Merge pull request #16492 from bernt-matthias/topic/consistent-profil…

…e-check

consistently compare profile versions

lib/galaxy/tool_util/deps/container_classes.py

@@ -16,6 +16,7 @@
 )
 from uuid import uuid4
 
+from packaging.version import Version
 from typing_extensions import Protocol
 
 from galaxy.util import (
@@ -360,7 +361,7 @@ def add_var(name, value):
                 defaults += ",$tool_directory:default_ro"
             if self.job_info.job_directory:
                 defaults += ",$job_directory:default_ro,$job_directory/outputs:rw"
-                if self.tool_info.profile <= 19.09:
+                if Version(str(self.tool_info.profile)) <= Version("19.09"):
                     defaults += ",$job_directory/configs:rw"
             if self.job_info.home_directory is not None:
                 defaults += ",$home_directory:rw"

lib/galaxy/tool_util/linters/general.py

@@ -6,6 +6,8 @@
     TYPE_CHECKING,
 )
 
+from packaging.version import Version
+
 from galaxy.tool_util.lint import Linter
 from galaxy.tool_util.version import (
     LegacyVersion,
@@ -161,7 +163,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
         _, tool_node = _tool_xml_and_root(tool_source)
         profile = tool_source.parse_profile()
         profile_valid = PROFILE_PATTERN.match(profile) is not None
-        if profile_valid and profile == "16.01":
+        if profile_valid and Version(profile) == Version("16.01"):
             lint_ctx.valid("Tool targets 16.01 Galaxy profile.", linter=cls.name(), node=tool_node)
 
 
@@ -171,7 +173,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
         _, tool_node = _tool_xml_and_root(tool_source)
         profile = tool_source.parse_profile()
         profile_valid = PROFILE_PATTERN.match(profile) is not None
-        if profile_valid and profile != "16.01":
+        if profile_valid and Version(profile) != Version("16.01"):
             lint_ctx.valid(f"Tool specifies profile version [{profile}].", linter=cls.name(), node=tool_node)
 
 

lib/galaxy/tool_util/linters/inputs.py

@@ -10,6 +10,8 @@
     TYPE_CHECKING,
 )
 
+from packaging.version import Version
+
 from galaxy.tool_util.lint import Linter
 from galaxy.util import string_as_bool
 from ._util import (
@@ -814,7 +816,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             profile = tool_source.parse_profile()
             truevalue = param.attrib.get("truevalue", "true")
             falsevalue = param.attrib.get("falsevalue", "false")
-            problematic_booleans_allowed = profile < "23.1"
+            problematic_booleans_allowed = Version(profile) < Version("23.1")
             lint_level = lint_ctx.warn if problematic_booleans_allowed else lint_ctx.error
             if truevalue == falsevalue:
                 lint_level(
@@ -840,7 +842,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             profile = tool_source.parse_profile()
             truevalue = param.attrib.get("truevalue", "true")
             falsevalue = param.attrib.get("falsevalue", "false")
-            problematic_booleans_allowed = profile < "23.1"
+            problematic_booleans_allowed = Version(profile) < Version("23.1")
             lint_level = lint_ctx.warn if problematic_booleans_allowed else lint_ctx.error
             if truevalue.lower() == "false":
                 lint_level(

lib/galaxy/tool_util/parser/xml.py

@@ -128,7 +128,7 @@ def __init__(self, xml_tree: ElementTree, source_path=None, macro_paths=None):
         self.root = self.xml_tree.getroot()
         self._source_path = source_path
         self._macro_paths = macro_paths or []
-        self.legacy_defaults = self.parse_profile() == "16.01"
+        self.legacy_defaults = Version(self.parse_profile()) == Version("16.01")
         self._string = xml_to_string(self.root)
 
     def to_string(self):
@@ -248,7 +248,7 @@ def parse_environment_variables(self):
         return environment_variables
 
     def parse_home_target(self):
-        target = "job_home" if self.parse_profile() >= "18.01" else "shared_home"
+        target = "job_home" if Version(self.parse_profile()) >= Version("18.01") else "shared_home"
         command_el = self._command_el
         command_legacy = (command_el is not None) and command_el.get("use_shared_home", None)
         if command_legacy is not None:
@@ -395,7 +395,7 @@ def parse_provided_metadata_style(self):
             style = out_elem.attrib["provided_metadata_style"]
 
         if style is None:
-            style = "legacy" if self.parse_profile() < "17.09" else "default"
+            style = "legacy" if Version(self.parse_profile()) < Version("17.09") else "default"
 
         assert style in ["legacy", "default"]
         return style
@@ -537,7 +537,7 @@ def _parse_output(
         output.filters = data_elem.findall("filter")
         output.tool = tool
         output.from_work_dir = data_elem.get("from_work_dir", None)
-        if output.from_work_dir and getattr(tool, "profile", 0) < 21.09:
+        if output.from_work_dir and Version(str(getattr(tool, "profile", 0))) < Version("21.09"):
             # We started quoting from_work_dir outputs in 21.09.
             # Prior to quoting, trailing spaces had no effect.
             # This ensures that old tools continue to work.
@@ -758,7 +758,7 @@ def __parse_element_tests(parent_element, profile=None):
         element_tests[identifier] = __parse_test_attributes(
             element, element_attrib, parse_elements=True, profile=profile
         )
-        if profile and profile >= "20.09":
+        if profile and Version(profile) >= Version("20.09"):
             element_tests[identifier][1]["expected_sort_order"] = idx
 
     return element_tests

lib/galaxy/tools/__init__.py

@@ -913,10 +913,10 @@ def requires_galaxy_python_environment(self):
         if self.tool_type not in ["default", "manage_data", "interactive", "data_source", "data_source_async"]:
             return True
 
-        if self.tool_type == "manage_data" and self.profile < 18.09:
+        if self.tool_type == "manage_data" and Version(str(self.profile)) < Version("18.09"):
             return True
 
-        if self.tool_type == "data_source" and self.profile < 21.09:
+        if self.tool_type == "data_source" and Version(str(self.profile)) < Version("21.09"):
             return True
 
         if self.tool_type == "data_source_async" and self.profile < 24.0:
@@ -1022,7 +1022,7 @@ def parse(self, tool_source: ToolSource, guid=None, dynamic=False):
         self.python_template_version = tool_source.parse_python_template_version()
         if self.python_template_version is None:
             # If python_template_version not specified we assume tools with profile versions >= 19.05 are python 3 ready
-            if self.profile >= 19.05:
+            if profile >= Version("19.05"):
                 self.python_template_version = Version("3.5")
             else:
                 self.python_template_version = Version("2.7")
@@ -1036,7 +1036,7 @@ def parse(self, tool_source: ToolSource, guid=None, dynamic=False):
 
         self.version = tool_source.parse_version()
         if not self.version:
-            if self.profile < 16.04:
+            if profile < Version("16.04"):
                 # For backward compatibility, some tools may not have versions yet.
                 self.version = "1.0.0"
             else:

lib/galaxy/tools/actions/__init__.py

@@ -14,6 +14,8 @@
     Union,
 )
 
+from packaging.version import Version
+
 from galaxy import model
 from galaxy.exceptions import ItemAccessibilityException
 from galaxy.job_execution.actions.post import ActionBox
@@ -420,7 +422,7 @@ def execute(
         # format='input" previously would give you a random extension from
         # the input extensions, now it should just give "input" as the output
         # format.
-        input_ext = "data" if tool.profile < 16.04 else "input"
+        input_ext = "data" if Version(str(tool.profile)) < Version("16.04") else "input"
         input_dbkey = incoming.get("dbkey", "?")
         for name, data in reversed(list(inp_data.items())):
             if not data:
@@ -432,7 +434,7 @@ def execute(
                 data = data.to_history_dataset_association(None)
                 inp_data[name] = data
 
-            if tool.profile < 16.04:
+            if Version(str(tool.profile)) < Version("16.04"):
                 input_ext = data.ext
 
             if data.dbkey not in [None, "?"]:

lib/galaxy/tools/evaluation.py

@@ -15,6 +15,8 @@
     Union,
 )
 
+from packaging.version import Version
+
 from galaxy import model
 from galaxy.authnz.util import provider_name_to_backend
 from galaxy.job_execution.compute_environment import ComputeEnvironment
@@ -741,7 +743,7 @@ def _build_param_file(self):
         param_dict = self.param_dict
         directory = self.local_working_directory
         command = self.tool.command
-        if self.tool.profile < 16.04 and command and "$param_file" in command:
+        if Version(str(self.tool.profile)) < Version("16.04") and command and "$param_file" in command:
             with tempfile.NamedTemporaryFile(mode="w", dir=directory, delete=False) as param:
                 for key, value in param_dict.items():
                     # parameters can be strings or lists of strings, coerce to list

lib/galaxy/tools/execute.py

@@ -18,6 +18,7 @@
 )
 
 from boltons.iterutils import remap
+from packaging.version import Version
 
 from galaxy import model
 from galaxy.exceptions import ToolInputsNotOKException
@@ -310,7 +311,7 @@ def output_name(self, trans, history, params, output):
         return output_collection_name
 
     def sliced_input_collection_structure(self, input_name):
-        unqualified_recurse = self.tool.profile < 18.09 and "|" not in input_name
+        unqualified_recurse = Version(str(self.tool.profile)) < Version("18.09") and "|" not in input_name
 
         def find_collection(input_dict, input_name):
             for key, value in input_dict.items():

lib/galaxy/tools/parameters/basic.py

@@ -21,6 +21,7 @@
     Union,
 )
 
+from packaging.version import Version
 from webob.compat import cgi_FieldStorage
 
 from galaxy import util
@@ -589,7 +590,7 @@ def __init__(self, tool, input_source):
         super().__init__(tool, input_source)
         truevalue = input_source.get("truevalue", "true")
         falsevalue = input_source.get("falsevalue", "false")
-        if tool and tool.profile >= 23.1:
+        if tool and Version(str(tool.profile)) >= Version("23.1"):
             if truevalue == falsevalue:
                 raise ParameterValueError("Cannot set true and false to the same value", self.name)
             if truevalue.lower() == "false":
@@ -1020,7 +1021,7 @@ def from_json(self, value, trans, other_values=None, require_legal_value=True):
                 "an invalid option (None) was selected, please verify", self.name, None, is_dynamic=self.is_dynamic
             )
         elif not legal_values:
-            if self.optional and self.tool.profile < 18.09:
+            if self.optional and Version(str(self.tool.profile)) < Version("18.09"):
                 # Covers optional parameters with default values that reference other optional parameters.
                 # These will have a value but no legal_values.
                 # See https://github.com/galaxyproject/tools-iuc/pull/1842#issuecomment-394083768 for context.

lib/galaxy/tools/wrappers.py

@@ -19,6 +19,8 @@
     Union,
 )
 
+from packaging.version import Version
+
 from galaxy.model import (
     DatasetCollection,
     DatasetCollectionElement,
@@ -128,7 +130,7 @@ def __init__(
             and input.type == "text"
             and input.optional
             and input.optionality_inferred
-            and (profile is None or profile < 23.0)
+            and (profile is None or Version(str(profile)) < Version("23.0"))
         ):
             # Tools with old profile versions may treat an optional text parameter as `""`
             value = ""