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Merge pull request #14524 from nsoranzo/misc_fixes_202208

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Misc fixes 202208
This commit is contained in:
John Chilton
2022-08-29 09:37:38 -04:00
committed by GitHub
parent c3fe860d1a d9326c8f2c
commit 11517ea8ea
16 changed files with 40 additions and 69 deletions
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CONTRIBUTING.md
+1 -1
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@@ -158,7 +158,7 @@ https://help.github.com/en/github/getting-started-with-github/git-and-github-lea
particular emphasis on readability being the ultimate goal:
- 4 spaces (not tabs!) per indentation level
- divergences from PEP-8 are listed in the `[flake8]` section of the
`setup.cfg` file
`.flake8` file
- The Python code base is automatically formatted using
[isort](https://pycqa.github.io/isort/) (for imports) and
[black](https://black.readthedocs.io). To easily format your Python code
contrib/galaxy_config_merger.py
-15
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@@ -6,21 +6,6 @@ Created by Anne Pajon on 31 Jan 2012
Copyright (c) 2012 Cancer Research UK - Cambridge Research Institute.
This source file is licensed under the Academic Free License version
3.0 available at http://www.opensource.org/licenses/AFL-3.0.
Permission is hereby granted to reproduce, translate, adapt, alter,
transform, modify, or arrange this source file (the "Original Work");
to distribute or communicate copies of it under any license of your
choice that does not contradict the terms and conditions; to perform
or display the Original Work publicly.
THE ORIGINAL WORK IS PROVIDED UNDER THIS LICENSE ON AN "AS IS" BASIS
AND WITHOUT WARRANTY, EITHER EXPRESS OR IMPLIED, INCLUDING, WITHOUT
LIMITATION, THE WARRANTIES OF NON-INFRINGEMENT, MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY OF
THE ORIGINAL WORK IS WITH YOU.
Script for merging specific local Galaxy config galaxy.ini.cri with default Galaxy galaxy.ini.sample
"""
lib/galaxy/job_execution/output_collect.py
+1 -1
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@@ -646,7 +646,7 @@ class DatasetCollector:
def __init__(self, dataset_collection_description):
self.discover_via = dataset_collection_description.discover_via
# dataset_collection_description is an abstract description
# built from the tool parsing module - see galaxy.tool_util.parser.output_colleciton_def
# built from the tool parsing module - see galaxy.tool_util.parser.output_collection_def
self.sort_key = dataset_collection_description.sort_key
self.sort_reverse = dataset_collection_description.sort_reverse
self.sort_comp = dataset_collection_description.sort_comp
lib/galaxy/jobs/__init__.py
+2 -4
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@@ -2128,10 +2128,8 @@ class MinimalJobWrapper(HasResourceParameters):
raise Exception(f"Unknown target type [{target}]")
def get_tool_provided_job_metadata(self):
if self.tool_provided_job_metadata is not None:
return self.tool_provided_job_metadata
self.tool_provided_job_metadata = self.tool.tool_provided_metadata(self)
if self.tool_provided_job_metadata is None:
self.tool_provided_job_metadata = self.tool.tool_provided_metadata(self)
return self.tool_provided_job_metadata
def get_dataset_finish_context(self, job_context, output_dataset_assoc):
lib/galaxy/tool_util/toolbox/base.py
+2 -2
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@@ -1322,9 +1322,9 @@ class AbstractToolBox(Dictifiable, ManagesIntegratedToolPanelMixin):
def _tool_from_lineage_version(self, lineage_tool_version):
if lineage_tool_version.id_based:
return self._tools_by_id.get(lineage_tool_version.id, None)
return self._tools_by_id.get(lineage_tool_version.id)
else:
return self._tool_versions_by_id.get(lineage_tool_version.id, {}).get(lineage_tool_version.version, None)
return self._tool_versions_by_id.get(lineage_tool_version.id, {}).get(lineage_tool_version.version)
def _build_filter_method(self, trans):
context = Bunch(toolbox=self, trans=trans)
lib/galaxy/tool_util/verify/interactor.py
-8
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@@ -1332,14 +1332,6 @@ def _verify_outputs(testdef, history, jobs, data_list, data_collection_list, gal
job_stdio = galaxy_interactor.get_job_stdio(job["id"])
if testdef.num_outputs is not None:
expected = testdef.num_outputs
actual = len(data_list) + len(data_collection_list)
if expected != actual:
message = f"Incorrect number of outputs - expected {expected}, found {actual}: datasets {data_list.keys()} collections {data_collection_list.keys()}"
error = AssertionError(message)
register_exception(error)
if testdef.num_outputs is not None:
expected = testdef.num_outputs
actual = len(data_list) + len(data_collection_list)
lib/galaxy/tools/__init__.py
+1 -1
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@@ -3528,7 +3528,7 @@ class RelabelFromFileTool(DatabaseOperationTool):
add_copied_value_to_new_elements(new_labels[i], dce_object)
for key in new_elements.keys():
if not re.match(r"^[\w\- \.,]+$", key):
raise Exception(f"Invalid new colleciton identifier [{key}]")
raise Exception(f"Invalid new collection identifier [{key}]")
self._add_datasets_to_history(history, new_elements.values())
output_collections.create_collection(
next(iter(self.outputs.values())), "output", elements=new_elements, propagate_hda_tags=False
lib/galaxy/tools/execute.py
+1 -1
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@@ -33,7 +33,7 @@ if typing.TYPE_CHECKING:
log = logging.getLogger(__name__)
SINGLE_EXECUTION_SUCCESS_MESSAGE = "Tool ${tool_id} created job ${job_id}"
BATCH_EXECUTION_MESSAGE = "Executed ${job_count} job(s) for tool ${tool_id} request"
BATCH_EXECUTION_MESSAGE = "Created ${job_count} job(s) for tool ${tool_id} request"
class PartialJobExecution(Exception):
lib/galaxy/webapps/base/webapp.py
+2 -4
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@@ -19,6 +19,7 @@ from urllib.parse import urlparse
import mako.lookup
import mako.runtime
from apispec import APISpec
from paste.urlmap import URLMap
from sqlalchemy import (
and_,
true,
@@ -47,6 +48,7 @@ from galaxy.web.framework import (
helpers,
url_for,
)
from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
try:
from importlib.resources import files # type: ignore[attr-defined]
@@ -1114,10 +1116,6 @@ def default_url_path(path):
def build_url_map(app, global_conf, **local_conf):
from paste.urlmap import URLMap
from galaxy.web.framework.middleware.static import CacheableStaticURLParser as Static
urlmap = URLMap()
# Merge the global and local configurations
conf = global_conf.copy()
lib/galaxy/webapps/galaxy/api/jobs.py
+12 -12
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@@ -260,7 +260,7 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
return {"has_empty_inputs": has_empty_inputs, "has_duplicate_inputs": has_duplicate_inputs}
@expose_api
def inputs(self, trans: ProvidesUserContext, id, **kwd):
def inputs(self, trans: ProvidesUserContext, id, **kwd) -> List[dict]:
"""
GET /api/jobs/{id}/inputs
@@ -269,14 +269,14 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
:type id: string
:param id: Encoded job id
:rtype: dictionary
:returns: dictionary containing input dataset associations
:rtype: list of dicts
:returns: list of dictionaries containing input dataset associations
"""
job = self.__get_job(trans, id)
return self.__dictify_associations(trans, job.input_datasets, job.input_library_datasets)
@expose_api
def outputs(self, trans: ProvidesUserContext, id, **kwd):
def outputs(self, trans: ProvidesUserContext, id, **kwd) -> List[dict]:
"""
outputs( trans, id )
* GET /api/jobs/{id}/outputs
@@ -285,8 +285,8 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
:type id: string
:param id: Encoded job id
:rtype: dictionary
:returns: dictionary containing output dataset associations
:rtype: list of dicts
:returns: list of dictionaries containing output dataset associations
"""
job = self.__get_job(trans, id)
return self.__dictify_associations(trans, job.output_datasets, job.output_library_datasets)
@@ -309,7 +309,7 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
return self.job_manager.stop(job, message=message)
@expose_api
def resume(self, trans: ProvidesUserContext, id, **kwd):
def resume(self, trans: ProvidesUserContext, id, **kwd) -> List[dict]:
"""
* PUT /api/jobs/{id}/resume
Resumes a paused job
@@ -317,8 +317,8 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
:type id: string
:param id: Encoded job id
:rtype: dictionary
:returns: dictionary containing output dataset associations
:rtype: list of dicts
:returns: list of dictionaries containing output dataset associations
"""
job = self.__get_job(trans, id)
if not job:
@@ -425,13 +425,13 @@ class JobController(BaseGalaxyAPIController, UsesVisualizationMixin):
raise exceptions.ConfigDoesNotAllowException(f"Tool '{job.tool_id}' cannot be rerun.")
return tool.to_json(trans, {}, job=job)
def __dictify_associations(self, trans, *association_lists):
rval = []
def __dictify_associations(self, trans, *association_lists) -> List[dict]:
rval: List[dict] = []
for association_list in association_lists:
rval.extend(self.__dictify_association(trans, a) for a in association_list)
return rval
def __dictify_association(self, trans, job_dataset_association):
def __dictify_association(self, trans, job_dataset_association) -> dict:
dataset_dict = None
dataset = job_dataset_association.dataset
if dataset:
lib/galaxy_test/api/test_history_contents.py
+1 -1
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@@ -434,7 +434,7 @@ class HistoryContentsApiTestCase(ApiTestCase):
assert post_combined_count == pre_combined_count + 1
assert pre_dataset_count == post_dataset_count
# Test show dataset colleciton.
# Test show dataset collection.
collection_url = f"histories/{self.history_id}/contents/dataset_collections/{dataset_collection['id']}"
show_response = self._get(collection_url)
self._assert_status_code_is(show_response, 200)
lib/galaxy_test/base/populators.py
+1 -1
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@@ -2662,7 +2662,7 @@ class BaseDatasetCollectionPopulator:
return element_identifiers
def __create(self, payload, wait=False):
# Create a colleciton - either from existing datasets using collection creation API
# Create a collection - either from existing datasets using collection creation API
# or from direct uploads with the fetch API. Dispatch on "targets" keyword in payload
# to decide which to use.
if "targets" not in payload:
lib/tool_shed/test/base/twilltestcase.py
-2
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@@ -43,8 +43,6 @@ from . import (
# Set a 10 minute timeout for repository installation.
repository_installation_timeout = 600
# Dial ClientCookie logging down (very noisy)
logging.getLogger("ClientCookie.cookies").setLevel(logging.WARNING)
log = logging.getLogger(__name__)
tc.options["equiv_refresh_interval"] = 0
lib/tool_shed/util/shed_util_common.py
+11 -10
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@@ -212,16 +212,17 @@ def get_repository_file_contents(app, file_path, repository_id, is_admin=False):
elif checkers.check_binary(file_path):
return "<br/>Binary file<br/>"
else:
for line in open(file_path):
safe_str = f"{safe_str}{basic_util.to_html_string(line)}"
# Stop reading after string is larger than MAX_CONTENT_SIZE.
if len(safe_str) > MAX_CONTENT_SIZE:
large_str = (
"<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>"
% util.nice_size(MAX_CONTENT_SIZE)
)
safe_str = f"{safe_str}{large_str}"
break
with open(file_path) as fh:
for line in fh:
safe_str = f"{safe_str}{basic_util.to_html_string(line)}"
# Stop reading after string is larger than MAX_CONTENT_SIZE.
if len(safe_str) > MAX_CONTENT_SIZE:
large_str = (
"<br/>File contents truncated because file size is larger than maximum viewing size of %s<br/>"
% util.nice_size(MAX_CONTENT_SIZE)
)
safe_str = f"{safe_str}{large_str}"
break
if len(safe_str) > basic_util.MAX_DISPLAY_SIZE:
# Eliminate the middle of the file to display a file no larger than basic_util.MAX_DISPLAY_SIZE.
lib/tool_shed/webapp/model/__init__.py
+4 -5
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@@ -11,6 +11,10 @@ from typing import (
TYPE_CHECKING,
)
from mercurial import (
hg,
ui,
)
from sqlalchemy import (
Boolean,
Column,
@@ -414,11 +418,6 @@ class Repository(Base, Dictifiable, _HasTable):
@property
def hg_repo(self):
from mercurial import (
hg,
ui,
)
if not WEAK_HG_REPO_CACHE.get(self):
WEAK_HG_REPO_CACHE[self] = hg.cachedlocalrepo(hg.repository(ui.ui(), self.repo_path().encode("utf-8")))
return WEAK_HG_REPO_CACHE[self].fetch()[0]
pyproject.toml
+1 -1
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@@ -49,7 +49,7 @@ cwltool = "==3.1.20211107152837"
dictobj = "*"
docutils = "!=0.17, !=0.17.1"
edam-ontology = "*"
fastapi = ">=0.68.2, !=0.69.0, !=0.70.0, !=0.70.1" # https://github.com/tiangolo/fastapi/issues/4041
fastapi = ">=0.71.0" # https://github.com/tiangolo/fastapi/issues/4041
fastapi-utils = "*"
fs = "*"
future = "*"