catch all exceptions

Add outer most broad exception chatchin to stop crash tracebac propagation
cas-bioinf · Jul 24, 2019 · 38d5143 · 38d5143
1 parent 74f215b
commit 38d5143
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Showing 2 changed files with 36 additions and 21 deletions.
diff --git a/rna_blast_analyze/BA.py b/rna_blast_analyze/BA.py
@@ -385,27 +385,42 @@ def check_if_rfam_needed(inargs):
 
 
 def main():
-
-    # outer envelope for the script
-    # ========= perform argument parsing =========
-
-    if download_name in sys.argv and not ('-q' in sys.argv or '--blast_query' in sys.argv):
-        # run download rfam here
-        # do not run, if given with normal run request
-        from rna_blast_analyze.BR_core.config import tools_paths, CONFIG
-        from rna_blast_analyze.BR_core import cmalign
-        if cfg_name in sys.argv:
-            CONFIG.override(tools_paths(config_file=sys.argv[sys.argv.index(cfg_name) + 1]))
-        cmalign.download_cmmodels_file()
-        # rfam database downloaded
+    try:
+        # outer envelope for the script
+        # ========= perform argument parsing =========
+
+        if download_name in sys.argv and not ('-q' in sys.argv or '--blast_query' in sys.argv):
+            # run download rfam here
+            # do not run, if given with normal run request
+            from rna_blast_analyze.BR_core.config import tools_paths, CONFIG
+            from rna_blast_analyze.BR_core import cmalign
+            if cfg_name in sys.argv:
+                CONFIG.override(tools_paths(config_file=sys.argv[sys.argv.index(cfg_name) + 1]))
+            cmalign.download_cmmodels_file()
+            # rfam database downloaded
+            sys.exit(0)
+
+        args = f_parser()
+
+        _ = lunch_with_args(args)
+
+        # if we reach here, exit with 0
         sys.exit(0)
+    except Exception as e:
+        print('Something went wrong.')
+        try:
+            import traceback
+            print(
+                'The error traceback is written to rboAnalyzer.log . '
+                'Please send it along with the query file and BLAST input to the developers.'
+            )
 
-    args = f_parser()
-
-    _ = lunch_with_args(args)
-
-    # if we reach here, exit with 0
-    sys.exit(0)
+            with open('rboAnalyzer.log', 'w') as fd:
+                fd.write(str(e))
+                fd.write(traceback.format_exc())
+        except:
+            pass
+        sys.exit(1)
 
 
 def lunch_with_args(args):

diff --git a/test_func/test_infer_homology.py b/test_func/test_infer_homology.py
@@ -20,6 +20,8 @@ def clean_object(self):
         self.data.query.annotations = dict()
         for h in self.data.hits:
             h.extension.annotations = dict()
+        self.data.args.blast_query = os.path.join(fwd, test_dir, 'RF00001.fasta')
+        self.data.cm_file = os.path.join(fwd, test_dir, 'RF00001.cm')
 
     def test_simple(self):
         self.clean_object()
@@ -29,15 +31,13 @@ def test_simple(self):
     def test_rfam(self):
         self.clean_object()
         self.data.args.use_rfam = True
-        self.data.args.blast_query = os.path.join(fwd, test_dir, 'RF00001.fasta')
         cm_file, _ = infer_homology.find_and_extract_cm_model(self.data.args, self.data)
         pred, sel, cmfile = infer_homology.infer_homology(self.data, self.data.args, cm_file)
         os.remove(cmfile)
 
     def test_with_cm_file(self):
         self.clean_object()
         self.data.args.use_rfam = False
-        self.data.cm_file = os.path.join(fwd, test_dir, 'RF00001.cm')
         cm_file, _ = infer_homology.find_and_extract_cm_model(self.data.args, self.data)
         pred, sel, _ = infer_homology.infer_homology(self.data, self.data.args, cm_file)