#!/usr/bin/env python

# Extracts subpaths from a map spreadsheet

import csv

import os.path

import sys

sys.path.append(os.path.dirname(__file__)+"/../lib")

import opts

def all_not_none(list_):

    return reduce(lambda a, b: a and b, map(lambda e: e != None, list_))

def main():

    # Get subpath config from env vars

    config_names = ['subpath', 'new_root']

    env_names = []

    configs = map(lambda col: opts.get_env_vars(config_names, col, env_names),

        ['left', 'right'])

    if not all_not_none(configs): raise SystemExit(

        'Usage: '+opts.env_usage(env_names)+' '+sys.argv[0]+' <map >submap')

    # Transform map

    for config in configs:

        config['prefix'] = config['subpath']+config['new_root']

        config['prefix_len'] = len(config['prefix'])

    reader = csv.reader(sys.stdin)

    col_names = reader.next()[:2]

    # TODO: replace col_names with new_roots

    writer = csv.writer(sys.stdout)

    writer.writerow(col_names)

    for row in reader:

        if row[0].startswith(configs[0]['prefix']):

            assert row[1].startswith(configs[1]['prefix'])

            for idx in range(len(configs)):

                row[idx] = row[idx][configs[idx]['prefix_len']:]

            writer.writerow(row)

main()

#!/bin/bash

# Extracts plot subpaths from VegX-VegBank.csv

selfDir="$(dirname -- "$0")"

cd "$selfDir"

export left_subpath='*ID->' left_new_root='/*s/plotObservation/' \

right_subpath= right_new_root=

../scripts/util/submap <VegX-VegBank.csv >VegX-VegBank.plots.csv

VegX/*s/individualOrganismObservation/,VegBank/

*UniqueIdentifierID->/*s/plot/country,namedPlace[placeSystem=area|country|territory]/placeName

*UniqueIdentifierID->/*s/plot/county,namedPlace[placeSystem=county]/placeName

*UniqueIdentifierID->/*s/plot/geospatial/CoordinateUncertaintyInMeters,plot/locationAccuracy

*UniqueIdentifierID->/*s/plot/geospatial/DecimalLatitude,plot/realLatitude

*UniqueIdentifierID->/*s/plot/geospatial/DecimalLongitude,plot/realLongitude

*UniqueIdentifierID->/*s/plot/geospatial/FootprintWKT,plot/dsgpoly

*UniqueIdentifierID->/*s/plot/geospatial/maximumDepthInMeters,observation/waterDepth/max

*UniqueIdentifierID->/*s/plot/geospatial/maximumElevationInMeters,"plot/{elevation/max,elevationRange/to}"

*UniqueIdentifierID->/*s/plot/geospatial/minimumDepthInMeters,observation/waterDepth/min

*UniqueIdentifierID->/*s/plot/geospatial/minimumElevationInMeters,"plot/{elevation/min,elevationRange/from}"

*UniqueIdentifierID->/*s/plot/plotUniqueIdentifier,plot/authorPlotCode

*UniqueIdentifierID->/*s/plot/relatedSpatialItem/relatedItem[relationshipType=parentPlot]/relatedItemID->/*s/plot/plotUniqueIdentifier,plot/PARENT_ID->/plot/authorPlotCode

*UniqueIdentifierID->/*s/plot/simpleUserdefined[name=locality]/value,namedPlace/placeDescription

*UniqueIdentifierID->/*s/plot/state,namedPlace[placeSystem=region|state|province]/placeName

obsStartDate,"stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/collectionDate,observation/authorObsCode"

obsStartDate/_date/day,stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/collectionDate/_date/day

obsStartDate/_date/month,stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/collectionDate/_date/month

obsStartDate/_date/year,stemLocation/taxonInterpretation[PLANTCONCEPT_ID=]/collectionDate/_date/year