Merge pull request #14993 from jdavcs/dev_datatypes_contbl

Refactor, add type hints to get_chunk() in datatypes

test/unit/data/datatypes/test_connectivity_table.py

@@ -0,0 +1,49 @@
+import os
+
+import pytest
+
+from galaxy.datatypes.tabular import ConnectivityTable
+from galaxy.util import galaxy_directory
+
+
+@pytest.fixture
+def dataset():
+    class MockDataset:
+        file_name = os.path.join(galaxy_directory(), "test-data/1.ct")
+
+    return MockDataset()
+
+
+@pytest.fixture
+def make_trans():
+    class Stub:
+        pass
+
+    class StubTransaction:
+        def __init__(self, chunk_size):
+            self.app = Stub()
+            self.app.config = Stub()  # type: ignore[attr-defined]
+            self.app.config.display_chunk_size = chunk_size  # type: ignore[attr-defined]
+
+    return StubTransaction
+
+
+def test_get_chunk(dataset, make_trans):
+    dt = ConnectivityTable()
+    chunk_size = 1000
+    trans = make_trans(chunk_size)
+    chunk = dt.get_chunk(trans, dataset)
+    assert (
+        chunk
+        == '{"ck_data": "363\\ttmRNA\\n1\\tG\\t0\\t2\\t359\\t1\\n2\\tG\\t1\\t3\\t358\\t2\\n", "offset": 38, "data_line_offset": 0}'
+    )
+
+
+def test_get_chunk_with_offset(dataset, make_trans):
+    dt = ConnectivityTable()
+    chunk_size = 10
+    trans = make_trans(chunk_size)
+
+    # reads chunk_size chars from offset 5 (line 1) to the end of line 2
+    chunk = dt.get_chunk(trans, dataset, 5)
+    assert chunk == '{"ck_data": "mRNA\\n1\\tG\\t0\\t2\\t359\\t1", "offset": 24, "data_line_offset": 0}'