Unverified Commit cc35a28a authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Add test for conda ``best_search_result()``

parent a0d6e87f

lib/galaxy/tool_util/deps/conda_util.py

+2 −0
Original line number Diff line number Diff line
@@ -517,6 +517,8 @@ def best_search_result( 


    Return ``None`` if no results match.

    """

    # Cannot specify the version here (i.e. conda_target.package_specifier)

    # because if the version is not found, the exec_search() call would fail.

    search_args = [conda_target.package]

    try:

        res = conda_context.exec_search(search_args, json=True, offline=offline, platform=platform)

test/unit/tool_util/test_conda_resolution.py

+28 −5
Original line number Diff line number Diff line
@@ -2,9 +2,13 @@ import os 
import shutil

from tempfile import mkdtemp



from galaxy.tool_util.deps import (

    conda_util,

    DependencyManager,

from galaxy.tool_util.deps import DependencyManager

from galaxy.tool_util.deps.conda_util import (

    best_search_result,

    CondaContext,

    CondaTarget,

    install_conda,

    installed_conda_targets,

)

from galaxy.tool_util.deps.requirements import ToolRequirement

from galaxy.tool_util.deps.resolvers.conda import CondaDependencyResolver
@@ -51,11 +55,30 @@ def test_against_conda_prefix_regression(): 
            use_path_exec=False,  # For the test ensure this is always a clean install

        )

        conda_context = resolver.conda_context

        assert len(list(conda_util.installed_conda_targets(conda_context))) == 0

        assert len(list(installed_conda_targets(conda_context))) == 0

        req = ToolRequirement(name="samtools", version="0.1.16", type="package")

        dependency = resolver.resolve(req, job_directory=job_dir)

        assert dependency.shell_commands() is not None  # install should not fail anymore

        installed_targets = list(conda_util.installed_conda_targets(conda_context))

        installed_targets = list(installed_conda_targets(conda_context))

        assert len(installed_targets) > 0

    finally:

        shutil.rmtree(base_path)





@external_dependency_management

def test_best_search_result(tmp_path) -> None:

    conda_context = CondaContext(

        conda_prefix=os.path.join(tmp_path, "_conda"), condarc_override=os.path.join(tmp_path, "_condarc")

    )

    install_conda(conda_context)

    (hit, exact) = best_search_result(CondaTarget("samtools"), conda_context)

    assert hit["name"] == "samtools"

    assert exact is True

    (hit, exact) = best_search_result(CondaTarget("samtools", version="1.3.1"), conda_context)

    assert hit["name"] == "samtools"

    assert hit["version"] == "1.3.1"

    assert exact is True

    # Search non-existent version

    (hit, exact) = best_search_result(CondaTarget("samtools", version="1.16"), conda_context)

    assert hit["name"] == "samtools"

    assert exact is False