def _raw_update_history_item(self, history_id, item_id, data):
update_url = self._api_url("histories/%s/contents/%s" %
(history_id, item_id),
use_key=True)
update_response = requests.put(update_url, json=data)
assert_status_code_is_ok(update_response)
return update_response
def test_page_encoding_markdown(self):
dataset = self.dataset_populator.new_dataset(self.history_id)
dataset_id = dataset["id"]
request = dict(
slug="mypage-markdown",
title="MY PAGE",
content='''```galaxy
history_dataset_display(history_dataset_id=%s)
```''' % dataset["id"],
content_format="markdown",
)
page_response = self._post("pages", request, json=True)
api_asserts.assert_status_code_is_ok(page_response)
sa_session = self._app.model.context
page_revision = sa_session.query(
model.PageRevision).filter_by(content_format="markdown").all()[0]
assert '''```galaxy
history_dataset_display(history_dataset_id=1)
```''' in page_revision.content, page_revision.content
assert '''::: history_dataset_display history_dataset_id=%s''' % dataset_id not in page_revision.content, page_revision.content
show_page_response = self._get("pages/%s" % page_response.json()["id"])
api_asserts.assert_status_code_is_ok(show_page_response)
content = show_page_response.json()["content"]
assert '''```galaxy
history_dataset_display(history_dataset_id=1)
```''' not in content, content
assert '''```galaxy
history_dataset_display(history_dataset_id=%s)
```''' % dataset_id in content, content
def test_vault_secret_per_user_in_file_source(self):
"""
This file source performs a user vault lookup. The secret stored for the first user is a
valid path and should succeed, while the second user's stored secret should fail.
"""
with self._different_user(email=self.USER_1_APP_VAULT_ENTRY):
app = self._app
user = app.model.context.query(app.model.User).filter(
app.model.User.email == self.USER_1_APP_VAULT_ENTRY).first()
user_vault = UserVaultWrapper(self._app.vault, user)
# use a valid symlink path so the posix list succeeds
user_vault.write_secret(
'posix/root_path',
app.config.user_library_import_symlink_allowlist[0])
data = {"target": "gxfiles://test_user_vault"}
list_response = self.galaxy_interactor.get("remote_files", data)
api_asserts.assert_status_code_is_ok(list_response)
remote_files = list_response.json()
print(remote_files)
with self._different_user(email=self.USER_2_APP_VAULT_ENTRY):
app = self._app
user = app.model.context.query(app.model.User).filter(
app.model.User.email == self.USER_2_APP_VAULT_ENTRY).first()
user_vault = UserVaultWrapper(self._app.vault, user)
# use an invalid symlink path so the posix list fails
user_vault.write_secret('posix/root_path', '/invalid/root')
data = {"target": "gxfiles://test_user_vault"}
list_response = self.galaxy_interactor.get("remote_files", data)
api_asserts.assert_status_code_is(list_response, 404)
def test_plugin_config(self):
plugin_config_response = self.galaxy_interactor.get(
"remote_files/plugins")
api_asserts.assert_status_code_is_ok(plugin_config_response)
plugins = plugin_config_response.json()
assert len(plugins) == 1
assert plugins[0]["type"] == "posix"
assert plugins[0]["uri_root"] == "gxfiles://posix_test"
assert plugins[0]["writable"] is True
assert plugins[0]["requires_roles"] == REQUIRED_ROLE
assert plugins[0]["requires_groups"] == REQUIRED_GROUP
def _assert_list_response_matches_fixtures(self, list_response):
api_asserts.assert_status_code_is_ok(list_response)
remote_files = list_response.json()
assert len(remote_files) == 2
if remote_files[0]["class"] == "Directory":
dir = remote_files[0]
file = remote_files[1]
else:
dir = remote_files[1]
file = remote_files[0]
assert file["name"] == "a"
assert dir["name"] == "subdir1"
def test_plugin_config(self):
# Default user has required role but not required group, so cannot see plugin
plugin_config_response = self.galaxy_interactor.get(
"remote_files/plugins")
api_asserts.assert_status_code_is_ok(plugin_config_response)
plugins = plugin_config_response.json()
assert len(plugins) == 0
# Admins can see plugins
plugin_config_response = self.galaxy_interactor.get(
"remote_files/plugins", admin=True)
api_asserts.assert_status_code_is_ok(plugin_config_response)
plugins = plugin_config_response.json()
assert len(plugins) == 1
assert plugins[0]["type"] == "posix"
assert plugins[0]["uri_root"] == "gxfiles://posix_test"
assert plugins[0]["writable"] is True
assert plugins[0]["requires_roles"] == REQUIRED_ROLE
assert plugins[0]["requires_groups"] == REQUIRED_GROUP
def test_simple_usage(self):
plugin_config_response = self.galaxy_interactor.get("remote_files/plugins")
api_asserts.assert_status_code_is_ok(plugin_config_response)
plugins = plugin_config_response.json()
assert len(plugins) == 1
assert plugins[0]["type"] == "webdav"
assert plugins[0]["uri_prefix"] == "gxfiles://test1"
data = {"target": "gxfiles://test1"}
list_response = self.galaxy_interactor.get("remote_files", data)
api_asserts.assert_status_code_is_ok(list_response)
remote_files = list_response.json()
print(remote_files)
with self.dataset_populator.test_history() as history_id:
new_dataset = self.dataset_populator.new_dataset(history_id, content="gxfiles://test1/a", assert_ok=True)
content = self.dataset_populator.get_history_dataset_content(history_id, dataset=new_dataset)
assert content == "a\n", content
def test_page_encoding(self):
request = dict(
slug="mypage",
title="MY PAGE",
content=
'''<p>Page!<div class="embedded-item" id="History-%s"></div></p>'''
% self.history_id,
)
page_response = self._post("pages", request, json=True)
api_asserts.assert_status_code_is_ok(page_response)
sa_session = self._app.model.context
page_revision = sa_session.query(
model.PageRevision).filter_by(content_format="html").all()[0]
assert '''id="History-1"''' in page_revision.content, page_revision.content
assert '''id="History-%s"''' % self.history_id not in page_revision.content, page_revision.content
show_page_response = self._get("pages/%s" % page_response.json()["id"])
api_asserts.assert_status_code_is_ok(show_page_response)
content = show_page_response.json()["content"]
assert '''id="History-1"''' not in content, content
assert '''id="History-%s"''' % self.history_id in content, content
def test_upload_file_from_remote_source(self):
with self._different_user(email=self.USER_1_APP_VAULT_ENTRY):
app = self._app
user = app.model.context.query(app.model.User).filter(
app.model.User.email == self.USER_1_APP_VAULT_ENTRY).first()
user_vault = UserVaultWrapper(self._app.vault, user)
# use a valid symlink path so the posix list succeeds
user_vault.write_secret(
'posix/root_path',
app.config.user_library_import_symlink_allowlist[0])
data = {"target": "gxfiles://test_user_vault"}
with open(
os.path.join(
app.config.user_library_import_symlink_allowlist[0],
'a_file'), 'w') as fh:
fh.write('I require access to the vault')
list_response = self.galaxy_interactor.get("remote_files", data)
api_asserts.assert_status_code_is_ok(list_response)
remote_files = list_response.json()
assert len(remote_files) == 1
with self.dataset_populator.test_history() as history_id:
element = dict(src="url",
url="gxfiles://test_user_vault/a_file")
target = {
"destination": {
"type": "hdas"
},
"elements": [element],
}
targets = json.dumps([target])
payload = {
"history_id": history_id,
"targets": targets,
}
new_dataset = self.dataset_populator.fetch(
payload, assert_ok=True).json()["outputs"][0]
content = self.dataset_populator.get_history_dataset_content(
history_id, dataset=new_dataset)
assert content == "I require access to the vault", content
def _get_history_item_as_admin(self, history_id, item_id):
response = self._get("histories/%s/contents/%s?view=detailed" %
(history_id, item_id),
admin=True)
assert_status_code_is_ok(response)
return response.json()
def _assert_status_code_is_ok(self, response):
assert_status_code_is_ok(response)
