From 10b4840ca5408655bc5d80684b4be821de652ba4 Mon Sep 17 00:00:00 2001
From: Jayaram Kancherla <jayaram.kancherla@gmail.com>
Date: Mon, 20 May 2024 16:34:55 -0700
Subject: [PATCH] use alt funcs and object readers and writers

---
 setup.cfg                                     |  2 +-
 .../read_single_cell_experiment.py            | 22 ++++------
 .../save_single_cell_experiment.py            | 40 ++++++++-----------
 3 files changed, 24 insertions(+), 40 deletions(-)

diff --git a/setup.cfg b/setup.cfg
index 182de57..f1fdf7e 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -49,7 +49,7 @@ python_requires = >=3.8
 # For more information, check out https://semver.org/.
 install_requires =
     importlib-metadata; python_version<"3.8"
-    dolomite-base>=0.2.0
+    dolomite-base>=0.2.3
     dolomite-se>=0.1.1
     singlecellexperiment>=0.4.3,<0.5.0
 
diff --git a/src/dolomite_sce/read_single_cell_experiment.py b/src/dolomite_sce/read_single_cell_experiment.py
index e8ca41b..f6b648b 100644
--- a/src/dolomite_sce/read_single_cell_experiment.py
+++ b/src/dolomite_sce/read_single_cell_experiment.py
@@ -3,7 +3,6 @@
 
 import dolomite_base as dl
 from dolomite_base.read_object import read_object_registry
-from dolomite_se import read_common_se_props
 from singlecellexperiment import SingleCellExperiment
 
 read_object_registry["single_cell_experiment"] = (
@@ -37,29 +36,22 @@ def read_single_cell_experiment(
         with file-backed arrays in the assays.
     """
 
-    _row_data, _column_data, _assays = read_common_se_props(path)
+    metadata["type"] = "range_summarized_experiment"
+    rse = dl.alt_read_object(path, metadata=metadata, **kwargs)
 
     _main_expt_name = None
     if "main_experiment_name" in metadata["single_cell_experiment"]:
         _main_expt_name = metadata["single_cell_experiment"]["main_experiment_name"]
 
     sce = SingleCellExperiment(
-        assays=_assays,
-        row_data=_row_data,
-        column_data=_column_data,
+        assays=rse.get_assays(),
+        row_data=rse.get_row_data(),
+        column_data=rse.get_column_data(),
+        row_ranges=rse.get_row_ranges(),
+        metadata=rse.get_metadata(),
         main_experiment_name=_main_expt_name,
     )
 
-    _meta_path = os.path.join(path, "other_data")
-    if os.path.exists(_meta_path):
-        _meta = dl.alt_read_object(_meta_path, **kwargs)
-        sce = sce.set_metadata(_meta.as_dict())
-
-    _ranges_path = os.path.join(path, "row_ranges")
-    if os.path.exists(_ranges_path):
-        _ranges = dl.alt_read_object(_ranges_path, **kwargs)
-        sce = sce.set_row_ranges(_ranges)
-
     _rdim_path = os.path.join(path, "reduced_dimensions")
     if os.path.exists(_rdim_path):
         _rdims = {}
diff --git a/src/dolomite_sce/save_single_cell_experiment.py b/src/dolomite_sce/save_single_cell_experiment.py
index 4ce0f35..0ca0fd9 100644
--- a/src/dolomite_sce/save_single_cell_experiment.py
+++ b/src/dolomite_sce/save_single_cell_experiment.py
@@ -65,34 +65,23 @@ def save_single_cell_experiment(
     if alt_expts_args is None:
         alt_expts_args = {}
 
-    _se_meta = f"{list(x.shape)}"
-
-    _sce_meta = '"single_cell_experiment": { "version": "1.0" }'
-    if x.get_main_experiment_name() is not None:
-        _sce_meta = (
-            '"single_cell_experiment": { "version": "1.0", "main_experiment_name": "'
-            + str(x.get_main_experiment_name())
-            + '" }'
-        )
-
-    with open(os.path.join(path, "OBJECT"), "w", encoding="utf-8") as handle:
-        handle.write(
-            '{ "type": "single_cell_experiment", '
-            + _sce_meta
-            + ", "
-            + '"ranged_summarized_experiment": { "version": "1.0" },'
-            + '"summarized_experiment": {"version": "1.0", "dimensions": '
-            + _se_meta
-            + " } }"
-        )
-
     save_common_se_props(
         x, path, data_frame_args=data_frame_args, assay_args=assay_args
     )
 
+    # Modify OBJECT
+    _info = dl.read_object_file(path)
+    _info["single_cell_experiment"] = {"version": "1.0"}
+    if x.get_main_experiment_name() is not None:
+        _info["single_cell_experiment"]["main_experiment_name"] = str(
+            x.get_main_experiment_name()
+        )
+    dl.save_object_file(path, "single_cell_experiment", _info)
+
+    # save row ranges
     _ranges = x.get_row_ranges()
     if _ranges is not None:
-        dl.save_object(_ranges, path=os.path.join(path, "row_ranges"))
+        dl.alt_save_object(_ranges, path=os.path.join(path, "row_ranges"), **kwargs)
 
     # save rdims
     _rdim_names = x.get_reduced_dim_names()
@@ -106,7 +95,9 @@ def save_single_cell_experiment(
         for _aidx, _aname in enumerate(_rdim_names):
             _rdim_save_path = os.path.join(_rdim_path, str(_aidx))
             try:
-                dl.save_object(x.reduced_dim(_aname), path=_rdim_save_path, **rdim_args)
+                dl.alt_save_object(
+                    x.reduced_dim(_aname), path=_rdim_save_path, **rdim_args, **kwargs
+                )
             except Exception as ex:
                 raise RuntimeError(
                     "failed to stage reduced dimension '"
@@ -129,10 +120,11 @@ def save_single_cell_experiment(
         for _aidx, _aname in enumerate(_alt_names):
             _alt_save_path = os.path.join(_alt_path, str(_aidx))
             try:
-                dl.save_object(
+                dl.alt_save_object(
                     x.alternative_experiment(_aname),
                     path=_alt_save_path,
                     **alt_expts_args,
+                    **kwargs,
                 )
             except Exception as ex:
                 raise RuntimeError(