Add validator for index files, Implements #130

src/dgenies/lib/job_manager.py

@@ -627,6 +627,12 @@ class JobManager:
                     self.set_job_status("fail", "Alignment file is invalid. Please check your file.")
                     return False, True, None
             elif input_type != "backup":
+                if my_input.get_path().endswith(".idx"):
+                    if not validators.idx(my_input.get_path()):
+                        self.set_job_status("fail",
+                                            "%s index file is invalid. Please check your file." %
+                                            input_type.capitalize())
+                        return False, True, None
                 if self.config.batch_system_type != "local" and file_size >= getattr(self.config,
                                                                                      "min_%s_size" % input_type):
                     should_be_local = False
@@ -1125,15 +1131,17 @@ class JobManager:
                 shutil.move(self.paf, self.paf_raw)
                 if not validators.paf(self.paf_raw):
                     return False
+                target_path = os.path.join(self.output_dir, "target.idx")
+                query_path = os.path.join(self.output_dir, "query.idx")
+                if not validators.idx(target_path) or not validators.idx(query_path):
+                    return False
                 self.align = Fasta(name="map", path=self.paf_raw, type_f="local")
                 self.aln_format = "paf"
                 with open(os.path.join(self.output_dir, ".align"), "w") as aln:
                     aln.write(self.paf_raw)
-                target_path = os.path.join(self.output_dir, "target.idx")
                 self.target = Fasta(name="target", path=target_path, type_f="local")
                 with open(os.path.join(self.output_dir, ".target"), "w") as trgt:
                     trgt.write(target_path)
-                query_path = os.path.join(self.output_dir, "query.idx")
                 self.query = Fasta(name="query", path=query_path, type_f="local")
                 with open(os.path.join(self.output_dir, ".query"), "w") as qr:
                     qr.write(query_path)
@@ -1185,7 +1193,7 @@ class JobManager:
                 self._after_start(success, error_set)
 
         except Exception:
-            print(traceback.print_exc())
+            traceback.print_exc()
             error = "<p>An unexpected error has occurred. Please contact the support to report the bug.</p>"
             if MODE == "webserver":
                 with Job.connect():

src/dgenies/lib/validators.py

@@ -56,4 +56,29 @@ def maf(in_file):
     except:
         return False
     else:
-        return True
\ No newline at end of file
+        return True
+
+
+def idx(in_file):
+    try:
+        with open(in_file, "r") as inf:
+            first_line = inf.readline()
+            if "\t" in first_line:
+                return False
+            must_be_last = False
+            for line in inf:
+                if must_be_last:
+                    return False
+                line = line.rstrip()
+                if line == "":
+                    must_be_last = True
+                else:
+                    cols = line.split("\t")
+                    if len(cols) != 2:
+                        return False
+                    if not cols[1].isdigit():
+                        return False
+    except:
+        return False
+    else:
+        return True

src/dgenies/views.py

@@ -391,7 +391,6 @@ def install():
         latest = json.loads(call.content.decode("utf-8"))
         if "tag_name" in latest:
             latest = latest["tag_name"][1:]
-    print(latest)
 
     with open(os.path.join(app_folder, "md", "INSTALL.md"), "r", encoding='utf-8') as install_instr:
         content = install_instr.read()