source: grass-addons/grass7/vector/v.in.pygbif/v.in.pygbif.py

Last change on this file was 73969, checked in by neteler, 6 years ago

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1#!/usr/bin/env python
2
3"""
4MODULE: v.in.pygbif
5
6AUTHOR(S): Stefan Blumentrath < stefan.blumentrath AT nina.no>
7 Helmut Kudrnovsky <alectoria AT gmx at>
8
9PURPOSE: Search and import GBIF species distribution data directly from
10 GBIF API using pygbif
11
12COPYRIGHT: (C) 2016 by the GRASS Development Team
13
14 This program is free software under the GNU General Public
15 License (>=v2). Read the file COPYING that comes with GRASS
16 for details.
17"""
18
19"""
20To Dos:
21- use proper cleanup routine, esp if using csv + vrt (copy from other modules)
22- handle layers in mask input
23- add progress bar
24- make date_from and date_to dependent on each other or use today as date_to if not specified
25
26"""
27
28#%module
29#% description: Search and import GBIF species distribution data
30#% keyword: vector
31#% keyword: geometry
32#%end
33
34#%option G_OPT_V_OUTPUT
35#% key: output
36#% description: Name of resulting vector map with occurrences
37#% required : yes
38#%end
39
40#%option
41#% key: taxa
42#% description: Comma separated list of taxon names or keys to fetch data for
43#% required : yes
44#%end
45
46#%option G_OPT_V_INPUT
47#% key: mask
48#% description: Vector map that delimits region of interest
49#% guisection: Spatial filter
50#% required: no
51#%end
52
53#%option
54#% key: date_from
55#% type: string
56#% description: Lower bound of acceptable dates (format: yyyy, yyyy-MM, yyyy-MM-dd, or MM-dd)
57#% guisection: Temporal filter
58#% required: no
59#%end
60
61#%option
62#% key: date_to
63#% type: string
64#% description: Upper bound of acceptable dates (format: yyyy, yyyy-MM, yyyy-MM-dd, or MM-dd)
65#% guisection: Temporal filter
66#% required: no
67#%end
68
69# Import will allways be limited to current region except for latlon locations
70#%flag
71#% key: b
72#% description: Do not build topology
73#%end
74
75#%flag
76#% key: r
77#% description: Do not limit import to current region (works only in lat/lon)
78#% guisection: Spatial filter
79#%end
80
81#%flag
82#% key: p
83#% description: Print result from matching taxa names and exit
84#% guisection: Print
85#% suppress_required: yes
86#%end
87
88#%flag
89#% key: i
90#% description: Produce individual map for each taxon
91#%end
92
93#%flag
94#% key: g
95#% description: Print result from matching taxon names in shell script style and exit
96#% guisection: Print
97#% suppress_required: yes
98#%end
99
100#%flag
101#% key: o
102#% description: Print number of matching occurrences per taxon and exit
103#% guisection: Print
104#% suppress_required: yes
105#%end
106
107#%flag
108#% key: t
109#% description: Print result of taxon matching in table format and exit
110#% guisection: Print
111#% suppress_required: yes
112#%end
113
114#%option
115#% key: basisofrecord
116#% type: string
117#% description: Accepted basis of records
118#% guisection: Context filter
119#% required: no
120#% multiple: no
121#% options: ALL,FOSSIL_SPECIMEN,HUMAN_OBSERVATION,LITERATURE,LIVING_SPECIMEN,MACHINE_OBSERVATION,OBSERVATION,PRESERVED_SPECIMEN,UNKNOWN
122#% answer: ALL
123#%end
124
125#%option
126#% key: rank
127#% type: string
128#% description: Rank of the taxon to search for
129#% guisection: Context filter
130#% required: yes
131#% multiple: no
132#% options: class,cultivar,cultivar_group,domain,family,form,genus,informal,infrageneric_name,infraorder,infraspecific_name,infrasubspecific_name,kingdom,order,phylum,section,series,species,strain,subclass,subfamily,subform,subgenus,subkingdom,suborder,subphylum,subsection,subseries,subspecies,subtribe,subvariety,superclass,superfamily,superorder,superphylum,suprageneric_name,tribe,unranked,variety
133#% answer: species
134#%end
135
136#%option
137#% key: recordedby
138#% type: string
139#% description: The person who recorded the occurrence.
140#% guisection: Context filter
141#%end
142
143#%option
144#% key: institutioncode
145#% type: string
146#% description: An identifier of any form assigned by the source to identify the institution the record belongs to.
147#% guisection: Context filter
148#%end
149
150#%option
151#% key: country
152#% type: string
153#% description: The 2-letter country code (as per ISO-3166-1) of the country in which the occurrence was recorded
154#% guisection: Spatial filter
155#%end
156
157#%option
158#% key: continent
159#% type: string
160#% description: The continent in which the occurrence was recorded
161#% guisection: Spatial filter
162#% options: africa,antarctica,asia,europe,north_america,oceania,south_america
163#%end
164
165#%flag
166#% key: n
167#% description: Do not limit search to records with coordinates
168#% guisection: Spatial filter
169#%end
170
171#%flag
172#% key: s
173#% description: Do also import occurrences with spatial issues
174#% guisection: Spatial filter
175#%end
176
177import sys
178import os
179import math
180from osgeo import ogr
181from osgeo import osr
182import grass.script as grass
183from grass.pygrass.vector import Vector
184from grass.pygrass.vector import VectorTopo
185from grass.pygrass.vector.geometry import Point
186from dateutil.parser import parse
187
188def set_output_encoding(encoding='utf-8'):
189 import sys
190 import codecs
191 '''When piping to the terminal, python knows the encoding needed, and
192 sets it automatically. But when piping to another program (for example,
193 | less), python can not check the output encoding. In that case, it
194 is None. What I am doing here is to catch this situation for both
195 stdout and stderr and force the encoding'''
196 current = sys.stdout.encoding
197 if current is None:
198 sys.stdout = codecs.getwriter(encoding)(sys.stdout)
199 current = sys.stderr.encoding
200 if current is None:
201 sys.stderr = codecs.getwriter(encoding)(sys.stderr)
202
203
204def main():
205
206 try:
207 from pygbif import occurrences
208 from pygbif import species
209 except ImportError:
210 grass.fatal(_("Cannot import pygbif (https://github.com/sckott/pygbif)"
211 " library."
212 " Please install it (pip install pygbif)"
213 " or ensure that it is on path"
214 " (use PYTHONPATH variable)."))
215
216 # Parse input options
217 output = options['output']
218 mask = options['mask']
219 species_maps = flags['i']
220 no_region_limit = flags['r']
221 no_topo = flags['b']
222 print_species = flags['p']
223 print_species_table = flags['t']
224 print_species_shell = flags['g']
225 print_occ_number = flags['o']
226 allow_no_geom = flags['n']
227 hasGeoIssue = flags['s']
228 taxa_list = options['taxa'].split(',')
229 institutionCode = options['institutioncode']
230 basisofrecord = options['basisofrecord']
231 recordedby = options['recordedby'].split(',')
232 date_from = options['date_from']
233 date_to = options['date_to']
234 country = options['country']
235 continent = options['continent']
236 rank = options['rank']
237
238 # Define static variable
239 #Initialize cat
240 cat = 0
241 # Number of occurrences to fetch in one request
242 chunk_size = 300
243 # lat/lon proj string
244 latlon_crs = ['+proj=longlat +no_defs +a=6378137 +rf=298.257223563 +towgs84=0.000,0.000,0.000',
245 '+proj=longlat +no_defs +a=6378137 +rf=298.257223563 +towgs84=0,0,0,0,0,0,0']
246 # List attributes available in Darwin Core
247 # not all attributes are returned in each request
248 # to avoid key errors when accessing the dictionary returned by pygbif
249 # presence of DWC keys in the returned dictionary is checked using this list
250 # The number of keys in this list has to be equal to the number of columns
251 # in the attribute table and the attributes written for each occurrence
252 dwc_keys = ['key', 'taxonRank', 'taxonKey', 'taxonID', 'scientificName',
253 'species', 'speciesKey', 'genericName', 'genus', 'genusKey',
254 'family', 'familyKey', 'order', 'orderKey', 'class',
255 'classKey', 'phylum', 'phylumKey', 'kingdom', 'kingdomKey',
256 'eventDate', 'verbatimEventDate', 'startDayOfYear',
257 'endDayOfYear', 'year', 'month', 'day', 'occurrenceID',
258 'occurrenceStatus', 'occurrenceRemarks', 'Habitat',
259 'basisOfRecord', 'preparations', 'sex', 'type', 'locality',
260 'verbatimLocality', 'decimalLongitude', 'decimalLatitude',
261 'geodeticDatum', 'higerGeography', 'continent', 'country',
262 'countryCode', 'stateProvince', 'gbifID', 'protocol',
263 'identifier', 'recordedBy', 'identificationID', 'identifiers',
264 'dateIdentified', 'modified', 'institutionCode',
265 'lastInterpreted', 'lastParsed', 'references', 'relations',
266 'catalogNumber', 'occurrenceDetails', 'datasetKey',
267 'datasetName', 'collectionCode', 'rights', 'rightsHolder',
268 'license', 'publishingOrgKey', 'publishingCountry',
269 'lastCrawled', 'specificEpithet', 'facts', 'issues',
270 'extensions', 'language']
271 # Deinfe columns for attribute table
272 cols = [('cat', 'INTEGER PRIMARY KEY'),
273 ('g_search', 'varchar(100)'),
274 ('g_key', 'integer'),
275 ('g_taxonrank', 'varchar(50)'),
276 ('g_taxonkey', 'integer'),
277 ('g_taxonid', 'varchar(50)'),
278 ('g_scientificname', 'varchar(255)'),
279 ('g_species', 'varchar(255)'),
280 ('g_specieskey', 'integer'),
281 ('g_genericname', 'varchar(255)'),
282 ('g_genus', 'varchar(50)'),
283 ('g_genuskey', 'integer'),
284 ('g_family', 'varchar(50)'),
285 ('g_familykey', 'integer'),
286 ('g_order', 'varchar(50)'),
287 ('g_orderkey', 'integer'),
288 ('g_class', 'varchar(50)'),
289 ('g_classkey', 'integer'),
290 ('g_phylum', 'varchar(50)'),
291 ('g_phylumkey', 'integer'),
292 ('g_kingdom', 'varchar(50)'),
293 ('g_kingdomkey', 'integer'),
294 ('g_eventdate', 'text'),
295 ('g_verbatimeventdate', 'varchar(50)'),
296 ('g_startDayOfYear', 'integer'),
297 ('g_endDayOfYear', 'integer'),
298 ('g_year', 'integer'),
299 ('g_month', 'integer'),
300 ('g_day', 'integer'),
301 ('g_occurrenceid', 'varchar(255)'),
302 ('g_occurrenceStatus', 'varchar(50)'),
303 ('g_occurrenceRemarks', 'varchar(50)'),
304 ('g_Habitat', 'varchar(50)'),
305 ('g_basisofrecord', 'varchar(50)'),
306 ('g_preparations', 'varchar(50)'),
307 ('g_sex', 'varchar(50)'),
308 ('g_type', 'varchar(50)'),
309 ('g_locality', 'varchar(255)'),
310 ('g_verbatimlocality', 'varchar(255)'),
311 ('g_decimallongitude', 'double precision'),
312 ('g_decimallatitude', 'double precision'),
313 ('g_geodeticdatum', 'varchar(50)'),
314 ('g_higerGeography', 'varchar(255)'),
315 ('g_continent', 'varchar(50)'),
316 ('g_country', 'varchar(50)'),
317 ('g_countryCode', 'varchar(50)'),
318 ('g_stateProvince', 'varchar(50)'),
319 ('g_gbifid', 'varchar(255)'),
320 ('g_protocol', 'varchar(255)'),
321 ('g_identifier', 'varchar(50)'),
322 ('g_recordedby', 'varchar(255)'),
323 ('g_identificationid', 'varchar(255)'),
324 ('g_identifiers', 'text'),
325 ('g_dateidentified', 'text'),
326 ('g_modified', 'text'),
327 ('g_institutioncode', 'varchar(50)'),
328 ('g_lastinterpreted', 'text'),
329 ('g_lastparsed', 'text'),
330 ('g_references', 'varchar(255)'),
331 ('g_relations', 'text'),
332 ('g_catalognumber', 'varchar(50)'),
333 ('g_occurrencedetails', 'text'),
334 ('g_datasetkey', 'varchar(50)'),
335 ('g_datasetname', 'varchar(255)'),
336 ('g_collectioncode', 'varchar(50)'),
337 ('g_rights', 'varchar(255)'),
338 ('g_rightsholder', 'varchar(255)'),
339 ('g_license', 'varchar(50)'),
340 ('g_publishingorgkey', 'varchar(50)'),
341 ('g_publishingcountry', 'varchar(50)'),
342 ('g_lastcrawled', 'text'),
343 ('g_specificepithet', 'varchar(50)'),
344 ('g_facts', 'text'),
345 ('g_issues', 'text'),
346 ('g_extensions', 'text'),
347 ('g_language', 'varchar(50)')]
348
349 set_output_encoding()
350 # Set temporal filter if requested by user
351 # Initialize eventDate filter
352 eventDate = None
353 # Check if date from is compatible (ISO compliant)
354 if date_from:
355 try:
356 parse(date_from)
357 except:
358 grass.fatal("Invalid invalid start date provided")
359
360 if date_from and not date_to:
361 eventDate = '{}'.format(date_from)
362 # Check if date to is compatible (ISO compliant)
363 if date_to:
364 try:
365 parse(date_to)
366 except:
367 grass.fatal("Invalid invalid end date provided")
368 # Check if date to is after date_from
369 if parse(date_from) < parse(date_to):
370 eventDate = '{},{}'.format(date_from, date_to)
371 else:
372 grass.fatal("Invalid date range: End date has to be after start date!")
373 # Set filter on basisOfRecord if requested by user
374 if basisofrecord == 'ALL':
375 basisOfRecord = None
376 else:
377 basisOfRecord = basisofrecord
378 # Allow also occurrences with spatial issues if requested by user
379 hasGeospatialIssue = False
380 if hasGeoIssue:
381 hasGeospatialIssue = True
382 # Allow also occurrences without coordinates if requested by user
383 hasCoordinate = True
384 if allow_no_geom:
385 hasCoordinate = False
386
387 # Set reprojection parameters
388 # Set target projection of current LOCATION
389 target_crs = grass.read_command('g.proj', flags='fj').rstrip(os.linesep)
390 target = osr.SpatialReference(target_crs)
391 target.ImportFromProj4(target_crs)
392 if target == 'XY location (unprojected)':
393 grass.fatal("Sorry, XY locations are not supported!")
394
395 # Set source projection from GBIF
396 source = osr.SpatialReference()
397 source.ImportFromEPSG(4326)
398 if target_crs not in latlon_crs:
399 transform = osr.CoordinateTransformation(source, target)
400 reverse_transform = osr.CoordinateTransformation(target, source)
401
402 # Generate WKT polygon to use for spatial filtering if requested
403 if mask:
404 if len(mask.split('@')) == 2:
405 m = VectorTopo(mask.split('@')[0], mapset=mask.split('@')[1])
406 else:
407 m = VectorTopo(mask)
408 if not m.exist():
409 grass.fatal('Could not find vector map <{}>'.format(mask))
410 m.open('r')
411 if not m.is_open():
412 grass.fatal('Could not open vector map <{}>'.format(mask))
413
414 # Use map Bbox as spatial filter if map contains <> 1 area
415 if m.number_of('areas') == 1:
416 region_pol = [area.to_wkt() for area in m.viter("areas")][0]
417 else:
418 bbox = str(m.bbox()).replace('Bbox(', '').replace(' ', '').rstrip(')').split(',')
419 region_pol = 'POLYGON(({0} {1}, {0} {3}, {2} {3}, {2} {1}, {0} {1}))'.format(bbox[2],
420 bbox[0], bbox[3], bbox[1])
421 m.close()
422 else:
423 # Do not limit import spatially if LOCATION is able to take global data
424 if no_region_limit:
425 if target_crs not in latlon_crs:
426 grass.fatal('Import of data from outside the current region is'
427 'only supported in a WGS84 location!')
428 region_pol = None
429 else:
430 # Limit import spatially to current region
431 # if LOCATION is !NOT! able to take global data
432 # to avoid pprojection ERRORS
433 region = grass.parse_command('g.region', flags='g')
434 region_pol = 'POLYGON(({0} {1}, {0} {3}, {2} {3}, {2} {1}, {0} {1}))'.format(region['e'],
435 region['n'], region['w'], region['s'])
436
437 # Do not reproject in latlon LOCATIONS
438 if target_crs not in latlon_crs:
439 pol = ogr.CreateGeometryFromWkt(region_pol)
440 pol.Transform(reverse_transform)
441 pol = pol.ExportToWkt()
442 else:
443 pol = region_pol
444
445 # Create output map if not output maps for each species are requested
446 if not species_maps and not print_species and not print_species_shell and not print_occ_number and not print_species_table:
447 mapname = output
448 new = Vector(mapname)
449 new.open('w', tab_name=mapname, tab_cols=cols)
450 cat = 1
451
452 # Import data for each species
453 for s in taxa_list:
454 # Get the taxon key if not the taxon key is provided as input
455 try:
456 key = int(s)
457 except:
458 try:
459 species_match = species.name_backbone(s, rank=rank,
460 strict=False,
461 verbose=True)
462 key = species_match['usageKey']
463 except:
464 grass.error('Data request for taxon {} failed. Are you online?'.format(s))
465 continue
466
467 # Return matching taxon and alternatives and exit
468 if print_species:
469 print('Matching taxon for {} is:'.format(s))
470 print('{} {}'.format(species_match['scientificName'], species_match['status']))
471 if 'alternatives' in list(species_match.keys()):
472 print('Alternative matches might be:'.format(s))
473 for m in species_match['alternatives']:
474 print('{} {}'.format(m['scientificName'], m['status']))
475 else:
476 print('No alternatives found for the given taxon')
477 continue
478 if print_species_shell:
479 print('match={}'.format(species_match['scientificName']))
480 if 'alternatives' in list(species_match.keys()):
481 alternatives = []
482 for m in species_match['alternatives']:
483 alternatives.append(m['scientificName'])
484 print('alternatives={}'.format(','.join(alternatives)))
485 continue
486 if print_species_table:
487 if 'alternatives' in list(species_match.keys()):
488 if len(species_match['alternatives']) == 0:
489 print('{0}|{1}|{2}|'.format(s, key, species_match['scientificName']))
490 else:
491 alternatives = []
492 for m in species_match['alternatives']:
493 alternatives.append(m['scientificName'])
494 print('{0}|{1}|{2}|{3}'.format(s, key, species_match['scientificName'],
495 ','.join(alternatives)))
496 continue
497 try:
498 returns_n = occurrences.search(taxonKey=key,
499 hasGeospatialIssue=hasGeospatialIssue,
500 hasCoordinate=hasCoordinate,
501 institutionCode=institutionCode,
502 basisOfRecord=basisOfRecord,
503 recordedBy=recordedby,
504 eventDate=eventDate,
505 continent=continent,
506 country=country,
507 geometry=pol,
508 limit=1)['count']
509 except:
510 grass.error('Data request for taxon {} faild. Are you online?'.format(s))
511 returns_n = 0
512
513 # Exit if search does not give a return
514 # Print only number of returns for the given search and exit
515 if print_occ_number:
516 grass.message('Found {0} occurrences for taxon {1}...'.format(returns_n, s))
517 continue
518 elif returns_n <= 0:
519 grass.warning('No occurrences for current search for taxon {0}...'.format(s))
520 continue
521 elif returns_n >= 200000:
522 grass.warning('Your search for {1} returns {0} records.\n'
523 'Unfortunately, the GBIF search API is limited to 200,000 records per request.\n'
524 'The download will be incomplete. Please consider to split up your search.'.format(returns_n, s))
525
526 # Get the number of chunks to download
527 chunks = int(math.ceil(returns_n / float(chunk_size)))
528 grass.verbose('Downloading {0} occurrences for taxon {1}...'.format(returns_n, s))
529
530 # Create a map for each species if requested using map name as suffix
531 if species_maps:
532 mapname = '{}_{}'.format(s.replace(' ', '_'), output)
533
534 new = Vector(mapname)
535 new.open('w', tab_name=mapname, tab_cols=cols)
536 cat = 0
537
538 # Download the data from GBIF
539 for c in range(chunks):
540 # Define offset
541 offset = c * chunk_size
542 # Adjust chunk_size to the hard limit of 200,000 records in GBIF API
543 # if necessary
544 if offset + chunk_size >= 200000:
545 chunk_size = 200000 - offset
546 # Get the returns for the next chunk
547 returns = occurrences.search(taxonKey=key,
548 hasGeospatialIssue=hasGeospatialIssue,
549 hasCoordinate=hasCoordinate,
550 institutionCode=institutionCode,
551 basisOfRecord=basisOfRecord,
552 recordedBy=recordedby,
553 eventDate=eventDate,
554 continent=continent,
555 country=country,
556 geometry=pol,
557 limit=chunk_size,
558 offset=offset)
559
560 # Write the returned data to map and attribute table
561 for res in returns['results']:
562 if target_crs not in latlon_crs:
563 point = ogr.CreateGeometryFromWkt('POINT ({} {})'.format(res['decimalLongitude'], res['decimalLatitude']))
564 point.Transform(transform)
565 x = point.GetX()
566 y = point.GetY()
567 else:
568 x = res['decimalLongitude']
569 y = res['decimalLatitude']
570
571 point = Point(x, y)
572
573 for k in dwc_keys:
574 if k not in list(res.keys()):
575 res.update({k: None})
576
577 cat = cat + 1
578 new.write(point, cat=cat, attrs=(
579 '{}'.format(s),
580 res['key'],
581 res['taxonRank'],
582 res['taxonKey'],
583 res['taxonID'],
584 res['scientificName'],
585 res['species'],
586 res['speciesKey'],
587 res['genericName'],
588 res['genus'],
589 res['genusKey'],
590 res['family'],
591 res['familyKey'],
592 res['order'],
593 res['orderKey'],
594 res['class'],
595 res['classKey'],
596 res['phylum'],
597 res['phylumKey'],
598 res['kingdom'],
599 res['kingdomKey'],
600 '{}'.format(res['eventDate']) if res['eventDate'] else None,
601 '{}'.format(res['verbatimEventDate']) if res['verbatimEventDate'] else None,
602 res['startDayOfYear'],
603 res['endDayOfYear'],
604 res['year'],
605 res['month'],
606 res['day'],
607 res['occurrenceID'],
608 res['occurrenceStatus'],
609 res['occurrenceRemarks'],
610 res['Habitat'],
611 res['basisOfRecord'],
612 res['preparations'],
613 res['sex'],
614 res['type'],
615 res['locality'],
616 res['verbatimLocality'],
617 res['decimalLongitude'],
618 res['decimalLatitude'],
619 res['geodeticDatum'],
620 res['higerGeography'],
621 res['continent'],
622 res['country'],
623 res['countryCode'],
624 res['stateProvince'],
625 res['gbifID'],
626 res['protocol'],
627 res['identifier'],
628 res['recordedBy'],
629 res['identificationID'],
630 ','.join(res['identifiers']),
631 '{}'.format(res['dateIdentified']) if res['dateIdentified'] else None,
632 '{}'.format(res['modified']) if res['modified'] else None,
633 res['institutionCode'],
634 '{}'.format(res['lastInterpreted']) if res['lastInterpreted'] else None,
635 '{}'.format(res['lastParsed']) if res['lastParsed'] else None,
636 res['references'],
637 ','.join(res['relations']),
638 res['catalogNumber'],
639 '{}'.format(res['occurrenceDetails']) if res['occurrenceDetails'] else None,
640 res['datasetKey'],
641 res['datasetName'],
642 res['collectionCode'],
643 res['rights'],
644 res['rightsHolder'],
645 res['license'],
646 res['publishingOrgKey'],
647 res['publishingCountry'],
648 '{}'.format(res['lastCrawled']) if res['lastCrawled'] else None,
649 res['specificEpithet'],
650 ','.join(res['facts']),
651 ','.join(res['issues']),
652 ','.join(res['extensions']),
653 res['language'],))
654
655 cat = cat + 1
656
657 # Close the current map if a map for each species is requested
658 if species_maps:
659 new.table.conn.commit()
660 new.close()
661 if not no_topo:
662 grass.run_command('v.build', map=mapname, option='build')
663
664 # Close the output map if not a map for each species is requested
665 if not species_maps and not print_species and not print_species_shell and not print_occ_number and not print_species_table:
666 new.table.conn.commit()
667 new.close()
668 if not no_topo:
669 grass.run_command('v.build', map=mapname, option='build')
670
671# Run the module
672# ToDo: Add an atexit procedure which closes and removes the current map
673if __name__ == "__main__":
674 options, flags = grass.parser()
675 sys.exit(main())
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