Add export and import as tar file

src/dgenies/lib/job_manager.py

@@ -101,7 +101,8 @@ class JobManager:
             with open(query_file) as q_f:
                 file_path = q_f.readline()
                 self.query = Fasta(
-                    name=os.path.splitext(os.path.basename(file_path.replace(".gz", "")).split("_", 1)[1])[0],
+                    name="target" if file_path.endswith(".idx") else
+                         os.path.splitext(os.path.basename(file_path.replace(".gz", "")).split("_", 1)[1])[0],
                     path=file_path,
                     type_f="local"
                 )
@@ -110,7 +111,8 @@ class JobManager:
             with open(target_file) as t_f:
                 file_path = t_f.readline()
                 self.target = Fasta(
-                    name=os.path.splitext(os.path.basename(file_path.replace(".gz", "")).split("_", 1)[1])[0],
+                    name="query" if file_path.endswith(".idx") else
+                         os.path.splitext(os.path.basename(file_path.replace(".gz", "")).split("_", 1)[1])[0],
                     path=file_path,
                     type_f="local"
                 )
@@ -501,7 +503,7 @@ class JobManager:
             save_file.write(finale_path)
         return True, False, finale_path, name
 
-    def __check_url(self, fasta: Fasta):
+    def __check_url(self, fasta: Fasta, formats: tuple):
         url = fasta.get_path()
         try:
             filename = self.__get_filename_from_url(url)
@@ -519,7 +521,7 @@ class JobManager:
                 self.set_status_standalone(status, error)
             return False
         if filename is not None:
-            allowed = Functions.allowed_file(filename)
+            allowed = Functions.allowed_file(filename, formats)
             if not allowed:
                 status = "fail"
                 error = "<p>File <b>%s</b> downloaded from <b>%s</b> is not a Fasta file!</p>" \
@@ -602,7 +604,7 @@ class JobManager:
                 if not getattr(validators, self.aln_format)(self.align.get_path()):
                     self.set_job_status("fail", "Alignment file is invalid. Please check your file.")
                     return False, True, None
-            else:
+            elif input_type != "backup":
                 if self.config.batch_system_type != "local" and file_size >= getattr(self.config,
                                                                                      "min_%s_size" % input_type):
                     should_be_local = False
@@ -694,7 +696,7 @@ class JobManager:
                                                                           max_upload_size_readable)
                     if not correct:
                         return False, error_set, True
-                elif self.__check_url(self.query):
+                elif self.__check_url(self.query, ("fasta",) if self.align is None else ("fasta", "idx")):
                     files_to_download.append([self.query, "query"])
                 else:
                     return False, True, True
@@ -705,7 +707,7 @@ class JobManager:
                                                                           max_upload_size_readable)
                     if not correct:
                         return False, error_set, True
-                elif self.__check_url(self.target):
+                elif self.__check_url(self.target, ("fasta",) if self.align is None else ("fasta", "idx")):
                     files_to_download.append([self.target, "target"])
                 else:
                     return False, True, True
@@ -714,7 +716,7 @@ class JobManager:
                     self.align.set_path(self.__getting_local_file(self.align, "align"))
                     correct, error_set, should_be_local = self.check_file("align", should_be_local,
                                                                           max_upload_size_readable)
-                elif self.__check_url(self.align):
+                elif self.__check_url(self.align, ("map",)):
                     files_to_download.append([self.align, "align"])
                 else:
                     return False, True, True
@@ -723,7 +725,7 @@ class JobManager:
                     self.backup.set_path(self.__getting_local_file(self.backup, "backup"))
                     correct, error_set, should_be_local = self.check_file("backup", should_be_local,
                                                                           max_upload_size_readable)
-                elif self.__check_url(self.backup):
+                elif self.__check_url(self.backup, ("backup",)):
                     files_to_download.append([self.backup, "backup"])
                 else:
                     return False, True, True
@@ -1188,7 +1190,7 @@ class JobManager:
                 print("Old job found without result dir existing: delete it from BDD!")
                 for j11 in j1:
                     j11.delete_instance()
-            if self.target is not None:
+            if self.target is not None or self.backup is not None:
                 job = Job.create(id_job=self.id_job, email=self.email, batch_type=self.config.batch_system_type,
                                  date_created=datetime.now(), tool=self.tool.name if self.tool is not None else None)
                 job.save()