#!/usr/bin/env python """ MODULE: v.in.gbif AUTHOR(S): Helmut Kudrnovsky PURPOSE: Imports GBIF species distribution data by saving original data to a GDAL VRT and importing the VRT by v.in.ogr COPYRIGHT: (C) 2015 by the GRASS Development Team This program is free software under the GNU General Public License (>=v2). Read the file COPYING that comes with GRASS for details. """ #%module #% description: importing of GBIF species distribution data #% keyword: vector #% keyword: geometry #%end #%option G_OPT_F_INPUT #% key: input #% required: yes #%end #%option G_OPT_V_OUTPUT #% key: output #% description: name of imported GBIF data set #% required : yes #%end #%flag #% key: c #% description: Create GDAL VRT data set of GBIF data #% guisection: vrt #%end #%option G_OPT_M_DIR #% key: dir #% description: Directory where the output will be found #% required : no #% guisection: vrt #%end #%flag #% key: r #% description: Reproject data on-the-fly if no latlon (WGS84) location #%end import sys import os import csv import math import shutil import tempfile import grass.script as grass def main(): gbifraw = options['input'] gbifimported = options['output'] directory = options['dir'] move_vrt_gbif_to_dir = flags['c'] gbifvrt = gbifimported+'.vrt' gbif_vrt_layer = gbifimported gbifcsv = gbifimported+'.csv' reproject_gbif = flags['r'] global tmp # check for unsupported locations or unsupported combination of option and projected location in_proj = grass.parse_command('g.proj', flags='g') if in_proj['name'].lower() == 'xy_location_unprojected': grass.fatal(_("xy-locations are not supported")) # import GBIF data grass.message( "Starting importing GBIF data ..." ) grass.message( "preparing data for vrt ..." ) # new quoted GBIF csv file gbiftempdir = tempfile.gettempdir() new_gbif_csv = os.path.join( gbiftempdir, gbifcsv ) # quote raw data with open('%s' % (gbifraw), 'rb') as csvinfile: gbifreader = csv.reader(csvinfile, delimiter='\t') with open ('%s' % (new_gbif_csv), 'wb') as csvoutfile: gbifwriter = csv.writer(csvoutfile, quotechar='"', quoting=csv.QUOTE_ALL) for row in gbifreader: gbifwriter.writerow(row) grass.message( "----" ) # write vrt grass.message( "writing vrt ..." ) new_gbif_vrt = os.path.join( gbiftempdir, gbifvrt ) f = open('%s' % (new_gbif_vrt), 'wt') f.write(""" %s wkbPoint WGS84 """ % (gbif_vrt_layer, gbifcsv) ) f.close() grass.message( "----" ) # Give information where output file are saved grass.message( "GBIF vrt files:" ) grass.message( gbifvrt ) grass.message( "-" ) grass.message( gbifcsv ) grass.message( "----" ) # import GBIF vrt grass.message( "importing GBIF vrt ..." ) # reprojection-on-the-fly if flag r if reproject_gbif : grass.message( "reprojecting data on-the-fly ..." ) grass.run_command("v.import", input = new_gbif_vrt, output = gbifimported, quiet = True) # no reprojection-on-the-fly else: grass.run_command("v.in.ogr", input = new_gbif_vrt, layer = gbif_vrt_layer, output = gbifimported, quiet = True) grass.message( "..." ) # v.in.gbif done! grass.message( "importing GBIF data done!" ) # move vrt and csv to user defined directory if move_vrt_gbif_to_dir : grass.message( "----" ) grass.message( "Create GBIF vrt data files ..." ) shutil.move(new_gbif_vrt, directory) shutil.move(new_gbif_csv, directory) grass.message( "in following user defined directory:" ) grass.message( directory ) grass.message( "----" ) else: grass.message( "----") grass.message("Some clean up ...") os.remove("%s" % new_gbif_vrt) os.remove("%s" % new_gbif_csv) grass.message("Clean up done.") grass.message( "----") if __name__ == "__main__": options, flags = grass.parser() sys.exit(main())