def fail_if_unauthorized(node_addon, auth, file_id):
node = node_addon.owner
user_settings = node_addon.user_settings
if file_id is None:
raise HTTPError(http.NOT_FOUND)
try:
connection = connect_from_settings_or_403(user_settings)
except HTTPError as error:
if error.code == 403:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
released_file_ids = [f.id for f in get_files(study, released=True)]
all_file_ids = [f.id for f in get_files(study)] + released_file_ids
if file_id not in all_file_ids:
raise HTTPError(http.FORBIDDEN)
elif not node.can_edit(auth) and file_id not in released_file_ids:
raise HTTPError(http.UNAUTHORIZED)
def dataverse_get_widget_contents(node_addon, **kwargs):
data = {
'connected': False,
}
if not node_addon.is_fully_configured:
return {'data': data}, http.OK
doi = node_addon.study_hdl
alias = node_addon.dataverse_alias
connection = connect_from_settings_or_403(node_addon.user_settings)
dataverse = get_dataverse(connection, alias)
study = get_study(dataverse, doi)
if study is None:
return {'data': data}, http.BAD_REQUEST
dataverse_url = 'http://{0}/dvn/dv/'.format(HOST) + alias
study_url = 'http://dx.doi.org/' + doi
data.update({
'connected': True,
'dataverse': node_addon.dataverse,
'dataverseUrl': dataverse_url,
'study': node_addon.study,
'doi': doi,
'studyUrl': study_url,
'citation': study.citation,
})
return {'data': data}, http.OK
def fail_if_unauthorized(node_addon, auth, file_id):
node = node_addon.owner
user_settings = node_addon.user_settings
if file_id is None:
raise HTTPError(httplib.NOT_FOUND)
try:
connection = connect_from_settings_or_403(user_settings)
except HTTPError as error:
if error.code == 403:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
released_file_ids = [f.id for f in get_files(study, released=True)]
all_file_ids = [f.id for f in get_files(study)] + released_file_ids
if file_id not in all_file_ids:
raise HTTPError(httplib.FORBIDDEN)
elif not node.can_edit(auth) and file_id not in released_file_ids:
raise HTTPError(httplib.UNAUTHORIZED)
def dataverse_get_widget_contents(node_addon, **kwargs):
data = {
'connected': False,
}
if not node_addon.is_fully_configured:
return {'data': data}, http.OK
doi = node_addon.study_hdl
alias = node_addon.dataverse_alias
connection = connect_from_settings_or_403(node_addon.user_settings)
dataverse = get_dataverse(connection, alias)
study = get_study(dataverse, doi)
if study is None:
return {'data': data}, http.BAD_REQUEST
dataverse_url = 'http://{0}/dvn/dv/'.format(HOST) + alias
study_url = 'http://dx.doi.org/' + doi
data.update({
'connected': True,
'dataverse': node_addon.dataverse,
'dataverseUrl': dataverse_url,
'study': node_addon.study,
'doi': doi,
'studyUrl': study_url,
'citation': study.citation,
})
return {'data': data}, http.OK
def test_get_study(self):
self.mock_study.get_state.return_value = 'DRAFT'
self.mock_dataverse.get_study_by_doi.return_value = self.mock_study
s = get_study(self.mock_dataverse, 'My hdl')
self.mock_dataverse.get_study_by_doi.assert_called_once_with('My hdl')
assert_equal(s, self.mock_study)
def test_get_bad_study(self):
error = UnicodeDecodeError('utf-8', b'', 1, 2, 'jeepers')
self.mock_study.get_state.side_effect = error
self.mock_dataverse.get_study_by_doi.return_value = self.mock_study
with assert_raises(HTTPError) as e:
s = get_study(self.mock_dataverse, 'My hdl')
self.mock_dataverse.get_study_by_doi.assert_called_once_with('My hdl')
assert_equal(e.exception.code, 406)
def test_get_deaccessioned_study(self):
self.mock_study.get_state.return_value = 'DEACCESSIONED'
self.mock_dataverse.get_study_by_doi.return_value = self.mock_study
with assert_raises(HTTPError) as e:
s = get_study(self.mock_dataverse, 'My hdl')
self.mock_dataverse.get_study_by_doi.assert_called_once_with('My hdl')
assert_equal(e.exception.code, 410)
def dataverse_hgrid_data_contents(node_addon, auth, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
state = request.args.get('state')
default_state = 'released'
state = 'released' if not node.can_edit(auth) else state or default_state
released = state == 'released'
can_edit = node.can_edit(auth) and not node.is_registration and not released
can_view = node.can_view(auth)
connection = connect_from_settings(user_settings)
if node_addon.study_hdl is None or connection is None:
return []
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
# Quit if hdl does not produce a study
if study is None:
return []
info = []
for f in get_files(study, released):
item = {
'addon': 'dataverse',
'provider': 'dataverse',
rubeus.KIND: 'file',
'name': f.name,
'path': f.name,
'file_id': f.id,
'ext': os.path.splitext(f.name)[1],
'urls': {
'view': node.web_url_for('dataverse_view_file',
path=f.id),
'download': node.web_url_for('dataverse_download_file',
path=f.id),
'delete': node.api_url_for('dataverse_delete_file',
path=f.id),
},
'permissions': {
'view': can_view,
'edit': can_edit,
},
}
info.append(item)
return {'data': info}
def dataverse_hgrid_data_contents(node_addon, auth, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
state = request.args.get('state')
default_state = 'released'
state = 'released' if not node.can_edit(auth) else state or default_state
released = state == 'released'
can_edit = node.can_edit(
auth) and not node.is_registration and not released
can_view = node.can_view(auth)
connection = connect_from_settings(user_settings)
if node_addon.study_hdl is None or connection is None:
return []
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
# Quit if hdl does not produce a study
if study is None:
return []
info = []
for f in get_files(study, released):
item = {
'addon': 'dataverse',
'provider': 'dataverse',
rubeus.KIND: 'file',
'name': f.name,
'path': f.name,
'file_id': f.id,
'ext': os.path.splitext(f.name)[1],
'urls': {
'view': node.web_url_for('dataverse_view_file', path=f.id),
'download': node.web_url_for('dataverse_download_file',
path=f.id),
'delete': node.api_url_for('dataverse_delete_file', path=f.id),
},
'permissions': {
'view': can_view,
'edit': can_edit,
},
}
info.append(item)
return {'data': info}
def set_dataverse_and_study(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')
hdl = request.json.get('study').get('hdl')
if hdl is None:
return HTTPError(http.BAD_REQUEST)
connection = client.connect_from_settings(user_settings)
dataverse = client.get_dataverse(connection, alias)
study = client.get_study(dataverse, hdl)
node_addon.dataverse_alias = dataverse.alias
node_addon.dataverse = dataverse.title
node_addon.study_hdl = study.doi
node_addon.study = study.title
node = node_addon.owner
node.add_log(
action='dataverse_study_linked',
params={
'project': node.parent_id,
'node': node._primary_key,
'study': study.title,
},
auth=auth,
)
node_addon.save()
return {'dataverse': dataverse.title, 'study': study.title}, http.OK
def set_dataverse_and_study(node_addon, auth, **kwargs):
user_settings = node_addon.user_settings
user = get_current_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')
hdl = request.json.get('study').get('hdl')
if hdl is None:
return HTTPError(http.BAD_REQUEST)
connection = connect_from_settings(user_settings)
dataverse = get_dataverse(connection, alias)
study = get_study(dataverse, hdl)
node_addon.dataverse_alias = dataverse.alias
node_addon.dataverse = dataverse.title
node_addon.study_hdl = study.doi
node_addon.study = study.title
node = node_addon.owner
node.add_log(
action='dataverse_study_linked',
params={
'project': node.parent_id,
'node': node._primary_key,
'study': study.title,
},
auth=auth,
)
node_addon.save()
return {'dataverse': dataverse.title, 'study': study.title}, http.OK
def dataverse_delete_file(node_addon, auth, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
now = datetime.datetime.utcnow()
file_id = kwargs.get('path')
if file_id is None:
raise HTTPError(http.NOT_FOUND)
try:
connection = connect_from_settings_or_403(user_settings)
except HTTPError as error:
if error.code == 403:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
file = get_file_by_id(study, file_id)
delete_file(file)
# Check if file was deleted
if get_file_by_id(study, file_id) is not None:
raise HTTPError(http.BAD_REQUEST)
node.add_log(
action='dataverse_file_removed',
params={
'project': node.parent_id,
'node': node._primary_key,
'filename': file.name,
'study': study.title,
},
auth=auth,
log_date=now,
)
return {}
def dataverse_delete_file(node_addon, auth, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
now = datetime.datetime.utcnow()
file_id = kwargs.get('path')
if file_id is None:
raise HTTPError(httplib.NOT_FOUND)
try:
connection = connect_from_settings_or_403(user_settings)
except HTTPError as error:
if error.code == httplib.FORBIDDEN:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
file = get_file_by_id(study, file_id)
delete_file(file)
# Check if file was deleted
if get_file_by_id(study, file_id) is not None:
raise HTTPError(httplib.BAD_REQUEST)
node.add_log(
action='dataverse_file_removed',
params={
'project': node.parent_id,
'node': node._primary_key,
'filename': file.name,
'study': study.title,
},
auth=auth,
log_date=now,
)
return {}
def dataverse_release_study(node_addon, auth, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
now = datetime.datetime.utcnow()
try:
connection = connect_from_settings_or_403(user_settings)
except HTTPError as error:
if error.code == 403:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
if study.get_state() == 'RELEASED':
raise HTTPError(httplib.CONFLICT)
release_study(study)
# Add a log
node.add_log(
action='dataverse_study_released',
params={
'project': node.parent_id,
'node': node._primary_key,
'study': study.title,
},
auth=auth,
log_date=now,
)
return {'study': study.title}, httplib.OK
def dataverse_release_study(node_addon, auth, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
now = datetime.datetime.utcnow()
try:
connection = connect_from_settings_or_403(user_settings)
except HTTPError as error:
if error.code == 403:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
if study.get_state() == 'RELEASED':
raise HTTPError(http.CONFLICT)
release_study(study)
# Add a log
node.add_log(
action='dataverse_study_released',
params={
'project': node.parent_id,
'node': node._primary_key,
'study': study.title,
},
auth=auth,
log_date=now,
)
return {'study': study.title}, http.OK
def dataverse_hgrid_root(node_addon, auth, state=None, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
default_state = 'released'
state = 'released' if not node.can_edit(auth) else state or default_state
connection = connect_from_settings(user_settings)
# Quit if no study linked
if node_addon.study_hdl is None or connection is None:
return []
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
# Quit if hdl does not produce a study
if study is None:
return []
released_files = get_files(study, released=True)
authorized = node.can_edit(auth)
# Produce draft version or quit if no released version is available
if not released_files:
if authorized:
state = 'draft'
else:
return []
study_name = node_addon.study
if len(study_name) > 23:
study_name = u'{0}...'.format(study_name[:20])
permissions = {
'edit': node.can_edit(auth) and not node.is_registration,
'view': node.can_view(auth)
}
urls = {
'upload': node.api_url_for('dataverse_upload_file'),
'fetch': node.api_url_for('dataverse_hgrid_data_contents', state=state),
'state': node.api_url_for('dataverse_root_folder_public'),
'release': node.api_url_for('dataverse_release_study'),
}
buttons = [rubeus.build_addon_button(
'<i class="fa fa-globe"></i> Release Study',
'releaseStudy')] if state == 'draft' else None
return [rubeus.build_addon_root(
node_addon,
study_name,
urls=urls,
permissions=permissions,
buttons=buttons,
study=study_name,
doi=study.doi,
dataverse=dataverse.title,
citation=study.citation,
hasReleasedFiles=bool(released_files),
state=state,
)]
def dataverse_upload_file(node_addon, auth, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
try:
name = request.args['name']
except KeyError:
raise HTTPError(httplib.BAD_REQUEST)
now = datetime.datetime.utcnow()
can_edit = node.can_edit(auth) and not node.is_registration
can_view = node.can_view(auth)
try:
connection = connect_from_settings_or_403(user_settings)
except HTTPError as error:
if error.code == httplib.FORBIDDEN:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
filename = secure_filename(name)
status_code = httplib.CREATED
old_id = None
# Fail if file is too small (Dataverse issue)
content = request.data
if len(content) < 5:
raise HTTPError(httplib.UNSUPPORTED_MEDIA_TYPE)
# Replace file if old version exists
old_file = get_file(study, filename)
if old_file is not None:
status_code = httplib.OK
old_id = old_file.id
delete_file(old_file)
# Check if file was deleted
if get_file_by_id(study, old_id) is not None:
raise HTTPError(httplib.BAD_REQUEST)
upload_file(study, filename, content)
file = get_file(study, filename)
if file is None:
raise HTTPError(httplib.BAD_REQUEST)
node.add_log(
action='dataverse_file_added',
params={
'project': node.parent_id,
'node': node._primary_key,
'filename': filename,
'path': node.web_url_for('dataverse_view_file', path=file.id),
'study': study.title,
},
auth=auth,
log_date=now,
)
info = {
'addon': 'dataverse',
'file_id': file.id,
'old_id': old_id,
'name': filename,
'path': filename,
'size': [
len(content),
rubeus.format_filesize(len(content))
],
rubeus.KIND: rubeus.FILE,
'urls': {
'view': node.web_url_for('dataverse_view_file',
path=file.id),
'download': node.web_url_for('dataverse_download_file',
path=file.id),
'delete': node.api_url_for('dataverse_delete_file',
path=file.id),
},
'permissions': {
'view': can_view,
'edit': can_edit,
},
}
return info, status_code
def dataverse_upload_file(node_addon, auth, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
try:
name = request.args['name']
except KeyError:
raise HTTPError(http.BAD_REQUEST)
now = datetime.datetime.utcnow()
can_edit = node.can_edit(auth) and not node.is_registration
can_view = node.can_view(auth)
try:
connection = connect_from_settings_or_403(user_settings)
except HTTPError as error:
if error.code == 403:
connection = None
else:
raise
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
filename = secure_filename(name)
action = 'file_uploaded'
old_id = None
# Fail if file is too small (Dataverse issue)
content = request.data
if len(content) < 5:
raise HTTPError(http.UNSUPPORTED_MEDIA_TYPE)
# Replace file if old version exists
old_file = get_file(study, filename)
if old_file is not None:
action = 'file_updated'
old_id = old_file.id
delete_file(old_file)
# Check if file was deleted
if get_file_by_id(study, old_id) is not None:
raise HTTPError(http.BAD_REQUEST)
upload_file(study, filename, content)
file = get_file(study, filename)
if file is None:
raise HTTPError(http.BAD_REQUEST)
node.add_log(
action='dataverse_file_added',
params={
'project': node.parent_id,
'node': node._primary_key,
'filename': filename,
'path': node.web_url_for('dataverse_view_file', path=file.id),
'study': study.title,
},
auth=auth,
log_date=now,
)
info = {
'addon': 'dataverse',
'file_id': file.id,
'old_id': old_id,
'name': filename,
'path': filename,
'size': [len(content),
rubeus.format_filesize(len(content))],
rubeus.KIND: rubeus.FILE,
'urls': {
'view': node.web_url_for('dataverse_view_file', path=file.id),
'download': node.web_url_for('dataverse_download_file',
path=file.id),
'delete': node.api_url_for('dataverse_delete_file', path=file.id),
},
'permissions': {
'view': can_view,
'edit': can_edit,
},
'actionTaken': action,
}
return info, 201
def dataverse_hgrid_root(node_addon, auth, state=None, **kwargs):
node = node_addon.owner
user_settings = node_addon.user_settings
default_state = 'released'
state = 'released' if not node.can_edit(auth) else state or default_state
connection = connect_from_settings(user_settings)
# Quit if no study linked
if node_addon.study_hdl is None or connection is None:
return []
dataverse = get_dataverse(connection, node_addon.dataverse_alias)
study = get_study(dataverse, node_addon.study_hdl)
# Quit if hdl does not produce a study
if study is None:
return []
released_files = get_files(study, released=True)
authorized = node.can_edit(auth)
# Produce draft version or quit if no released version is available
if not released_files:
if authorized:
state = 'draft'
else:
return []
study_name = node_addon.study
if len(study_name) > 23:
study_name = u'{0}...'.format(study_name[:20])
permissions = {
'edit': node.can_edit(auth) and not node.is_registration,
'view': node.can_view(auth)
}
urls = {
'upload': node.api_url_for('dataverse_upload_file'),
'fetch': node.api_url_for('dataverse_hgrid_data_contents',
state=state),
'state': node.api_url_for('dataverse_root_folder_public'),
'release': node.api_url_for('dataverse_release_study'),
}
buttons = [
rubeus.build_addon_button('<i class="fa fa-globe"></i> Release Study',
'releaseStudy')
] if state == 'draft' else None
return [
rubeus.build_addon_root(
node_addon,
study_name,
urls=urls,
permissions=permissions,
buttons=buttons,
study=study_name,
doi=study.doi,
dataverse=dataverse.title,
citation=study.citation,
hasReleasedFiles=bool(released_files),
state=state,
)
]
