mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Nicola Soranzo
6b3f672770
Fix warnings during py34-unit tests like:
```
/home/travis/build/galaxyproject/galaxy/test/unit/workflows/test_extract_summary.py:46: DeprecationWarning: Please use assertEqual instead.
self.assertEquals(job_dict[hda.job], [('out1', derived_hda_2)])
```
See e.g. https://travis-ci.org/galaxyproject/galaxy/jobs/438829277
287 lines
12 KiB
Python
287 lines
12 KiB
Python
# -*- coding: utf-8 -*-
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from requests import (
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get,
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post,
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put
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)
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from base import api # noqa: I100,I202
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from base.populators import ( # noqa: I100
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DatasetCollectionPopulator,
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DatasetPopulator,
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wait_on
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)
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class HistoriesApiTestCase(api.ApiTestCase):
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def setUp(self):
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super(HistoriesApiTestCase, self).setUp()
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self.dataset_populator = DatasetPopulator(self.galaxy_interactor)
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self.dataset_collection_populator = DatasetCollectionPopulator(self.galaxy_interactor)
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def test_create_history(self):
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# Create a history.
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create_response = self._create_history("TestHistory1")
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created_id = create_response["id"]
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# Make sure new history appears in index of user's histories.
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index_response = self._get("histories").json()
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indexed_history = [h for h in index_response if h["id"] == created_id][0]
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self.assertEqual(indexed_history["name"], "TestHistory1")
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def test_show_history(self):
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history_id = self._create_history("TestHistoryForShow")["id"]
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show_response = self._show(history_id)
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self._assert_has_key(
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show_response,
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'id', 'name', 'annotation', 'size', 'contents_url',
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'state', 'state_details', 'state_ids'
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)
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state_details = show_response["state_details"]
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state_ids = show_response["state_ids"]
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states = [
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'discarded', 'empty', 'error', 'failed_metadata', 'new',
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'ok', 'paused', 'queued', 'running', 'setting_metadata', 'upload'
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]
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assert isinstance(state_details, dict)
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assert isinstance(state_ids, dict)
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self._assert_has_keys(state_details, *states)
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self._assert_has_keys(state_ids, *states)
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def test_show_most_recently_used(self):
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history_id = self._create_history("TestHistoryRecent")["id"]
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show_response = self._get("histories/most_recently_used").json()
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assert show_response["id"] == history_id
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def test_index_order(self):
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slightly_older_history_id = self._create_history("TestHistorySlightlyOlder")["id"]
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newer_history_id = self._create_history("TestHistoryNewer")["id"]
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index_response = self._get("histories").json()
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assert index_response[0]["id"] == newer_history_id
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assert index_response[1]["id"] == slightly_older_history_id
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def test_delete(self):
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# Setup a history and ensure it is in the index
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history_id = self._create_history("TestHistoryForDelete")["id"]
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index_response = self._get("histories").json()
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assert index_response[0]["id"] == history_id
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show_response = self._show(history_id)
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assert not show_response["deleted"]
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# Delete the history
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self._delete("histories/%s" % history_id)
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# Check can view it - but it is deleted
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show_response = self._show(history_id)
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assert show_response["deleted"]
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# Verify it is dropped from history index
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index_response = self._get("histories").json()
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assert len(index_response) == 0 or index_response[0]["id"] != history_id
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# Add deleted filter to index to view it
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index_response = self._get("histories", {"deleted": "true"}).json()
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assert index_response[0]["id"] == history_id
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def test_purge(self):
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history_id = self._create_history("TestHistoryForPurge")["id"]
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data = {'purge': True}
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self._delete("histories/%s" % history_id, data=data)
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show_response = self._show(history_id)
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assert show_response["deleted"]
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assert show_response["purged"]
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def test_undelete(self):
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history_id = self._create_history("TestHistoryForDeleteAndUndelete")["id"]
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self._delete("histories/%s" % history_id)
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self._post("histories/deleted/%s/undelete" % history_id)
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show_response = self._show(history_id)
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assert not show_response["deleted"]
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def test_update(self):
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history_id = self._create_history("TestHistoryForUpdating")["id"]
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self._update(history_id, {"name": "New Name"})
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show_response = self._show(history_id)
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assert show_response["name"] == "New Name"
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unicode_name = u'桜ゲノム'
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self._update(history_id, {"name": unicode_name})
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show_response = self._show(history_id)
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assert show_response["name"] == unicode_name, show_response
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quoted_name = "'MooCow'"
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self._update(history_id, {"name": quoted_name})
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show_response = self._show(history_id)
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assert show_response["name"] == quoted_name
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self._update(history_id, {"deleted": True})
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show_response = self._show(history_id)
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assert show_response["deleted"], show_response
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self._update(history_id, {"deleted": False})
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show_response = self._show(history_id)
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assert not show_response["deleted"]
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self._update(history_id, {"published": True})
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show_response = self._show(history_id)
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assert show_response["published"]
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self._update(history_id, {"genome_build": "hg18"})
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show_response = self._show(history_id)
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assert show_response["genome_build"] == "hg18"
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self._update(history_id, {"annotation": "The annotation is cool"})
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show_response = self._show(history_id)
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assert show_response["annotation"] == "The annotation is cool"
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self._update(history_id, {"annotation": unicode_name})
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show_response = self._show(history_id)
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assert show_response["annotation"] == unicode_name, show_response
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self._update(history_id, {"annotation": quoted_name})
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show_response = self._show(history_id)
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assert show_response["annotation"] == quoted_name
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def test_update_invalid_attribute(self):
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history_id = self._create_history("TestHistoryForInvalidUpdating")["id"]
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put_response = self._update(history_id, {"invalidkey": "moo"})
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assert "invalidkey" not in put_response.json()
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def test_update_invalid_types(self):
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history_id = self._create_history("TestHistoryForUpdatingInvalidTypes")["id"]
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for str_key in ["name", "annotation"]:
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assert self._update(history_id, {str_key: False}).status_code == 400
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for bool_key in ['deleted', 'importable', 'published']:
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assert self._update(history_id, {bool_key: "a string"}).status_code == 400
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assert self._update(history_id, {"tags": "a simple string"}).status_code == 400
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assert self._update(history_id, {"tags": [True]}).status_code == 400
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def test_invalid_keys(self):
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invalid_history_id = "1234123412341234"
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assert self._get("histories/%s" % invalid_history_id).status_code == 400
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assert self._update(invalid_history_id, {"name": "new name"}).status_code == 400
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assert self._delete("histories/%s" % invalid_history_id).status_code == 400
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assert self._post("histories/deleted/%s/undelete" % invalid_history_id).status_code == 400
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def test_create_anonymous_fails(self):
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post_data = dict(name="CannotCreate")
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# Using lower-level _api_url will cause key to not be injected.
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histories_url = self._api_url("histories")
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create_response = post(url=histories_url, data=post_data)
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self._assert_status_code_is(create_response, 403)
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def test_import_export(self):
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history_name = "for_export"
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history_id = self.dataset_populator.new_history(name=history_name)
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self.dataset_populator.new_dataset(history_id, content="1 2 3")
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imported_history_id = self._reimport_history(history_id, history_name)
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contents_response = self._get("histories/%s/contents" % imported_history_id)
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self._assert_status_code_is(contents_response, 200)
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contents = contents_response.json()
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assert len(contents) == 1
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imported_content = self.dataset_populator.get_history_dataset_content(
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history_id=imported_history_id,
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dataset_id=contents[0]["id"]
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)
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assert imported_content == "1 2 3\n"
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def test_import_export_collection(self):
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from nose.plugins.skip import SkipTest
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raise SkipTest("Collection import/export not yet implemented")
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history_name = "for_export_with_collections"
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history_id = self.dataset_populator.new_history(name=history_name)
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self.dataset_collection_populator.create_list_in_history(history_id, contents=["Hello", "World"])
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imported_history_id = self._reimport_history(history_id, history_name)
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contents_response = self._get("histories/%s/contents" % imported_history_id)
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self._assert_status_code_is(contents_response, 200)
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contents = contents_response.json()
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assert len(contents) == 3
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def _reimport_history(self, history_id, history_name):
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# Ensure the history is ready to go...
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self.dataset_populator.wait_for_history(history_id, assert_ok=True)
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# Export the history.
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download_path = self._export(history_id)
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# Create download for history
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full_download_url = "%s%s?key=%s" % (self.url, download_path, self.galaxy_interactor.api_key)
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download_response = get(full_download_url)
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self._assert_status_code_is(download_response, 200)
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def history_names():
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history_index = self._get("histories")
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return dict((h["name"], h) for h in history_index.json())
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import_name = "imported from archive: %s" % history_name
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assert import_name not in history_names()
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import_data = dict(archive_source=full_download_url, archive_type="url")
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import_response = self._post("histories", data=import_data)
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self._assert_status_code_is(import_response, 200)
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def has_history_with_name():
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histories = history_names()
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return histories.get(import_name, None)
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imported_history = wait_on(has_history_with_name, desc="import history")
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imported_history_id = imported_history["id"]
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self.dataset_populator.wait_for_history(imported_history_id)
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return imported_history_id
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def test_create_tag(self):
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post_data = dict(name="TestHistoryForTag")
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history_id = self._post("histories", data=post_data).json()["id"]
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tag_data = dict(value="awesometagvalue")
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tag_url = "histories/%s/tags/awesometagname" % history_id
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tag_create_response = self._post(tag_url, data=tag_data)
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self._assert_status_code_is(tag_create_response, 200)
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def _export(self, history_id):
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export_url = self._api_url("histories/%s/exports" % history_id, use_key=True)
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put_response = put(export_url)
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self._assert_status_code_is(put_response, 202)
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def export_ready_response():
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put_response = put(export_url)
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if put_response.status_code == 202:
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return None
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return put_response
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put_response = wait_on(export_ready_response, desc="export ready")
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self._assert_status_code_is(put_response, 200)
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response = put_response.json()
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self._assert_has_keys(response, "download_url")
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download_path = response["download_url"]
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return download_path
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def _show(self, history_id):
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return self._get("histories/%s" % history_id).json()
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def _update(self, history_id, data):
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update_url = self._api_url("histories/%s" % history_id, use_key=True)
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put_response = put(update_url, json=data)
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return put_response
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def _create_history(self, name):
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post_data = dict(name=name)
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create_response = self._post("histories", data=post_data).json()
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self._assert_has_keys(create_response, "name", "id")
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self.assertEqual(create_response["name"], name)
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return create_response
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# TODO: (CE) test_create_from_copy
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