def test_get_dataset_calls_patched_timeout_method(self, mock_requests):
# Verify optional timeout parameter is passed to requests by dataverse client.
# https://github.com/IQSS/dataverse-client-python/pull/27
dataverse = Dataverse(mock.Mock(), mock.Mock())
dataverse.connection.auth = 'me'
dataverse.collection.get.return_value = '123'
mock_requests.get.side_effect = Exception('Done Testing')
with assert_raises(Exception) as e:
get_dataset(dataverse, 'My hdl')
assert_is(mock_requests.get.assert_called_once_with('123', auth='me', timeout=settings.REQUEST_TIMEOUT), None)
assert_equal(e.exception.message, 'Done Testing')
def test_get_dataset_calls_patched_timeout_method(self, mock_requests):
# Verify optional timeout parameter is passed to requests by dataverse client.
# https://github.com/IQSS/dataverse-client-python/pull/27
dataverse = Dataverse(mock.Mock(), mock.Mock())
dataverse.connection.auth = 'me'
dataverse.collection.get.return_value = '123'
mock_requests.get.side_effect = Exception('Done Testing')
with assert_raises(Exception) as e:
get_dataset(dataverse, 'My hdl')
assert_is(mock_requests.get.assert_called_once_with('123', auth='me', timeout=settings.REQUEST_TIMEOUT), None)
assert_equal(e.exception.message, 'Done Testing')
def dataverse_get_widget_contents(node_addon, **kwargs):
data = {
'connected': False,
}
if not node_addon.complete:
return {'data': data}, http.OK
doi = node_addon.dataset_doi
alias = node_addon.dataverse_alias
connection = connect_from_settings_or_401(node_addon.user_settings)
dataverse = get_dataverse(connection, alias)
dataset = get_dataset(dataverse, doi)
if dataset is None:
return {'data': data}, http.BAD_REQUEST
dataverse_url = 'http://{0}/dataverse/'.format(HOST) + alias
dataset_url = 'http://dx.doi.org/' + doi
data.update({
'connected': True,
'dataverse': node_addon.dataverse,
'dataverseUrl': dataverse_url,
'dataset': node_addon.dataset,
'doi': doi,
'datasetUrl': dataset_url,
'citation': dataset.citation,
})
return {'data': data}, http.OK
def dataverse_get_widget_contents(node_addon, **kwargs):
data = {
'connected': False,
}
if not node_addon.complete:
return {'data': data}, http.OK
doi = node_addon.dataset_doi
alias = node_addon.dataverse_alias
connection = client.connect_from_settings_or_401(node_addon)
dataverse = client.get_dataverse(connection, alias)
dataset = client.get_dataset(dataverse, doi)
if dataset is None:
return {'data': data}, http.BAD_REQUEST
dataverse_host = node_addon.external_account.oauth_key
dataverse_url = 'http://{0}/dataverse/{1}'.format(dataverse_host, alias)
dataset_url = 'http://dx.doi.org/' + doi
data.update({
'connected': True,
'dataverse': node_addon.dataverse,
'dataverseUrl': dataverse_url,
'dataset': node_addon.dataset,
'doi': doi,
'datasetUrl': dataset_url,
'citation': dataset.citation,
})
return {'data': data}, http.OK
def dataverse_set_config(node_addon, auth, **kwargs):
"""Saves selected Dataverse and dataset to node settings"""
user_settings = node_addon.user_settings
user = auth.user
if user_settings and user_settings.owner != user:
raise HTTPError(http.FORBIDDEN)
try:
assert_clean(request.json)
except AssertionError:
# TODO: Test me!
raise HTTPError(http.NOT_ACCEPTABLE)
alias = request.json.get('dataverse', {}).get('alias')
doi = request.json.get('dataset', {}).get('doi')
if doi is None or alias is None:
return HTTPError(http.BAD_REQUEST)
connection = client.connect_from_settings(node_addon)
dataverse = client.get_dataverse(connection, alias)
dataset = client.get_dataset(dataverse, doi)
node_addon.set_folder(dataverse, dataset, auth)
return {'dataverse': dataverse.title, 'dataset': dataset.title}, http.OK
def dataverse_publish_dataset(node_addon, auth, **kwargs):
node = node_addon.owner
publish_both = request.json.get('publish_both', False)
now = timezone.now()
connection = client.connect_from_settings_or_401(node_addon)
dataverse = client.get_dataverse(connection, node_addon.dataverse_alias)
dataset = client.get_dataset(dataverse, node_addon.dataset_doi)
if publish_both:
client.publish_dataverse(dataverse)
client.publish_dataset(dataset)
# Add a log
node.add_log(
action='dataverse_dataset_published',
params={
'project': node.parent_id,
'node': node._id,
'dataset': dataset.title,
},
auth=auth,
log_date=now,
)
return {'dataset': dataset.title}, http.OK
def dataverse_publish(node_addon, auth, publish_both=False):
node = node_addon.owner
user_settings = node_addon.user_settings
now = datetime.datetime.utcnow()
try:
connection = connect_from_settings_or_401(user_settings)
except HTTPError as error:
if error.code == httplib.UNAUTHORIZED:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
dataset = get_dataset(dataverse, node_addon.dataset_doi)
if publish_both:
publish_dataverse(dataverse)
publish_dataset(dataset)
# Add a log
node.add_log(
action="dataverse_dataset_published",
params={"project": node.parent_id, "node": node._primary_key, "dataset": dataset.title},
auth=auth,
log_date=now,
)
return {"dataset": dataset.title}, httplib.OK
def dataverse_publish_dataset(node_addon, auth, **kwargs):
node = node_addon.owner
publish_both = request.json.get('publish_both', False)
now = datetime.datetime.utcnow()
try:
connection = connect_from_settings_or_401(node_addon)
except HTTPError as error:
if error.code == httplib.UNAUTHORIZED:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
dataset = get_dataset(dataverse, node_addon.dataset_doi)
if publish_both:
publish_dataverse(dataverse)
publish_dataset(dataset)
# Add a log
node.add_log(
action='dataverse_dataset_published',
params={
'project': node.parent_id,
'node': node._primary_key,
'dataset': dataset.title,
},
auth=auth,
log_date=now,
)
return {'dataset': dataset.title}, httplib.OK
def dataverse_get_widget_contents(node_addon, **kwargs):
data = {
'connected': False,
}
if not node_addon.complete:
return {'data': data}, http.OK
doi = node_addon.dataset_doi
alias = node_addon.dataverse_alias
connection = client.connect_from_settings_or_401(node_addon)
dataverse = client.get_dataverse(connection, alias)
dataset = client.get_dataset(dataverse, doi)
if dataset is None:
return {'data': data}, http.BAD_REQUEST
dataverse_host = node_addon.external_account.oauth_key
dataverse_url = 'http://{0}/dataverse/{1}'.format(dataverse_host, alias)
dataset_url = 'https://doi.org/' + doi
data.update({
'connected': True,
'dataverse': node_addon.dataverse,
'dataverseUrl': dataverse_url,
'dataset': node_addon.dataset,
'doi': doi,
'datasetUrl': dataset_url,
'citation': dataset.citation,
})
return {'data': data}, http.OK
def dataverse_publish(node_addon, auth, publish_both=False):
node = node_addon.owner
user_settings = node_addon.user_settings
now = datetime.datetime.utcnow()
try:
connection = connect_from_settings_or_401(user_settings)
except HTTPError as error:
if error.code == httplib.UNAUTHORIZED:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
dataset = get_dataset(dataverse, node_addon.dataset_doi)
if publish_both:
publish_dataverse(dataverse)
publish_dataset(dataset)
# Add a log
node.add_log(
action='dataverse_dataset_published',
params={
'project': node.parent_id,
'node': node._primary_key,
'dataset': dataset.title,
},
auth=auth,
log_date=now,
)
return {'dataset': dataset.title}, httplib.OK
def dataverse_publish_dataset(node_addon, auth, **kwargs):
node = node_addon.owner
publish_both = request.json.get('publish_both', False)
now = datetime.datetime.utcnow()
connection = client.connect_from_settings_or_401(node_addon)
dataverse = client.get_dataverse(connection, node_addon.dataverse_alias)
dataset = client.get_dataset(dataverse, node_addon.dataset_doi)
if publish_both:
client.publish_dataverse(dataverse)
client.publish_dataset(dataset)
# Add a log
node.add_log(
action='dataverse_dataset_published',
params={
'project': node.parent_id,
'node': node._id,
'dataset': dataset.title,
},
auth=auth,
log_date=now,
)
return {'dataset': dataset.title}, http.OK
def dataverse_set_config(node_addon, auth, **kwargs):
"""Saves selected Dataverse and dataset to node settings"""
user_settings = node_addon.user_settings
user = auth.user
if user_settings and user_settings.owner != user:
raise HTTPError(http.FORBIDDEN)
try:
assert_clean(request.json)
except AssertionError:
# TODO: Test me!
raise HTTPError(http.NOT_ACCEPTABLE)
alias = request.json.get('dataverse', {}).get('alias')
doi = request.json.get('dataset', {}).get('doi')
if doi is None or alias is None:
return HTTPError(http.BAD_REQUEST)
connection = client.connect_from_settings(node_addon)
dataverse = client.get_dataverse(connection, alias)
dataset = client.get_dataset(dataverse, doi)
node_addon.set_folder(dataverse, dataset, auth)
return {'dataverse': dataverse.title, 'dataset': dataset.title}, http.OK
def dataverse_hgrid_root(node_addon, auth, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
default_version = 'latest-published'
version = 'latest-published' if not node.can_edit(auth) else default_version
# Quit if no dataset linked
if not node_addon.complete:
return []
can_edit = node.can_edit(auth)
permissions = {
'edit': can_edit and not node.is_registration,
'view': node.can_view(auth)
}
try:
connection = connect_from_settings(user_settings)
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
dataset = get_dataset(dataverse, node_addon.dataset_doi)
except SSLError:
return [rubeus.build_addon_root(
node_addon,
node_addon.dataset,
permissions=permissions
)]
# Quit if doi does not produce a dataset
if dataset is None:
return []
published_files = get_files(dataset, published=True)
# Produce draft version or quit if no published version is available
if not published_files:
if can_edit:
version = 'latest'
else:
return []
urls = {
'publish': node.api_url_for('dataverse_publish_dataset'),
'publishBoth': node.api_url_for('dataverse_publish_both')
}
return [rubeus.build_addon_root(
node_addon,
node_addon.dataset,
urls=urls,
permissions=permissions,
dataset=node_addon.dataset,
doi=dataset.doi,
dataverse=dataverse.title,
hasPublishedFiles=bool(published_files),
dataverseIsPublished=dataverse.is_published,
version=version,
)]
def test_get_dataset(self):
self.mock_dataset.get_state.return_value = 'DRAFT'
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
s = get_dataset(self.mock_dataverse, 'My hdl')
assert_is(self.mock_dataverse.get_dataset_by_doi.assert_called_once_with('My hdl', timeout=settings.REQUEST_TIMEOUT), None)
assert_equal(s, self.mock_dataset)
def test_get_dataset(self):
self.mock_dataset.get_state.return_value = 'DRAFT'
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
s = get_dataset(self.mock_dataverse, 'My hdl')
assert_is(self.mock_dataverse.get_dataset_by_doi.assert_called_once_with('My hdl', timeout=settings.REQUEST_TIMEOUT), None)
assert_equal(s, self.mock_dataset)
def test_get_dataset(self):
self.mock_dataset.get_state.return_value = 'DRAFT'
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
s = get_dataset(self.mock_dataverse, 'My hdl')
self.mock_dataverse.get_dataset_by_doi.assert_called_once_with('My hdl')
assert_equal(s, self.mock_dataset)
def test_get_dataset(self):
self.mock_dataset.get_state.return_value = "DRAFT"
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
s = get_dataset(self.mock_dataverse, "My hdl")
self.mock_dataverse.get_dataset_by_doi.assert_called_once_with("My hdl")
assert_equal(s, self.mock_dataset)
def test_get_bad_dataset(self):
error = UnicodeDecodeError("utf-8", b"", 1, 2, "jeepers")
self.mock_dataset.get_state.side_effect = error
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
with assert_raises(HTTPError) as e:
s = get_dataset(self.mock_dataverse, "My hdl")
self.mock_dataverse.get_dataset_by_doi.assert_called_once_with("My hdl")
assert_equal(e.exception.code, 406)
def test_get_deaccessioned_dataset(self):
self.mock_dataset.get_state.return_value = "DEACCESSIONED"
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
with assert_raises(HTTPError) as e:
s = get_dataset(self.mock_dataverse, "My hdl")
self.mock_dataverse.get_dataset_by_doi.assert_called_once_with("My hdl")
assert_equal(e.exception.code, 410)
def test_get_bad_dataset(self):
error = UnicodeDecodeError('utf-8', b'', 1, 2, 'jeepers')
self.mock_dataset.get_state.side_effect = error
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
with assert_raises(HTTPError) as e:
s = get_dataset(self.mock_dataverse, 'My hdl')
assert_is(self.mock_dataverse.get_dataset_by_doi.assert_called_once_with('My hdl', timeout=settings.REQUEST_TIMEOUT), None)
assert_equal(e.exception.code, 406)
def test_get_deaccessioned_dataset(self):
self.mock_dataset.get_state.return_value = 'DEACCESSIONED'
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
with assert_raises(HTTPError) as e:
s = get_dataset(self.mock_dataverse, 'My hdl')
assert_is(self.mock_dataverse.get_dataset_by_doi.assert_called_once_with('My hdl', timeout=settings.REQUEST_TIMEOUT), None)
assert_equal(e.exception.code, 410)
def test_get_deaccessioned_dataset(self):
self.mock_dataset.get_state.return_value = 'DEACCESSIONED'
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
with assert_raises(HTTPError) as e:
s = get_dataset(self.mock_dataverse, 'My hdl')
assert_is(self.mock_dataverse.get_dataset_by_doi.assert_called_once_with('My hdl', timeout=settings.REQUEST_TIMEOUT), None)
assert_equal(e.exception.code, 410)
def test_get_bad_dataset(self):
error = UnicodeDecodeError('utf-8', b'', 1, 2, 'jeepers')
self.mock_dataset.get_state.side_effect = error
self.mock_dataverse.get_dataset_by_doi.return_value = self.mock_dataset
with assert_raises(HTTPError) as e:
s = get_dataset(self.mock_dataverse, 'My hdl')
assert_is(self.mock_dataverse.get_dataset_by_doi.assert_called_once_with('My hdl', timeout=settings.REQUEST_TIMEOUT), None)
assert_equal(e.exception.code, 406)
def dataverse_set_config(node_addon, auth, **kwargs):
"""Saves selected Dataverse and dataset to node settings"""
user_settings = node_addon.user_settings
user = auth.user
if user_settings and user_settings.owner != user:
raise HTTPError(http.FORBIDDEN)
try:
assert_clean(request.json)
except AssertionError:
# TODO: Test me!
raise HTTPError(http.NOT_ACCEPTABLE)
alias = request.json.get('dataverse').get('alias')
doi = request.json.get('dataset').get('doi')
if doi is None:
return HTTPError(http.BAD_REQUEST)
connection = client.connect_from_settings(node_addon)
dataverse = client.get_dataverse(connection, alias)
dataset = client.get_dataset(dataverse, doi)
node_addon.dataverse_alias = dataverse.alias
node_addon.dataverse = dataverse.title
node_addon.dataset_doi = dataset.doi
node_addon.dataset_id = dataset.id
node_addon.dataset = dataset.title
node = node_addon.owner
node.add_log(
action='dataverse_dataset_linked',
params={
'project': node.parent_id,
'node': node._primary_key,
'dataset': dataset.title,
},
auth=auth,
)
node_addon.save()
return {'dataverse': dataverse.title, 'dataset': dataset.title}, http.OK
def dataverse_set_config(node_addon, auth, **kwargs):
"""Saves selected Dataverse and dataset to node settings"""
user_settings = node_addon.user_settings
user = auth.user
if user_settings and user_settings.owner != user:
raise HTTPError(http.FORBIDDEN)
try:
assert_clean(request.json)
except AssertionError:
# TODO: Test me!
raise HTTPError(http.NOT_ACCEPTABLE)
alias = request.json.get('dataverse').get('alias')
doi = request.json.get('dataset').get('doi')
if doi is None:
return HTTPError(http.BAD_REQUEST)
connection = client.connect_from_settings(node_addon)
dataverse = client.get_dataverse(connection, alias)
dataset = client.get_dataset(dataverse, doi)
node_addon.dataverse_alias = dataverse.alias
node_addon.dataverse = dataverse.title
node_addon.dataset_doi = dataset.doi
node_addon.dataset_id = dataset.id
node_addon.dataset = dataset.title
node = node_addon.owner
node.add_log(
action='dataverse_dataset_linked',
params={
'project': node.parent_id,
'node': node._primary_key,
'dataset': dataset.title,
},
auth=auth,
)
node_addon.save()
return {'dataverse': dataverse.title, 'dataset': dataset.title}, http.OK
def set_dataverse_and_dataset(node_addon, auth, **kwargs):
user_settings = node_addon.user_settings
user = auth.user
if user_settings and user_settings.owner != user:
raise HTTPError(http.FORBIDDEN)
try:
assert_clean(request.json)
except AssertionError:
# TODO: Test me!
raise HTTPError(http.NOT_ACCEPTABLE)
alias = request.json.get("dataverse").get("alias")
doi = request.json.get("dataset").get("doi")
if doi is None:
return HTTPError(http.BAD_REQUEST)
connection = client.connect_from_settings(user_settings)
dataverse = client.get_dataverse(connection, alias)
dataset = client.get_dataset(dataverse, doi)
node_addon.dataverse_alias = dataverse.alias
node_addon.dataverse = dataverse.title
node_addon.dataset_doi = dataset.doi
node_addon.dataset_id = dataset.id
node_addon.dataset = dataset.title
node = node_addon.owner
node.add_log(
action="dataverse_dataset_linked",
params={"project": node.parent_id, "node": node._primary_key, "dataset": dataset.title},
auth=auth,
)
node_addon.save()
return {"dataverse": dataverse.title, "dataset": dataset.title}, http.OK
def _dataverse_root_folder(node_addon, auth, **kwargs):
node = node_addon.owner
default_version = 'latest-published'
version = 'latest-published' if not node.can_edit(auth) else default_version
# Quit if no dataset linked
if not node_addon.complete:
return []
can_edit = node.can_edit(auth)
permissions = {
'edit': can_edit and not node.is_registration,
'view': node.can_view(auth)
}
try:
connection = client.connect_from_settings(node_addon)
dataverse = client.get_dataverse(connection, node_addon.dataverse_alias)
dataset = client.get_dataset(dataverse, node_addon.dataset_doi)
except SSLError:
return [rubeus.build_addon_root(
node_addon,
node_addon.dataset,
permissions=permissions,
private_key=kwargs.get('view_only', None),
)]
# Quit if doi does not produce a dataset
if dataset is None:
return []
published_files = client.get_files(dataset, published=True)
# Produce draft version or quit if no published version is available
if not published_files:
if can_edit:
version = 'latest'
else:
return []
urls = {
'publish': node.api_url_for('dataverse_publish_dataset'),
}
# determine if there are any changes between the published and draft
# versions of the dataset
try:
dataset.get_metadata('latest-published')
dataset_is_published = True
dataset_draft_modified = dataset.get_state() == 'DRAFT'
except VersionJsonNotFoundError:
dataset_is_published = False
dataset_draft_modified = True
# Get the dataverse host
# (stored in oauth_key because dataverse doesn't use that)
dataverse_host = node_addon.external_account.oauth_key
return [rubeus.build_addon_root(
node_addon,
node_addon.dataset,
urls=urls,
permissions=permissions,
dataset=node_addon.dataset,
doi=dataset.doi,
dataverse=dataverse.title,
hasPublishedFiles=bool(published_files),
dataverseIsPublished=dataverse.is_published,
datasetIsPublished=dataset_is_published,
datasetDraftModified=dataset_draft_modified,
version=version,
host=dataverse_host,
private_key=kwargs.get('view_only', None),
)]
def _dataverse_root_folder(node_addon, auth, **kwargs):
node = node_addon.owner
default_version = 'latest-published'
version = 'latest-published' if not node.can_edit(auth) else default_version
# Quit if no dataset linked
if not node_addon.complete:
return []
can_edit = node.can_edit(auth)
permissions = {
'edit': can_edit and not node.is_registration,
'view': node.can_view(auth)
}
try:
connection = client.connect_from_settings(node_addon)
dataverse = client.get_dataverse(connection, node_addon.dataverse_alias)
dataset = client.get_dataset(dataverse, node_addon.dataset_doi)
except SSLError:
return [rubeus.build_addon_root(
node_addon,
node_addon.dataset,
permissions=permissions
)]
# Quit if doi does not produce a dataset
if dataset is None:
return []
published_files = client.get_files(dataset, published=True)
# Produce draft version or quit if no published version is available
if not published_files:
if can_edit:
version = 'latest'
else:
return []
urls = {
'publish': node.api_url_for('dataverse_publish_dataset'),
}
# determine if there are any changes between the published and draft
# versions of the dataset
try:
dataset.get_metadata('latest-published')
dataset_is_published = True
dataset_draft_modified = dataset.get_state() == 'DRAFT'
except VersionJsonNotFoundError:
dataset_is_published = False
dataset_draft_modified = True
# Get the dataverse host
# (stored in oauth_key because dataverse doesn't use that)
dataverse_host = node_addon.external_account.oauth_key
return [rubeus.build_addon_root(
node_addon,
node_addon.dataset,
urls=urls,
permissions=permissions,
dataset=node_addon.dataset,
doi=dataset.doi,
dataverse=dataverse.title,
hasPublishedFiles=bool(published_files),
dataverseIsPublished=dataverse.is_published,
datasetIsPublished=dataset_is_published,
datasetDraftModified=dataset_draft_modified,
version=version,
host=dataverse_host,
)]
