MRG: add more output information when sketches fail to load

src/lib.rs

@@ -450,33 +450,38 @@ fn load_sketches_above_threshold(
         .filter_map(|m| {
             let sigs = Signature::from_path(m);
 
-            let mut mm = None;
-            if let Ok(sigs) = sigs {
-                for sig in &sigs {
-                    if let Some(mh) = prepare_query(sig, template) {
-                        if let Ok(overlap) = mh.count_common(query, false) {
-                            if overlap >= threshold_hashes {
-                                let result = PrefetchResult {
-                                    name: sig.name(),
-                                    minhash: mh,
-                                    overlap,
-                                };
-                                mm = Some(result);
-                                break;
+            match sigs {
+                Ok(sigs) => {
+                    let mut mm = None;
+                    for sig in &sigs {
+                        if let Some(mh) = prepare_query(sig, template) {
+                            if let Ok(overlap) = mh.count_common(query, false) {
+                                if overlap >= threshold_hashes {
+                                    let result = PrefetchResult {
+                                        name: sig.name(),
+                                        minhash: mh,
+                                        overlap,
+                                    };
+                                    mm = Some(result);
+                                    break;
+                                }
                             }
+                        } else {
+                            eprintln!("WARNING: no compatible sketches in path '{}'",
+                                      m.display());
+                            let _i = skipped_paths.fetch_add(1, atomic::Ordering::SeqCst);
                         }
-                    } else {
-                        eprintln!("WARNING: no compatible sketches in path '{}'",
-                                  m.display());
-                        let _i = skipped_paths.fetch_add(1, atomic::Ordering::SeqCst);
                     }
+                    mm
                 }
-            } else {
-                let _ = failed_paths.fetch_add(1, atomic::Ordering::SeqCst);
-                eprintln!("WARNING: could not load sketches from path '{}'",
+                Err(err) => {
+                    eprintln!("Sketch loading error: {}", err);
+                    let _ = failed_paths.fetch_add(1, atomic::Ordering::SeqCst);
+                    eprintln!("WARNING: could not load sketches from path '{}'",
                           m.display());
+                    None
+                }
             }
-            mm
         })
         .collect();
 

src/python/tests/test_gather.py

@@ -199,6 +199,34 @@ def test_bad_against_2(runtmp, capfd):
     assert "WARNING: 1 signature paths failed to load. See error messages above." in captured.err
 
 
+def test_bad_against_3(runtmp, capfd):
+    # test bad 'against' file - in this case, one containing an empty file
+    query = get_test_data('SRR606249.sig.gz')
+    against_list = runtmp.output('against.txt')
+
+    sig2 = get_test_data('2.fa.sig.gz')
+    empty_file = runtmp.output('empty.sig')
+    with open(empty_file, 'wb') as fp:
+        pass
+    make_file_list(against_list, [sig2, empty_file])
+
+
+    g_output = runtmp.output('gather.csv')
+    p_output = runtmp.output('prefetch.csv')
+
+    runtmp.sourmash('scripts', 'fastgather', query, against_list,
+                    '-o', g_output, '--output-prefetch', p_output,
+                    '-s', '100000')
+
+    captured = capfd.readouterr()
+    print(captured.err)
+
+    assert "Sketch loading error: File is too short, less than five bytes" in captured.err
+    assert "WARNING: could not load sketches from path" in captured.err
+
+    assert "WARNING: 1 signature paths failed to load. See error messages above." in captured.err
+
+
 def test_against_multisigfile(runtmp):
     # test against a sigfile that contains multiple sketches
     query = get_test_data('SRR606249.sig.gz')