Call fsaccess.realpath before comparing paths in _relocate. (#1560)

Co-authored-by: Michael R. Crusoe <[email protected]>

Author: tetron

MANIFEST.in

@@ -10,6 +10,9 @@ include tests/tmp4/alpha/*
 include tests/wf/*
 include tests/wf/operation/*
 include tests/override/*
+include tests/reloc/*.cwl
+include tests/reloc/dir1/*
+include tests/reloc/dir2/*
 include tests/checker_wf/*
 include tests/subgraph/*
 include tests/trs/*

cwltool/process.py

@@ -354,11 +354,13 @@ def _collectDirEntries(
                 yield from _collectDirEntries(sub_obj)
 
     def _relocate(src: str, dst: str) -> None:
+        src = fs_access.realpath(src)
+        dst = fs_access.realpath(dst)
+
         if src == dst:
             return
 
         # If the source is not contained in source_directories we're not allowed to delete it
-        src = fs_access.realpath(src)
         src_can_deleted = any(
             os.path.commonprefix([p, src]) == p for p in source_directories
         )

requirements.txt

@@ -2,7 +2,7 @@ requests>=2.4.3
 ruamel.yaml>=0.15,<0.17.17
 rdflib>=4.2.2,<6.1
 shellescape>=3.4.1,<3.9
-schema-salad>=8.2.20210914115719,<9
+schema-salad>=8.2.20211104054942,<9
 prov==1.5.1
 bagit==1.8.1
 mypy-extensions

setup.py

@@ -111,9 +111,7 @@
         "ruamel.yaml >= 0.15, < 0.17.17",
         "rdflib >= 4.2.2, < 6.1.0",
         "shellescape >= 3.4.1, < 3.9",
-        # 7.1.20210518142926 or later required due to
-        # https://github.com/common-workflow-language/schema_salad/issues/385
-        "schema-salad >= 8.2.20210914115719, < 9",
+        "schema-salad >= 8.2.20211104054942, < 9",
         "mypy-extensions",
         "psutil >= 5.6.6",
         "prov == 1.5.1",

tests/reloc/dir1/foo

@@ -0,0 +1 @@
+dir1

tests/reloc/dir2

@@ -0,0 +1,15 @@
+cwlVersion: v1.2
+class: CommandLineTool
+inputs:
+  inp: Directory
+outputs:
+  bar:
+    type: File
+    outputBinding:
+      glob: dir2/foo
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - $(inputs.inp)
+arguments: [ls, -l]

tests/reloc/test.cwl

@@ -1,8 +1,12 @@
 import json
 import sys
 from pathlib import Path
+import tempfile
 
 from cwltool.main import main
+from cwltool.process import relocateOutputs
+from cwltool.stdfsaccess import StdFsAccess
+from cwltool.pathmapper import PathMapper
 
 from .util import get_data, needs_docker
 
@@ -33,3 +37,19 @@ def test_for_conflict_file_names(tmp_path: Path) -> None:
     out = json.loads(stream.getvalue())
     assert out["b1"]["basename"] == out["b2"]["basename"]
     assert out["b1"]["location"] != out["b2"]["location"]
+
+
+def test_relocate_symlinks(tmp_path: Path) -> None:
+    assert (
+        main(
+            [
+                "--debug",
+                "--outdir",
+                get_data("tests/reloc") + "/dir2",
+                get_data("tests/reloc/test.cwl"),
+                "--inp",
+                get_data("tests/reloc") + "/dir2",
+            ]
+        )
+        == 0
+    )