galaxy/test/unit/app/tools/test_toolbox.py

import collections
import json
import logging
import os
import string
import time
from typing import Optional

import pytest
import routes

from galaxy import model
from galaxy.app_unittest_utils.tools_support import UsesTools
from galaxy.config_watchers import ConfigWatchers
from galaxy.model import tool_shed_install
from galaxy.model.tool_shed_install import mapping
from galaxy.tool_util.unittest_utils import mock_trans
from galaxy.tool_util.unittest_utils.sample_data import (
    SIMPLE_MACRO,
    SIMPLE_TOOL_WITH_MACRO,
)
from galaxy.tools import ToolBox
from galaxy.tools.cache import ToolCache
from galaxy.util.unittest import TestCase

log = logging.getLogger(__name__)


CONFIG_TEST_TOOL_VERSION_TEMPLATE = string.Template(
    """    <tool file="tool.xml" guid="github.com/galaxyproject/example/test_tool/0.${version}">
            <tool_shed>github.com</tool_shed>
            <repository_name>example</repository_name>
            <repository_owner>galaxyproject</repository_owner>
            <installed_changeset_revision>${version}</installed_changeset_revision>
            <id>github.com/galaxyproject/example/test_tool/0.${version}</id>
            <version>0.${version}</version>
        </tool>
    """
)
CONFIG_TEST_TOOL_VERSION_1 = CONFIG_TEST_TOOL_VERSION_TEMPLATE.safe_substitute(dict(version="1"))
CONFIG_TEST_TOOL_VERSION_2 = CONFIG_TEST_TOOL_VERSION_TEMPLATE.safe_substitute(dict(version="2"))

REPO_TYPE = collections.namedtuple(
    "REPO_TYPE",
    "tool_shed owner name changeset_revision installed_changeset_revision description status",
)
DEFAULT_TEST_REPO = REPO_TYPE("github.com", "galaxyproject", "example", "1", "1", "description", "OK")


class SimplifiedToolBox(ToolBox):
    def __init__(self, test_case: "BaseToolBoxTestCase"):
        app = test_case.app
        app.watchers.tool_config_watcher.reload_callback = lambda: reload_callback(test_case)
        # Handle app/config stuff needed by toolbox but not by tools.
        app.tool_cache = ToolCache() if not hasattr(app, "tool_cache") else app.tool_cache
        config_files = test_case.config_files
        tool_root_dir = test_case.test_directory
        super().__init__(
            config_files,
            tool_root_dir,
            app,
        )
        # Need to start thread now for new reload callback to take effect
        self.app.watchers.start()


class BaseToolBoxTestCase(TestCase, UsesTools):
    _toolbox: Optional[SimplifiedToolBox] = None

    @property
    def integrated_tool_panel_path(self):
        return os.path.join(self.test_directory, "integrated_tool_panel.xml")

    def assert_integerated_tool_panel(self, exists=True):
        does_exist = os.path.exists(self.integrated_tool_panel_path)
        if exists:
            assert does_exist
        else:
            assert not does_exist

    @property
    def toolbox(self):
        if self._toolbox is None:
            self.app.toolbox = self._toolbox = SimplifiedToolBox(self)
        return self._toolbox

    def setUp(self):
        self.reindexed = False
        self.setup_app()
        install_model = mapping.init("sqlite:///:memory:", create_tables=True)
        self.app.tool_cache = ToolCache()
        self.app.install_model = install_model
        self.app.reindex_tool_search = self.__reindex  # type: ignore[assignment]
        itp_config = os.path.join(self.test_directory, "integrated_tool_panel.xml")
        self.app.config.integrated_tool_panel_config = itp_config
        self.app.watchers = ConfigWatchers(self.app)
        self._toolbox = None
        self.config_files = []

    def tearDown(self):
        self.app.watchers.shutdown()

    def _repo_install(self, changeset, config_filename=None):
        metadata = {
            "tools": [
                {
                    "add_to_tool_panel": False,  # to have repository.includes_tools_for_display_in_tool_panel=False in InstalledRepositoryManager.activate_repository()
                    "guid": f"github.com/galaxyproject/example/test_tool/0.{changeset}",
                    "tool_config": "tool.xml",
                }
            ],
        }
        if config_filename:
            metadata["shed_config_filename"] = config_filename
        repository = tool_shed_install.ToolShedRepository(metadata_=metadata)
        repository.tool_shed = DEFAULT_TEST_REPO.tool_shed
        repository.owner = DEFAULT_TEST_REPO.owner
        repository.name = DEFAULT_TEST_REPO.name
        repository.changeset_revision = changeset
        repository.installed_changeset_revision = changeset
        repository.deleted = False
        repository.uninstalled = False
        self.app.install_model.context.add(repository)
        self.app.install_model.context.flush()
        return repository

    def _setup_two_versions(self):
        self._repo_install(changeset="1")
        version1 = tool_shed_install.ToolVersion()
        version1.tool_id = "github.com/galaxyproject/example/test_tool/0.1"
        self.app.install_model.context.add(version1)
        self.app.install_model.context.flush()

        self._repo_install(changeset="2")
        version2 = tool_shed_install.ToolVersion()
        version2.tool_id = "github.com/galaxyproject/example/test_tool/0.2"
        self.app.install_model.context.add(version2)
        self.app.install_model.context.flush()

        version_association = tool_shed_install.ToolVersionAssociation()
        version_association.parent_id = version1.id
        version_association.tool_id = version2.id

        self.app.install_model.context.add(version_association)
        self.app.install_model.context.flush()

    def _setup_two_versions_in_config(self, section=False):
        if section:
            template = """<toolbox tool_path="%s">
    <section id="tid" name="TID" version="">
        %s
    </section>
    <section id="tid" name="TID" version="">
        %s
    </section>
</toolbox>"""
        else:
            template = """<toolbox tool_path="%s">
    %s
    %s
</toolbox>"""
        self._add_config(template % (self.test_directory, CONFIG_TEST_TOOL_VERSION_1, CONFIG_TEST_TOOL_VERSION_2))

    def _add_config(self, content, name="tool_conf.xml"):
        is_json = name.endswith(".json")
        path = self._tool_conf_path(name=name)
        with open(path, "w") as f:
            if not is_json or isinstance(content, str):
                f.write(content)
            else:
                json.dump(content, f)
        self.config_files.append(path)

    def _init_dynamic_tool_conf(self):
        # Add a dynamic tool conf (such as a ToolShed managed one) to list of configs.
        self._add_config(f"""<toolbox tool_path="{self.test_directory}"></toolbox>""")

    def _tool_conf_path(self, name="tool_conf.xml"):
        path = os.path.join(self.test_directory, name)
        return path

    def _tool_path(self, name="tool.xml"):
        path = os.path.join(self.test_directory, name)
        return path

    def __reindex(self):
        self.reindexed = True


class TestToolBox(BaseToolBoxTestCase):
    def test_load_file(self):
        self._init_tool()
        self._add_config("""<toolbox><tool file="tool.xml" /></toolbox>""")

        toolbox = self.toolbox
        assert toolbox.get_tool("test_tool") is not None
        assert toolbox.get_tool("not_a_test_tool") is None

    def test_record_macros(self):
        self._init_tool()
        self._init_tool(
            filename="tool_with_macro.xml",
            tool_contents=SIMPLE_TOOL_WITH_MACRO,
            extra_file_contents=SIMPLE_MACRO.substitute(tool_version="2.0"),
            extra_file_path="external.xml",
        )
        self._add_config("""<toolbox><tool file="tool_with_macro.xml"/><tool file="tool.xml" /></toolbox>""")
        toolbox = self.toolbox
        tool = toolbox.get_tool("test_tool")
        assert tool is not None
        assert len(tool._macro_paths) == 0
        tool = toolbox.get_tool("tool_with_macro")
        assert tool is not None
        assert len(tool._macro_paths) == 1

    @pytest.mark.xfail(raises=AssertionError)
    def test_tool_reload_when_macro_is_altered(self):
        self._init_tool(
            filename="tool_with_macro.xml",
            tool_contents=SIMPLE_TOOL_WITH_MACRO,
            extra_file_contents=SIMPLE_MACRO.substitute(tool_version="2.0"),
            extra_file_path="external.xml",
        )
        self._add_config("""<toolbox><tool file="tool_with_macro.xml"/></toolbox>""")
        toolbox = self.toolbox
        tool = toolbox.get_tool("tool_with_macro")
        assert tool is not None
        assert len(tool._macro_paths) == 1
        macro_path = tool._macro_paths[0]
        with open(macro_path, "w") as macro_out:
            macro_out.write(SIMPLE_MACRO.substitute(tool_version="3.0"))

        def check_tool_macro():
            tool = self.toolbox.get_tool("tool_with_macro")
            assert tool.version == "3.0"

        self._try_until_no_errors(check_tool_macro)

    @pytest.mark.xfail(raises=AssertionError)
    def test_tool_reload_for_broken_tool(self):
        self._init_tool(filename="simple_tool.xml", version="1.0")
        self._add_config("""<toolbox><tool file="simple_tool.xml"/></toolbox>""")
        toolbox = self.toolbox
        tool = toolbox.get_tool("test_tool")
        assert tool is not None
        assert tool.version == "1.0"
        assert tool.tool_errors is None
        # Tool is loaded, now let's break it
        tool_path = tool.config_file
        with open(tool.config_file, "w") as out:
            out.write("certainly not a valid tool")

        def check_tool_errors():
            tool = self.toolbox.get_tool("test_tool")
            assert tool is not None
            assert tool.version == "1.0"
            assert tool.tool_errors == "Current on-disk tool is not valid"

        self._try_until_no_errors(check_tool_errors)

        # Tool is still loaded, lets restore it with a new version
        self._init_tool(filename="simple_tool.xml", version="2.0")

        def check_no_tool_errors():
            tool = self.toolbox.get_tool("test_tool")
            assert tool is not None
            assert tool.version == "2.0"
            assert tool.tool_errors is None
            assert tool_path == tool.config_file, "config file"

        self._try_until_no_errors(check_no_tool_errors)

    def _try_until_no_errors(self, f):
        e = None
        for _ in range(40):
            try:
                f()
                return
            except AssertionError as error:
                e = error
                time.sleep(0.25)

        if e:
            raise e

    def test_enforce_tool_profile(self):
        self._init_tool(filename="old_tool.xml", version="1.0", profile="17.01", tool_id="test_old_tool_profile")
        with self.assertRaisesRegex(Exception, r"The tool \[test_new_tool_profile\] targets version 37\.01 of Galaxy"):
            # This will write the file but fail to load the tool
            self._init_tool(filename="new_tool.xml", version="2.0", profile="37.01", tool_id="test_new_tool_profile")
        self._add_config("""<toolbox><tool file="old_tool.xml"/><tool file="new_tool.xml"/></toolbox>""")
        toolbox = self.toolbox
        assert toolbox.get_tool("test_old_tool_profile") is not None
        assert toolbox.get_tool("test_new_tool_profile") is None

    def test_to_dict_in_panel(self):
        for json_conf in [True, False]:
            self._init_tool_in_section(json=json_conf)
            mapper = routes.Mapper()
            mapper.connect("tool_runner", "/test/tool_runner")
            as_dict = self.toolbox.to_dict(mock_trans())
            test_section = self._find_section(as_dict, "t")
            assert len(test_section["elems"]) == 1
            assert test_section["elems"][0]["id"] == "test_tool"

    def test_to_dict_out_of_panel(self):
        for json_conf in [True, False]:
            self._init_tool_in_section(json=json_conf)
            mapper = routes.Mapper()
            mapper.connect("tool_runner", "/test/tool_runner")
            as_dict = self.toolbox.to_dict(mock_trans(), in_panel=False)
            assert as_dict[0]["id"] == "test_tool"

    def test_out_of_panel_filtering(self):
        self._init_tool_in_section()

        mapper = routes.Mapper()
        mapper.connect("tool_runner", "/test/tool_runner")
        as_dict = self.toolbox.to_dict(mock_trans(), in_panel=False)
        assert len(as_dict) == 1

        def allow_user_access(user, attempting_access):
            assert not attempting_access
            return False

        # Disable access to the tool, make sure it is filtered out.
        self.toolbox.get_tool("test_tool").allow_user_access = allow_user_access
        as_dict = self.toolbox.to_dict(mock_trans(), in_panel=False)
        assert len(as_dict) == 0, as_dict

    def _find_section(self, as_dict, section_id):
        for elem in as_dict:
            if elem.get("id") == section_id:
                assert elem["model_class"] == "ToolSection"
                return elem
        raise AssertionError(f"Failed to find section with id [{section_id}]")

    def test_tool_shed_properties(self):
        self._init_tool()
        self._setup_two_versions_in_config(section=False)
        self._setup_two_versions()

        test_tool = self.toolbox.get_tool("test_tool")
        assert test_tool.tool_shed == "github.com"
        assert test_tool.repository_owner == "galaxyproject"
        assert test_tool.repository_name == "example"
        # TODO: Not deterministc, probably should be?
        assert test_tool.installed_changeset_revision in ["1", "2"]

    def test_tool_shed_properties_only_on_installed_tools(self):
        self._init_tool()
        self._add_config("""<toolbox><tool file="tool.xml" /></toolbox>""")
        toolbox = self.toolbox
        test_tool = toolbox.get_tool("test_tool")
        assert test_tool.tool_shed is None
        assert test_tool.repository_name is None
        assert test_tool.repository_owner is None
        assert test_tool.installed_changeset_revision is None

    def test_tool_shed_request_version(self):
        self._init_tool()
        self._setup_two_versions_in_config(section=False)
        self._setup_two_versions()

        test_tool = self.toolbox.get_tool("test_tool", tool_version="0.1")
        assert test_tool.version == "0.1"

        test_tool = self.toolbox.get_tool("test_tool", tool_version="0.2")
        assert test_tool.version == "0.2"

        # there is no version 3, return newest version
        test_tool = self.toolbox.get_tool("test_tool", tool_version="3")
        assert test_tool.version == "0.2"

    def test_load_file_in_section(self):
        self._init_tool_in_section()

        toolbox = self.toolbox
        assert toolbox.get_tool("test_tool") is not None
        assert toolbox.get_tool("not_a_test_tool") is None

    def test_writes_integrate_tool_panel(self):
        self._init_tool()
        self._add_config("""<toolbox><tool file="tool.xml" /></toolbox>""")

        self.assert_integerated_tool_panel(exists=False)
        self.toolbox
        self.assert_integerated_tool_panel(exists=True)

    def test_groups_tools_in_section(self):
        self._init_tool()
        self._setup_two_versions_in_config(section=True)
        self._setup_two_versions()
        self.toolbox
        self.__verify_two_test_tools()

        # Assert only newer version of the tool loaded into the panel.
        section = self.toolbox._tool_panel["tid"]
        assert len(section.elems) == 1
        assert next(iter(section.elems.values())).id == "github.com/galaxyproject/example/test_tool/0.2"

        test_tool = self.toolbox.get_tool("test_tool", tool_version="0.1")
        section_pair = self.toolbox.get_section_for_tool(test_tool)
        assert section_pair == ("tid", "TID")

    def test_group_tools_out_of_section(self):
        self._init_tool()
        self._setup_two_versions_in_config(section=False)
        self._setup_two_versions()
        self.__verify_two_test_tools()

        # Assert tools merged in tool panel.
        assert len(self.toolbox._tool_panel) == 1

    def test_get_section_by_label(self):
        self._add_config(
            """<toolbox><section id="tid" name="Completely unrelated"><label id="lab1" text="Label 1" /><label id="lab2" text="Label 2" /></section></toolbox>"""
        )
        assert len(self.toolbox._tool_panel) == 1
        section = self.toolbox._tool_panel["tid"]
        tool_panel_section_key, section_by_label = self.toolbox.get_section(
            section_id="nope", new_label="Completely unrelated", create_if_needed=True
        )
        assert section_by_label is section
        assert tool_panel_section_key == "tid"

    def test_get_tool(self):
        self._init_tool()
        self._setup_two_versions_in_config()
        self._setup_two_versions()
        assert self.toolbox.get_tool("test_tool").id in [
            "github.com/galaxyproject/example/test_tool/0.1",
            "github.com/galaxyproject/example/test_tool/0.2",
        ]
        assert (
            self.toolbox.get_tool("github.com/galaxyproject/example/test_tool/0.1").id
            == "github.com/galaxyproject/example/test_tool/0.1"
        )
        assert (
            self.toolbox.get_tool("github.com/galaxyproject/example/test_tool/0.2").id
            == "github.com/galaxyproject/example/test_tool/0.2"
        )
        assert (
            self.toolbox.get_tool("github.com/galaxyproject/example/test_tool/0.3").id
            != "github.com/galaxyproject/example/test_tool/0.3"
        )

    def test_tool_dir(self):
        self._init_tool()
        self._add_config(f"""<toolbox><tool_dir dir="{self.test_directory}" /></toolbox>""")

        toolbox = self.toolbox
        assert toolbox.get_tool("test_tool") is not None

    def test_tool_dir_json(self):
        self._init_tool()
        self._add_config({"items": [{"type": "tool_dir", "dir": self.test_directory}]}, name="tool_conf.json")

        toolbox = self.toolbox
        assert toolbox.get_tool("test_tool") is not None

    def test_workflow_in_panel(self):
        stored_workflow = self.__test_workflow()
        encoded_id = self.app.security.encode_id(stored_workflow.id)
        self._add_config(f"""<toolbox><workflow id="{encoded_id}" /></toolbox>""")
        assert len(self.toolbox._tool_panel) == 1
        panel_workflow = next(iter(self.toolbox._tool_panel.values()))
        assert panel_workflow == stored_workflow.latest_workflow
        # TODO: test to_dict with workflows

    def test_workflow_in_section(self):
        stored_workflow = self.__test_workflow()
        encoded_id = self.app.security.encode_id(stored_workflow.id)
        self._add_config(
            f"""<toolbox><section id="tid" name="TID"><workflow id="{encoded_id}" /></section></toolbox>"""
        )
        assert len(self.toolbox._tool_panel) == 1
        section = self.toolbox._tool_panel["tid"]
        assert len(section.elems) == 1
        panel_workflow = next(iter(section.elems.values()))
        assert panel_workflow == stored_workflow.latest_workflow

    def test_label_in_panel(self):
        self._add_config("""<toolbox><label id="lab1" text="Label 1" /><label id="lab2" text="Label 2" /></toolbox>""")
        assert len(self.toolbox._tool_panel) == 2
        self.__check_test_labels(self.toolbox._tool_panel)

    def test_label_in_section(self):
        self._add_config(
            """<toolbox><section id="tid" name="TID"><label id="lab1" text="Label 1" /><label id="lab2" text="Label 2" /></section></toolbox>"""
        )
        assert len(self.toolbox._tool_panel) == 1
        section = self.toolbox._tool_panel["tid"]
        self.__check_test_labels(section.elems)

    def _init_tool_in_section(self, json=False):
        self._init_tool()
        if not json:
            self._add_config("""<toolbox><section id="t" name="test"><tool file="tool.xml" /></section></toolbox>""")
        else:
            section = {
                "type": "section",
                "id": "t",
                "name": "test",
                "items": [{"type": "tool", "file": "tool.xml"}],
            }
            self._add_config({"items": [section]}, name="tool_conf.json")

    def __check_test_labels(self, panel_dict):
        assert list(panel_dict.keys()) == ["label_lab1", "label_lab2"]
        label1 = next(iter(panel_dict.values()))
        assert label1.id == "lab1"
        assert label1.text == "Label 1"

        label2 = panel_dict["label_lab2"]
        assert label2.id == "lab2"
        assert label2.text == "Label 2"

    def __test_workflow(self):
        stored_workflow = model.StoredWorkflow()
        workflow = model.Workflow()
        workflow.stored_workflow = stored_workflow
        stored_workflow.latest_workflow = workflow
        user = model.User()
        user.email = "test@example.com"
        user.password = "passw0rD1"
        stored_workflow.user = user
        self.app.model.context.add(workflow)
        self.app.model.context.add(stored_workflow)
        self.app.model.context.flush()
        return stored_workflow

    def __verify_two_test_tools(self):
        # Assert tool versions of the tool with simple id 'test_tool'
        all_versions = self.toolbox.get_tool("test_tool", get_all_versions=True)
        assert len(all_versions) == 2

        # Verify lineage_ids on both tools is correctly ordered.
        for version in ["0.1", "0.2"]:
            guid = "github.com/galaxyproject/example/test_tool/" + version
            lineage_ids = self.toolbox.get_tool(guid).lineage.get_version_ids()
            assert lineage_ids[0] == "github.com/galaxyproject/example/test_tool/0.1"
            assert lineage_ids[1] == "github.com/galaxyproject/example/test_tool/0.2"

        # Test tool_version attribute.
        assert (
            self.toolbox.get_tool("test_tool", tool_version="0.1").guid
            == "github.com/galaxyproject/example/test_tool/0.1"
        )
        assert (
            self.toolbox.get_tool("test_tool", tool_version="0.2").guid
            == "github.com/galaxyproject/example/test_tool/0.2"
        )

    def test_default_lineage(self):
        self.__init_versioned_tools()
        self._add_config("""<toolbox><tool file="tool_v01.xml" /><tool file="tool_v02.xml" /></toolbox>""")
        self.__verify_get_tool_for_default_lineage()

    def test_default_lineage_reversed(self):
        # Run same test as above but with entries in tool_conf reversed to
        # ensure versioning is at work and not order effects.
        self.__init_versioned_tools()
        self._add_config("""<toolbox><tool file="tool_v02.xml" /><tool file="tool_v01.xml" /></toolbox>""")
        self.__verify_get_tool_for_default_lineage()

    def test_grouping_with_default_lineage(self):
        self.__init_versioned_tools()
        self._add_config("""<toolbox><tool file="tool_v01.xml" /><tool file="tool_v02.xml" /></toolbox>""")
        self.__verify_tool_panel_for_default_lineage()

    def test_grouping_with_default_lineage_reversed(self):
        # Run same test as above but with entries in tool_conf reversed to
        # ensure versioning is at work and not order effects.
        self.__init_versioned_tools()
        self._add_config("""<toolbox><tool file="tool_v02.xml" /><tool file="tool_v02.xml" /></toolbox>""")
        self.__verify_tool_panel_for_default_lineage()

    def __init_versioned_tools(self):
        self._init_tool(filename="tool_v01.xml", version="0.1")
        self._init_tool(filename="tool_v02.xml", version="0.2")

    def __verify_tool_panel_for_default_lineage(self):
        assert len(self.toolbox._tool_panel) == 1
        tool = self.toolbox._tool_panel["tool_test_tool"]
        assert tool.version == "0.2", tool.version
        assert tool.id == "test_tool"

    def __verify_get_tool_for_default_lineage(self):
        tool_v01 = self.toolbox.get_tool("test_tool", tool_version="0.1")
        tool_v02 = self.toolbox.get_tool("test_tool", tool_version="0.2")
        assert tool_v02.id == "test_tool"
        assert tool_v02.version == "0.2", tool_v02.version
        assert tool_v01.id == "test_tool"
        assert tool_v01.version == "0.1"

        # Newer variant gets to be default for that id.
        default_tool = self.toolbox.get_tool("test_tool")
        assert default_tool.id == "test_tool"
        assert default_tool.version == "0.2"

    def __setup_shed_tool_conf(self):
        self._add_config("""<toolbox tool_path="."></toolbox>""")

        self.toolbox  # create toolbox
        assert not self.reindexed

        os.remove(self.integrated_tool_panel_path)


def reload_callback(test_case):
    test_case.app.tool_cache.cleanup()
    log.debug("Reload callback called, toolbox contains %s", test_case._toolbox._tool_versions_by_id)
    test_case._toolbox = test_case.app.toolbox = SimplifiedToolBox(test_case)
    log.debug("After callback toolbox contains %s", test_case._toolbox._tool_versions_by_id)