Commit 43999021 authored by Duggan, John's avatar Duggan, John
Browse files

Merge branch '149-fix-missing-rucio-temp-directory' into 'dev' 

Resolve "Fix missing Rucio temp directory"

Closes #149

See merge request !143
parents 6847d699 816da430

.gitlab-ci.yml

+2 −2
Original line number Diff line number Diff line
@@ -9,8 +9,8 @@ variables: 
  CONTAINER_GALAXY_URL: "${NDIP_DOCKER_REPOSITORY}/${CI_PROJECT_PATH}"

  CONTAINER_GALAXY_BASE_URL: "${CONTAINER_GALAXY_URL}/base"

  CONTAINER_GALAXY_COMMIT_URL: "${CONTAINER_GALAXY_URL}/commit"

  GALAXY_VERSION_PYTHON: 25.1.dev3+ornl

  GALAXY_VERSION_DOCKER: 25.1.dev3.ornl

  GALAXY_VERSION_PYTHON: 25.1.dev4+ornl

  GALAXY_VERSION_DOCKER: 25.1.dev4.ornl



# This import is for the func_rse_docker_* functions

before_script:

lib/galaxy/objectstore/rucio.py

+1 −0
Original line number Diff line number Diff line
@@ -165,6 +165,7 @@ class RucioBroker: 
            temp_directory = self.extra_dirs["temp"]

            self.rucio_config_path = os.path.join(temp_directory, "rucio.cfg")

            key_for_pass = "password"

            os.makedirs(temp_directory, exist_ok=True)

            with open(self.rucio_config_path, "w") as f:

                f.write(

                    f"""[client]

test/unit/tool_shed/test_files/toolshed_community_files.tgz

0 → 100644
+20 KiB

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test/unit/tool_shed/test_shed_index.py

+10 −6
Original line number Diff line number Diff line
@@ -3,6 +3,7 @@ import shutil 
import tempfile

from collections import namedtuple

from io import BytesIO

from pathlib import Path



import pytest

import requests
@@ -11,7 +12,7 @@ from whoosh import index 
from galaxy.util.compression_utils import CompressedFile

from tool_shed.util.shed_index import build_index



URL = "https://github.com/mvdbeek/toolshed-test-data/blob/master/toolshed_community_files.tgz?raw=true"

PATH = Path(__file__).resolve().parent / "test_files" / "toolshed_community_files.tgz"





@pytest.fixture
@@ -26,9 +27,8 @@ def whoosh_index_dir(): 
@pytest.fixture(scope="module")

def community_file_dir():

    extracted_archive_dir = tempfile.mkdtemp()

    response = requests.get(URL)

    response.raise_for_status()

    b = BytesIO(response.content)

    with open(PATH, "rb") as community_file:

        b = BytesIO(community_file.read())

    with CompressedFile.open_tar(b) as tar:

        tar.extractall(extracted_archive_dir)

    try:
@@ -39,12 +39,16 @@ def community_file_dir(): 


@pytest.fixture()

def community_file_structure(community_file_dir):

    community = namedtuple("community", "file_path hgweb_config_dir hgweb_repo_prefix dburi")

    community = namedtuple(

        "community", "file_path hgweb_config_dir hgweb_repo_prefix dburi"

    )

    return community(

        file_path=os.path.join(community_file_dir, "database", "community_files"),

        hgweb_config_dir=community_file_dir,

        hgweb_repo_prefix="repos/",

        dburi="sqlite:///{}".format(os.path.join(community_file_dir, "database", "community.sqlite")),

        dburi="sqlite:///{}".format(

            os.path.join(community_file_dir, "database", "community.sqlite")

        ),

    )