Unverified Commit 7fb43de9 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #19626 from nsoranzo/release_24.0_fix_mulled_tests 

[24.0] Fix mulled tests
parents d550b77e 0c09d02d

lib/galaxy/tool_util/deps/mulled/invfile.lua

+3 −2
Original line number Diff line number Diff line
@@ -88,13 +88,14 @@ inv.task('build') 
    .using(conda_image)

        .withHostConfig({binds = bind_args})

        .run('/bin/sh', '-c', preinstall

            .. conda_bin .. ' create --quiet --yes -p /usr/local/env --copy  && '

            .. conda_bin .. ' install '

            .. channel_args .. ' '

            .. target_args

            .. ' --strict-channel-priority -p /usr/local --copy --yes '

            .. ' --strict-channel-priority -p /usr/local/env --copy --yes '

            .. verbose

            .. postinstall)

    .wrap('build/dist')

    .wrap('build/dist/env')

        .at('/usr/local')

        .inImage(destination_base_image)

        .as(repo)

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

+14 −2
Original line number Diff line number Diff line
@@ -5,6 +5,10 @@ import json 
import logging

import sys

import tempfile

from typing import (

    Dict,

    List,

)



import requests
@@ -123,7 +127,7 @@ class CondaSearch: 
    def __init__(self, channel):

        self.channel = channel



    def get_json(self, search_string):

    def get_json(self, search_string) -> List[Dict[str, str]]:

        """

        Function takes search_string variable and returns results from the bioconda channel in JSON format
@@ -136,8 +140,16 @@ class CondaSearch: 
        except Exception as e:

            logging.info(f"Search failed with: {e}")

            return []

        header_found = False

        lines_fields: List[List[str]] = []

        for line in raw_out.splitlines():

            if line.startswith("#"):

                header_found = True

            elif header_found:

                lines_fields.append(line.split())

        return [

            {"package": n.split()[0], "version": n.split()[1], "build": n.split()[2]} for n in raw_out.split("\n")[2:-1]

            {"package": line_fields[0], "version": line_fields[1], "build": line_fields[2]}

            for line_fields in lines_fields

        ]

test/unit/tool_util/mulled/test_mulled_search.py

+4 −4
Original line number Diff line number Diff line
@@ -25,10 +25,10 @@ def test_quay_search(): 
@skip_unless_executable("conda")

def test_conda_search():

    t = CondaSearch("bioconda")

    search1 = t.get_json("asdfasdf")

    search2 = t.get_json("bioconductor-gosemsim")

    assert search1 == []

    assert all(r["package"] == "bioconductor-gosemsim" for r in search2)

    search = t.get_json("asdfasdf")

    assert search == []

    search = t.get_json("bioconductor-gosemsim")

    assert all(r["package"] == "bioconductor-gosemsim" for r in search)





@external_dependency_management