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Merge pull request #13330 from mvdbeek/exp_imp_anonymous

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[22.01] Fix history exports import by url
This commit is contained in:
Marius van den Beek
2022-02-10 12:11:19 +01:00
committed by GitHub
parent bf3a5420ef 96d89a4f5c
commit c1f959d909
4 changed files with 25 additions and 19 deletions
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lib/galaxy/webapps/galaxy/api/histories.py
+2 -2
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@@ -59,7 +59,7 @@ from galaxy.web import (
expose_api,
expose_api_anonymous,
expose_api_anonymous_and_sessionless,
expose_api_raw,
expose_api_raw_anonymous_and_sessionless,
)
from galaxy.webapps.galaxy.api.common import (
parse_serialization_params,
@@ -765,7 +765,7 @@ class HistoriesController(BaseGalaxyAPIController):
trans.response.status = 202
return export_result
@expose_api_raw
@expose_api_raw_anonymous_and_sessionless
def archive_download(self, trans, id, jeha_id, **kwds):
"""
GET /api/histories/{id}/exports/{jeha_id}
lib/galaxy_test/api/test_histories.py
+1 -1
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@@ -390,7 +390,7 @@ class ImportExportTests(BaseHistories):
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, api_key=self.galaxy_interactor.api_key
history_id, history_name, wait_on_history_length=wait_on_history_length, export_kwds=export_kwds,
)
def _import_history_and_wait(self, import_data, history_name, wait_on_history_length=None):
lib/galaxy_test/api/test_workflow_extraction.py
+1 -1
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@@ -499,7 +499,7 @@ test_data:
history_length = self.dataset_populator.history_length(history_id)
new_history_id = self.dataset_populator.reimport_history(
history_id, history_name, wait_on_history_length=history_length, export_kwds={}, api_key=self.galaxy_interactor.api_key
history_id, history_name, wait_on_history_length=history_length, export_kwds={},
)
# wait a little more for those jobs, todo fix to wait for history imported false or
# for a specific number of jobs...
lib/galaxy_test/base/populators.py
+21 -15
View File
@@ -555,7 +555,7 @@ class BaseDatasetPopulator(BasePopulator):
self.wait_for_history(history_id, assert_ok=True, timeout=timeout)
def wait_for_job(self, job_id: str, assert_ok: bool = False, timeout: timeout_type = DEFAULT_TIMEOUT):
return wait_on_state(lambda: self.get_job_details(job_id), desc="job state", assert_ok=assert_ok, timeout=timeout)
return wait_on_state(lambda: self.get_job_details(job_id, full=True), desc="job state", assert_ok=assert_ok, timeout=timeout)
def get_job_details(self, job_id: str, full: bool = False) -> Response:
return self._get(f"jobs/{job_id}?full={full}")
@@ -913,6 +913,11 @@ class BaseDatasetPopulator(BasePopulator):
assert update_response.status_code == 200, update_response.content
return update_response.json()
def make_public(self, history_id: str) -> dict:
sharing_response = self._put(f"histories/{history_id}/publish")
assert sharing_response.status_code == 200
return sharing_response.json()
def validate_dataset(self, history_id: str, dataset_id: str) -> Dict[str, Any]:
url = f"histories/{history_id}/contents/{dataset_id}/validate"
update_response = self._put(url)
@@ -967,20 +972,19 @@ class BaseDatasetPopulator(BasePopulator):
assert "job_id" in job_desc
return self.wait_for_job(job_desc["job_id"])
def export_url(self, history_id: str, data, api_key: str, check_download: bool = True) -> str:
def export_url(self, history_id: str, data, check_download: bool = True) -> str:
put_response = self.prepare_export(history_id, data)
response = put_response.json()
api_asserts.assert_has_keys(response, "download_url")
download_url = urllib.parse.urljoin(self.galaxy_interactor.api_url, response["download_url"].strip('/'))
if check_download:
self.get_export_url(download_url, api_key)
self.get_export_url(download_url)
return download_url
def get_export_url(self, export_url, api_key) -> Response:
full_download_url = f"{export_url}?key={api_key}"
download_response = self._get(full_download_url)
def get_export_url(self, export_url) -> Response:
download_response = self._get(export_url)
api_asserts.assert_status_code_is(download_response, 200)
return download_response
@@ -991,6 +995,7 @@ class BaseDatasetPopulator(BasePopulator):
files["archive_file"] = archive_file
import_response = self._post("histories", data=import_data, files=files)
api_asserts.assert_status_code_is(import_response, 200)
return import_response.json()['id']
def import_history_and_wait_for_name(self, import_data, history_name):
def history_names():
@@ -999,7 +1004,8 @@ class BaseDatasetPopulator(BasePopulator):
import_name = f"imported from archive: {history_name}"
assert import_name not in history_names()
self.import_history(import_data)
job_id = self.import_history(import_data)
self.wait_for_job(job_id, assert_ok=True)
def has_history_with_name():
histories = history_names()
@@ -1034,14 +1040,13 @@ class BaseDatasetPopulator(BasePopulator):
contents = contents_response.json()
return len(contents)
def reimport_history(self, history_id, history_name, wait_on_history_length, export_kwds, api_key):
def reimport_history(self, history_id, history_name, wait_on_history_length, export_kwds):
# Make history public so we can import by url
self.make_public(history_id)
# Export the history.
download_path = self.export_url(history_id, export_kwds, api_key, check_download=True)
download_url = self.export_url(history_id, export_kwds, check_download=True)
# Create download for history
full_download_url = urllib.parse.urljoin(download_path, f"?key={api_key}")
import_data = dict(archive_source=full_download_url, archive_type="url")
import_data = dict(archive_source=download_url, archive_type="url")
imported_history_id = self.import_history_and_wait_for_name(import_data, history_name)
@@ -2151,12 +2156,13 @@ def wait_on_state(state_func: Callable, desc="state", skip_states=None, ok_state
def get_state():
response = state_func()
assert response.status_code == 200, f"Failed to fetch state update while waiting. [{response.content}]"
state = response.json()["state"]
state_response = response.json()
state = state_response["state"]
if state in skip_states:
return None
else:
if assert_ok:
assert state in ok_states, f"Final state - {state} - not okay."
assert state in ok_states, f"Final state - {state} - not okay. Full response: {state_response}"
return state
if skip_states is None: