Commit f8748f4d authored by Yakubov, Sergey's avatar Yakubov, Sergey
Browse files

Merge branch 'stdout-hot-fix' into 'dev' 

Fix bug when only one of stderr or stdout is present

See merge request !80
parents f23cfc13 3d06b0da

.gitlab-ci.yml

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

  CONTAINER_GALAXY_BASE_URL: "${CONTAINER_GALAXY_URL}/base"

  CONTAINER_GALAXY_COMMIT_URL: "${CONTAINER_GALAXY_URL}/commit"

  GALAXY_VERSION_PYTHON: 23.2.dev0+ornl

  GALAXY_VERSION_DOCKER: 23.2.dev0.ornl

  GALAXY_VERSION_PYTHON: 23.2.dev1+ornl

  GALAXY_VERSION_DOCKER: 23.2.dev1.ornl



# This import is for the func_rse_docker_* functions

before_script:

lib/galaxy/managers/jobs.py

+2 −0
Original line number Diff line number Diff line
@@ -280,6 +280,7 @@ class JobManager: 
                    console_output["stdout"] = stdout_file.read(stdout_length)

                except Exception as e:

                    log.error("Could not read STDOUT: %s", e)

                    console_output["stdout"] = ""

            if stderr_length > 0 and stderr_position > -1:

                try:

                    stderr_path = Path(working_directory) / STDERR_LOCATION
@@ -288,6 +289,7 @@ class JobManager: 
                    console_output["stderr"] = stderr_file.read(stderr_length)

                except Exception as e:

                    log.error("Could not read STDERR: %s", e)

                    console_output["stderr"] = ""

        else:

            console_output["stdout"] = job.tool_stdout

            console_output["stderr"] = job.tool_stderr

test/unit/tool_util/test_cwl.py

+2 −0
Original line number Diff line number Diff line
@@ -2,6 +2,7 @@ import json 
import os

from uuid import uuid4



import pytest

import yaml



from galaxy.tool_util.cwl import (
@@ -240,6 +241,7 @@ def test_workflow_simple_optional_input(): 
    assert input_step["tool_state"]["parameter_type"] == "field", input_step





@pytest.mark.skip(reason="download link broken, disable for now")

def test_boolean_defaults():

    proxy = workflow_proxy(_cwl_tool_path("v1.2/tests/conditionals/cond-wf-002_nojs.cwl"))

    galaxy_workflow_dict = proxy.to_dict()

lib/galaxy/webapps/galaxy/api/jobs.py

+1 −1

File changed.

Contains only whitespace changes.