From a5f9f6f2bb101002b0adc6b0ed2257548a6a042e Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Wed, 25 Sep 2024 15:41:52 -0700 Subject: [PATCH 1/2] Add more debugging output when checking expected files --- fetch.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/fetch.py b/fetch.py index 5cc16a1..baafd44 100755 --- a/fetch.py +++ b/fetch.py @@ -100,12 +100,17 @@ def _check_prefetch_against_manifest(self, directory, manifest): """Check that prefetch downloaded all the files in the manifest.""" expected_files = self._read_manifest(manifest) downloaded_files = os.listdir(directory) + print("Found downloaded files:") + print(sorted(downloaded_files)) + print("Expected {} files; found {} files.", len(expected_files), len(downloaded_files)) return set(downloaded_files) == set(expected_files) def _check_prefetch_against_n_files(self, directory, n_files): """Check that prefetch downloaded the expected number of files.""" downloaded_files = os.listdir(directory) - print(downloaded_files) + print("Found downloaded files:") + print(sorted(downloaded_files)) + print("Expected {} files; found {} files.", n_files, len(downloaded_files)) return len(downloaded_files) == n_files def _untar(self, directory): From 3ba9d7cf5da56ecb689bc7beb6cd6c59e1b72edf Mon Sep 17 00:00:00 2001 From: Adrienne Stilp Date: Wed, 25 Sep 2024 15:45:18 -0700 Subject: [PATCH 2/2] Update Docker version in WDL --- fetch_dbgap_files.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/fetch_dbgap_files.wdl b/fetch_dbgap_files.wdl index 715d484..35c1bc4 100644 --- a/fetch_dbgap_files.wdl +++ b/fetch_dbgap_files.wdl @@ -50,7 +50,7 @@ task fetch_files { } runtime { # Pull from DockerHub - docker: "uwgac/fetch-dbgap-files:0.2.0" + docker: "uwgac/fetch-dbgap-files:0.2.1" disks: "local-disk ${disk_gb} SSD" } }