revert Python 3.8 changes for packages/packages_for_pulsar_by_dep_dag…

….txt

.github/workflows/test_galaxy_packages_for_pulsar.yaml

@@ -20,7 +20,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ['3.8']
+        python-version: ['3.7']  # don't upgrade, see https://github.com/galaxyproject/galaxy/pull/16649
     steps:
       - uses: actions/checkout@v3
         with:

lib/galaxy/files/sources/__init__.py

@@ -463,7 +463,8 @@ def _get_error_msg_for(rule_name: str) -> str:
 
 def uri_join(*args):
     # url_join doesn't work with non-standard scheme
-    if "://" in (arg0 := args[0]):
+    arg0 = args[0]
+    if "://" in arg0:
         scheme, path = arg0.split("://", 1)
         rval = f"{scheme}://{slash_join(path, *args[1:]) if path else slash_join(*args[1:])}"
     else:

lib/galaxy/files/sources/http.py

@@ -85,7 +85,8 @@ def _serialization_props(self, user_context=None) -> HTTPFilesSourceProperties:
         return cast(HTTPFilesSourceProperties, effective_props)
 
     def score_url_match(self, url: str):
-        if match := self._url_regex.match(url):
+        match = self._url_regex.match(url)
+        if match:
             return match.span()[1]
         else:
             return 0

lib/galaxy/job_metrics/instrumenters/cgroup.py

@@ -90,7 +90,8 @@ class CgroupPlugin(InstrumentPlugin):
     def __init__(self, **kwargs):
         self.verbose = asbool(kwargs.get("verbose", False))
         self.cgroup_mount = kwargs.get("cgroup_mount", "/sys/fs/cgroup")
-        if params_str := kwargs.get("params", None):
+        params_str = kwargs.get("params", None)
+        if params_str:
             params = [v.strip() for v in params_str.split(",")]
         else:
             params = list(TITLES.keys())

lib/galaxy/job_metrics/instrumenters/env.py

@@ -28,7 +28,8 @@ class EnvPlugin(InstrumentPlugin):
     default_safety = Safety.UNSAFE
 
     def __init__(self, **kwargs):
-        if variables_str := kwargs.get("variables", None):
+        variables_str = kwargs.get("variables", None)
+        if variables_str:
             self.variables = [v.strip() for v in variables_str.split(",")]
         else:
             self.variables = None

lib/galaxy/objectstore/__init__.py

@@ -1183,7 +1183,8 @@ def _create(self, obj, **kwargs):
             return self.backends[object_store_id]
 
     def _call_method(self, method, obj, default, default_is_exception, **kwargs):
-        if (object_store_id := self.__get_store_id_for(obj, **kwargs)) is not None:
+        object_store_id = self.__get_store_id_for(obj, **kwargs)
+        if object_store_id is not None:
             return self.backends[object_store_id].__getattribute__(method)(obj, **kwargs)
         if default_is_exception:
             raise default(

lib/galaxy/objectstore/caching.py

@@ -57,7 +57,8 @@ def check_cache(cache_target: CacheTarget):
     # Initiate cleaning once we reach cache_monitor_cache_limit percentage of the defined cache size?
     # Convert GBs to bytes for comparison
     cache_size_in_gb = cache_target.size * ONE_GIGA_BYTE
-    if total_size > (cache_limit := cache_size_in_gb * cache_target.limit):
+    cache_limit = cache_size_in_gb * cache_target.limit
+    if total_size > cache_limit:
         log.debug(
             "Initiating cache cleaning: current cache size: %s; clean until smaller than: %s",
             nice_size(total_size),

lib/galaxy/objectstore/pithos.py

@@ -126,7 +126,8 @@ def to_dict(self):
     def _authenticate(self):
         auth = self.config_dict["auth"]
         url, token = auth["url"], auth["token"]
-        if ca_certs := auth.get("ca_certs"):
+        ca_certs = auth.get("ca_certs")
+        if ca_certs:
             utils.https.patch_with_certs(ca_certs)
         elif auth.get("ignore_ssl").lower() in ("true", "yes", "on"):
             utils.https.patch_ignore_ssl()
@@ -411,7 +412,8 @@ def _update_from_file(self, obj, **kwargs):
 
         path = self._construct_path(obj, **kwargs)
         cache_path = self._get_cache_path(path)
-        if file_name := kwargs.get("file_name"):
+        file_name = kwargs.get("file_name")
+        if file_name:
             source_path = os.path.abspath(file_name)
             try:
                 if source_path != cache_path:

lib/galaxy/tool_util/biotools/interface.py

@@ -55,7 +55,8 @@ def simplify_edam_dicts(a_list: List[Dict[str, str]]):
 
 def simplify_edam_dict(as_dict: Dict[str, str]) -> Optional[str]:
     uri = as_dict["uri"]
-    if match := TERM_PATTERN.match(uri):
+    match = TERM_PATTERN.match(uri)
+    if match:
         return match.group(1)
     else:
         # TODO: log problem...

lib/galaxy/tool_util/cwl/parser.py

@@ -132,9 +132,10 @@ def id(self):
         return raw_id
 
     def galaxy_id(self) -> str:
+        raw_id = self.id
         tool_id = None
         # don't reduce "search.cwl#index" to search
-        if raw_id := self.id:
+        if raw_id:
             tool_id = os.path.basename(raw_id)
             # tool_id = os.path.splitext(os.path.basename(raw_id))[0]
         if not tool_id:
@@ -228,7 +229,9 @@ def doc(self):
         return doc
 
     def label(self):
-        if (label := self._tool.tool.get("label")) is not None:
+        label = self._tool.tool.get("label")
+
+        if label is not None:
             return label.partition(":")[0]  # return substring before ':'
         else:
             return ""

lib/galaxy/tool_util/cwl/runtime_actions.py

@@ -118,7 +118,8 @@ def move_output(output, target_path, output_name=None):
         file_description = file_dict_to_description(output)
         file_description.write_to(target_path)
 
-        if secondary_files := output.get("secondaryFiles", []):
+        secondary_files = output.get("secondaryFiles", [])
+        if secondary_files:
             order = []
             index_contents = {"order": order}
 

lib/galaxy/tool_util/cwl/util.py

@@ -253,8 +253,9 @@ def replacement_file(value):
 
             return value
 
+        secondary_files = value.get("secondaryFiles", [])
         secondary_files_tar_path = None
-        if secondary_files := value.get("secondaryFiles", []):
+        if secondary_files:
             tmp = tempfile.NamedTemporaryFile(delete=False)
             tf = tarfile.open(fileobj=tmp, mode="w:")
             order: List[str] = []

lib/galaxy/tool_util/data/__init__.py

@@ -341,7 +341,8 @@ def configure_and_load(
         self.parse_column_spec(config_element)
 
         # store repo info if available:
-        if (repo_elem := config_element.find("tool_shed_repository")) is not None:
+        repo_elem = config_element.find("tool_shed_repository")
+        if repo_elem is not None:
             repo_info = dict(
                 tool_shed=repo_elem.find("tool_shed").text,
                 name=repo_elem.find("repository_name").text,

lib/galaxy/tool_util/data/bundles/models.py

@@ -202,7 +202,8 @@ def _xml_to_data_table_output_column_move(move_elem: Element) -> DataTableBundle
 def _xml_to_data_table_output_column_translation(
     value_translation_elem: Element,
 ) -> Optional[DataTableBundleProcessorDataTableOutputColumnTranslation]:
-    if (value_translation := value_translation_elem.text) is not None:
+    value_translation = value_translation_elem.text
+    if value_translation is not None:
         value_translation_type = value_translation_elem.get("type", DEFAULT_VALUE_TRANSLATION_TYPE)
         return DataTableBundleProcessorDataTableOutputColumnTranslation(
             value=value_translation, type=value_translation_type

lib/galaxy/tool_util/deps/brew_exts.py

@@ -521,7 +521,8 @@ def __action(sys):
 def recipe_cellar_path(cellar_path, recipe, version):
     recipe_base = recipe.split("/")[-1]
     recipe_base_path = os.path.join(cellar_path, recipe_base, version)
-    if revision_paths := glob.glob(f"{recipe_base_path}_*"):
+    revision_paths = glob.glob(f"{recipe_base_path}_*")
+    if revision_paths:
         revisions = map(lambda x: int(x.rsplit("_", 1)[-1]), revision_paths)
         max_revision = max(revisions)
         recipe_path = "%s_%d" % (recipe_base_path, max_revision)

lib/galaxy/tool_util/deps/conda_util.py

@@ -5,7 +5,6 @@
 import os
 import platform
 import re
-import shlex
 import shutil
 import sys
 import tempfile
@@ -29,6 +28,7 @@
     commands,
     download_to_file,
     listify,
+    shlex_join,
     smart_str,
     which,
 )
@@ -253,7 +253,7 @@ def exec_command(self, operation: str, args: List[str], stdout_path: Optional[st
         env = {}
         if self.condarc_override:
             env["CONDARC"] = self.condarc_override
-        cmd_string = shlex.join(cmd)
+        cmd_string = shlex_join(cmd)
         kwds = dict()
         try:
             if stdout_path:

lib/galaxy/tool_util/deps/container_classes.py

@@ -389,7 +389,8 @@ def add_var(name, value):
 
         # Not all tools have a tool_directory - strip this out if supplied by
         # job_conf.
-        if (tool_directory_index := volumes_str.find("$tool_directory")) > 0:
+        tool_directory_index = volumes_str.find("$tool_directory")
+        if tool_directory_index > 0:
             end_index = volumes_str.find(",", tool_directory_index)
             if end_index < 0:
                 end_index = len(volumes_str)

lib/galaxy/tool_util/deps/container_resolvers/mulled.py

@@ -325,9 +325,10 @@ def docker_cached_container_description(
         return None
 
     cached_images = list_docker_cached_mulled_images(namespace, hash_func=hash_func, resolution_cache=resolution_cache)
+    image = find_best_matching_cached_image(targets, cached_images, hash_func)
 
     container = None
-    if image := find_best_matching_cached_image(targets, cached_images, hash_func):
+    if image:
         container = ContainerDescription(
             image.image_identifier,
             type="docker",
@@ -350,9 +351,10 @@ def singularity_cached_container_description(
         return None
 
     cached_images = cache_directory.list_cached_mulled_images_from_path()
+    image = find_best_matching_cached_image(targets, cached_images, hash_func)
 
     container = None
-    if image := find_best_matching_cached_image(targets, cached_images, hash_func):
+    if image:
         container = ContainerDescription(
             os.path.abspath(os.path.join(cache_directory.path, image.image_identifier)),
             type="singularity",

lib/galaxy/tool_util/deps/containers.py

@@ -214,12 +214,15 @@ def __build_container_id_from_parts(
     ) -> str:
         repo = ""
         owner = ""
-        if (repo_key := f"{container_type}_repo_{mode}") in destination_info:
+        repo_key = f"{container_type}_repo_{mode}"
+        owner_key = f"{container_type}_owner_{mode}"
+        if repo_key in destination_info:
             repo = f"{destination_info[repo_key]}/"
-        if (owner_key := f"{container_type}_owner_{mode}") in destination_info:
+        if owner_key in destination_info:
             owner = f"{destination_info[owner_key]}/"
         cont_id = repo + owner + destination_info[f"{container_type}_image_{mode}"]
-        if (tag_key := f"{container_type}_tag_{mode}") in destination_info:
+        tag_key = f"{container_type}_tag_{mode}"
+        if tag_key in destination_info:
             cont_id += f":{destination_info[tag_key]}"
         return cont_id
 

lib/galaxy/tool_util/deps/dockerfiles.py

@@ -46,7 +46,8 @@ def dockerfile_build(path, dockerfile=None, error=log.error, **kwds):
         commands.execute(docker_command_parts)
 
     commands.execute(docker_command_parts)
-    if docker_image_cache := kwds["docker_image_cache"]:
+    docker_image_cache = kwds["docker_image_cache"]
+    if docker_image_cache:
         destination = docker_cache_path(docker_image_cache, image_identifier)
         save_image_command_parts = docker_util.build_save_image_command(
             image_identifier, destination, **docker_host_args(**kwds)

lib/galaxy/tool_util/deps/mulled/mulled_build.py

@@ -12,7 +12,6 @@
 import json
 import logging
 import os
-import shlex
 import shutil
 import stat
 import string
@@ -39,6 +38,7 @@
     commands,
     download_to_file,
     safe_makedirs,
+    shlex_join,
     unicodify,
 )
 from ._cli import arg_parser
@@ -335,7 +335,7 @@ def mull_targets(
             involucro_args.insert(6, "-set")
             involucro_args.insert(7, f"TEST_BINDS={','.join(test_bind)}")
     cmd = involucro_context.build_command(involucro_args)
-    print(f"Executing: {shlex.join(cmd)}")
+    print(f"Executing: {shlex_join(cmd)}")
     if dry_run:
         return 0
     ensure_installed(involucro_context, True)

lib/galaxy/tool_util/deps/mulled/util.py

@@ -194,7 +194,8 @@ def parse_tag(tag: str) -> PARSED_TAG:
     version = tag.rsplit(":")[-1]
     build_string = "-1"
     build_number = -1
-    if match := BUILD_NUMBER_REGEX.search(version):
+    match = BUILD_NUMBER_REGEX.search(version)
+    if match:
         build_number = int(match.group(0))
     if "--" in version:
         version, build_string = version.rsplit("--", 1)

lib/galaxy/tool_util/deps/resolvers/__init__.py

@@ -252,7 +252,8 @@ def _expand_specs(self, requirement):
         version = requirement.version
         specs = requirement.specs
 
-        if (spec := self._find_specification(specs)) is not None:
+        spec = self._find_specification(specs)
+        if spec is not None:
             name = spec.short_name
             version = spec.version or version
 

lib/galaxy/tool_util/linters/general.py

@@ -31,7 +31,8 @@
 def lint_general(tool_source, lint_ctx):
     """Check tool version, name, and id."""
     # determine line to report for general problems with outputs
-    if tool_xml := getattr(tool_source, "xml_tree", None):
+    tool_xml = getattr(tool_source, "xml_tree", None)
+    if tool_xml:
         tool_node = tool_xml.getroot()
     else:
         tool_node = None

lib/galaxy/tool_util/linters/help.py

@@ -33,7 +33,8 @@ def lint_help(tool_xml, lint_ctx):
     if "TODO" in help_text:
         lint_ctx.warn("Help contains TODO text.", node=helps[0])
 
-    if invalid_rst := rst_invalid(help_text):
+    invalid_rst = rst_invalid(help_text)
+    if invalid_rst:
         lint_ctx.warn(f"Invalid reStructuredText found in help - [{invalid_rst}].", node=helps[0])
     else:
         lint_ctx.valid("Help contains valid reStructuredText.", node=helps[0])

lib/galaxy/tool_util/linters/inputs.py

@@ -552,7 +552,8 @@ def lint_inputs(tool_source: "ToolSource", lint_ctx: "LintContext"):
             lint_ctx.warn("Found no input parameters.", node=tool_node)
 
     # check if there is an output with the same name as an input
-    if (outputs := tool_xml.find("./outputs")) is not None:
+    outputs = tool_xml.find("./outputs")
+    if outputs is not None:
         for output in outputs:
             if output.get("name") in input_names:
                 lint_ctx.error(

lib/galaxy/tool_util/linters/stdio.py

@@ -60,7 +60,8 @@ def _lint_regex(tool_xml, child, lint_ctx):
     for key in child.attrib.keys():
         if key not in ["description", "level", "match", "source"]:
             lint_ctx.warn(f"Unknown attribute [{key}] encountered on regex tag.", node=child)
-    if match := child.attrib.get("match"):
+    match = child.attrib.get("match")
+    if match:
         try:
             re.compile(match)
         except Exception as e:

lib/galaxy/tool_util/parser/cwl.py

@@ -151,7 +151,8 @@ def _parse_output(self, tool, output_instance):
 
     def parse_requirements_and_containers(self):
         containers = []
-        if docker_identifier := self.tool_proxy.docker_identifier():
+        docker_identifier = self.tool_proxy.docker_identifier()
+        if docker_identifier:
             containers.append({"type": "docker", "identifier": docker_identifier})
 
         software_requirements = self.tool_proxy.software_requirements()

lib/galaxy/tool_util/parser/interface.py

@@ -314,7 +314,8 @@ def parse_tests_to_dict(self) -> ToolSourceTests:
         return {"tests": []}
 
     def __str__(self):
-        if source_path := self.source_path:
+        source_path = self.source_path
+        if source_path:
             as_str = f"{self.__class__.__name__}[{source_path}]"
         else:
             as_str = f"{self.__class__.__name__}[In-memory]"