Merge pull request galaxyproject#18728 from jmchilton/tool_upgrade

Implement tool upgrade assistant.

lib/galaxy/tool_util/parser/xml.py

@@ -376,6 +376,10 @@ def _get_option_value(self, key, default):
     def _command_el(self):
         return self.root.find("command")
 
+    @property
+    def _outputs_el(self):
+        return self.root.find("outputs")
+
     def _get_attribute_as_bool(self, attribute, default, elem=None):
         if elem is None:
             elem = self.root
@@ -411,7 +415,7 @@ def parse_input_pages(self) -> "XmlPagesSource":
 
     def parse_provided_metadata_style(self):
         style = None
-        out_elem = self.root.find("outputs")
+        out_elem = self._outputs_el
         if out_elem is not None and "provided_metadata_style" in out_elem.attrib:
             style = out_elem.attrib["provided_metadata_style"]
 

lib/galaxy/tool_util/upgrade/__init__.py

@@ -0,0 +1,319 @@
+# Documented profile changes not covered.
+# - Allow invalid values. @mvdbeek any clue what to say here. The PR is here:
+# - https://github.com/galaxyproject/galaxy/pull/6264
+#
+# I don't want to declare these TODO but somethings could be more percise.
+# - We could inspect the XML source and tell when tools are using galaxy.json and improve
+#   the messaging on 17.09 for that. We can't be absolutely sure these would or would not be
+#   problems but we can be more confident they might be.
+# - Ditto for $HOME and the 18.01 migration.
+# - We could try to walk parameters and give more specific advice on structured_like qualification.
+from json import loads
+from typing import (
+    Any,
+    cast,
+    Dict,
+    List,
+    Optional,
+    Type,
+)
+
+from typing_extensions import (
+    Literal,
+    NotRequired,
+    TypedDict,
+)
+
+from galaxy.tool_util.parameters.case import validate_test_cases_for_tool_source
+from galaxy.tool_util.parser.factory import get_tool_source
+from galaxy.tool_util.parser.xml import XmlToolSource
+from galaxy.util import Element
+from galaxy.util.resources import resource_string
+
+TOOL_TOO_NEW = "Target tool has a profile that is too new, consider upgrading this script for the latest advice."
+TARGET_TOO_NEW = (
+    "Target upgrade version is too new for this script, consider upgrading this script for the latest advice."
+)
+
+TYPE_LEVEL = Literal["must_fix", "consider", "ready", "info"]
+
+
+class AdviceCode(TypedDict):
+    name: str
+    level: TYPE_LEVEL
+    message: str
+    niche: NotRequired[bool]
+    url: NotRequired[str]
+
+
+upgrade_codes_json = resource_string(__package__, "upgrade_codes.json")
+upgrade_codes_by_name: Dict[str, AdviceCode] = {}
+
+for name, upgrade_object in loads(upgrade_codes_json).items():
+    upgrade_object["name"] = name
+    upgrade_codes_by_name[name] = cast(AdviceCode, upgrade_object)
+
+
+class Advice:
+    advice_code: AdviceCode
+    message: Optional[str]
+
+    def __init__(self, advice_code: AdviceCode, message: Optional[str]):
+        self.advice_code = advice_code
+        self.message = message
+
+    @property
+    def url(self) -> Optional[str]:
+        return self.advice_code.get("url")
+
+    @property
+    def level(self) -> TYPE_LEVEL:
+        return self.advice_code["level"]
+
+    @property
+    def niche(self) -> bool:
+        return self.advice_code.get("niche", False)
+
+    @property
+    def advice_code_message(self) -> str:
+        return self.advice_code["message"]
+
+    def to_dict(self) -> Dict[str, Any]:
+        as_dict = cast(Dict[str, Any], self.advice_code.copy())
+        as_dict["advice_code_message"] = self.advice_code_message
+        as_dict["message"] = self.message
+        return as_dict
+
+
+class AdviceCollection:
+    _advice: List[Advice]
+
+    def __init__(self):
+        self._advice = []
+
+    def add(self, code: str, message: Optional[str] = None):
+        self._advice.append(Advice(upgrade_codes_by_name[code], message))
+
+    def to_list(self) -> List[Advice]:
+        return self._advice
+
+
+class ProfileMigration:
+    """A class offering advice on upgrading a Galaxy tool between two profile versions."""
+
+    from_version: str
+    to_version: str
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        return None
+
+
+class ProfileMigration16_04(ProfileMigration):
+    from_version = "16.01"
+    to_version = "16.04"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        interpreter = tool_source.parse_interpreter()
+        if interpreter:
+            advice_collection.add("16_04_fix_interpreter")
+        else:
+            advice_collection.add("16_04_ready_interpreter")
+        advice_collection.add("16_04_consider_implicit_extra_file_collection")
+
+        if _has_matching_xpath(tool_source, ".//data[@format = 'input']"):
+            advice_collection.add("16_04_fix_output_format")
+
+        if not _has_matching_xpath(tool_source, ".//stdio") and not _has_matching_xpath(
+            tool_source, ".//command[@detect_errors]"
+        ):
+            advice_collection.add("16_04_exit_code")
+
+
+class ProfileMigration17_09(ProfileMigration):
+    from_version = "16.04"
+    to_version = "17.09"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+
+        outputs_el = tool_source._outputs_el
+        if outputs_el is not None and outputs_el.get("`provided_metadata_style`", None) is not None:
+            advice_collection.add("17_09_consider_provided_metadata_style")
+
+
+class ProfileMigration18_01(ProfileMigration):
+    from_version = "17.09"
+    to_version = "18.01"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        command_el = tool_source._command_el
+        if command_el is not None and command_el.get("use_shared_home", None) is None:
+            advice_collection.add("18_01_consider_home_directory")
+
+        if _has_matching_xpath(tool_source, ".//outputs/collection[@structured_like]"):
+            advice_collection.add("18_01_consider_structured_like")
+
+
+class ProfileMigration18_09(ProfileMigration):
+    from_version = "18.01"
+    to_version = "18.09"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        tool_type = tool_source.parse_tool_type()
+        if tool_type == "manage_data":
+            advice_collection.add("18_09_consider_python_environment")
+
+
+class ProfileMigration20_05(ProfileMigration):
+    from_version = "18.09"
+    to_version = "20.05"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+
+        if _has_matching_xpath(tool_source, ".//configfiles/inputs"):
+            advice_collection.add("20_05_consider_inputs_as_json_changes")
+
+
+class ProfileMigration20_09(ProfileMigration):
+    from_version = "20.05"
+    to_version = "20.09"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+
+        tests = tool_source.parse_tests_to_dict()
+        for test in tests["tests"]:
+            output_collections = test.get("output_collections")
+            if not output_collections:
+                continue
+
+            for output_collection in output_collections:
+                if output_collection.get("element_tests"):
+                    advice_collection.add("20_09_consider_output_collection_order")
+
+        command_el = tool_source._command_el
+        if command_el is not None:
+            strict = command_el.get("strict", None)
+            if strict is None:
+                advice_collection.add("20_09_consider_set_e")
+
+
+class ProfileMigration21_09(ProfileMigration):
+    from_version = "20.09"
+    to_version = "21.09"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        for el in _find_all(tool_source, ".//data[@from_work_dir]"):
+            from_work_dir = el.get("from_work_dir") or ""
+            if from_work_dir != from_work_dir.strip():
+                advice_collection.add("")
+
+        tool_type = tool_source.parse_tool_type()
+        if tool_type == "data_source":
+            advice_collection.add("21_09_consider_python_environment")
+
+
+class ProfileMigration23_0(ProfileMigration):
+    from_version = "21.09"
+    to_version = "23.0"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        for text_param in _find_all(tool_source, ".//input[@type='text']"):
+            optional_tag_set = text_param.get("optional", None) is not None
+            if not optional_tag_set:
+                advice_collection.add("23_0_consider_optional_text")
+
+
+class ProfileMigration24_0(ProfileMigration):
+    from_version = "23.0"
+    to_version = "24.0"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        tool_type = tool_source.parse_tool_type()
+        if tool_type == "data_source_async":
+            advice_collection.add("24_0_consider_python_environment")
+        if tool_type in ["data_source_async", "data_source"]:
+            advice_collection.add("24_0_request_cleaning")
+
+
+class ProfileMigration24_2(ProfileMigration):
+    from_version = "24.0"
+    to_version = "24.2"
+
+    @classmethod
+    def advise(cls, advice_collection: AdviceCollection, xml_file: str) -> None:
+        tool_source = _xml_tool_source(xml_file)
+        results = validate_test_cases_for_tool_source(tool_source, use_latest_profile=True)
+        for result in results:
+            if result.validation_error:
+                advice_collection.add("24_2_fix_test_case_validation", str(result.validation_error))
+
+
+profile_migrations: List[Type[ProfileMigration]] = [
+    ProfileMigration16_04,
+    ProfileMigration17_09,
+    ProfileMigration18_01,
+    ProfileMigration18_09,
+    ProfileMigration20_05,
+    ProfileMigration20_09,
+    ProfileMigration21_09,
+    ProfileMigration23_0,
+    ProfileMigration24_0,
+    ProfileMigration24_2,
+]
+
+latest_supported_version = "24.2"
+
+
+def advise_on_upgrade(xml_file: str, to_version: Optional[str] = None) -> List[Advice]:
+    to_version = to_version or latest_supported_version
+    tool_source = _xml_tool_source(xml_file)
+    initial_version = tool_source.parse_profile()
+    if initial_version > latest_supported_version:
+        raise Exception(TOOL_TOO_NEW)
+    elif to_version > latest_supported_version:
+        raise Exception(TARGET_TOO_NEW)
+    advice_collection = AdviceCollection()
+
+    for migration in profile_migrations:
+        if migration.to_version < initial_version:
+            # tool started past here... just skip this advice
+            continue
+        if migration.to_version > to_version:
+            # we're not advising on upgrading past this point
+            break
+        migration.advise(advice_collection, xml_file)
+
+    return advice_collection.to_list()
+
+
+def _xml_tool_source(xml_file: str) -> XmlToolSource:
+    tool_source = get_tool_source(xml_file)
+    if not isinstance(tool_source, XmlToolSource):
+        raise Exception("Can only provide upgrade advice for XML tools.")
+    return cast(XmlToolSource, tool_source)
+
+
+def _has_matching_xpath(tool_source: XmlToolSource, xpath: str) -> bool:
+    return tool_source.xml_tree.find(xpath) is not None
+
+
+def _find_all(tool_source: XmlToolSource, xpath: str) -> List[Element]:
+    return cast(List[Element], tool_source.xml_tree.findall(".//data[@from_work_dir]") or [])