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harvest_metadata.py
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harvest_metadata.py
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#!/usr/bin/python2.7
""" Script for harvesting metadata from a variety of protocols i.e:
- OAI-PMH
- OGC-CSW
- OpenSearch
Inspired by:
- harvest-metadata from https://github.com/steingod/mdharvest/tree/master/src
- code from http://lightonphiri.org/blog/metadata-harvesting-via-oai-pmh-using-python
AUTHOR: Trygve Halsne, 25.01.2017
USAGE:
Harvesting initiated with internal methods in class. Run this script and
edit the main() method or import class in other scripts.
COMMENTS (for further development):
- Implement hprotocol: ISO 19115
- Does OGC-CSW metadata have some kind of resumptionToken analog?
"""
import urllib2 as ul2
import urllib as ul
from xml.dom.minidom import parseString
import codecs
import sys
from datetime import datetime
import lxml.etree as ET
class MetadataHarvester(object):
""" Creates metadata-harvester object with methods for harvesting and writing.
"""
def __init__(self, baseURL, records, outputDir, hProtocol, username=None, pw=None):
""" Set initial variables in class
baseURL - URL to repository i.e. Internet host and port
records - key-value arguments for querying database
outputDir - Output directory for data harvested
hProtocol - Harvesting protocol. E.g. OAI-PMH, OpenSearch
username - In case authentication is required from server
pw - In case authentication is required from server
"""
self.baseURL = baseURL
self.records = records
self.outputDir = outputDir
self.hProtocol = hProtocol
self.username = username
self.pw = pw
def harvest(self):
""" Inititates harvester. Chooses strategy depending on
harvesting protocol
"""
baseURL, records, hProtocol, uname, pw = self.baseURL, self.records, self.hProtocol, self.username, self.pw
if hProtocol == 'OAI-PMH':
getRecordsURL = str(baseURL + records)
print "Harvesting metadata from: \n\tURL: %s \n\tprotocol: %s \n" % (getRecordsURL,hProtocol)
start_time = datetime.now()
# Initial phase
resumptionToken = self.oaipmh_resumptionToken(getRecordsURL)
dom = self.harvestContent(getRecordsURL)
if dom != None:
self.oaipmh_writeToFile(dom)
pageCounter = 1
while resumptionToken != []:
print "\n"
print "Handling resumptionToken: %.0f \n" % pageCounter
resumptionToken = ul.urlencode({'resumptionToken':resumptionToken}) # create resumptionToken URL parameter
getRecordsURLLoop = str(baseURL+'?verb=ListRecords&'+resumptionToken)
print getRecordsURLLoop
dom = self.harvestContent(getRecordsURLLoop)
if dom != None:
self.oaipmh_writeToFile(dom)
else:
print "dom = " + str(dom) + ', for page ' + str(pageCounter)
resumptionToken = self.oaipmh_resumptionToken(getRecordsURLLoop)
pageCounter += 1
print "\n\nHarvesting took: %s [h:mm:ss]" % str(datetime.now()-start_time)
elif hProtocol == 'OGC-CSW':
getRecordsURL = str(baseURL + records)
print "Harvesting metadata from: \n\tURL: %s \n\tprotocol: %s \n" % (getRecordsURL,hProtocol)
start_time = datetime.now()
dom = self.harvestContent(getRecordsURL)
if dom != None:
self.ogccsw_writeCSWISOtoFile(dom)
print "\n\nHarvesting took: %s [h:mm:ss]\n" % str(datetime.now()-start_time)
elif hProtocol == "OpenSearch":
getRecordsURL = str(baseURL + records)
print "Harvesting metadata from: \n\tURL: %s \n\tprotocol: %s \n" % (getRecordsURL,hProtocol)
start_time = datetime.now()
dom = self.harvestContent(getRecordsURL,credentials=True,uname=uname,pw=pw)
if dom != None:
self.openSearch_writeENTRYtoFile(dom)
# get all results by iteration
tree = ET.fromstring(dom.toxml())
nsmap = tree.nsmap
default_ns = nsmap.pop(None)
totalResults = int(tree.xpath('./opensearch:totalResults',namespaces=nsmap)[0].text)
startIndex = int(tree.xpath('./opensearch:startIndex',namespaces=nsmap)[0].text)
itemsPerPage = int(tree.xpath('./opensearch:itemsPerPage',namespaces=nsmap)[0].text)
current_results = itemsPerPage
# looping through the rest of the results updating start and rows values
if totalResults > itemsPerPage:
print "\nCould not display all results on single page. Starts iterating..."
while current_results < totalResults:
print "\n\n\tHandling results (%s - %s) / %s" %(current_results, current_results + itemsPerPage, totalResults)
from_to = "?start=%s&rows=%s&" % (current_results,itemsPerPage)
getRecordsURLLoop = str(baseURL + from_to + records[1:])
dom = self.harvestContent(getRecordsURLLoop,credentials=True,uname=uname,pw=pw)
if dom != None:
self.openSearch_writeENTRYtoFile(dom)
current_results += itemsPerPage
print "\n\nHarvesting took: %s [h:mm:ss]\n" % str(datetime.now()-start_time)
else:
print '\nProtocol %s is not accepted.' % hProtocol
exit()
def openSearch_writeENTRYtoFile(self,dom):
""" Write OpenSearch ENTRY elements in fom to file"""
print("Writing OpenSearch ENTRY metadata elements to disk... ")
entries = dom.getElementsByTagName('entry')
print "\tFound %.f ENTRY elements." % entries.length
counter = 1
has_fname = False
for entry in entries:
# Depending on usage; choose naming convention
fname = entry.getElementsByTagName('title')[0].childNodes[0].nodeValue
if fname != None:
has_fname = True
"""
# Use UUID as naming convention
str_elements = entry.getElementsByTagName('str')
for s in reversed(str_elements):
if s.getAttribute('name') == 'uuid':
fname = s.childNodes[0].nodeValue
has_fname = True
break;
"""
if has_fname:
sys.stdout.write('\tWriting OpenSearch ENTRY elements %.f / %d \r' %(counter,entries.length))
sys.stdout.flush()
self.write_to_file(entry,fname)
counter += 1
else:
sys.stdout.write('\tNo filename availible. Not able to write OpenSearch entry (%s) to file' % dom)
def ogccsw_writeCSWISOtoFile(self,dom):
""" Write CSW-ISO elements in dom to file """
print("Writing CSW ISO metadata elements to disk... ")
mD_metadata_elements = dom.getElementsByTagName('gmd:MD_Metadata')
mDsize = mD_metadata_elements.length
size_idInfo = dom.getElementsByTagName('gmd:identificationInfo').length
print "\tFound %.f ISO records." %mDsize
if mDsize>0:
counter = 1
for md_element in mD_metadata_elements:
# Check if element contains valid metadata
idInfo = md_element.getElementsByTagName('gmd:identificationInfo')
try:
# Use unique ID as filename
fileIdentifier = md_element.getElementsByTagName('gmd:fileIdentifier')[0]
cs = fileIdentifier.getElementsByTagName('gco:CharacterString')[0]
fname = cs.firstChild.nodeValue
except:
print "\n\tMetadata element did not contain unique ID"
fname = "tmp_" + str(counter)
continue
if idInfo !=[]:
sys.stdout.write('\tWriting CSW-ISO elements %.f / %d \r' %(counter,size_idInfo))
sys.stdout.flush()
self.write_to_file(md_element,fname)
counter += 1
def oaipmh_writeToFile(self, dom):
""" Write OAI-PMH metadata elements to file
dom - minidom object
NOTE: If record contains header, extract unique identifier and
check if dataset is deleted by means of having an attribute.
"""
print "Writing OAI-PMH metadata to disk... "
record_elements = dom.getElementsByTagName('record')
nb_elements = len(record_elements)
if nb_elements != 0:
counter = 1
for record in record_elements:
for child in record.childNodes:
if str(child.nodeName) == 'header':
out_fname = child.getElementsByTagName('identifier')[0].childNodes[0].nodeValue
has_attrib = child.hasAttributes()
if not has_attrib:
sys.stdout.write('\tWriting metadata element %.f / %d \r' %(counter,nb_elements))
sys.stdout.flush()
md_element = record.getElementsByTagName('metadata')[0]
for cn in md_element.childNodes:
if cn.hasChildNodes():
element = cn
break
if 'element' in locals():
self.write_to_file(element,out_fname)
else:
print "\tRecord contains insufficient metadata. Change metadataPrefix?"
counter += 1
else:
print "\tRecord: %s is deleted. Thus, not harvested." % out_fname
else:
print "\trecords did not contain DIF elements"
def write_to_file(self, root, fname):
""" Function for storing harvested metadata to file
- root: root Element to be stored. <DOM Element>
- fname: unique id. <String>
- output_path: output directory. <String>
"""
outputDir = self.outputDir
total_fname = outputDir + fname + '.xml'
output = codecs.open(total_fname ,'w','utf-8')
output.write(root.toxml())
output.close()
def harvestContent(self,URL,credentials=False,uname="foo",pw="bar"):
""" Function for harvesting content from URL."""
try:
if not credentials:
file = ul2.urlopen(URL,timeout=40) # Timeout depends on user/server
data = file.read()
file.close()
return parseString(data)
else:
p = ul2.HTTPPasswordMgrWithDefaultRealm()
p.add_password(None, URL, uname, pw)
handler = ul2.HTTPBasicAuthHandler(p)
opener = ul2.build_opener(handler)
ul2.install_opener(opener)
return parseString(ul2.urlopen(URL).read())
except ul2.HTTPError:
print("There was an error with the URL request. " +
"Could not open or parse content from: \n\t %s" % URL)
def oaipmh_resumptionToken(self,URL):
""" Function for handeling resumptionToken in OAI-PMH"""
try:
file = ul2.urlopen(URL, timeout=40)
data = file.read()
file.close()
dom = parseString(data)
if dom.getElementsByTagName('resumptionToken').length == 0:
return dom.getElementsByTagName('resumptionToken')
else:
if dom.getElementsByTagName('resumptionToken')[0].firstChild != None:
return dom.getElementsByTagName('resumptionToken')[0].firstChild.nodeValue
else:
return []
except ul2.HTTPError:
print "There was an error with the URL request"
def main():
''' Main method with examples for isolated running of script'''
baseURL = 'https://oaipmh.met.no/oai/'
records = '?verb=ListRecords&set=NBS&metadataPrefix=mmd'
outputDir = 'output/'
hProtocol = 'OAI-PMH'
#mh = MetadataHarvester(baseURL,records, outputDir, hProtocol)
#mh.harvest()
'''
baseURL = 'http://metadata.bgs.ac.uk/geonetwork/srv/en/csw'
records = '?SERVICE=CSW&VERSION=2.0.2&request=GetRecords&constraintLanguage=CQL_TEXT&typeNames=csw:Record&resultType=results&outputSchema=http://www.isotc211.org/2005/gmd'
outputDir = 'output/'
hProtocol = 'OGC-CSW'
mh2 = MetadataHarvester(baseURL,records, outputDir, hProtocol)
mh2.harvest()
'''
with open('myValues.txt','r') as code:
cred_tmp = code.readline()
cred = cred_tmp.split(';')
baseURL = 'https://colhub.met.no/search'
#records = '?q=*'
#records = '?q=platformname:Sentinel-1%20AND%20ingestionDate:[NOW-2DAY%20TO%20NOW]'
#records = '?q=S2A_MSIL1C*%20AND%20footprint:%22Intersects(POLYGON((-10.25%2071.41,%20-10.20%2070.61,%20-6.79%2070.60,%20-6.70%2071.44,%20-10.25%2071.41)))%22%20AND%20ingestiondate:[NOW-3HOUR%20TO%20NOW]'
records = '?&q=S1A_IW_GRDH_*'
records = '?&q=S3A_OL_1_EFR____20180213T101722_20180213T102022_20180214T135646_0179_028_008_1980_LN1_O_NT_002'
records = '?&q=(%20footprint:"Intersects(POLYGON((-10.84%2056.73,33.63%2056.73,33.63%2072.96,-10.84%2072.96,-10.84%2056.73)))"%20)%20AND%20ingestiondate:[NOW-2HOUR%20TO%20NOW]%20AND%20(platformname:Sentinel-1%20AND%20producttype:GRD)'
records = '?q=S2A_MSIL1C*%20AND%20(%20footprint:%22Intersects(POLYGON((-10.839960226907229%2056.73364306430818,33.632696023092755%2056.73364306430818,33.632696023092755%2072.96099707011066,-10.839960226907229%2072.96099707011066,-10.839960226907229%2056.73364306430818)))%22%20)%20AND%20ingestiondate:[2018-03-22T18:00:00.000Z%20TO%202018-03-22T20:00:59.999Z%20]'
outputDir = 'output/'
hProtocol = 'OpenSearch'
mh3 = MetadataHarvester(baseURL,records, outputDir, hProtocol,cred[0],cred[1])
mh3.harvest()
if __name__ == '__main__':
main()
# Some TEMPORARY VALUES
# List all recordsets: http://arcticdata.met.no/metamod/oai?verb=ListRecords&set=nmdc&metadataPrefix=dif
# List identifier: http://arcticdata.met.no/metamod/oai?verb=GetRecord&identifier=urn:x-wmo:md:no.met.arcticdata.test3::ADC_svim-oha-monthly&metadataPrefix=dif
# Recordset with resumptionToken: http://union.ndltd.org/OAI-PMH/?verb=ListRecords&metadataPrefix=oai_dc
# Recordset with DIF elements and resumptionToken (Slow server..): http://ws.pangaea.de/oai/provider?verb=ListRecords&metadataPrefix=dif
# Recordset with DIF elements and resumptionToken: https://esg.prototype.ucar.edu/oai/repository.htm?verb=ListRecords&metadataPrefix=dif
# Recordset with gcmd(DIF) elements: http://oai.nerc-bas.ac.uk:8080/oai/provider?verb=ListRecords&metadataPrefix=gcmd
# OGC-CSW recordset: http://metadata.bgs.ac.uk/geonetwork/srv/en/csw?SERVICE=CSW&VERSION=2.0.2&request=GetRecords&constraintLanguage=CQL_TEXT&typeNames=csw:Record&resultType=results&outputSchema=http://www.isotc211.org/2005/gmd
# OpenSearch from sentinel scihub: https://scihub.copernicus.eu/dhus/search?q=S2A*