Use less memory in the Giraffe WDL test (#4541)

* Use a Giraffe demo workflow with lower memory requirements * Improve reporting accessed files
DataBiosphere · Jul 20, 2023 · f0f3133 · f0f3133
1 parent aaa451b
commit f0f3133
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Showing 2 changed files with 10 additions and 3 deletions.
diff --git a/src/toil/fileStores/abstractFileStore.py b/src/toil/fileStores/abstractFileStore.py
@@ -346,7 +346,14 @@ def _dumpAccessLogs(self) -> None:
                 # For each access record
                 if len(item) == 2:
                     # If it has a name, dump wit the name
-                    logger.warning('Downloaded file \'%s\' to path \'%s\'', *item)
+                    file_id, dest_path = item
+                    if os.path.exists(dest_path):
+                        if os.path.islink(dest_path):
+                            logger.warning('Symlinked file \'%s\' to path \'%s\'', file_id, dest_path)
+                        else:
+                            logger.warning('Downloaded file \'%s\' to path \'%s\'', file_id, dest_path)
+                    else:
+                        logger.warning('Downloaded file \'%s\' to path \'%s\' (gone!)', file_id, dest_path)
                 else:
                     # Otherwise dump without the name
                     logger.warning('Streamed file \'%s\'', *item)

diff --git a/src/toil/test/wdl/wdltoil_test.py b/src/toil/test/wdl/wdltoil_test.py
@@ -90,7 +90,7 @@ def test_giraffe_deepvariant(self):
         # TODO: enable test if nvidia-container-runtime and Singularity are installed but Docker isn't.
 
         json_dir = self._createTempDir()
-        base_uri = 'https://raw.githubusercontent.com/vgteam/vg_wdl/44a03d9664db3f6d041a2f4a69bbc4f65c79533f'
+        base_uri = 'https://raw.githubusercontent.com/vgteam/vg_wdl/65dd739aae765f5c4dedd14f2e42d5a263f9267a'
 
         wdl_file = f"{base_uri}/workflows/giraffe_and_deepvariant.wdl"
         json_file = os.path.abspath(os.path.join(json_dir, 'inputs.json'))
@@ -133,7 +133,7 @@ def test_giraffe(self):
         # TODO: enable test if nvidia-container-runtime and Singularity are installed but Docker isn't.
 
         json_dir = self._createTempDir()
-        base_uri = 'https://raw.githubusercontent.com/vgteam/vg_wdl/44a03d9664db3f6d041a2f4a69bbc4f65c79533f'
+        base_uri = 'https://raw.githubusercontent.com/vgteam/vg_wdl/65dd739aae765f5c4dedd14f2e42d5a263f9267a'
         wdl_file = f"{base_uri}/workflows/giraffe.wdl"
         json_file = f"{base_uri}/params/giraffe.json"