Commit 1e05ac04 authored by Matthias Bernt's avatar Matthias Bernt
Browse files

move and fix tests

parent 708ea0e0

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

+6 −45
Original line number Diff line number Diff line
@@ -10,6 +10,7 @@ import json 
import logging

from glob import glob

from typing import (

    Any,

    Dict,

    Optional,

)
@@ -36,7 +37,7 @@ INSTALL_JINJA_EXCEPTION = ( 
)





def get_commands_from_yaml(yaml_content):

def get_commands_from_yaml(yaml_content: bytes) -> Optional[Dict[str, Any]]:

    """

    Parse tests from Conda's meta.yaml file contents

    """
@@ -81,7 +82,7 @@ def get_commands_from_yaml(yaml_content): 
    return package_tests





def get_run_test(file: str) -> Dict:

def get_run_test(file: str) -> Dict[str, Any]:

    r"""

    Get tests from a run_test.sh file

    """
@@ -105,60 +106,20 @@ def prepend_anaconda_url(url): 
    return f"https://anaconda.org{url}"





def get_test_from_anaconda(url: str) -> Optional[Dict]:

def get_test_from_anaconda(url: str) -> Optional[Dict[str, Any]]:

    """

    Given the URL of an anaconda tarball, return tests



    >>> # test for info/recipe/meta.yaml

    >>> tests = get_test_from_anaconda("https://anaconda.org/conda-forge/chopin2/1.0.6/download/noarch/chopin2-1.0.6-pyhd8ed1ab_0.tar.bz2")

    >>> assert tests == {'commands': ['pip check', 'chopin2 --version'], 'imports': ['chopin2'], 'import_lang': 'python -c'}, tests

    >>> tests = get_test_from_anaconda("https://anaconda.org/conda-forge/chopin2/1.0.7/download/noarch/chopin2-1.0.7-pyhd8ed1ab_1.conda")

    >>> assert tests == {'commands': ['pip check', 'chopin2 --version'], 'imports': ['chopin2'], 'import_lang': 'python -c'}, tests

    >>> # test for info/recipe/run_test.sh

    >>> tests = get_test_from_anaconda("https://anaconda.org/bioconda/ucsc-pslmap/366/download/linux-64/ucsc-pslmap-366-hdd26221_0.tar.bz2")

    >>> assert tests == {'commands': ['#!/bin/bash && pslMap 2> /dev/null || [[ "$?" == 255 ]] && ']}, tests

    """

    name, content = get_file_from_conda_package(

        url, ["info/recipe/meta.yaml", "info/recipe/meta.yaml.template", "info/recipe/run_test.sh"]

    )

    if name.startswith("info/recipe/meta.yaml"):

    if name and content and name.startswith("info/recipe/meta.yaml"):

        package_tests = get_commands_from_yaml(content)

        if package_tests:

            return package_tests

    if name == "info/recipe/run_test.sh":

    if name and content and name == "info/recipe/run_test.sh":

        return get_run_test(unicodify(content))

    return None

    # try:

    #     tarball = get_file_from_recipe_url(url)

    # except tarfile.ReadError:

    #     return None



    # try:

    #     metafile = tarball.extractfile("info/recipe/meta.yaml")

    # except (tarfile.ReadError, KeyError, TypeError):

    #     pass

    # else:

    #     package_tests = get_commands_from_yaml(metafile.read())

    #     if package_tests:

    #         return package_tests



    # # this part is perhaps unnecessary, but some of the older tarballs have a testfile with .yaml.template ext

    # try:

    #     metafile = tarball.extractfile("info/recipe/meta.yaml.template")

    # except (tarfile.ReadError, KeyError, TypeError):

    #     pass

    # else:

    #     package_tests = get_commands_from_yaml(metafile)

    #     if package_tests:

    #         return package_tests



    # # if meta.yaml was not present or there were no tests in it, try and get run_test.sh instead

    # try:

    #     run_test = tarball.extractfile("info/recipe/run_test.sh")

    #     return get_run_test(run_test)

    # except KeyError:

    #     logging.info("run_test.sh file not present.")

    #     return None





def find_anaconda_versions(name, anaconda_channel="bioconda"):

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

+4 −1
Original line number Diff line number Diff line
@@ -18,7 +18,10 @@ import string 
import subprocess

import sys

from sys import platform as _platform

from typing import List, TYPE_CHECKING

from typing import (

    List,

    TYPE_CHECKING,

)



import yaml

test/unit/tool_util/mulled/test_get_tests.py

+20 −5
Original line number Diff line number Diff line
@@ -32,9 +32,9 @@ test: 


def test_get_commands_from_yaml():

    commands = get_commands_from_yaml(smart_str(TEST_RECIPE))

    assert commands["imports"] == ["eagle"]

    assert commands["commands"] == ["eagle --help"]

    assert commands["import_lang"] == "python -c"

    assert commands and commands["imports"] == ["eagle"]

    assert commands and commands["commands"] == ["eagle --help"]

    assert commands and commands["import_lang"] == "python -c"





def test_get_run_test():
@@ -55,11 +55,26 @@ def test_prepend_anaconda_url(): 


@external_dependency_management

def test_get_test_from_anaconda():

    # test old fashion tar.bz2 package

    tests = get_test_from_anaconda(

        "https://anaconda.org/bioconda/samtools/1.3.1/download/linux-64/samtools-1.3.1-5.tar.bz2"

    )

    assert tests["commands"] == ["samtools --help"]

    assert tests["import_lang"] == "python -c"

    assert tests and tests["commands"] == ["samtools --help"]

    assert tests and tests["import_lang"] == "python -c"



    # test new conda package

    tests = get_test_from_anaconda(

        "https://anaconda.org/conda-forge/chopin2/1.0.7/download/noarch/chopin2-1.0.7-pyhd8ed1ab_1.conda"

    )

    assert tests and tests["commands"] == ["pip check", "chopin2 --version"]

    assert tests and tests["imports"] == ["chopin2"]

    assert tests and tests["import_lang"] == "python -c"



    # test for package defining tests in info/recipe/run_test.sh

    tests = get_test_from_anaconda(

        "https://anaconda.org/bioconda/ucsc-pslmap/366/download/linux-64/ucsc-pslmap-366-hdd26221_0.tar.bz2"

    )

    assert tests and tests["commands"] == ['#!/bin/bash && pslMap 2> /dev/null || [[ "$?" == 255 ]] && ']





@external_dependency_management