diff --git a/.github/workflows/galaxy_framework.yaml b/.github/workflows/galaxy_framework.yaml index 52f08d32..6ccaea96 100644 --- a/.github/workflows/galaxy_framework.yaml +++ b/.github/workflows/galaxy_framework.yaml @@ -52,7 +52,7 @@ jobs: GALAXY_TEST_JOB_CONFIG_FILE: ../pulsar/test_data/test_job_conf.yaml GALAXY_CONFIG_OVERRIDE_METADATA_STRATEGY: ${{ matrix.metadata-strategy }} continue-on-error: ${{ matrix.galaxy-branch == 'master' }} - - uses: actions/upload-artifact@v2 + - uses: actions/upload-artifact@v4 with: name: Framework test results (${{ matrix.python-version }}) path: 'galaxy/run_framework_tests.html' diff --git a/pulsar/managers/base/__init__.py b/pulsar/managers/base/__init__.py index 5c89eb66..6ca07e91 100644 --- a/pulsar/managers/base/__init__.py +++ b/pulsar/managers/base/__init__.py @@ -186,7 +186,7 @@ def _check_execution(self, job_id, tool_id, command_line): for file in self._list_dir(tool_files_dir): if os.path.isdir(join(tool_files_dir, file)): continue - contents = open(join(tool_files_dir, file)).read() + contents = open(join(tool_files_dir, file), "rb").read() log.debug("job_id: {} - checking tool file {}".format(job_id, file)) authorization.authorize_tool_file(basename(file), contents) config_files_dir = job_directory.configs_directory() diff --git a/pulsar/tools/authorization.py b/pulsar/tools/authorization.py index 32412c31..3783f59e 100644 --- a/pulsar/tools/authorization.py +++ b/pulsar/tools/authorization.py @@ -43,7 +43,7 @@ def authorize_tool_file(self, name, contents): tool = self.tool tool_dir = tool.get_tool_dir() tool_dir_file = join(tool_dir, name) - allowed_contents = open(tool_dir_file).read() + allowed_contents = open(tool_dir_file, "rb").read() if contents != allowed_contents: self.__unauthorized("Attempt to write tool file with contents differing from Pulsar copy of tool file.")