Unverified Commit ffb52910 authored by Nicola Soranzo's avatar Nicola Soranzo
Browse files

Fix parsing of mulled tsv files containing comments and tabs

parent cc35a28a

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

+12 −10
Original line number Diff line number Diff line
@@ -130,7 +130,7 @@ def find_anaconda_versions(name, anaconda_channel="bioconda"): 
    """

    r = requests.get(f"https://anaconda.org/{anaconda_channel}/{name}/files", timeout=MULLED_SOCKET_TIMEOUT)

    urls = []

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

    for line in r.text.splitlines():

        if "download/linux" in line:

            urls.append(line.split('"')[1])

    return urls
@@ -271,22 +271,24 @@ def import_test_to_command_list(import_lang: str, import_: str) -> List[str]: 




def hashed_test_search(

    container, recipes_path=None, deep=False, anaconda_channel="bioconda", github_repo="bioconda/bioconda-recipes"

):

    container: str, recipes_path=None, deep=False, anaconda_channel="bioconda", github_repo="bioconda/bioconda-recipes"

) -> Dict[str, Any]:

    """

    Get test for hashed containers

    """

    package_tests = {"commands": [], "imports": [], "container": container, "import_lang": "python -c"}

    package_tests: Dict[str, Any] = {"commands": [], "imports": [], "container": container, "import_lang": "python -c"}



    githubpage = requests.get(

    response = requests.get(

        f"https://raw.githubusercontent.com/BioContainers/multi-package-containers/master/combinations/{container}.tsv",

        timeout=MULLED_SOCKET_TIMEOUT,

    )

    if githubpage.status_code == 200:

        packages = githubpage.text.split(",")  # get names of packages from github

        packages = [package.split("=") for package in packages]

    else:

        packages = []

    response.raise_for_status()

    for line in response.text.splitlines():

        if not line.startswith("#"):

            break

    concatenated_targets = line.split("\t")[0]

    targets = concatenated_targets.split(",")

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



    containers = []

    for package in packages: