def generateTaxonReport(tNode, results, subDirectory):
workingResults = subsetResults(taxonId=int(tNode['index']))
fn = "report.html"
baseDir = os.path.join(reportDir, subDirectory)
print baseDir
# Make directory if it does not exist
if not os.path.exists(baseDir):
os.makedirs(baseDir)
outFn = os.path.join(baseDir, fn)
with open(outFn, 'w') as outF:
outF.write('<html>\n')
outF.write(' <head>\n')
outF.write(' <title>Report for %s - %s</title>\n' % (tNode['rank'], tNode['name']))
outF.write(' </head>\n')
outF.write(' <body>\n')
outF.write(' <h1>%s - %s</h1>\n' % (tNode['rank'], tNode['name']))
if tNode.has_key('taxon_name'):
outF.write(' <h3>Taxon Name: %s</h3>\n' % tNode['taxon_name'])
outF.write(' <br /><br />\n')
# Write out children
if tNode.has_key('children'):
outF.write(' <h2>Children</h2>\n')
outF.write(' <ul>\n')
for child in tNode['children']:
sDir = '%s/%s' % (subDirectory, child['name'])
try:
outF.write(' <li><a href="%s/report.html">%s</a></li>\n' % (sDir, child['name']))
except:
pass
generateTaxonReport(child, results, sDir)
outF.write(' </ul>\n')
outF.write(' <br /><br />\n')
# Global top 10
top10 = getHighestCounts(workingResults)
outF.write(' <h2>Global Top 10</h2>\n')
outF.write(' <ol>\n')
for r in top10:
try:
outF.write(' <li>%s : %s</li>\n' % (PROVIDERS[r[0]], r[3]))
except:
pass
outF.write(' </ol>\n')
outF.write(' <br /><br />\n')
# For each continent
outF.write(' <h2>Continents Top 10</h2>\n')
for k in CONTINENTS_LOOKUP:
regionId = CONTINENTS_LOOKUP[k]
continentTop10 = getHighestCounts(subsetResults(results=workingResults, regionId=regionId))
if len(continentTop10) > 0:
outF.write(' <h3>%s</h3>\n' % k)
outF.write(' <ol>\n')
for r in continentTop10:
try:
outF.write(' <li>%s : %s</li>\n' % (PROVIDERS[r[0]], r[3]))
except:
pass
outF.write(' </ol>\n')
outF.write(' <br /><br />')
outF.write(' <br /><br />\n')
# For each country
outF.write(' <h2>Countries Top 10</h2>\n')
for k in COUNTRIES_LOOKUP:
regionId = COUNTRIES_LOOKUP[k]
countryTop10 = getHighestCounts(subsetResults(results=workingResults, regionId=regionId))
if len(countryTop10) > 0:
outF.write(' <h3>%s</h3>\n' % k)
outF.write(' <ol>\n')
for r in countryTop10:
try:
outF.write(' <li>%s : %s</li>\n' % (PROVIDERS[r[0]], r[3]))
except:
pass
outF.write(' </ol>\n')
outF.write(' <br /><br />\n')
outF.write(' <br /><br />\n')
# For each state
outF.write(' <h2>States Top 10</h2>\n')
for k in STATES_LOOKUP:
regionId = STATES_LOOKUP[k]
statesTop10 = getHighestCounts(subsetResults(results=workingResults, regionId=regionId))
if len(statesTop10) > 0:
outF.write(' <h3>%s</h3>\n' % k)
outF.write(' <ol>\n')
for r in statesTop10:
try:
outF.write(' <li>%s : %s</li>\n' % (PROVIDERS[r[0]], r[3]))
except:
pass
outF.write(' </ol>\n')
outF.write(' <br /><br />\n')
# For each ocean
outF.write(' <h2>Oceans Top 10</h2>\n')
for k in OCEANS_LOOKUP:
regionId = OCEANS_LOOKUP[k]
oceansTop10 = getHighestCounts(subsetResults(results=workingResults, regionId=regionId))
if len(oceansTop10) > 0:
outF.write(' <h3>%s</h3>\n' % k)
outF.write(' <ol>\n')
for r in oceansTop10:
try:
outF.write(' <li>%s : %s</li>\n' % (PROVIDERS[r[0]], r[3]))
except:
pass
outF.write(' </ol>\n')
outF.write(' <br /><br />\n')
outF.write(' </body>\n')
outF.write('</html>')
outF.write(' <br /><br />\n')
# For each ocean
outF.write(' <h2>Oceans Top 10</h2>\n')
for k in OCEANS_LOOKUP:
regionId = OCEANS_LOOKUP[k]
oceansTop10 = getHighestCounts(subsetResults(results=workingResults, regionId=regionId))
if len(oceansTop10) > 0:
outF.write(' <h3>%s</h3>\n' % k)
outF.write(' <ol>\n')
for r in oceansTop10:
try:
outF.write(' <li>%s : %s</li>\n' % (PROVIDERS[r[0]], r[3]))
except:
pass
outF.write(' </ol>\n')
outF.write(' <br /><br />\n')
outF.write(' </body>\n')
outF.write('</html>')
# .............................................................................
if __name__ == "__main__":
import json
taxTreeFn = "/home/cjgrady/workspace/occDataMiningPOC/data/taxonTree/fishTaxa.json"
# May need to make directories first
with open(taxTreeFn) as taxF:
taxonTree = json.load(taxF)
results = subsetResults()
generateTaxonReport(taxonTree, results, reportDir)
