dwca-python/coverage.py at master · godfoder/dwca-python · GitHub

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#!/usr/bin/env python

from __future__ importdivision
importoptparse
importos
importsys
importdwca
importjson
importpprint

parser=optparse.OptionParser()
parser.add_option("-f", "--file", help="DWC-a file to read")
parser.add_option("-q", "--quiet",
action="store_false", dest="verbose", default=True,
help="don't print status messages to stdout")
parser.add_option("-n", "--nocount", dest="count", action="store_false", default=True,
help="print out record counts")
parser.add_option("-j", "--json", action="store_true", default=False,
help="print out record JSON")

(options, args) =parser.parse_args()

coverage= { "Taxon": {
"Scientific Name": { "divisior": 1, "fields": ["dwc:scientificName"]},
"Taxon Rank": { "divisior": 1, "fields": ["dwc:taxonRank"]},
"Higher Order Taxa": { "divisior": 1, "fields": ["dwc:kingdom","dwc:family"]},
"Scientific Name Status": { "divisior": 1, "fields": ["dwc:scientificNameAuthorship","dwc:nomenclaturalStatus","dwc:dateIdentified","dwc:identifiedBy" ]},
"Remarks": { "divisior": 1, "fields": ["dwc:identificationRemarks"]},
 },
"Locality": {
"Decimal Coordiantes": { "divisior": 2, "fields": ["dwc:decimalLatitude","dwc:decimalLongitude"]},
"Verbatim Coordinates": { "divisior": 2, "fields": ["dwc:verbatimLatitude","dwc:verbatimLongitude"]},
"Administrative Boundaries": { "divisior": 4, "fields": ["dwc:continent","dwc:country","dwc:stateProvince","dwc:county"]},
"Water Body": { "divisior": 1, "fields": ["dwc:waterBody"]},
"Locality": { "divisior": 1, "fields": ["dwc:locality"]},
"Verbatim Locality": { "divisior": 1, "fields": ["dwc:verbatimLocality"]},
"Depth": { "divisior": 1, "fields": ["dwc:maximumDepthInMeters","dwc:maximumDepthInMeters"]},
"Elevation": { "divisior": 1, "fields": ["dwc:maximumElevationInMeters",""]},
"Identifier": { "divisior": 1, "fields": ["dwc:locationID"]},
 },
"Temporal": {
"Event Date": { "divisior": 1, "fields": ["dwc:eventDate"]},
"Verbatim Event Date": { "divisior": 1, "fields": ["dwc:verbatimEventDate"]},
 },
"Provenance": {
"Collector": { "divisior": 1, "fields": ["dwc:recordedBy","dwc:recordNumber"]},
"Basis of Record": { "divisior": 1, "fields": ["dwc:basisOfRecord"]},
"DwC Triple": { "divisior": 3, "fields": ["dwc:institutionCode","dwc:collectionCode","dwc:catalogNumber"]},
 },
 }

coverageInversion= {}
forlevelincoverage:
l=coverage[level]
forgroupinl:
g=l[group]
forkeying['fields']:
ifkeyincoverageInversion:
coverageInversion[key].append((level,group))
else:
coverageInversion[key] = [(level,group)]

ifoptions.file==None:
parser.print_help()
sys.exit(1)
else:
dwcaobj=dwca.Dwca(options.file)
keycounts= {"core": {}}
reccount= {"core": 0}
coverageIndex= {}
forrecordindwcaobj.core:
reccount["core"] +=1
forkeyinrecord:
ifkeyinkeycounts["core"]:
keycounts["core"][key] +=1
else:
keycounts["core"][key] =1

ifkeyincoverageInversion:
for (level,group) incoverageInversion[key]:
iflevelnotincoverageIndex:
coverageIndex[level] = {}
ifgroupnotincoverageIndex[level]:
coverageIndex[level][group] =0
coverageIndex[level][group] +=1
ifoptions.json:
print(json.dumps(record,separators=(',',':')))
fordwcrfindwcaobj.extensions:
keycounts[dwcrf.name] = {}
reccount[dwcrf.name] =0
forrecordindwcrf:
reccount[dwcrf.name] +=1
forkeyinrecord:
ifkeyinkeycounts[dwcrf.name]:
keycounts[dwcrf.name][key] +=1
else:
keycounts[dwcrf.name][key] =1
ifoptions.json:
print(json.dumps(record,separators=(',',':')))
pass
ifoptions.json:
print(json.dumps(dwcaobj.metadata,separators=(',',':')))
ifoptions.count:

forkeyinreccount:
cci=float(0)
ccc=0
count=reccount[key]
forreckeyinkeycounts[key]:
total=keycounts[key][reckey]
pct=total/count
cci+=pct
ccc+=1
print"{0}/{1}: {2}".format(key,reckey,pct*100)
ifkey=="core":
forlevelincoverageIndex:
print"Coverages for {0}".format(level)
forgroupincoverageIndex[level]:
ci=coverageIndex[level][group]
cic=coverage[level][group]['divisior']
cipct=ci/(count*cic) *100
print"Coverage Index for {0}/{1}: {2}".format(level,group,cipct)
print"Composite coverage index for {0}: {1}".format(key,cci/ccc*100)