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import_dataset.py
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import_dataset.py
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import csv
import os
from os.path import join
import lxml.html
from pyDataverse.exceptions import ApiAuthorizationError
from pyDataverse.api import Api
from requests import post
import json
import dvconfig
import lxml.etree as et
base_url = dvconfig.base_url
native_api_base_url = f'{base_url}/api'
api_token = dvconfig.api_token
dataverse_id = dvconfig.dataverse_name
input_path = dvconfig.liss_dc_path
release = 'no'
fail_counter = 0
total_counter = 0
ns = {
'xmlns': 'http://www.openarchives.org/OAI/2.0/',
'oai_dc': 'http://www.openarchives.org/OAI/2.0/oai_dc/',
'dc': 'http://purl.org/dc/elements/1.1/',
'xsi': 'http://www.w3.org/2001/XMLSchema-instance'
}
api = Api(base_url, api_token)
print('API status: ' + api.status)
# print(f'curl -u {api_token}: {base_url}/dvn/api/data-deposit/v1.1/swordv2/service-document')
def get_primitive_field(list_elements, typeName, typeClass='primitive', multiple=False):
result = dict()
result['typeName'] = typeName
result['multiple'] = multiple
result['typeClass'] = typeClass
if not multiple:
if isinstance(list_elements[0], str):
result['value'] = list_elements[0]
else:
result['value'] = list_elements[0].text
return result
else:
if isinstance(list_elements[0], str):
result['value'] = [i for i in list_elements]
else:
result['value'] = [i.text for i in list_elements]
return result
def get_compound_field(list_elements, typeName, inner_typeName, typeClass='compound', inner_typeClass='primitive', multiple=True, inner_multiple=False):
result = dict()
result['typeName'] = typeName
result['multiple'] = multiple
result['typeClass'] = typeClass
if multiple:
value_list = list()
for i in list_elements:
value_list.append({inner_typeName: get_primitive_field([i], inner_typeName, inner_typeClass, inner_multiple)})
result['value'] = value_list
return result
raise Exception('Does not support compound field with non-multiple value yet')
def get_pid(dom):
pids = dom.xpath('./dc:identifier', namespaces=ns)
is_doi: bool = False
protocol = None
authority = None
local_id = None
if pids is not None and len(pids) == 1:
print('checking pids')
pid_uri = pids[0].text
print(f'checking pids {pid_uri}')
"""if pid uri starts with doi.org set is_doi to True and protocol to doi"""
if pid_uri.lower().strip().startswith('https://doi.org/'):
is_doi = True
protocol = 'doi'
"""get all the components of the uri"""
pid_components: list = pid_uri.split('/')
if len(pid_components) == 5:
authority = pid_components[-2]
local_id = pid_components[-1]
return protocol, authority, local_id, is_doi
def convert_dc_to_dv_json(dc_root):
# dc_tags = ['title', 'creator', 'description', 'publisher', 'date', 'identifier', 'rights']
fields = list()
"""get pid"""
protocol, authority, local_id, is_doi = get_pid(dc_root)
pid = f'{protocol}:{authority}/{local_id}'
if is_doi:
result = {
'datasetVersion': {
"termsOfUse": "N/A",
'license': 'NONE',
'protocol': protocol,
'authority': authority,
'identifier': pid,
'metadataBlocks': {
'citation': {
'displayName': 'Citation Metadata',
'fields': [
]
}
}
}
}
else:
result = {
'datasetVersion': {
"termsOfUse": "N/A",
'license': 'NONE',
'metadataBlocks': {
'citation': {
'displayName': 'Citation Metadata',
'fields': [
]
}
}
}
}
# get subject
fields.append(get_primitive_field([f'Social Sciences'], 'subject', 'controlledVocabulary', True))
# # print(dc_root.xpath('./dc:identifier', namespaces=ns))
# ids = dc_root.xpath('./dc:identifier', namespaces=ns)
# if ids is not None and len(ids) > 0:
# # result['datasetVersion']['id'] = ids[0].text
# fields.append(get_compound_field(ids, 'otherId', 'otherIdValue'))
# print(dc_root.xpath('./dc:title', namespaces=ns))
titles = dc_root.xpath('./dc:title', namespaces=ns)
if titles is not None and len(titles) > 0:
fields.append(get_primitive_field([titles[0]], 'title'))
# print(dc_root.xpath('./dc:publisher', namespaces=ns))
publishers = dc_root.xpath('./dc:publisher', namespaces=ns)
publisher_dict = dict()
if publishers is not None and len(publishers) > 0:
publisher_dict = get_primitive_field(publishers, 'authorAffiliation')
# print(dc_root.xpath('./dc:creator', namespaces=ns))
creators = dc_root.xpath('./dc:creator', namespaces=ns)
if creators is not None and len(creators) > 0:
creators_dict = get_compound_field(creators, 'author', 'authorName', 'compound', 'primitive', True, False)
if publisher_dict is not None:
for i in creators_dict['value']:
i['authorAffiliation'] = publisher_dict
fields.append(creators_dict)
# print(dc_root.xpath('./dc:description', namespaces=ns))
descriptions = dc_root.xpath('./dc:description', namespaces=ns)
if descriptions is not None and len(descriptions) > 0:
fields.append(get_compound_field(descriptions, 'dsDescription', 'dsDescriptionValue', 'compound', 'primitive', True, False))
# add date as distributionDate
dates = dc_root.xpath('./dc:date', namespaces=ns)
if dates is not None and len(dates) > 0:
fields.append(get_primitive_field(dates, 'distributionDate'))
# add dataset contact
fields.append(get_compound_field(['[email protected]'], 'datasetContact', 'datasetContactEmail', 'compound', 'primitive', True, False))
# print(dc_root.xpath('./dc:date', namespaces=ns))
# print(dc_root.xpath('./dc:rights', namespaces=ns))
result['datasetVersion']['metadataBlocks']['citation']['fields'] = fields
return json.dumps(result), is_doi, pid
error_file = '/Users/vic/Documents/DANS/projects/ODISSEI/liss-data/liss-dc/error_file'
def write_error_to_file(resp, others=None):
with open(error_file, 'a+') as f:
json.dump(resp.json(), f)
if others is not None:
f.writelines(others)
f.writelines('\n')
def post_request(query_str, metadata=None, auth=False, params=None):
"""Make a POST request.
Parameters
----------
query_str : string
Query string for the request. Will be concatenated to
`native_api_base_url`.
metadata : string
Metadata as a json-formatted string. Defaults to `None`.
auth : bool
Should an api token be sent in the request. Defaults to `False`.
params : dict
Dictionary of parameters to be passed with the request.
Defaults to `None`.
Returns
-------
requests.Response
Response object of requests library.
"""
global fail_counter, total_counter
url = '{0}{1}'.format(native_api_base_url, query_str)
if auth:
if api_token:
if not params:
params = {}
params['key'] = api_token
else:
ApiAuthorizationError(
'ERROR: POST - Api token not passed to '
'`post_request` {}.'.format(url)
)
try:
data = open(metadata, mode='rb').read()
except OSError:
data = metadata
try:
resp = post(
url,
# data=open(metadata, mode='rb').read(),
data=data,
params=params
)
if resp.status_code < 200 or resp.status_code > 299:
fail_counter += 1
write_error_to_file(resp, )
return resp
except ConnectionError:
raise ConnectionError(
'ERROR: POST - Could not establish connection to api {}.'
''.format(url)
)
def import_dataset(dataverse, metadata, pid=None, release='no', auth=True):
query_str = f'/dataverses/{dataverse}/datasets/:import?pid={pid}&release={release}'
resp = post_request(query_str, metadata, auth)
if resp.status_code == 201:
identifier = resp.json()['data']['persistentId']
print('Dataset {} created.'.format(identifier))
return resp
def get_titles_from_csv(filename):
with open(filename, 'r') as csvf:
rows = csv.reader(csvf)
return [row[0] for row in rows]
def get_titles():
liss = '/Users/vic/Documents/DANS/projects/ODISSEI/liss-data/liss-dc/liss panel and immigrant panel - liss.csv'
immigrant = '/Users/vic/Documents/DANS/projects/ODISSEI/liss-data/liss-dc/liss panel and immigrant panel - immigrant.csv'
no_arrow = '/Users/vic/Documents/DANS/projects/ODISSEI/liss-data/liss-dc/liss panel and immigrant panel - no_arrow.csv'
liss_titles = get_titles_from_csv(liss)
immigrant_titles = get_titles_from_csv(immigrant)
no_arrow_titles = get_titles_from_csv(no_arrow)
return liss_titles + immigrant_titles + no_arrow_titles
def main(doi_only=True):
counter = 1
all_top_level_titles = get_titles()
for root, dirs, files in os.walk(input_path):
for name in files:
full_input_file = join(root, name)
if full_input_file.endswith('xml'):
print(f'{counter} working on {full_input_file}')
counter += 1
dom = et.parse(full_input_file)
xml_root = dom.getroot()
dc_root = xml_root.xpath('./xmlns:metadata', namespaces=ns)
title_root = xml_root.xpath('./xmlns:metadata', namespaces=ns)
try:
title_root = title_root[0].getchildren()
except IndexError as ex:
print(ex)
continue
titles = title_root[0].xpath('./dc:title', namespaces=ns)
title = titles[0].text
if isinstance(dc_root, list) and len(dc_root) == 1:
dc_root = dc_root[0].getchildren()
if isinstance(dc_root, list) and len(dc_root) == 1:
if title in all_top_level_titles:
print(title)
dc_root = dc_root[0]
dc_json, is_doi, pid = convert_dc_to_dv_json(dc_root)
# print(dc_json)
# exit()
if is_doi and pid is not None:
resp = import_dataset(dataverse_id, dc_json, pid=pid)
else:
if not doi_only:
resp = api.create_dataset(dataverse_id, dc_json)
print(resp.status_code)
if not 300 > resp.status_code > 199:
print(resp.text)
print(dc_json)
raise Exception('error occurred')
else:
print(f'{full_input_file} with title {title} is not top level')
else:
raise Exception('invalid metadata block, cannot find dc block')
else:
raise Exception('invalid LISS format, cannot find metadata block')
# exit()
if __name__ == '__main__':
# import all top level studies
# main(False)
# import top level studies with doi
main(True)