Merge pull request #247 from umccr/bugfix/no-doc-cache

Use --no-doc-cache to stop cwltool from locking
umccr · Nov 29, 2023 · ec93d33 · ec93d33
2 parents 7571695 + 7a5aaa7
commit ec93d33
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Showing 5 changed files with 10 additions and 10 deletions.
diff --git a/bin/create_typescript_interface_from_schema.py b/bin/create_typescript_interface_from_schema.py
@@ -101,7 +101,7 @@ def create_packed_schema_json(cwl_yaml_path: Path) -> Dict:
             "outputs: {}\n"
         )
 
-    cwltool_pack_proc: CompletedProcess = run(["cwltool", "--pack", cwl_tool_file.name], capture_output=True)
+    cwltool_pack_proc: CompletedProcess = run(["cwltool", "--no-doc-cache", "--pack", cwl_tool_file.name], capture_output=True)
 
     if not cwltool_pack_proc.returncode == 0:
         logger.error(f"cwltool failed with error '{cwltool_pack_proc.stderr.decode()}'")

diff --git a/classes/cwl.py b/classes/cwl.py
@@ -192,7 +192,7 @@ def run_cwltool_pack(self, packed_file: NamedTemporaryFile):
             [
                  "conda", "run",
                  "--name", ICAV1_CWLTOOL_CONDA_ENV_NAME,
-                 "cwltool", "--pack", self.cwl_file_path
+                 "cwltool", "--no-doc-cache", "--pack", self.cwl_file_path
 
             ],
             capture_output=True)
@@ -207,7 +207,7 @@ def run_cwltool_pack(self, packed_file: NamedTemporaryFile):
     @staticmethod
     def run_cwltool_validate(cwl_file_path: Path):
         """
-        Run subprocess command ["cwltool", "--validate", "/path/to/cwl"]
+        Run subprocess command ["cwltool", "--no-doc-cache", "--validate", "/path/to/cwl"]
         :return:
         """
 
@@ -219,7 +219,7 @@ def run_cwltool_validate(cwl_file_path: Path):
                 [
                     "conda", "run",
                     "--name", ICAV1_CWLTOOL_CONDA_ENV_NAME,
-                    "cwltool", "--validate", cwl_file_path
+                    "cwltool", "--no-doc-cache", "--validate", cwl_file_path
 
                 ],
                 capture_output=True)
@@ -234,7 +234,7 @@ def run_cwltool_validate(cwl_file_path: Path):
             [
                 "conda", "run",
                 "--name", f"{LATEST_CWLTOOL_CONDA_ENV_NAME}",
-                "cwltool", "--validate", cwl_file_path
+                "cwltool", "--no-doc-cache", "--validate", cwl_file_path
 
             ],
             capture_output=True)

diff --git a/subcommands/v2/zip_v2_workflow.py b/subcommands/v2/zip_v2_workflow.py
@@ -251,7 +251,7 @@ def zip_workflow(self):
         )
         proc_returncode, proc_stdout, proc_stderr = run_subprocess_proc(
             [
-                "cwltool", "--validate", str(output_tempdir / "workflow.cwl")
+                "cwltool", "--no-doc-cache", "--validate", str(output_tempdir / "workflow.cwl")
             ],
             cwd=str(output_tempdir),
             capture_output=True

diff --git a/utils/cwl_workflow_helper_utils.py b/utils/cwl_workflow_helper_utils.py
@@ -133,7 +133,7 @@ def collect_objects_by_print_deps(cwl_path: Path) -> List:
 
     returncode, stdout, stderr = run_subprocess_proc(
         [
-            "cwltool", "--print-deps", str(cwl_path)
+            "cwltool", "--no-doc-cache", "--print-deps", str(cwl_path)
         ],
         capture_output=True
     )
@@ -396,7 +396,7 @@ def zip_workflow(cwl_obj: CWLWorkflow, output_zip_path: Path):
     logger.info("Now all files have been transferred, confirming successful 'zip' with cwltool --validate")
     proc_returncode, proc_stdout, proc_stderr = run_subprocess_proc(
         [
-            "cwltool", "--validate", str(output_tempdir / "workflow.cwl")
+            "cwltool", "--no-doc-cache", "--validate", str(output_tempdir / "workflow.cwl")
         ],
         cwd=str(output_tempdir),
         capture_output=True
@@ -442,7 +442,7 @@ def create_packed_workflow_from_zipped_workflow_path(zipped_path: Path, output_p
         # Pack workflow
         pack_returncode, pack_stdout, pack_stderr = run_subprocess_proc(
             [
-                "cwltool", "--pack", extracted_main_workflow_path
+                "cwltool", "--no-doc-cache", "--pack", extracted_main_workflow_path
             ],
             capture_output=True
         )

diff --git a/utils/pydot_utils.py b/utils/pydot_utils.py
@@ -41,7 +41,7 @@ def build_cwl_dot(cwl_item: CWL, dot_out_path: Path):
     with open(str(dot_out_path), 'w') as write_h:
         build_dot_returncode, _, build_dot_stderr = run_subprocess_proc(
             [
-                "cwltool", "--debug",
+                "cwltool", "--debug", "--no-doc-cache",
                 "--print-dot", cwl_packed_temp_file.name
             ],
             stdout=write_h, stderr=subprocess.PIPE