Unverified Commit 759065dc authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #14100 from mvdbeek/upload_dir_fix 

[22.05] Write temporary files created within celery tasks to working directory
parents 88163ff5 1b4bbe09

lib/galaxy/tools/data_fetch.py

+1 −1
Original line number Diff line number Diff line
@@ -485,7 +485,7 @@ def _has_src_to_path(upload_config, item, is_dataset=False) -> Tuple[str, str]: 
    if src == "url":

        url = item.get("url")

        try:

            path = stream_url_to_file(url, file_sources=upload_config.file_sources)

            path = stream_url_to_file(url, file_sources=upload_config.file_sources, dir=upload_config.working_directory)

        except Exception as e:

            raise Exception(f"Failed to fetch url {url}. {str(e)}")

test/unit/app/tools/test_data_fetch.py

+30 −0
Original line number Diff line number Diff line 
import json

import os

import tempfile

from contextlib import contextmanager

from os import environ

from shutil import rmtree
@@ -35,6 +36,30 @@ def test_simple_path_get(): 
        assert output





def test_simple_uri_get():

    with _execute_context() as execute_context:

        request = {

            "targets": [

                {

                    "destination": {

                        "type": "hdas",

                    },

                    "elements": [

                        {

                            "src": "url",

                            "url": "https://raw.githubusercontent.com/galaxyproject/galaxy/dev/test-data/1.bed",

                        }

                    ],

                }

            ]

        }

        execute_context.execute_request(request)

        output = _unnamed_output(execute_context)

        hda_result = output["elements"][0]

        assert hda_result["state"] == "ok"

        assert hda_result["ext"] == "bed"





def test_deferred_uri_get():

    with _execute_context() as execute_context:

        request = {
@@ -222,8 +247,13 @@ def test_hdca_failed_expansion(): 
def _execute_context():

    job_directory = mkdtemp()

    try:

        # temporarily set tempdir to non-existing location

        # to make sure all intermediate files are created in the working

        # directory

        tempfile.tempdir = "/abcdefgh123456"

        yield ExecuteContext(job_directory)

    finally:

        tempfile.tempdir = None

        rmtree(job_directory)