Unverified Commit 8f0e11b9 authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Use ``best_search_result()`` function instead of parsing anaconda.org web pages 

Fix the following mulled unit test:

```
FAILED test/unit/tool_util/mulled/test_get_tests.py::test_hashed_test_search - AssertionError: assert ['samtools --help'] == ['bamtools --help', 'samtools --help']
  At index 0 diff: 'samtools --help' != 'bamtools --help'
  Right contains one more item: 'samtools --help'
  Full diff:
  - ['bamtools --help', 'samtools --help']
  + ['samtools --help']
```

that started not finding bamtools-2.4.0 inside
https://anaconda.org/bioconda/bamtools/files any more.

Also:
- Add type annotation to `CondaInDockerContext` and fix ensuing issues.
parent 302acfbc

lib/galaxy/tool_util/deps/conda_util.py

+6 −4
Original line number Diff line number Diff line
@@ -101,7 +101,7 @@ class CondaContext(installable.InstallableContext): 
    def __init__(

        self,

        conda_prefix: Optional[str] = None,

        conda_exec: Optional[str] = None,

        conda_exec: Optional[Union[str, List[str]]] = None,

        shell_exec: Optional[Callable[..., int]] = None,

        debug: bool = False,

        ensure_channels: Union[str, List[str]] = "",
@@ -204,11 +204,12 @@ class CondaContext(installable.InstallableContext): 


    def is_conda_installed(self) -> bool:

        """

        Check if conda_exec exists

        Check if conda_info() works

        """

        if os.path.exists(self.conda_exec):

        try:

            self.conda_info()

            return True

        else:

        except Exception:

            return False



    def can_install_conda(self) -> bool:
@@ -218,6 +219,7 @@ class CondaContext(installable.InstallableContext): 
        If conda_exec equals conda_prefix/bin/conda, we can install conda if either conda_prefix

        does not exist or is empty.

        """

        assert isinstance(self.conda_exec, str), "conda_exec is not a str"

        conda_exec = os.path.abspath(self.conda_exec)

        conda_prefix_plus_exec = os.path.abspath(os.path.join(self.conda_prefix, "bin/conda"))

        if conda_exec == conda_prefix_plus_exec:

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

+1 −1
Original line number Diff line number Diff line
@@ -42,13 +42,13 @@ from ..container_classes import ( 
)

from ..docker_util import build_docker_images_command

from ..mulled.mulled_build import (

    DEFAULT_CHANNELS,

    ensure_installed,

    InvolucroContext,

    mull_targets,

)

from ..mulled.mulled_build_tool import requirements_to_mulled_targets

from ..mulled.util import (

    DEFAULT_CHANNELS,

    default_mulled_conda_channels_from_env,

    mulled_tags_for,

    split_tag,

lib/galaxy/tool_util/deps/dependencies.py

+1 −1
Original line number Diff line number Diff line
@@ -12,7 +12,7 @@ from galaxy.tool_util.deps.requirements import ( 
    ToolRequirements,

)

from galaxy.util import bunch

from .mulled.mulled_build import DEFAULT_CHANNELS

from .mulled.util import DEFAULT_CHANNELS





class AppInfo:

lib/galaxy/tool_util/deps/installable.py

+1 −1
Original line number Diff line number Diff line
@@ -34,7 +34,7 @@ class InstallableContext(metaclass=abc.ABCMeta): 
        """Return parent path of the location the installable will be created within."""





def ensure_installed(installable_context, install_func, auto_init):

def ensure_installed(installable_context: InstallableContext, install_func, auto_init):

    """Make sure target is installed - handle multiple processes potentially attempting installation."""

    parent_path = installable_context.parent_path

    desc = installable_context.installable_description

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

+17 −13
Original line number Diff line number Diff line
@@ -25,12 +25,17 @@ except ImportError: 
    Template = None  # type: ignore[assignment,misc]

    UndefinedError = Exception  # type: ignore[assignment,misc]



from galaxy.tool_util.deps.conda_util import (

    best_search_result,

    CondaTarget,

)

from galaxy.util import (

    check_github_api_response_rate_limit,

    unicodify,

)

from galaxy.util.commands import argv_to_str

from .util import (

    CondaInDockerContext,

    get_files_from_conda_package,

    MULLED_SOCKET_TIMEOUT,

    split_container_name,
@@ -291,20 +296,19 @@ def hashed_test_search( 
    targets = concatenated_targets.split(",")

    packages = [target.split("=") for target in targets]



    conda_context = CondaInDockerContext(ensure_channels=[anaconda_channel])

    containers = []

    for package in packages:

        r = requests.get(f"https://anaconda.org/bioconda/{package[0]}/files", timeout=MULLED_SOCKET_TIMEOUT)

        r.raise_for_status()

        p = "-".join(package)

        for line in r.text.split("\n"):

    for package_name, package_version in packages:

        conda_target = CondaTarget(package_name, package_version)

        # include only linux-64 builds since that is hardcoded in get_anaconda_url and the only target for container builds

            if p in line and "linux-64" in line:

                build = line.split(p)[1].split(".tar.bz2")[0]

                if build == "":

                    containers.append(f"{package[0]}:{package[1]}")

        hit, exact = best_search_result(conda_target, conda_context, platform="linux-64")

        if not hit or not exact:

            raise Exception(f"Could not find {conda_target}")

        build = hit["build"]

        if build:

            containers.append(f"{package_name}:{package_version}--{build}")

        else:

                    containers.append(f"{package[0]}:{package[1]}-{build}")

                break

            containers.append(f"{package_name}:{package_version}")



    for container in containers:

        tests = main_test_search(container, recipes_path, deep, anaconda_channel, github_repo)