From 032bcfb3733bd54953cd29be54b9de8cfb1f5cc4 Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Mon, 17 Jun 2013 17:19:22 -0700 Subject: [PATCH] copy_tree_from wasn't actually making any symlinks. It turns out at some point the results class switched to using full paths. this meant my os.path.join's didn't work as it didn't modify fullly qualified paths. This patch converts the result lib path to a relative path based on the destination so it can compute source paths more easily. --- htsworkflow/submission/results.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/htsworkflow/submission/results.py b/htsworkflow/submission/results.py index c9000e4..4f815ad 100644 --- a/htsworkflow/submission/results.py +++ b/htsworkflow/submission/results.py @@ -52,7 +52,9 @@ class ResultMap(MutableMapping): destpath = os.getcwd() for lib_id in self.results_order: - lib_path = self.results[lib_id] + abs_lib_path = os.path.abspath(self.results[lib_id]) + lib_path = os.path.relpath(abs_lib_path, destpath) + LOGGER.debug('lib_path: %s', lib_path) lib_destination = os.path.join(destpath, lib_path) if not os.path.exists(lib_destination): LOGGER.info("Making dir {0}".format(lib_destination)) @@ -60,6 +62,7 @@ class ResultMap(MutableMapping): source_rel_dir = os.path.join(source_path, lib_path) source_lib_dir = os.path.abspath(source_rel_dir) + LOGGER.debug("source_lib_dir: %s", source_lib_dir) for filename in os.listdir(source_lib_dir): source_pathname = os.path.join(source_lib_dir, filename) -- 2.30.2