Rebuild cache-test cache dir, force add file for paranoid test

rki-mf1 · Sep 30, 2023 · dab81da · dab81da
1 parent 159e484
commit dab81da
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Showing 31 changed files with 97 additions and 2,755 deletions.
diff --git a/src/covsonar/cache.py b/src/covsonar/cache.py
@@ -405,7 +405,7 @@ def cache_sequence(self, seqhash: str, sequence: str) -> str:
             LOGGER.critical(
                 "Seqhash collision: sequences differ for seqhash " + seqhash + "."
             )
-            # sys.exit(1)
+            sys.exit(1)
 
         os.makedirs(os.path.dirname(fname), exist_ok=True)
         with open(fname, "w") as handle:
@@ -1017,7 +1017,7 @@ def paranoid_test(
                 + cigar
             )
             LOGGER.error("Paranoid test failed.")
-            return False
+            sys.exit(1)
         return True
 
 

diff --git a/src/covsonar/dbm.py b/src/covsonar/dbm.py
@@ -2744,6 +2744,7 @@ def handle_vcf_format(
                     LEFT JOIN element e ON v.element_id = e.id
                     LEFT JOIN molecule m ON e.molecule_id = m.id
                     WHERE {genome_condition}{nuc_filter}
+                    ORDER BY fs.name
                 ) as rows
                 GROUP BY
                     "molecule.accession", "variant.start", "variant.ref", "variant.alt"

diff --git a/tests/data/cache-test/cache/ref/1.cds b/tests/data/cache-test/cache/ref/1.cds
diff --git a/tests/data/cache-test/ref/1.lift → tests/data/cache-test/cache/ref/1.lift b/tests/data/cache-test/ref/1.lift → tests/data/cache-test/cache/ref/1.lift
diff --git a/tests/data/cache-test/ref/1.seq → tests/data/cache-test/cache/ref/1.seq b/tests/data/cache-test/ref/1.seq → tests/data/cache-test/cache/ref/1.seq
diff --git a/tests/data/cache-test/ref/1.tt → tests/data/cache-test/cache/ref/1.tt b/tests/data/cache-test/ref/1.tt → tests/data/cache-test/cache/ref/1.tt
diff --git a/...cache-test/cache/samples/Mz/MzliZGEwMGFhOTA0NjUzM2FjNDZmYjQ0YjNhYTExOWVmMDc0YjYzNA.sample b/...cache-test/cache/samples/Mz/MzliZGEwMGFhOTA0NjUzM2FjNDZmYjQ0YjNhYTExOWVmMDc0YjYzNA.sample
diff --git a/...cache-test/cache/samples/Nm/NmJlODBjNjAyNDBiN2QwN2E2MTcwOWZlN2FiMmMwOTkzYmJhOWI4Ng.sample b/...cache-test/cache/samples/Nm/NmJlODBjNjAyNDBiN2QwN2E2MTcwOWZlN2FiMmMwOTkzYmJhOWI4Ng.sample
diff --git a/...cache-test/cache/samples/OW/OWIxYjk5OGY2NDhmNmUwNzUwMzExMzU5MjkzYmIzOTU5ZDY3MWFmOA.sample b/...cache-test/cache/samples/OW/OWIxYjk5OGY2NDhmNmUwNzUwMzExMzU5MjkzYmIzOTU5ZDY3MWFmOA.sample
diff --git a/...cache-test/cache/samples/YT/YTFkOTE2MmVkMWY5MDVmZjU5YWU5M2MzYzI4YmExMmFmNjU4MmQzNA.sample b/...cache-test/cache/samples/YT/YTFkOTE2MmVkMWY5MDVmZjU5YWU5M2MzYzI4YmExMmFmNjU4MmQzNA.sample
diff --git a/...cache-test/cache/samples/ZT/ZTA5ZmI3NzEzMzU5ZDk1ZGNjOGMzMDdjZTMxNjBkZWU0MzI3NTg2ZA.sample b/...cache-test/cache/samples/ZT/ZTA5ZmI3NzEzMzU5ZDk1ZGNjOGMzMDdjZTMxNjBkZWU0MzI3NTg2ZA.sample
diff --git a/.../L0Z0a3N2YWxZNkVycUNOaXhSTEFER2R0QUhZ.seq → ...jYxMWVkZjQwODc0ZTBkNTBiM2QzMjg4M2Q4ZQ.seq b/.../L0Z0a3N2YWxZNkVycUNOaXhSTEFER2R0QUhZ.seq → ...jYxMWVkZjQwODc0ZTBkNTBiM2QzMjg4M2Q4ZQ.seq
diff --git a/.../d1ZIRXlkUlpqTktXbjN1YmYvK09NWHhRMVdR.seq → ...DEzYWNjZTZjOTM4NTYyMjQ1ZDE1NWRiNmQ3ZQ.seq b/.../d1ZIRXlkUlpqTktXbjN1YmYvK09NWHhRMVdR.seq → ...DEzYWNjZTZjOTM4NTYyMjQ1ZDE1NWRiNmQ3ZQ.seq
diff --git a/.../ODRuQ2Q0S0QrME9WcG1vWkNTRFRuYy9tbjA4.seq → ...Dg0YjQwMWIwYzc2MDk4ODY1NDc5NGFiZjMwOA.seq b/.../ODRuQ2Q0S0QrME9WcG1vWkNTRFRuYy9tbjA4.seq → ...Dg0YjQwMWIwYzc2MDk4ODY1NDc5NGFiZjMwOA.seq
diff --git a/...DI4ZTE4ZTg4ZjgwYmIzYTA3ZTQzZGM3NGEzZDk5NjZhMDhjNDM4MjYwYjY3MjFlNzM1MjM5Y2VjY2QzNzAyZA.seq b/...DI4ZTE4ZTg4ZjgwYmIzYTA3ZTQzZGM3NGEzZDk5NjZhMDhjNDM4MjYwYjY3MjFlNzM1MjM5Y2VjY2QzNzAyZA.seq
diff --git a/.../SjhYR28zTStJdXc0WGlrc3A2ZDZGOW0rOG1N.seq → ...Dc0ZDljYjAzNzMxNGIwOWU3MTRkN2E0YWM0Yw.seq b/.../SjhYR28zTStJdXc0WGlrc3A2ZDZGOW0rOG1N.seq → ...Dc0ZDljYjAzNzMxNGIwOWU3MTRkN2E0YWM0Yw.seq
diff --git a/.../data/cache-test/samples/Mz/MzliZGEwMGFhOTA0NjUzM2FjNDZmYjQ0YjNhYTExOWVmMDc0YjYzNA.sample b/.../data/cache-test/samples/Mz/MzliZGEwMGFhOTA0NjUzM2FjNDZmYjQ0YjNhYTExOWVmMDc0YjYzNA.sample
diff --git a/.../data/cache-test/samples/Nm/NmJlODBjNjAyNDBiN2QwN2E2MTcwOWZlN2FiMmMwOTkzYmJhOWI4Ng.sample b/.../data/cache-test/samples/Nm/NmJlODBjNjAyNDBiN2QwN2E2MTcwOWZlN2FiMmMwOTkzYmJhOWI4Ng.sample
diff --git a/.../data/cache-test/samples/OW/OWIxYjk5OGY2NDhmNmUwNzUwMzExMzU5MjkzYmIzOTU5ZDY3MWFmOA.sample b/.../data/cache-test/samples/OW/OWIxYjk5OGY2NDhmNmUwNzUwMzExMzU5MjkzYmIzOTU5ZDY3MWFmOA.sample
diff --git a/.../data/cache-test/samples/YT/YTFkOTE2MmVkMWY5MDVmZjU5YWU5M2MzYzI4YmExMmFmNjU4MmQzNA.sample b/.../data/cache-test/samples/YT/YTFkOTE2MmVkMWY5MDVmZjU5YWU5M2MzYzI4YmExMmFmNjU4MmQzNA.sample
diff --git a/.../data/cache-test/samples/ZT/ZTA5ZmI3NzEzMzU5ZDk1ZGNjOGMzMDdjZTMxNjBkZWU0MzI3NTg2ZA.sample b/.../data/cache-test/samples/ZT/ZTA5ZmI3NzEzMzU5ZDk1ZGNjOGMzMDdjZTMxNjBkZWU0MzI3NTg2ZA.sample
diff --git a/...est/var/K3/K3lSQmp5QkVmNmQyTFMzUy94NkZ2bnNtczlrQFRHbXZUMnZLVFh4OC8rZFNORWRlZnh3VHJlWQ.var b/...est/var/K3/K3lSQmp5QkVmNmQyTFMzUy94NkZ2bnNtczlrQFRHbXZUMnZLVFh4OC8rZFNORWRlZnh3VHJlWQ.var