Fetch configs from app setting and pass them down

Fix the code to avoid using global variables holding configuration
variables to avoid the failures caused by action-at-a-distance effects
due to change of a value elsewhere.

This way, all code consistently receives the same configuration values
passed on from callers.

We pass on the following configuration settings:
* TMPDIR
* SQL_URI
* TEXTDIR

1 files changed, 1 insertions, 0 deletions

diff --git a/gn3/heatmaps.py b/gn3/heatmaps.py
index 511996a..80c38e8 100644
--- a/gn3/heatmaps.py
+++ b/gn3/heatmaps.py
@@ -145,6 +145,7 @@ def build_heatmap(
         app.config['REAPER_COMMAND'],
         genotype_filename,
         traits_filename,
+        output_dir=app.config["TMPDIR"],
         separate_nperm_output=True
     )