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Merge branch 'release_21.05' into dev

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This commit is contained in:
mvdbeek
2021-07-01 10:03:48 +02:00
parent 91109c98ae 292cd4d31d
commit 9952be7a80
4 changed files with 41 additions and 38 deletions
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lib/galaxy/tools/parameters/basic.py
+7 -8
View File
@@ -1900,13 +1900,12 @@ class DataToolParameter(BaseDataToolParameter):
rval.append(trans.sa_session.query(trans.app.model.LibraryDatasetDatasetAssociation).get(decoded_id))
else:
raise ValueError(f"Unknown input source {single_value['src']} passed to job submission API.")
elif isinstance(single_value, trans.app.model.HistoryDatasetCollectionAssociation):
rval.append(single_value)
elif isinstance(single_value, trans.app.model.DatasetCollectionElement):
rval.append(single_value)
elif isinstance(single_value, trans.app.model.HistoryDatasetAssociation):
rval.append(single_value)
elif isinstance(single_value, trans.app.model.LibraryDatasetDatasetAssociation):
elif isinstance(single_value, (
trans.app.model.HistoryDatasetCollectionAssociation,
trans.app.model.DatasetCollectionElement,
trans.app.model.HistoryDatasetAssociation,
trans.app.model.LibraryDatasetDatasetAssociation
)):
rval.append(single_value)
else:
if len(str(single_value)) == 16:
@@ -1919,7 +1918,7 @@ class DataToolParameter(BaseDataToolParameter):
for val in rval:
if not isinstance(val, trans.app.model.HistoryDatasetCollectionAssociation):
raise ParameterValueError("if collections are supplied to multiple data input parameter, only collections may be used", self.name)
elif isinstance(value, trans.app.model.HistoryDatasetAssociation):
elif isinstance(value, (trans.app.model.HistoryDatasetAssociation, trans.app.model.LibraryDatasetDatasetAssociation)):
rval = value
elif isinstance(value, dict) and 'src' in value and 'id' in value:
if value['src'] == 'hda':
lib/galaxy_test/api/test_libraries.py
+26 -28
View File
@@ -1,5 +1,4 @@
import json
import time
import unittest
from galaxy_test.base.populators import (
@@ -340,44 +339,43 @@ class LibrariesApiTestCase(ApiTestCase):
container_update_time = container_fetch_response.json()['folder_contents'][0]['update_time']
assert dataset_update_time == container_update_time, container_fetch_response
def test_update_dataset_in_folder(self):
ld = self._create_dataset_in_folder_in_library("ForUpdateDataset", wait=True)
data = {'name': 'updated_name', 'file_ext': 'fastq', 'misc_info': 'updated_info', 'genome_build': 'updated_genome_build'}
create_response = self._patch(f"libraries/datasets/{ld.json()['id']}", data=data)
def _patch_library_dataset(self, library_dataset_id, data):
create_response = self._patch(f"libraries/datasets/{library_dataset_id}", data=data)
self._assert_status_code_is(create_response, 200)
self._assert_has_keys(create_response.json(), "name", "file_ext", "misc_info", "genome_build")
ld = create_response.json()
library_id = ld['parent_library_id']
return self.library_populator.wait_on_library_dataset(library={'id': library_id}, dataset=ld)
def test_update_dataset_in_folder(self):
ld = self._create_dataset_in_folder_in_library("ForUpdateDataset", content=">seq\nATGC", wait=True).json()
data = {'name': 'updated_name', 'file_ext': 'fasta', 'misc_info': 'updated_info', 'genome_build': 'updated_genome_build'}
ld_updated = self._patch_library_dataset(ld['id'], data)
self._assert_has_keys(ld_updated, "name", "file_ext", "misc_info", "genome_build")
def test_update_dataset_tags(self):
ld = self._create_dataset_in_folder_in_library("ForTagtestDataset")
ld = self._create_dataset_in_folder_in_library("ForTagtestDataset", wait=True).json()
data = {"tags": ["#Lancelot", "name:Holy Grail", "blue"]}
create_response = self._patch(f"libraries/datasets/{ld.json()['id']}", data=data)
self._assert_status_code_is(create_response, 200)
self._assert_has_keys(create_response.json(), "tags")
assert create_response.json()["tags"] == "name:Lancelot, name:HolyGrail, blue"
ld_updated = self._patch_library_dataset(ld['id'], data)
self._assert_has_keys(ld_updated, "tags")
assert ld_updated["tags"] == "name:Lancelot, name:HolyGrail, blue"
def test_invalid_update_dataset_in_folder(self):
ld = self._create_dataset_in_folder_in_library("ForInvalidUpdateDataset")
ld = self._create_dataset_in_folder_in_library("ForInvalidUpdateDataset", wait=True).json()
data = {'file_ext': 'nonexisting_type'}
create_response = self._patch(f"libraries/datasets/{ld.json()['id']}", data=data)
create_response = self._patch(f"libraries/datasets/{ld['id']}", data=data)
self._assert_status_code_is(create_response, 400)
assert 'This Galaxy does not recognize the datatype of:' in create_response.json()['err_msg']
def test_detect_datatype_of_dataset_in_folder(self):
ld = self._create_dataset_in_folder_in_library("ForDetectDataset")
# Wait for metadata job to finish.
time.sleep(2)
ld = self._create_dataset_in_folder_in_library("ForDetectDataset", wait=True).json()
data = {'file_ext': 'data'}
create_response = self._patch(f"libraries/datasets/{ld.json()['id']}", data=data)
self._assert_status_code_is(create_response, 200)
self._assert_has_keys(create_response.json(), "file_ext")
assert create_response.json()["file_ext"] == "data"
# Wait for metadata job to finish.
time.sleep(2)
ld_updated = self._patch_library_dataset(ld['id'], data)
self._assert_has_keys(ld_updated, "file_ext")
assert ld_updated["file_ext"] == "data"
data = {'file_ext': 'auto'}
create_response = self._patch(f"libraries/datasets/{ld.json()['id']}", data=data)
self._assert_status_code_is(create_response, 200)
self._assert_has_keys(create_response.json(), "file_ext")
assert create_response.json()["file_ext"] == "txt"
ld_updated = self._patch_library_dataset(ld['id'], data)
self._assert_has_keys(ld_updated, "file_ext")
assert ld_updated["file_ext"] == "txt"
def test_ldda_collection_import_to_history(self):
self._import_to_history(visible=True)
@@ -482,13 +480,13 @@ class LibrariesApiTestCase(ApiTestCase):
)
return self._post(f"folders/{containing_folder_id}", data=create_data)
def _create_dataset_in_folder_in_library(self, library_name, wait=False):
def _create_dataset_in_folder_in_library(self, library_name, content="1 2 3", wait=False):
library = self.library_populator.new_private_library(library_name)
folder_response = self._create_folder(library)
self._assert_status_code_is(folder_response, 200)
folder_id = folder_response.json()[0]['id']
history_id = self.dataset_populator.new_history()
hda_id = self.dataset_populator.new_dataset(history_id, content="1 2 3", wait=wait)['id']
hda_id = self.dataset_populator.new_dataset(history_id, content=content, wait=wait)['id']
payload = {'from_hda_id': hda_id, 'create_type': 'file', 'folder_id': folder_id}
ld = self._post(f"libraries/{folder_id}/contents", payload)
return ld
lib/galaxy_test/base/populators.py
+1 -1
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@@ -1742,7 +1742,7 @@ def wait_on_state(state_func: Callable, desc="state", skip_states=None, ok_state
return state
if skip_states is None:
skip_states = ["running", "queued", "new", "ready", "stop", "stopped"]
skip_states = ["running", "queued", "new", "ready", "stop", "stopped", "setting_metadata"]
if ok_states is None:
ok_states = ["ok", "scheduled"]
try:
packages/tool_util/HISTORY.rst
+7 -1
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@@ -6,7 +6,13 @@ History
.. to_doc
---------------------
21.1.2.dev0
21.1.3.dev0
---------------------
---------------------
21.1.2 (2021-06-23)
---------------------