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Source code for galaxy_test.api.test_histories
import time
from requests import (
post,
put
)
from galaxy_test.api.sharable import SharingApiTests
from galaxy_test.base.populators import (
DatasetCollectionPopulator,
DatasetPopulator,
skip_without_tool,
)
from ._framework import ApiTestCase
[docs]class BaseHistories:
def _show(self, history_id):
return self._get(f"histories/{history_id}").json()
def _update(self, history_id, data):
update_url = self._api_url(f"histories/{history_id}", use_key=True)
put_response = put(update_url, json=data)
return put_response
def _create_history(self, name):
post_data = dict(name=name)
create_response = self._post("histories", data=post_data).json()
self._assert_has_keys(create_response, "name", "id")
self.assertEqual(create_response["name"], name)
return create_response
[docs]class HistoriesApiTestCase(ApiTestCase, BaseHistories):
[docs] def setUp(self):
super().setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
[docs] def test_create_history(self):
# Create a history.
create_response = self._create_history("TestHistory1")
created_id = create_response["id"]
# Make sure new history appears in index of user's histories.
index_response = self._get("histories").json()
indexed_history = [h for h in index_response if h["id"] == created_id][0]
self.assertEqual(indexed_history["name"], "TestHistory1")
[docs] def test_show_history(self):
history_id = self._create_history("TestHistoryForShow")["id"]
show_response = self._show(history_id)
self._assert_has_key(
show_response,
'id', 'name', 'annotation', 'size', 'contents_url',
'state', 'state_details', 'state_ids'
)
state_details = show_response["state_details"]
state_ids = show_response["state_ids"]
states = [
'discarded', 'empty', 'error', 'failed_metadata', 'new',
'ok', 'paused', 'queued', 'running', 'setting_metadata', 'upload'
]
assert isinstance(state_details, dict)
assert isinstance(state_ids, dict)
self._assert_has_keys(state_details, *states)
self._assert_has_keys(state_ids, *states)
[docs] def test_show_most_recently_used(self):
history_id = self._create_history("TestHistoryRecent")["id"]
show_response = self._get("histories/most_recently_used").json()
assert show_response["id"] == history_id
[docs] def test_index_order(self):
slightly_older_history_id = self._create_history("TestHistorySlightlyOlder")["id"]
newer_history_id = self._create_history("TestHistoryNewer")["id"]
index_response = self._get("histories").json()
assert index_response[0]["id"] == newer_history_id
assert index_response[1]["id"] == slightly_older_history_id
[docs] def test_delete(self):
# Setup a history and ensure it is in the index
history_id = self._create_history("TestHistoryForDelete")["id"]
index_response = self._get("histories").json()
assert index_response[0]["id"] == history_id
show_response = self._show(history_id)
assert not show_response["deleted"]
# Delete the history
self._delete(f"histories/{history_id}")
# Check can view it - but it is deleted
show_response = self._show(history_id)
assert show_response["deleted"]
# Verify it is dropped from history index
index_response = self._get("histories").json()
assert len(index_response) == 0 or index_response[0]["id"] != history_id
# Add deleted filter to index to view it
index_response = self._get("histories", {"deleted": "true"}).json()
assert index_response[0]["id"] == history_id
[docs] def test_purge(self):
history_id = self._create_history("TestHistoryForPurge")["id"]
data = {'purge': True}
self._delete(f"histories/{history_id}", data=data)
show_response = self._show(history_id)
assert show_response["deleted"]
assert show_response["purged"]
[docs] def test_undelete(self):
history_id = self._create_history("TestHistoryForDeleteAndUndelete")["id"]
self._delete(f"histories/{history_id}")
self._post(f"histories/deleted/{history_id}/undelete")
show_response = self._show(history_id)
assert not show_response["deleted"]
[docs] def test_update(self):
history_id = self._create_history("TestHistoryForUpdating")["id"]
self._update(history_id, {"name": "New Name"})
show_response = self._show(history_id)
assert show_response["name"] == "New Name"
unicode_name = '桜ゲノム'
self._update(history_id, {"name": unicode_name})
show_response = self._show(history_id)
assert show_response["name"] == unicode_name, show_response
quoted_name = "'MooCow'"
self._update(history_id, {"name": quoted_name})
show_response = self._show(history_id)
assert show_response["name"] == quoted_name
self._update(history_id, {"deleted": True})
show_response = self._show(history_id)
assert show_response["deleted"], show_response
self._update(history_id, {"deleted": False})
show_response = self._show(history_id)
assert not show_response["deleted"]
self._update(history_id, {"published": True})
show_response = self._show(history_id)
assert show_response["published"]
self._update(history_id, {"genome_build": "hg18"})
show_response = self._show(history_id)
assert show_response["genome_build"] == "hg18"
self._update(history_id, {"annotation": "The annotation is cool"})
show_response = self._show(history_id)
assert show_response["annotation"] == "The annotation is cool"
self._update(history_id, {"annotation": unicode_name})
show_response = self._show(history_id)
assert show_response["annotation"] == unicode_name, show_response
self._update(history_id, {"annotation": quoted_name})
show_response = self._show(history_id)
assert show_response["annotation"] == quoted_name
[docs] def test_update_invalid_attribute(self):
history_id = self._create_history("TestHistoryForInvalidUpdating")["id"]
put_response = self._update(history_id, {"invalidkey": "moo"})
assert "invalidkey" not in put_response.json()
[docs] def test_update_invalid_types(self):
history_id = self._create_history("TestHistoryForUpdatingInvalidTypes")["id"]
for str_key in ["name", "annotation"]:
assert self._update(history_id, {str_key: False}).status_code == 400
for bool_key in ['deleted', 'importable', 'published']:
assert self._update(history_id, {bool_key: "a string"}).status_code == 400
assert self._update(history_id, {"tags": "a simple string"}).status_code == 400
assert self._update(history_id, {"tags": [True]}).status_code == 400
[docs] def test_invalid_keys(self):
invalid_history_id = "1234123412341234"
assert self._get(f"histories/{invalid_history_id}").status_code == 400
assert self._update(invalid_history_id, {"name": "new name"}).status_code == 400
assert self._delete(f"histories/{invalid_history_id}").status_code == 400
assert self._post(f"histories/deleted/{invalid_history_id}/undelete").status_code == 400
[docs] def test_create_anonymous_fails(self):
post_data = dict(name="CannotCreate")
# Using lower-level _api_url will cause key to not be injected.
histories_url = self._api_url("histories")
create_response = post(url=histories_url, data=post_data)
self._assert_status_code_is(create_response, 403)
[docs] def test_create_without_session_fails(self):
post_data = dict(name="SessionNeeded")
# Using admin=True will boostrap an Admin user without session
create_response = self._post("histories", data=post_data, admin=True)
self._assert_status_code_is(create_response, 400)
[docs] def test_create_tag(self):
post_data = dict(name="TestHistoryForTag")
history_id = self._post("histories", data=post_data).json()["id"]
tag_data = dict(value="awesometagvalue")
tag_url = f"histories/{history_id}/tags/awesometagname"
tag_create_response = self._post(tag_url, data=tag_data)
self._assert_status_code_is(tag_create_response, 200)
[docs] def test_copy_history(self):
history_id = self.dataset_populator.new_history()
fetch_response = self.dataset_collection_populator.create_list_in_history(history_id, contents=["Hello", "World"], direct_upload=True)
dataset_collection = self.dataset_collection_populator.wait_for_fetched_collection(fetch_response.json())
copied_history_response = self.dataset_populator.copy_history(history_id)
copied_history_response.raise_for_status()
copied_history = copied_history_response.json()
copied_collection = self.dataset_populator.get_history_collection_details(history_id=copied_history['id'], history_content_type="dataset_collection")
assert dataset_collection['name'] == copied_collection['name']
assert dataset_collection['id'] != copied_collection['id']
assert len(dataset_collection['elements']) == len(copied_collection['elements']) == 2
source_element = dataset_collection['elements'][0]
copied_element = copied_collection['elements'][0]
assert source_element['element_identifier'] == copied_element['element_identifier'] == 'data0'
assert source_element['id'] != copied_element['id']
source_hda = source_element['object']
copied_hda = copied_element['object']
assert source_hda['name'] == copied_hda['name'] == 'data0'
assert source_hda['id'] != copied_hda['id']
assert source_hda['history_id'] != copied_hda['history_id']
assert source_hda['hid'] == copied_hda['hid'] == 2
[docs]class ImportExportHistoryTestCase(ApiTestCase, BaseHistories):
[docs] def setUp(self):
super().setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
[docs] def test_import_export(self):
history_name = "for_export_default"
history_id = self.dataset_populator.setup_history_for_export_testing(history_name)
imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=2)
def upload_job_check(job):
assert job["tool_id"] == "upload1"
def check_discarded(hda):
assert hda["deleted"]
assert hda["state"] == "discarded", hda
assert hda["purged"] is True
self._check_imported_dataset(history_id=imported_history_id, hid=1, job_checker=upload_job_check)
self._check_imported_dataset(history_id=imported_history_id, hid=2, has_job=False, hda_checker=check_discarded, job_checker=upload_job_check)
imported_content = self.dataset_populator.get_history_dataset_content(
history_id=imported_history_id,
hid=1,
)
assert imported_content == "1 2 3\n"
[docs] def test_import_1901_histories(self):
f = open(self.test_data_resolver.get_filename("exports/1901_two_datasets.tgz"), 'rb')
import_data = dict(archive_source='', archive_file=f)
self._import_history_and_wait(import_data, "API Test History", wait_on_history_length=2)
[docs] def test_import_export_include_deleted(self):
history_name = "for_export_include_deleted"
history_id = self.dataset_populator.new_history(name=history_name)
self.dataset_populator.new_dataset(history_id, content="1 2 3")
deleted_hda = self.dataset_populator.new_dataset(history_id, content="1 2 3", wait=True)
self.dataset_populator.delete_dataset(history_id, deleted_hda["id"])
imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=2, export_kwds={"include_deleted": "True"})
self._assert_history_length(imported_history_id, 2)
def upload_job_check(job):
assert job["tool_id"] == "upload1"
def check_deleted_not_purged(hda):
assert hda["state"] == "ok", hda
assert hda["deleted"] is True, hda
assert hda["purged"] is False, hda
self._check_imported_dataset(history_id=imported_history_id, hid=1, job_checker=upload_job_check)
self._check_imported_dataset(history_id=imported_history_id, hid=2, hda_checker=check_deleted_not_purged, job_checker=upload_job_check)
imported_content = self.dataset_populator.get_history_dataset_content(
history_id=imported_history_id,
hid=1,
)
assert imported_content == "1 2 3\n"
[docs] @skip_without_tool("job_properties")
def test_import_export_failed_job(self):
history_name = "for_export_include_failed_job"
history_id = self.dataset_populator.new_history(name=history_name)
self.dataset_populator.run_tool('job_properties', inputs={'failbool': True}, history_id=history_id, assert_ok=False)
self.dataset_populator.wait_for_history(history_id, assert_ok=False)
imported_history_id = self._reimport_history(history_id, history_name, assert_ok=False, wait_on_history_length=4, export_kwds={"include_deleted": "True"})
self._assert_history_length(imported_history_id, 4)
def check_failed(hda_or_job):
print(hda_or_job)
assert hda_or_job["state"] == "error", hda_or_job
self.dataset_populator._summarize_history(imported_history_id)
self._check_imported_dataset(history_id=imported_history_id, hid=1, assert_ok=False, hda_checker=check_failed, job_checker=check_failed)
[docs] def test_import_metadata_regeneration(self):
history_name = "for_import_metadata_regeneration"
history_id = self.dataset_populator.new_history(name=history_name)
self.dataset_populator.new_dataset(history_id, content=open(self.test_data_resolver.get_filename("1.bam"), 'rb'), file_type='bam', wait=True)
imported_history_id = self._reimport_history(history_id, history_name)
self._assert_history_length(imported_history_id, 1)
self._check_imported_dataset(history_id=imported_history_id, hid=1)
import_bam_metadata = self.dataset_populator.get_history_dataset_details(
history_id=imported_history_id,
hid=1,
)
# The cleanup() method of the __IMPORT_HISTORY__ job (which is executed
# after the job has entered its final state):
# - creates a new dataset with 'ok' state and adds it to the history
# - starts a __SET_METADATA__ job to regenerate the dataset metadata, if
# needed
# We need to wait a bit for the creation of the __SET_METADATA__ job.
time.sleep(1)
self.dataset_populator.wait_for_history_jobs(imported_history_id, assert_ok=True)
bai_metadata = import_bam_metadata["meta_files"][0]
assert bai_metadata["file_type"] == "bam_index"
api_url = bai_metadata["download_url"].split("api/", 1)[1]
bai_response = self._get(api_url)
self._assert_status_code_is(bai_response, 200)
assert len(bai_response.content) > 4
[docs] def test_import_export_collection(self):
history_name = "for_export_with_collections"
history_id = self.dataset_populator.new_history(name=history_name)
self.dataset_collection_populator.create_list_in_history(history_id, contents=["Hello", "World"], direct_upload=True)
imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=3)
self._assert_history_length(imported_history_id, 3)
def check_elements(elements):
assert len(elements) == 2
element0 = elements[0]["object"]
element1 = elements[1]["object"]
for element in [element0, element1]:
assert not element["visible"]
assert not element["deleted"]
assert element["state"] == "ok"
assert element0["hid"] == 2
assert element1["hid"] == 3
self._check_imported_collection(imported_history_id, hid=1, collection_type="list", elements_checker=check_elements)
[docs] def test_import_export_nested_collection(self):
history_name = "for_export_with_nested_collections"
history_id = self.dataset_populator.new_history(name=history_name)
self.dataset_collection_populator.create_list_of_pairs_in_history(history_id)
imported_history_id = self._reimport_history(history_id, history_name, wait_on_history_length=3)
self._assert_history_length(imported_history_id, 3)
def check_elements(elements):
assert len(elements) == 1
element0 = elements[0]["object"]
self._assert_has_keys(element0, "elements", "collection_type")
child_elements = element0["elements"]
assert len(child_elements) == 2
assert element0["collection_type"] == "paired"
self._check_imported_collection(imported_history_id, hid=1, collection_type="list:paired", elements_checker=check_elements)
def _reimport_history(self, history_id, history_name, wait_on_history_length=None, assert_ok=True, export_kwds=None):
# Ensure the history is ready to go...
export_kwds = export_kwds or {}
self.dataset_populator.wait_for_history(history_id, assert_ok=assert_ok)
return self.dataset_populator.reimport_history(
history_id, history_name, wait_on_history_length=wait_on_history_length, export_kwds=export_kwds, url=self.url, api_key=self.galaxy_interactor.api_key
)
def _import_history_and_wait(self, import_data, history_name, wait_on_history_length=None):
imported_history_id = self.dataset_populator.import_history_and_wait_for_name(import_data, history_name)
if wait_on_history_length:
self.dataset_populator.wait_on_history_length(imported_history_id, wait_on_history_length)
return imported_history_id
def _assert_history_length(self, history_id, n):
contents_response = self._get(f"histories/{history_id}/contents")
self._assert_status_code_is(contents_response, 200)
contents = contents_response.json()
assert len(contents) == n, contents
def _check_imported_dataset(self, history_id, hid, assert_ok=True, has_job=True, hda_checker=None, job_checker=None):
imported_dataset_metadata = self.dataset_populator.get_history_dataset_details(
history_id=history_id,
hid=hid,
assert_ok=assert_ok,
)
assert imported_dataset_metadata["history_content_type"] == "dataset"
assert imported_dataset_metadata["history_id"] == history_id
if hda_checker is not None:
hda_checker(imported_dataset_metadata)
assert "creating_job" in imported_dataset_metadata
job_id = imported_dataset_metadata["creating_job"]
if has_job:
assert job_id
job_details = self.dataset_populator.get_job_details(job_id, full=True)
assert job_details.status_code == 200, job_details.content
job = job_details.json()
assert 'history_id' in job, job
assert job['history_id'] == history_id, job
if job_checker is not None:
job_checker(job)
def _check_imported_collection(self, history_id, hid, collection_type=None, elements_checker=None):
imported_collection_metadata = self.dataset_populator.get_history_collection_details(
history_id=history_id,
hid=hid,
)
assert imported_collection_metadata["history_content_type"] == "dataset_collection"
assert imported_collection_metadata["history_id"] == history_id
assert "collection_type" in imported_collection_metadata
assert "elements" in imported_collection_metadata
if collection_type is not None:
assert imported_collection_metadata["collection_type"] == collection_type, imported_collection_metadata
if elements_checker is not None:
elements_checker(imported_collection_metadata["elements"])
[docs]class SharingHistoryTestCase(ApiTestCase, BaseHistories, SharingApiTests):
"""Tests specific for the particularities of sharing Histories."""
api_name = "histories"
[docs] def create(self, name: str) -> str:
response_json = self._create_history(name)
history_id = response_json["id"]
# History to share cannot be empty
populator = DatasetPopulator(self.galaxy_interactor)
populator.new_dataset(history_id)
return history_id
[docs] def setUp(self):
super().setUp()
self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
[docs] def test_sharing_with_private_datasets(self):
history_id = self.dataset_populator.new_history()
hda = self.dataset_populator.new_dataset(history_id)
hda_id = hda["id"]
self.dataset_populator.make_private(history_id, hda_id)
with self._different_user():
target_user_id = self.dataset_populator.user_id()
payload = {"user_ids": [target_user_id]}
sharing_response = self._share_history_with_payload(history_id, payload)
# If no share_option is provided, the extra field will contain the
# datasets that need to be accessible before sharing
assert sharing_response["extra"]
assert sharing_response["extra"]["can_share"] is False
assert sharing_response["extra"]["can_change"][0]["id"] == hda_id
assert not sharing_response["users_shared_with"]
# Now we provide the share_option
payload = {
"user_ids": [target_user_id],
"share_option": "make_accessible_to_shared"
}
sharing_response = self._share_history_with_payload(history_id, payload)
assert sharing_response["users_shared_with"]
assert sharing_response["users_shared_with"][0]["id"] == target_user_id
[docs] def test_sharing_without_manage_permissions(self):
history_id = self.dataset_populator.new_history()
hda = self.dataset_populator.new_dataset(history_id)
hda_id = hda["id"]
owner_role_id = self.dataset_populator.user_private_role_id()
with self._different_user():
target_user_id = self.dataset_populator.user_id()
with self._different_user("alice@test.com"):
alice_role_id = self.dataset_populator.user_private_role_id()
# We have one dataset that we cannot manage
payload = {"access": [owner_role_id], "manage": [alice_role_id]}
update_response = self._update_permissions(history_id, hda_id, payload)
self._assert_status_code_is(update_response, 200)
# We will get an error if none of the datasets can be made accessible
payload = {"user_ids": [target_user_id]}
sharing_response = self._share_history_with_payload(history_id, payload)
assert sharing_response["extra"]
assert sharing_response["extra"]["can_share"] is False
assert sharing_response["extra"]["cannot_change"][0]["id"] == hda_id
assert sharing_response["errors"]
assert not sharing_response["users_shared_with"]
# Trying to change the permissions when sharing should fail
# because we don't have manage permissions
payload = {
"user_ids": [target_user_id],
"share_option": "make_public"
}
sharing_response = self._share_history_with_payload(history_id, payload)
assert sharing_response["extra"]
assert sharing_response["extra"]["can_share"] is False
assert sharing_response["errors"]
assert not sharing_response["users_shared_with"]
# we can share if we don't try to make any permission changes
payload = {
"user_ids": [target_user_id],
"share_option": "no_changes"
}
sharing_response = self._share_history_with_payload(history_id, payload)
assert not sharing_response["errors"]
assert sharing_response["users_shared_with"]
assert sharing_response["users_shared_with"][0]["id"] == target_user_id
[docs] def test_sharing_empty_not_allowed(self):
history_id = self.dataset_populator.new_history()
with self._different_user():
target_user_id = self.dataset_populator.user_id()
payload = {"user_ids": [target_user_id]}
sharing_response = self._share_history_with_payload(history_id, payload)
assert sharing_response["extra"]["can_share"] is False
assert sharing_response["errors"]
assert "empty" in sharing_response["errors"][0]
[docs] def test_sharing_with_duplicated_users(self):
history_id = self.create("HistoryToShareWithDuplicatedUser")
with self._different_user():
target_user_id = self.dataset_populator.user_id()
# Ignore repeated users in the same request
payload = {"user_ids": [target_user_id, target_user_id]}
sharing_response = self._share_history_with_payload(history_id, payload)
assert sharing_response["users_shared_with"]
assert len(sharing_response["users_shared_with"]) == 1
assert sharing_response["users_shared_with"][0]["id"] == target_user_id
[docs] def test_sharing_private_history_makes_datasets_public(self):
history_id = self.dataset_populator.new_history()
hda = self.dataset_populator.new_dataset(history_id)
hda_id = hda["id"]
self.dataset_populator.make_private(history_id, hda_id)
# Other users cannot access the dataset
with self._different_user():
show_response = self._get(f"datasets/{hda_id}")
self._assert_status_code_is(show_response, 403)
sharing_response = self._set_resource_sharing(history_id, "publish")
assert sharing_response["published"] is True
# Other users can access the dataset after publishing
with self._different_user():
show_response = self._get(f"datasets/{hda_id}")
self._assert_status_code_is(show_response, 200)
hda = show_response.json()
assert hda["id"] == hda_id
def _share_history_with_payload(self, history_id, payload):
sharing_response = self._put(f"histories/{history_id}/share_with_users", data=payload, json=True)
self._assert_status_code_is(sharing_response, 200)
return sharing_response.json()
def _update_permissions(self, history_id: str, dataset_id: str, payload):
url = f"histories/{history_id}/contents/{dataset_id}/permissions"
update_url = self._api_url(url, **{"use_admin_key": True})
update_response = put(update_url, json=payload)
return update_response