Revert "fix: isa-tab add-ped now only modifies values on process node…

…s of ped supplied samples #207"

This reverts commit 55f0f24.

cubi_tk/isa_tab/add_ped.py

@@ -178,9 +178,6 @@ def on_visit_material(self, material, node_path, study=None, assay=None):
 
     def on_visit_process(self, process, node_path, study=None, assay=None):
         super().on_visit_process(process, node_path, study, assay)
-        donor_name = node_path[0].name if _is_source(node_path[0]) else _sample_to_donor_name(node_path[0].name)
-        if donor_name not in self.donor_map:
-            return None
         proc_config_pairs = {
             "library construction ": {
                 "library type": "library_type",
@@ -481,8 +478,6 @@ def _append_assay_line_protocol(
     counter += 1
     return counter, curr
 
-def _sample_to_donor_name(sample_name):
-    return sample_name.rstrip("-N1")
 
 def _donor_to_sample_name(donor_name):
     return "%s-N1" % donor_name

tests/test_isa_tab_add_ped.py

@@ -100,27 +100,3 @@ def test_add_ped_just_update(tmpdir):
         str(scratch_dir),
         str(pathlib.Path(__file__).parent / "data" / "isa_tab" / "expected_output"),
     )
-
-def test_add_ped_sheet_subset_update(tmpdir):
-    """Test updating study and assay, but only a subset of the sheet."""
-    scratch_dir = tmpdir / "scratch"
-    path_ped = pathlib.Path(__file__).parent / "data" / "isa_tab" / "in_sheet_subset" / "input.ped"
-    shutil.copytree(
-        str(pathlib.Path(__file__).parent / "data" / "isa_tab" / "in_just_update"), str(scratch_dir)
-    )
-
-    # Update metadata
-    args = BASE_ARGS[:]
-    args[12] = "S00000XYZ"
-
-    argv = args + [str(scratch_dir / "i_Investigation.txt"), str(path_ped)]
-
-    # Actually exercise code and perform test.
-    res = main(argv)
-
-    assert not res
-
-    compare_input_output(
-        str(scratch_dir),
-        str(pathlib.Path(__file__).parent / "data" / "isa_tab" / "expected_output2"),
-    )