occurrences.search(catalogNumber=["49366","Bird.27847588"], limit=20)
# Use paging parameters (limit and offset) to page. Note the different results
# for the two queries below.
occurrences.search(datasetKey='7b5d6a48-f762-11e1-a439-00145eb45e9a', offset=10, limit=5)
occurrences.search(datasetKey='7b5d6a48-f762-11e1-a439-00145eb45e9a', offset=20, limit=5)
# Many dataset keys
# occurrences.search(datasetKey=["50c9509d-22c7-4a22-a47d-8c48425ef4a7", "7b5d6a48-f762-11e1-a439-00145eb45e9a"], limit=20)
# Search by collector name
res = occurrences.search(recordedBy="smith", limit=20)
[ x['recordedBy'] for x in res['results'] ]
# Many collector names
# occurrences.search(recordedBy=["smith","BJ Stacey"], limit=20)
# recordedByID
occurrences.search(recordedByID="https://orcid.org/0000-0003-1691-239X", limit = 3)
# identifiedByID
occurrences.search(identifiedByID="https://orcid.org/0000-0003-1691-239X", limit = 3)
# Search for many species
splist = ['Cyanocitta stelleri', 'Junco hyemalis', 'Aix sponsa']
keys = [ species.name_suggest(x)[0]['key'] for x in splist ]
out = [ occurrences.search(taxonKey = x, limit=1) for x in keys ]
[ x['results'][0]['speciesKey'] for x in out ]
# Search - q parameter
occurrences.search(q = "kingfisher", limit=20)
## spell check - only works with the `search` parameter
### spelled correctly - same result as above call
occurrences.search(q = "kingfisher", limit=20, spellCheck = True)
### spelled incorrectly - stops with suggested spelling
occurrences.search(q = "kajsdkla", limit=20, spellCheck = True)
### spelled incorrectly - stops with many suggested spellings
### and number of results for each
occurrences.search(q = "helir", limit=20, spellCheck = True)
# Search on latitidue and longitude
occurrences.search(decimalLatitude=50, decimalLongitude=10, limit=2)
# Search on a bounding box
## in well known text format
occurrences.search(geometry='POLYGON((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1))', limit=20)
from pygbif import species
key = species.name_suggest(q='Aesculus hippocastanum')[0]['key']
occurrences.search(taxonKey=key, geometry='POLYGON((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1))', limit=20)
## multipolygon
wkt = 'MULTIPOLYGON(((-123 38, -123 43, -116 43, -116 38, -123 38)),((-97 41, -97 45, -93 45, -93 41, -97 41)))'
occurrences.search(geometry = wkt, limit = 20)
# Search on country
occurrences.search(country='US', limit=20)
occurrences.search(country='FR', limit=20)
occurrences.search(country='DE', limit=20)
# Get only occurrences with lat/long data
occurrences.search(taxonKey=key, hasCoordinate=True, limit=20)
# Get only occurrences that were recorded as living specimens
occurrences.search(taxonKey=key, basisOfRecord="LIVING_SPECIMEN", hasCoordinate=True, limit=20)
# Get occurrences for a particular eventDate
occurrences.search(taxonKey=key, eventDate="2013", limit=20)
occurrences.search(taxonKey=key, year="2013", limit=20)
occurrences.search(taxonKey=key, month="6", limit=20)
# Get occurrences based on depth
key = species.name_backbone(name='Salmo salar', kingdom='animals')['usageKey']
occurrences.search(taxonKey=key, depth="5", limit=20)
# Get occurrences based on elevation
key = species.name_backbone(name='Puma concolor', kingdom='animals')['usageKey']
occurrences.search(taxonKey=key, elevation=50, hasCoordinate=True, limit=20)
# Get occurrences based on institutionCode
occurrences.search(institutionCode="TLMF", limit=20)
# Get occurrences based on collectionCode
occurrences.search(collectionCode="Floristic Databases MV - Higher Plants", limit=20)
# Get only those occurrences with spatial issues
occurrences.search(taxonKey=key, hasGeospatialIssue=True, limit=20)
# Search using a query string
occurrences.search(q="kingfisher", limit=20)
# Range queries
## See Detail for parameters that support range queries
### this is a range depth, with lower/upper limits in character string
occurrences.search(depth='50,100')
## Range search with year
occurrences.search(year='1999,2000', limit=20)
## Range search with latitude
occurrences.search(decimalLatitude='29.59,29.6')
# Search by specimen type status
## Look for possible values of the typeStatus parameter looking at the typestatus dataset
occurrences.search(typeStatus = 'allotype')
# Search by specimen record number
## This is the record number of the person/group that submitted the data, not GBIF's numbers
## You can see that many different groups have record number 1, so not super helpful
occurrences.search(recordNumber = 1)
# Search by last time interpreted: Date the record was last modified in GBIF
## The lastInterpreted parameter accepts ISO 8601 format dates, including
## yyyy, yyyy-MM, yyyy-MM-dd, or MM-dd. Range queries are accepted for lastInterpreted
occurrences.search(lastInterpreted = '2014-04-01')
# Search by continent
## One of africa, antarctica, asia, europe, north_america, oceania, or south_america
occurrences.search(continent = 'south_america')
occurrences.search(continent = 'africa')
occurrences.search(continent = 'oceania')
occurrences.search(continent = 'antarctica')
# Search for occurrences with images
occurrences.search(mediatype = 'StillImage')
occurrences.search(mediatype = 'MovingImage')
x = occurrences.search(mediatype = 'Sound')
[z['media'] for z in x['results']]
# Query based on issues
occurrences.search(taxonKey=1, issue='DEPTH_UNLIKELY')
occurrences.search(taxonKey=1, issue=['DEPTH_UNLIKELY','COORDINATE_ROUNDED'])
# Show all records in the Arizona State Lichen Collection that cant be matched to the GBIF
# backbone properly:
occurrences.search(datasetKey='84c0e1a0-f762-11e1-a439-00145eb45e9a', issue=['TAXON_MATCH_NONE','TAXON_MATCH_HIGHERRANK'])
# If you pass in an invalid polygon you get hopefully informative errors
### the WKT string is fine, but GBIF says bad polygon
wkt = 'POLYGON((-178.59375 64.83258989321493,-165.9375 59.24622380205539,
-147.3046875 59.065977905449806,-130.78125 51.04484764446178,-125.859375 36.70806354647625,
-112.1484375 23.367471303759686,-105.1171875 16.093320185359257,-86.8359375 9.23767076398516,
-82.96875 2.9485268155066175,-82.6171875 -14.812060061226388,-74.8828125 -18.849111862023985,
-77.34375 -47.661687803329166,-84.375 -49.975955187343295,174.7265625 -50.649460483096114,
179.296875 -42.19189902447192,-176.8359375 -35.634976650677295,176.8359375 -31.835565983656227,
163.4765625 -6.528187613695323,152.578125 1.894796132058301,135.703125 4.702353722559447,
127.96875 15.077427674847987,127.96875 23.689804541429606,139.921875 32.06861069132688,
149.4140625 42.65416193033991,159.2578125 48.3160811030533,168.3984375 57.019804336633165,
178.2421875 59.95776046458139,-179.6484375 61.16708631440347,-178.59375 64.83258989321493))'
occurrences.search(geometry = wkt)
# Faceting
## return no occurrence records with limit=0
x = occurrences.search(facet = "country", limit = 0)
x['facets']
## also return occurrence records
x = occurrences.search(facet = "establishmentMeans", limit = 10)
x['facets']
x['results']
## multiple facet variables
x = occurrences.search(facet = ["country", "basisOfRecord"], limit = 10)
x['results']
x['facets']
x['facets']['country']
x['facets']['basisOfRecord']
x['facets']['basisOfRecord']['count']
## set a minimum facet count
x = occurrences.search(facet = "country", facetMincount = 30000000L, limit = 0)
x['facets']
## paging per each faceted variable
### do so by passing in variables like "country" + "_facetLimit" = "country_facetLimit"
### or "country" + "_facetOffset" = "country_facetOffset"
x = occurrences.search(
facet = ["country", "basisOfRecord", "hasCoordinate"],
country_facetLimit = 3,
basisOfRecord_facetLimit = 6,
limit = 0
)
x['facets']
# requests package options
## There's an acceptable set of requests options (['timeout', 'cookies', 'auth',
## 'allow_redirects', 'proxies', 'verify', 'stream', 'cert']) you can pass
## in via **kwargs, e.g., set a timeout
x = occurrences.search(timeout = 1)
"""
url = gbif_baseurl + "occurrence/search"
args = {
"taxonKey": taxonKey,
"repatriated": repatriated,
"kingdomKey": kingdomKey,
"phylumKey": phylumKey,
"classKey": classKey,
"orderKey": orderKey,
"familyKey": familyKey,
"genusKey": genusKey,
"subgenusKey": subgenusKey,
"scientificName": scientificName,
"country": country,
"publishingCountry": publishingCountry,
"hasCoordinate": bool2str(hasCoordinate),
"typeStatus": typeStatus,
"recordNumber": recordNumber,
"lastInterpreted": lastInterpreted,
"continent": continent,
"geometry": geometry,
"recordedBy": recordedBy,
"recordedByID": recordedByID,
"identifiedByID": identifiedByID,
"basisOfRecord": basisOfRecord,
"datasetKey": datasetKey,
"eventDate": eventDate,
"catalogNumber": catalogNumber,
"year": year,
"month": month,
"decimalLatitude": decimalLatitude,
"decimalLongitude": decimalLongitude,
"elevation": elevation,
"depth": depth,
"institutionCode": institutionCode,
"collectionCode": collectionCode,
"hasGeospatialIssue": bool2str(hasGeospatialIssue),
"issue": issue,
"q": q,
"spellCheck": bool2str(spellCheck),
"mediatype": mediatype,
"limit": limit,
"offset": offset,
"establishmentMeans": establishmentMeans,
"facetMincount": facetMincount,
"facet": facet,
"facetMultiselect": bool2str(facetMultiselect),
}
gbif_kwargs = {key: kwargs[key] for key in kwargs if key not in requests_argset}
if gbif_kwargs is not None:
xx = dict(
zip([re.sub("_", ".", x) for x in gbif_kwargs.keys()], gbif_kwargs.values())
)
args.update(xx)
kwargs = {key: kwargs[key] for key in kwargs if key in requests_argset}
out = gbif_GET(url, args, **kwargs)
return out