Merge pull request #372 from mvdbeek/fix_tool_file_authorization_bina…

…ry_files

Open tool file contents in `rb`

.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'

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()

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.")