Merge pull request #13665 from nsoranzo/release_22.01_update_uvicorn

[22.01] Update uvicorn from broken 0.17.1

lib/galaxy/celery/_serialization.py

@@ -34,8 +34,8 @@ def schema_decoder(obj):
             assert clazz_str.startswith(SCHEMA_MODELS_PACKAGE_BASE) and ".." not in clazz_str, f"Invalid class str {clazz_str}"
             module_name, class_name = clazz_str.rsplit('.', 1)
             module = import_module(module_name)
-            clazz = getattr(module, class_name, None)
-            obj = clazz(**obj['__object__'])
+            clazz = getattr(module, class_name)
+            obj = clazz(**obj["__object__"])
             return obj
 
     return obj

lib/galaxy/datatypes/binary.py

@@ -19,8 +19,10 @@ from typing import Optional
 import h5py
 import numpy as np
 import pysam
-import pysam.bcftools
-from bx.seq.twobit import TWOBIT_MAGIC_NUMBER, TWOBIT_MAGIC_NUMBER_SWAP
+from bx.seq.twobit import (
+    TWOBIT_MAGIC_NUMBER,
+    TWOBIT_MAGIC_NUMBER_SWAP,
+)
 
 from galaxy import util
 from galaxy.datatypes import metadata

lib/galaxy/datatypes/converters/cram_to_bam.py

@@ -7,7 +7,7 @@ usage: %prog in_file out_file
 import optparse
 import os
 
-import pysam
+from pysam import sort  # type: ignore[attr-defined]
 
 
 def main():
@@ -15,8 +15,8 @@ def main():
     parser = optparse.OptionParser()
     (options, args) = parser.parse_args()
     input_fname, output_fname = args
-    slots = os.getenv('GALAXY_SLOTS', 1)
-    pysam.sort(f"-@{slots}", '-o', output_fname, '-O', 'bam', '-T', '.', input_fname)
+    slots = os.getenv("GALAXY_SLOTS", 1)
+    sort(f"-@{slots}", "-o", output_fname, "-O", "bam", "-T", ".", input_fname)
 
 
 if __name__ == "__main__":

lib/galaxy/dependencies/dev-requirements.txt

@@ -220,7 +220,7 @@ typing-extensions==4.0.1; python_version >= "3.6"
 tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
 ubiquerg==0.6.2
 urllib3==1.26.8; python_version >= "3.7" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.7"
-uvicorn==0.17.1; python_version >= "3.7"
+uvicorn==0.17.6; python_version >= "3.7"
 uvloop==0.16.0; python_version >= "3.7"
 vine==5.0.0; python_version >= "3.7"
 watchdog==2.1.6; python_version >= "3.6"

lib/galaxy/dependencies/lint-requirements.txt

@@ -1,7 +1,7 @@
 flake8
 flake8-bugbear
 flake8-import-order
-mypy==0.910
+mypy
 types-bleach
 types-boto
 types-contextvars

lib/galaxy/dependencies/pinned-lint-requirements.txt

@@ -4,11 +4,11 @@ flake8-bugbear==22.1.11
 flake8-import-order==0.18.1
 importlib-metadata==4.2.0
 mccabe==0.6.1
-mypy==0.910
+mypy==0.942
 mypy-extensions==0.4.3
 pycodestyle==2.8.0
 pyflakes==2.4.0
-toml==0.10.2
+tomli==2.0.1
 typed-ast==1.4.3
 types-bleach==4.1.4
 types-boto==2.49.7

lib/galaxy/dependencies/pinned-requirements.txt

@@ -158,7 +158,7 @@ typing-extensions==4.0.1; python_version >= "3.6"
 tzlocal==2.1; python_version >= "2.7" and python_full_version < "3.0.0" or python_full_version >= "3.5.0" and python_version < "4"
 ubiquerg==0.6.2
 urllib3==1.26.8; python_version >= "3.6" and python_full_version < "3.0.0" and python_version < "4" or python_full_version >= "3.6.0" and python_version < "4" and python_version >= "3.6"
-uvicorn==0.17.1; python_version >= "3.7"
+uvicorn==0.17.6; python_version >= "3.7"
 uvloop==0.16.0; python_version >= "3.7"
 vine==5.0.0; python_version >= "3.7"
 wcwidth==0.2.5; python_full_version >= "3.6.2" and python_version >= "3.7"

lib/galaxy/schema/fields.py

@@ -1,11 +1,7 @@
-import inspect
 import re
 from typing import Optional
 
-from pydantic import (
-    BaseModel,
-    Field,
-)
+from pydantic import Field
 
 from galaxy.security.idencoding import IdEncodingHelper
 
@@ -110,22 +106,3 @@ def OrderParamField(default_order: str) -> Optional[str]:
         ),
         example="name-dsc,create_time",
     )
-
-
-def optional(*fields):
-    """Decorator function used to modify a pydantic model's fields to all be optional.
-    Alternatively, you can  also pass the field names that should be made optional as arguments
-    to the decorator.
-    Taken from https://github.com/samuelcolvin/pydantic/issues/1223#issuecomment-775363074
-    """
-    def dec(_cls):
-        for field in fields:
-            _cls.__fields__[field].required = False
-        return _cls
-
-    if fields and inspect.isclass(fields[0]) and issubclass(fields[0], BaseModel):
-        cls = fields[0]
-        fields = cls.__fields__
-        return dec(cls)
-
-    return dec

lib/galaxy/tool_util/cwl/util.py

@@ -10,7 +10,12 @@ import tarfile
 import tempfile
 import urllib.parse
 from collections import namedtuple
-from typing import Any, List, Optional
+from typing import (
+    Any,
+    BinaryIO,
+    List,
+    Optional,
+)
 
 import yaml
 from typing_extensions import TypedDict
@@ -57,6 +62,7 @@ def output_properties(
 ) -> OutputPropertiesType:
     checksum = hashlib.sha1()
     properties: OutputPropertiesType = {"class": "File", "checksum": "", "size": 0}
+    f: BinaryIO
     if path is not None:
         properties["path"] = path
         f = open(path, "rb")

lib/galaxy/util/compression_utils.py

@@ -113,8 +113,9 @@ def get_fileobj_raw(
     compressed_format = None
     if 'gzip' in compressed_formats and is_gzip(filename):
         fh: Union[gzip.GzipFile, bz2.BZ2File, IO[bytes]] = gzip.GzipFile(filename, mode)
-        compressed_format = 'gzip'
-    elif 'bz2' in compressed_formats and is_bz2(filename):
+        compressed_format = "gzip"
+    elif "bz2" in compressed_formats and is_bz2(filename):
+        mode = cast(Literal["a", "ab", "r", "rb", "w", "wb", "x", "xb"], mode)
         fh = bz2.BZ2File(filename, mode)
         compressed_format = 'bz2'
     elif 'zip' in compressed_formats and zipfile.is_zipfile(filename):
@@ -123,7 +124,7 @@ def get_fileobj_raw(
         # since it always opens files in binary mode.
         # For emulating text mode, we will be returning the binary fh in a
         # TextIOWrapper.
-        zf_mode = mode.replace('b', '')
+        zf_mode = cast(Literal["r", "w"], mode.replace("b", ""))
         with zipfile.ZipFile(filename, zf_mode) as zh:
             fh = zh.open(zh.namelist()[0], zf_mode)
         compressed_format = 'zip'
@@ -325,6 +326,7 @@ class CompressedFile:
         return tarfile.open(filepath, mode, errorlevel=0)
 
     def open_zip(self, filepath: str, mode: str) -> zipfile.ZipFile:
+        mode = cast(Literal["a", "r", "w", "x"], mode)
         return zipfile.ZipFile(filepath, mode)
 
     def zipfile_ok(self, path_to_archive: str) -> bool:

lib/galaxy/util/properties.py

@@ -138,11 +138,7 @@ class NicerConfigParser(ConfigParser):
     def __init__(self, filename, *args, **kw):
         ConfigParser.__init__(self, *args, **kw)
         self.filename = filename
-        if hasattr(self, '_interpolation'):
-            self._interpolation = self.InterpolateWrapper(self._interpolation)
-
-    read_file = getattr(ConfigParser, 'read_file', ConfigParser.readfp)
-    read_file.__doc__ = ""
+        self._interpolation = self.InterpolateWrapper(self._interpolation)
 
     def defaults(self):
         """Return the defaults, with their values interpolated (with the
@@ -155,21 +151,7 @@ class NicerConfigParser(ConfigParser):
             defaults[key] = self.get('DEFAULT', key) or val
         return defaults
 
-    def _interpolate(self, section, option, rawval, vars):
-        # Python < 3.2
-        try:
-            return ConfigParser._interpolate(
-                self, section, option, rawval, vars)
-        except Exception:
-            e = sys.exc_info()[1]
-            args = list(e.args)
-            args[0] = f'Error in file {self.filename}: {e}'
-            e.args = tuple(args)
-            e.message = args[0]
-            raise
-
     class InterpolateWrapper:
-        # Python >= 3.2
         def __init__(self, original):
             self._original = original
 

lib/galaxy/webapps/galaxy/api/__init__.py

@@ -83,12 +83,11 @@ class GalaxyTypeDepends(Depends):
         self.galaxy_type_depends = dep_type
 
 
-def depends(dep_type: Type[T]) -> Any:
-
+def depends(dep_type: Type[T]) -> T:
     def _do_resolve(request: Request):
         return get_app().resolve(dep_type)
 
-    return GalaxyTypeDepends(_do_resolve, dep_type)
+    return cast(T, GalaxyTypeDepends(_do_resolve, dep_type))
 
 
 def get_session_manager(app: StructuredApp = DependsOnApp) -> GalaxySessionManager:

lib/galaxy/workflow/modules.py

@@ -1755,8 +1755,8 @@ class ToolModule(WorkflowModule):
                         # See https://github.com/galaxyproject/galaxy/pull/1693 for context.
                         replacement = dataset_instance
                         temp = iteration_elements[prefixed_name]
-                        if hasattr(temp, 'element_identifier') and temp.element_identifier:
-                            replacement.element_identifier = temp.element_identifier  # type: ignore[attr-defined]
+                        if hasattr(temp, "element_identifier") and temp.element_identifier:
+                            replacement.element_identifier = temp.element_identifier  # type: ignore[union-attr]
                     else:
                         # If collection - just use element model object.
                         replacement = iteration_elements[prefixed_name]

lib/galaxy_test/driver/driver_util.py

@@ -1022,6 +1022,8 @@ class GalaxyTestDriver(TestDriver):
 
         self.testing_shed_tools = getattr(config_object, "testing_shed_tools", False)
 
+        default_tool_conf: Optional[str]
+        datatypes_conf_override: Optional[str]
         if getattr(config_object, "framework_tool_and_types", False):
             default_tool_conf = FRAMEWORK_SAMPLE_TOOLS_CONF
             datatypes_conf_override = FRAMEWORK_DATATYPES_CONF
@@ -1065,8 +1067,8 @@ class GalaxyTestDriver(TestDriver):
                 if callable(galaxy_config):
                     galaxy_config = galaxy_config()
                 if galaxy_config is None:
-                    setup_galaxy_config_kwds = dict(
-                        allow_path_paste=getattr(config_object, "allow_path_paste", False),
+                    galaxy_config = setup_galaxy_config(
+                        galaxy_db_path,
                         use_test_file_dir=not self.testing_shed_tools,
                         default_install_db_merged=True,
                         default_tool_conf=self.default_tool_conf,
@@ -1077,10 +1079,7 @@ class GalaxyTestDriver(TestDriver):
                         conda_auto_install=getattr(config_object, "conda_auto_install", False),
                         use_shared_connection_for_amqp=getattr(config_object, "use_shared_connection_for_amqp", False),
                         allow_tool_conf_override=self.allow_tool_conf_override,
-                    )
-                    galaxy_config = setup_galaxy_config(
-                        galaxy_db_path,
-                        **setup_galaxy_config_kwds
+                        allow_path_paste=getattr(config_object, "allow_path_paste", False),
                     )
 
                     isolate_galaxy_config = getattr(config_object, "isolate_galaxy_config", False)

lib/tool_shed/tools/tool_validator.py

@@ -89,12 +89,9 @@ class ToolValidator(GalaxyToolValidator):
                         # 'ncbi_blastp_wrapper.xml' was moved to 'tools/ncbi_blast_plus/ncbi_blastp_wrapper.xml',
                         # so keep looking for the file until we find the new location.
                         continue
-                    fh = tempfile.NamedTemporaryFile('wb', prefix="tmp-toolshed-gltcrfrm")
-                    tmp_filename = fh.name
-                    fh.close()
-                    fh = open(tmp_filename, 'wb')
-                    fh.write(fctx.data())
-                    fh.close()
+                    with tempfile.NamedTemporaryFile("wb", prefix="tmp-toolshed-gltcrfrm", delete=False) as fh:
+                        tmp_filename = fh.name
+                        fh.write(fctx.data())
                     return tmp_filename
         return None
 

test/integration_selenium/test_user_library_permissions.py

@@ -1,5 +1,6 @@
 import os
 
+from galaxy_test.selenium.framework import retry_assertion_during_transitions
 from .framework import (
     selenium_test,
     SeleniumIntegrationTestCase,
@@ -90,7 +91,8 @@ class TestUserLibraryImport(SeleniumIntegrationTestCase):
         # search for created user and add him to permission field
         self.components.libraries.add_items_permission.wait_for_and_click()
         self.components.libraries.add_items_permission_input_field.wait_for_and_send_keys(email)
-        self.components.libraries.add_items_permission_option.wait_for_and_click()
+
+        self.select_add_items_permission_option(email)
 
         # assert that the right email has been saved
         allowed_user_email = self.components.libraries.add_items_permission_field_text.wait_for_text()
@@ -102,3 +104,9 @@ class TestUserLibraryImport(SeleniumIntegrationTestCase):
         self.logout()
         # login back to the 'regular' user account
         self.submit_login(email=email)
+
+    @retry_assertion_during_transitions
+    def select_add_items_permission_option(self, option_text):
+        el = self.components.libraries.add_items_permission_option.wait_for_visible()
+        assert option_text == el.text
+        el.click()

test/unit/data/datatypes/test_bam.py

@@ -1,4 +1,7 @@
-import pysam
+from pysam import (  # type: ignore[attr-defined]
+    AlignmentFile,
+    view,
+)
 
 from galaxy.datatypes.binary import Bam
 from .util import (
@@ -11,8 +14,8 @@ from .util import (
 def test_merge_bam():
     with get_input_files('1.bam', '1.bam') as input_files, get_tmp_path() as outpath:
         Bam.merge(input_files, outpath)
-        alignment_count_output = int(pysam.view('-c', outpath).strip())
-        alignment_count_input = int(pysam.view('-c', input_files[0]).strip()) * 2
+        alignment_count_output = int(view("-c", outpath).strip())
+        alignment_count_input = int(view("-c", input_files[0]).strip()) * 2
         assert alignment_count_input == alignment_count_output
 
 
@@ -42,9 +45,8 @@ def test_set_meta_presorted():
     b = Bam()
     with get_dataset('1.bam') as dataset:
         b.set_meta(dataset=dataset)
-        assert dataset.metadata.sort_order == 'coordinate'
-        bam_file = pysam.AlignmentFile(dataset.file_name, mode='rb',
-                                       index_filename=dataset.metadata.bam_index.file_name)
+        assert dataset.metadata.sort_order == "coordinate"
+        bam_file = AlignmentFile(dataset.file_name, mode="rb", index_filename=dataset.metadata.bam_index.file_name)
         assert bam_file.has_index() is True