Commit bfe680f0 authored by Duggan, John's avatar Duggan, John
Browse files

Merge branch 'dev' into 'main' 

Merge 'dev' into 'main'

See merge request !125
parents b9c5098f 77b66bda

.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: 24.2.dev3+ornl

  GALAXY_VERSION_DOCKER: 24.2.dev3.ornl

  GALAXY_VERSION_PYTHON: 24.2.dev4+ornl

  GALAXY_VERSION_DOCKER: 24.2.dev4.ornl



# This import is for the func_rse_docker_* functions

before_script:

lib/galaxy/jobs/runners/__init__.py

+3 −0
Original line number Diff line number Diff line
@@ -541,6 +541,7 @@ class BaseJobRunner: 
            return



        set_user = user_oidc_config.get("docker_set_user", False)

        set_user_groups = user_oidc_config.get("docker_set_user_groups", False)

        env_var = user_oidc_config.get("docker_add_user_to_env", None)



        if not set_user and not env_var:
@@ -572,6 +573,8 @@ class BaseJobRunner: 


        if set_user:

            destination_info["set_host_user"] = username

        if set_user_groups:

            destination_info["host_user_to_set_groups_from"] = username

        if env_var:

            destination_info["pass_host_user_to_env"] = env_var + "=" + username

        return

lib/galaxy/tool_util/deps/container_classes.py

+4 −0
Original line number Diff line number Diff line
@@ -481,8 +481,12 @@ class DockerContainer(Container, HasDockerLikeVolumes): 
        run_extra_arguments = self.prop("run_extra_arguments", docker_util.DEFAULT_RUN_EXTRA_ARGUMENTS)

        group_command = ""

        host_user = self.destination_info.get("set_host_user", None)

        user_with_groups = self.destination_info.get("host_user_to_set_groups_from", None)

        if host_user:

            group_command = string.Template(SET_USER_GROUPS_TEMPLATE).safe_substitute(username=host_user)

        elif user_with_groups:

            group_command = string.Template(SET_USER_GROUPS_TEMPLATE).safe_substitute(username=user_with_groups)

        if group_command:

            if run_extra_arguments:

                run_extra_arguments = run_extra_arguments + " $GROUPADD"

            else: