From f0f3133896b1004769e52ca8141dd8177ed62fc9 Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Thu, 20 Jul 2023 13:56:44 -0400 Subject: [PATCH] Use less memory in the Giraffe WDL test (#4541) * Use a Giraffe demo workflow with lower memory requirements * Improve reporting accessed files --- src/toil/fileStores/abstractFileStore.py | 9 ++++++++- src/toil/test/wdl/wdltoil_test.py | 4 ++-- 2 files changed, 10 insertions(+), 3 deletions(-) diff --git a/src/toil/fileStores/abstractFileStore.py b/src/toil/fileStores/abstractFileStore.py index 9e1616f4d5..c95b3121f8 100644 --- 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 index da7b6a3863..241594af8c 100644 --- 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"