From 67dfecd863fba6163edbd61cf4c3e8aa5dbbce7b Mon Sep 17 00:00:00 2001
From: Jan Eglinger <jan.eglinger@fmi.ch>
Date: Mon, 16 Oct 2023 14:54:37 +0200
Subject: [PATCH] Add simple test for mobie functionality

Also remove 'compute_aggregate_table_values' as we do not use it.
---
 src/faim_hcs/mobie.py |  44 -----------------
 tests/test_mobie.py   | 109 ++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 109 insertions(+), 44 deletions(-)
 create mode 100644 tests/test_mobie.py

diff --git a/src/faim_hcs/mobie.py b/src/faim_hcs/mobie.py
index 9ab1ec82..3cbe3130 100644
--- a/src/faim_hcs/mobie.py
+++ b/src/faim_hcs/mobie.py
@@ -226,50 +226,6 @@ def add_labels_view(
     wells_table.to_csv(wells_table_path, sep="\t", index=False)
 
 
-def compute_aggregate_table_values(
-    dataset_folder,
-    table_suffix,
-    aggregation_dict=None,
-):
-    """Aggregate all tables with given suffix, and write summarized values to wells table.
-
-    :param dataset_folder: location of the MoBIE dataset to be modified
-    :param table_suffix: common suffix of all tables to be included (e.g. 'my_seg' for 'A01_my_seg' etc.)
-    :param aggregation_dict: mapping of column names to (one or multiple) aggregation methods
-    """
-    if aggregation_dict is None:
-        aggregation_dict = {"area": ["mean", "min", "max"]}
-
-    # read wells table and get list of wells (region_id)
-    wells_table_path = join(dataset_folder, "tables", "wells", "default.tsv")
-    wells_table = read_table(wells_table_path)
-    wells = wells_table["region_id"]
-
-    # read and concatenate each table from segmentations
-    tables = []
-    for well in wells:
-        well_table = read_table(
-            join(dataset_folder, "tables", f"{well}_{table_suffix}", "default.tsv")
-        )
-        well_table["region_id"] = well
-        tables.append(well_table)
-    joined_table = pd.concat(tables)
-
-    # aggregate given columns with given functions
-    summary = joined_table.groupby("region_id").aggregate(aggregation_dict)
-
-    # flatten table index
-    summary.columns = ["_".join(headers) for headers in summary.columns.to_flat_index()]
-    # add suffix to column names
-    summary.columns = [f"{header}_{table_suffix}" for header in summary.columns]
-    print(summary)
-
-    # join with original wells table
-    wells_table.join(summary, on="region_id").to_csv(
-        wells_table_path, sep="\t", index=False
-    )
-
-
 def _add_channel_plate_overviews(
     dataset_folder, plate_hists, plate_colors, sources, view_name
 ):
diff --git a/tests/test_mobie.py b/tests/test_mobie.py
new file mode 100644
index 00000000..7a21964e
--- /dev/null
+++ b/tests/test_mobie.py
@@ -0,0 +1,109 @@
+import json
+from pathlib import Path
+
+import pytest
+from mobie.metadata.dataset_metadata import (
+    create_dataset_metadata,
+    create_dataset_structure,
+)
+from mobie.metadata.project_metadata import add_dataset, create_project_metadata
+from mobie.validation import validate_project
+
+from faim_hcs.io.MolecularDevicesImageXpress import parse_single_plane_multi_fields
+from faim_hcs.MetaSeriesUtils import get_well_image_CYX
+from faim_hcs.mobie import add_wells_to_project
+from faim_hcs.Zarr import build_zarr_scaffold, write_cyx_image_to_well
+
+ROOT_DIR = Path(__file__).parent.parent
+
+
+@pytest.fixture
+def files():
+    return parse_single_plane_multi_fields(ROOT_DIR / "resources" / "Projection-Mix")
+
+
+@pytest.fixture
+def zarr_group(files, zarr_dir):
+    plate = build_zarr_scaffold(
+        root_dir=zarr_dir,
+        files=files,
+        name="",
+        layout=384,
+        order_name="",
+        barcode="",
+    )
+    for well in ["E07", "E08"]:
+        img, hists, ch_metadata, metadata, roi_tables = get_well_image_CYX(
+            well_files=files[files["well"] == well],
+            channels=["w1"],
+        )
+        field = plate[well[0]][str(int(well[1:]))][0]
+        write_cyx_image_to_well(img, hists, ch_metadata, metadata, field)
+    return plate
+
+
+@pytest.fixture
+def mobie_project_folder(tmp_path_factory):
+    return tmp_path_factory.mktemp("mobie")
+
+
+@pytest.fixture
+def zarr_dir(tmp_path_factory):
+    return tmp_path_factory.mktemp("zarr")
+
+
+def test_add_wells_to_project(zarr_group, mobie_project_folder):
+    # setup OME-ZARR folder
+    # setup MoBIE project
+    dataset_name = "mobie_test_dataset"
+    create_project_metadata(
+        root=mobie_project_folder,
+        #    description="MoBIE test project",
+    )
+    create_dataset_structure(
+        root=mobie_project_folder,
+        dataset_name=dataset_name,
+        file_formats=["ome.zarr"],
+    )
+    create_dataset_metadata(
+        dataset_folder=(mobie_project_folder / dataset_name),
+        description="MoBIE test dataset",
+        is2d=True,
+    )
+    add_dataset(
+        root=mobie_project_folder,
+        dataset_name=dataset_name,
+        is_default=True,
+    )
+
+    # add_wells_to_project
+    add_wells_to_project(
+        plate=zarr_group,
+        dataset_folder=(mobie_project_folder / dataset_name),
+        well_group="0",
+        view_name="default",
+    )
+
+    # assert
+    validate_project(
+        root=mobie_project_folder,
+    )
+
+    dataset_json_path: Path = mobie_project_folder / dataset_name / "dataset.json"
+
+    assert dataset_json_path.exists()
+
+    with open(dataset_json_path) as f:
+        json_data = json.load(f)
+    assert "views" in json_data
+    assert "sourceDisplays" in json_data["views"]["default"]
+    assert "sourceTransforms" in json_data["views"]["default"]
+
+    table_path: Path = (
+        mobie_project_folder / dataset_name / "tables" / "wells" / "default.tsv"
+    )
+    assert table_path.exists()
+
+
+def test_add_labels_view():
+    pass