Merge pull request #138 from inab/137-error-when-adding-dot-file-to-o…

…utput-ro-crate Fixed several path handling issues in several parts of RO-Crate gener…
inab · Dec 8, 2024 · e3c066e · e3c066e
2 parents 6ce9872 + 51cd40f
commit e3c066e
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Showing 2 changed files with 25 additions and 9 deletions.
diff --git a/wfexs_backend/__main__.py b/wfexs_backend/__main__.py
@@ -1061,7 +1061,9 @@ def processStagedWorkdirCommand(
                             )
                             expanded_licences = wB.curate_licence_list(op_licences)
                             wfInstance.createStageResearchObject(
-                                filename=args.staged_workdir_command_args[1],
+                                filename=pathlib.Path(
+                                    args.staged_workdir_command_args[1]
+                                ),
                                 payloads=doMaterializedROCrate,
                                 licences=expanded_licences,
                                 resolved_orcids=resolved_orcids,
@@ -1078,7 +1080,9 @@ def processStagedWorkdirCommand(
                                 )
                                 expanded_licences = wB.curate_licence_list(op_licences)
                                 wfInstance.createResultsResearchObject(
-                                    filename=args.staged_workdir_command_args[1],
+                                    filename=pathlib.Path(
+                                        args.staged_workdir_command_args[1]
+                                    ),
                                     payloads=doMaterializedROCrate,
                                     licences=expanded_licences,
                                     resolved_orcids=resolved_orcids,

diff --git a/wfexs_backend/ro_crate.py b/wfexs_backend/ro_crate.py
@@ -2631,19 +2631,26 @@ def addWorkflowExecution(
         crate_meta_outputs: "MutableSequence[rocrate.model.entity.Entity]" = []
         if stagedExec.diagram is not None:
             # This is the original diagram, in DOT format (for now)
-            abs_diagram = os.path.join(self.work_dir, stagedExec.diagram)
+            abs_diagram = (
+                stagedExec.diagram
+                if stagedExec.diagram.is_absolute()
+                else (self.work_dir / stagedExec.diagram).resolve()
+            )
+            rel_diagram = stagedExec.diagram.relative_to(self.work_dir)
             dot_file = WorkflowDiagram(
                 self.crate,
-                source=os.path.join(self.work_dir, stagedExec.diagram),
-                dest_path=stagedExec.diagram,
+                source=abs_diagram,
+                dest_path=rel_diagram,
                 fetch_remote=False,
                 validate_url=False,
                 properties={
-                    "contentSize": str(os.stat(abs_diagram).st_size),
+                    "contentSize": str(abs_diagram.stat().st_size),
                     "sha256": ComputeDigestFromFile(
                         abs_diagram, "sha256", repMethod=hexDigest
                     ),
-                    "encodingFormat": magic.from_file(abs_diagram, mime=True),
+                    "encodingFormat": magic.from_file(
+                        abs_diagram.as_posix(), mime=True
+                    ),
                 },
             )
             self.crate.add(dot_file)
@@ -2663,7 +2670,12 @@ def addWorkflowExecution(
             os.close(png_dot_handle)
 
             with tempfile.NamedTemporaryFile() as d_err:
-                dot_cmd = [self.dot_binary, "-Tpng", "-o" + png_dot_path, abs_diagram]
+                dot_cmd = [
+                    self.dot_binary,
+                    "-Tpng",
+                    "-o" + png_dot_path,
+                    abs_diagram.as_posix(),
+                ]
 
                 diagram_dot_path_for_rocrate = stagedExec.diagram.relative_to(
                     self.work_dir
@@ -2687,7 +2699,7 @@ def addWorkflowExecution(
                     png_dot_file = WorkflowDiagram(
                         self.crate,
                         source=png_dot_path,
-                        dest_path=stagedExec.diagram.as_posix() + ".png",
+                        dest_path=rel_diagram.as_posix() + ".png",
                         fetch_remote=False,
                         validate_url=False,
                         properties={