add get method

cubi_tk/irods_common.py

@@ -220,3 +220,33 @@ def chksum(self):
                     logger.error("Problem during iRODS checksumming.")
                     logger.error(self.get_irods_error(e))
 
+    def get(self):
+        """Download files from SODAR."""
+        self.__jobs = [
+            attrs.evolve(job, bytes=self.session.data_objects.get(job.path_remote).size)
+            for job in self.__jobs
+        ]
+        self.__total_bytes = sum([job.bytes for job in self.__jobs])
+        # Double tqdm for currently transferred file info
+        # TODO: add more parenthesis after python 3.10
+        with tqdm(
+            total=self.__total_bytes,
+            unit="B",
+            unit_scale=True,
+            unit_divisor=1024,
+            position=1,
+        ) as t, tqdm(total=0, position=0, bar_format="{desc}", leave=False) as file_log:
+            for n, job in enumerate(self.__jobs):
+                file_log.set_description_str(
+                    f"File [{n + 1}/{len(self.__jobs)}]: {Path(job.path_local).name}"
+                )
+                try:
+                    self.session.data_objects.get(job.path_remote, job.path_local)
+                    t.update(job.bytes)
+                except FileNotFoundError:  # pragma: no cover
+                    raise
+                except Exception as e:  # pragma: no cover
+                    logger.error(f"Problem during transfer of {job.path_remote}")
+                    logger.error(self.get_irods_error(e))
+                    sys.exit(1)
+            t.clear()

tests/test_irods_common.py

@@ -12,6 +12,7 @@
 def test_transfer_job_bytes(fs):
     fs.create_file("test_file", st_size=123)
     assert TransferJob("test_file", "remote/path").bytes == 123
+    assert TransferJob("no_file.no", "remote/path").bytes == -1
 
 
 @patch("cubi_tk.irods_common.iRODSSession")
@@ -90,7 +91,9 @@ def test_get_irods_sessions(mocksession):
 def jobs():
     return (
         TransferJob(path_local="myfile.csv", path_remote="dest_dir/myfile.csv", bytes=123),
-        TransferJob(path_local="folder/file.csv", path_remote="dest_dir/folder/file.csv", bytes=1024),
+        TransferJob(
+            path_local="folder/file.csv", path_remote="dest_dir/folder/file.csv", bytes=1024
+        ),
     )
 
 
@@ -151,3 +154,16 @@ def test_irods_transfer_chksum(itransfer):
         assert mock_data_object.chksum.call_count == len(itransfer.destinations)
         for path in itransfer.destinations:
             mockget.assert_any_call(path)
+
+
+def test_irods_transfer_get(itransfer, jobs, fs):
+    with patch.object(itransfer.session.data_objects, "get") as mockget:
+        mockget.return_value.size = 111
+        itransfer.get()
+
+        for job in jobs:
+            # size check
+            mockget.assert_any_call(job.path_remote)
+            # download
+            mockget.assert_any_call(job.path_remote, job.path_local)
+        assert itransfer.size == 222