github workflow corrected.

.github/workflows/test.yml

@@ -24,14 +24,13 @@ jobs:
           pytest
       - name: Compare to moh_v3_template.csv
         shell: bash {0}
-        # Script based largely on update_moh_template.sh
         run: |
-          python src/clinical_etl/generate_schema.py  --out tmp_template
-          diff tmp_template.csv moh_v3_template.csv > tests/moh_diffs.txt
-          rm tmp_template.csv
-          bytes=$(head -5 tests/moh_diffs.txt | wc -c)
-          dd if=tests/moh_diffs.txt bs="$bytes" skip=1 conv=notrunc of=tests/moh_diffs1.txt
-          diff tests/moh_diffs1.txt tests/moh_diffs.txt
+          # Script based largely on update_moh_template.sh
+          python src/clinical_etl/generate_schema.py --out moh_template
+          diff moh_template.csv moh_v3_template.csv > curr_diff.txt
+          bytes=$(head -5 curr_diff.txt | wc -c)
+          dd if=curr_diff.txt bs="$bytes" skip=1 conv=notrunc of=new_diff.txt
+          diff new_diff.txt tests/moh_diffs.txt
           if [[ $? == 1 ]]; then echo MoH template checking needs to be updated! See https://github.com/CanDIG/clinical_ETL_code#mapping-template for information.
           exit 1
           fi

update_moh_template.sh

@@ -1,9 +1,10 @@
 #!/usr/bin/env bash
+# Updates the moh_template based on the schema.
+# Manual differences are recorded in tests/moh_diffs.txt
 
-
-python src/clinical_etl/generate_schema.py --out tmp_template
-diff tmp_template.csv moh_v3_template.csv > tests/moh_diffs.txt
-rm tmp_template.csv
-bytes=$(head -5 tests/moh_diffs.txt | wc -c)
-dd if=tests/moh_diffs.txt  bs="$bytes" skip=1 conv=notrunc of=tests/moh_diffs1.txt
+python src/clinical_etl/generate_schema.py --out moh_template
+diff moh_template.csv moh_v3_template.csv > curr_diff.txt
+bytes=$(head -5 curr_diff.txt | wc -c)
+dd if=curr_diff.txt  bs="$bytes" skip=1 conv=notrunc of=tests/moh_diffs1.txt
 mv tests/moh_diffs1.txt tests/moh_diffs.txt
+rm curr_diff.txt