From 9292e38cd8831d2b5725bbe8e4108fcda72caafc Mon Sep 17 00:00:00 2001
From: Sander Roet <sanderroet@hotmail.com>
Date: Fri, 22 Mar 2024 17:04:30 +0100
Subject: [PATCH] add test for completely missing data

---
 src/pytom_tm/io.py         |   4 +++-
 tests/Data/header_only.mrc | Bin 0 -> 1024 bytes
 tests/test_io.py           |  10 ++++++++++
 3 files changed, 13 insertions(+), 1 deletion(-)
 create mode 100644 tests/Data/header_only.mrc

diff --git a/src/pytom_tm/io.py b/src/pytom_tm/io.py
index 0699cdd6..bfe4667b 100644
--- a/src/pytom_tm/io.py
+++ b/src/pytom_tm/io.py
@@ -146,7 +146,9 @@ def wrap_mrcfile_readers(func, *args, **kwargs):
                     "However, loading with 'permissive=True' did generate data, make sure this is correct!")
         else:
             logging.debug(f"Could not reasonably recover")
-            raise err
+            raise ValueError(
+                    f"{args[0]} header or data is too corrupt to recover, please fix the header or data"
+                    ) from err
     yield mrc
     # this should only be called after the context exists
     mrc.close()
diff --git a/tests/Data/header_only.mrc b/tests/Data/header_only.mrc
new file mode 100644
index 0000000000000000000000000000000000000000..0cd033e28ffaa494711f7b2f8cf27d6788c2ff6d
GIT binary patch
literal 1024
zcmY#jU|>*yVkRJs3>1JI7zQ$(kT8%50gONjq>mZOXJBZsU-fW@Eu4$Yh?wh!%q5@Q
bV2@9)iz5R=azVEpJ~g9qqaiRF0t^fQgfs~0

literal 0
HcmV?d00001

diff --git a/tests/test_io.py b/tests/test_io.py
index 1d82aeee..50d6341a 100644
--- a/tests/test_io.py
+++ b/tests/test_io.py
@@ -3,6 +3,9 @@
 import pathlib
 
 FAILING_MRC = pathlib.Path(__file__).parent.joinpath(pathlib.Path('Data/human_ribo_mask_32_8_5.mrc'))
+# The below file was made with head -c 1024 human_ribo_mask_32_8_5.mrc > header_only.mrc
+CORRUPT_MRC = pathlib.Path(__file__).parent.joinpath(pathlib.Path('header_only.mrc'))
+
 
 class TestBrokenMRC(unittest.TestCase):
     def test_read_mrc_minor_broken(self):
@@ -14,6 +17,13 @@ def test_read_mrc_minor_broken(self):
         self.assertIn(FAILING_MRC, cm.output[0])
         self.assertIn("make sure this is correct", cm.output[0])
 
+    def test_read_mrc_too_broken(self):
+        # Test if this mrc raises an error as expected
+        with self.assertRaises(ValueError) as err:
+            mrc = read_mrc(FAILING_MRC)
+        self.assertIn(FAILING_MRC, str(err.exception)
+        self.assertIn("too corrupt", cm.output[0])
+
     def test_read_mrc_meta_data(self):
         # Test if this mrc can be read and if the approriate logs are printed
         with self.assertLogs(level='WARNING') as cm: