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dataset.py
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359 lines (291 loc) · 11.6 KB
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from __future__ import absolute_import
import os
import json
try:
from StringIO import StringIO
except ImportError:
from io import BytesIO as StringIO
from zipfile import ZipFile
from lxml import etree
import requests
from .exceptions import (
NoContainerError, OperationFailedError, UnpublishedDataverseError,
ConnectionError, MetadataNotFoundError, VersionJsonNotFoundError,
)
from dataverse.file import DataverseFile
from dataverse.settings import SWORD_BOOTSTRAP
from dataverse.utils import get_element, get_files_in_path, add_field
class Dataset(object):
def __init__(self, entry=SWORD_BOOTSTRAP, dataverse=None, edit_uri=None,
edit_media_uri=None, statement_uri=None, **kwargs):
"""
Datasets must have a title, description, and author.
This can be specified in the atom entry or as kwargs
"""
self.dataverse = dataverse
self.edit_uri = edit_uri
self.edit_media_uri = edit_media_uri
self.statement_uri = statement_uri
self.is_deleted = False
self._entry = etree.XML(entry) if isinstance(entry, str) else entry
self._statement = None
self._metadata = {}
self._id = None
# Updates sword entry from keyword arguments
for key in kwargs:
value = kwargs[key]
if isinstance(value, list):
for item in value:
add_field(self._entry, key, item, 'dcterms')
else:
add_field(self._entry, key, value, 'dcterms')
self.title = get_element(
self._entry, tag='title', namespace='dcterms'
).text
@classmethod
def from_xml_file(cls, xml_file):
with open(xml_file) as f:
xml = f.read()
return cls(xml)
@classmethod
def from_dataverse(cls, entry_element, dataverse):
# Entry not in appropriate format--extract relevant metadata
id_element = get_element(entry_element, tag='id')
title_element = get_element(entry_element, tag='title')
edit_media_element = get_element(
entry_element,
tag='link',
attribute='rel',
attribute_value='edit-media',
)
return cls(
title=title_element.text,
id=id_element.text,
dataverse=dataverse,
edit_uri=entry_element.base,
edit_media_uri=edit_media_element.get('href'),
)
@property
def doi(self):
if not self.dataverse:
raise NoContainerError('This dataset has not been added to a Dataverse.')
# Note: This depends strongly on URL structure, and may break easily
return self.edit_media_uri.rsplit('/study/', 1)[-1]
@property
def id(self):
if self._id:
return self._id
if not self.dataverse:
raise NoContainerError('This dataset has not been added to a Dataverse.')
for dataset in self.dataverse.get_contents(refresh=True):
if dataset['type'] == 'dataset':
doi = '{0}:{1}/{2}'.format(
dataset['protocol'],
dataset['authority'],
dataset['identifier'],
)
if doi == self.doi:
self._id = dataset['id']
return self._id
raise MetadataNotFoundError('The dataset ID could not be found.')
@property
def citation(self):
return get_element(
self.get_entry(),
namespace='http://purl.org/dc/terms/',
tag='bibliographicCitation'
).text
@property
def connection(self):
return self.dataverse.connection if self.dataverse else None
def get_entry(self, refresh=False):
if not refresh and self._entry is not None:
return etree.tostring(self._entry)
resp = requests.get(self.edit_uri, auth=self.connection.auth)
if resp.status_code != 200:
raise ConnectionError('Atom entry could not be retrieved.')
entry_string = resp.content
self._entry = etree.XML(entry_string)
return entry_string
def get_statement(self, refresh=False):
if not refresh and self._statement:
return self._statement
if not self.dataverse:
raise NoContainerError('This dataset has not been added to a Dataverse.')
if not self.statement_uri:
# Try to find statement uri without a request to the server
link = get_element(
self.get_entry(),
tag='link',
attribute='rel',
attribute_value='http://purl.org/net/sword/terms/statement',
)
if link is None:
# Find link with request to server
link = get_element(
self.get_entry(refresh=True),
tag='link',
attribute='rel',
attribute_value='http://purl.org/net/sword/terms/statement',
)
self.statement_uri = link.get('href')
resp = requests.get(self.statement_uri, auth=self.connection.auth)
if resp.status_code != 200:
raise ConnectionError('Statement could not be retrieved.')
self._statement = resp.content
return self._statement
def get_state(self, refresh=False):
if self.is_deleted:
return 'DEACCESSIONED'
return get_element(
self.get_statement(refresh),
tag='category',
attribute='term',
attribute_value='latestVersionState'
).text
def get_metadata(self, version='latest', refresh=False):
if not refresh and self._metadata.get(version):
return self._metadata[version]
if not self.dataverse:
raise NoContainerError('This dataset has not been added to a Dataverse.')
url = '{0}/datasets/{1}/versions/:{2}'.format(
self.connection.native_base_url,
self.id,
version,
)
resp = requests.get(url, params={'key': self.connection.token})
if resp.status_code == 404:
raise VersionJsonNotFoundError(
'JSON metadata could not be found for this version.'
)
elif resp.status_code != 200:
raise ConnectionError('JSON metadata could not be retrieved.')
metadata = resp.json()['data']
self._metadata[version] = metadata
# Update corresponding version metadata if retrieving 'latest'
if version == 'latest':
latest_version = (
'latest-published'
if metadata['versionState'] == 'RELEASED'
else 'draft'
)
self._metadata[latest_version] = metadata
return metadata
def update_metadata(self, metadata):
"""Updates dataset draft with provided metadata.
Will create a draft version if none exists.
:param dict metadata: json retrieved from `get_version_metadata`
"""
url = '{0}/datasets/{1}/versions/:draft'.format(
self.connection.native_base_url,
self.id,
)
resp = requests.put(
url,
headers={'Content-type': 'application/json'},
data=json.dumps(metadata),
params={'key': self.connection.token},
)
if resp.status_code != 200:
raise OperationFailedError('JSON metadata could not be updated.')
updated_metadata = resp.json()['data']
self._metadata['draft'] = updated_metadata
self._metadata['latest'] = updated_metadata
def create_draft(self):
"""Create draft version of dataset without changing metadata"""
metadata = self.get_metadata(refresh=True)
if metadata.get('versionState') == 'RELEASED':
self.update_metadata(metadata)
def publish(self):
if not self.dataverse.is_published:
raise UnpublishedDataverseError('Host Dataverse must be published.')
resp = requests.post(
self.edit_uri,
headers={'In-Progress': 'false', 'Content-Length': '0'},
auth=self.connection.auth,
)
if resp.status_code != 200:
raise OperationFailedError('The Dataset could not be published.')
self._metadata.pop('draft', None)
self._refresh(receipt=resp.content)
def get_file(self, file_name, version='latest', refresh=False):
files = self.get_files(version, refresh)
return next((f for f in files if f.name == file_name), None)
def get_file_by_id(self, file_id, version='latest', refresh=False):
files = self.get_files(version, refresh)
return next((f for f in files if f.id == file_id), None)
def get_files(self, version='latest', refresh=False):
try:
files_json = self.get_metadata(version, refresh)['files']
return [DataverseFile.from_json(self, file_json)
for file_json in files_json]
except VersionJsonNotFoundError:
return []
def upload_filepath(self, filepath):
self.upload_filepaths([filepath])
def upload_filepaths(self, filepaths):
# Convert a directory to a list of files
if len(filepaths) == 1 and os.path.isdir(filepaths[0]):
filepaths = get_files_in_path(filepaths[0])
# Zip up files
s = StringIO()
zip_file = ZipFile(s, 'w')
for filepath in filepaths:
zip_file.write(filepath)
zip_file.close()
content = s.getvalue()
self.upload_file('temp.zip', content, zip_files=False)
def upload_file(self, filename, content, zip_files=True):
if zip_files:
s = StringIO()
zip_file = ZipFile(s, 'w')
zip_file.writestr(filename, content)
zip_file.close()
# filename, content should reflect zipped file
filename = 'temp.zip'
content = s.getvalue()
headers = {
'Content-Disposition': 'filename={0}'.format(filename),
'Content-Type': 'application/zip',
'Packaging': 'http://purl.org/net/sword/package/SimpleZip',
}
requests.post(
self.edit_media_uri,
data=content,
headers=headers,
auth=self.connection.auth,
)
self.get_metadata(refresh=True)
# Note: We can't determine which file was uploaded. Returns None
def delete_file(self, dataverse_file):
resp = requests.delete(
dataverse_file.edit_media_uri,
auth=self.connection.auth,
)
if resp.status_code != 204:
raise OperationFailedError('The file could not be deleted.')
self.get_metadata(refresh=True)
# If we perform a server operation, we should refresh the dataset object
def _refresh(self, receipt=None):
if receipt:
self.edit_uri = get_element(
receipt,
tag='link',
attribute='rel',
attribute_value='edit'
).get('href')
self.edit_media_uri = get_element(
receipt,
tag='link',
attribute='rel',
attribute_value='edit-media'
).get('href')
self.statement_uri = get_element(
receipt,
tag='link',
attribute='rel',
attribute_value='http://purl.org/net/sword/terms/statement'
).get('href')
self.get_statement(refresh=True)
self.get_entry(refresh=True)
self.get_metadata('latest', refresh=True)