From 6407cbd6b63a7c45c9e8a79c81aba5b82f4bd868 Mon Sep 17 00:00:00 2001
From: Lena Trnovec <115463806+lenatr99@users.noreply.github.com>
Date: Wed, 29 May 2024 14:20:29 +0200
Subject: [PATCH] [FIX] LoadData - Bugs with gene and cell annotations (#403)

* Load Data bugfix

* Add Spatial Autocorrelation Scorer to documentation json, index.rst
---
 doc/index.rst                                 |  1 +
 doc/widgets.json                              |  7 ++++
 .../single_cell/widgets/load_data.py          | 32 +++++++++++++------
 .../single_cell/widgets/owloaddata.py         |  2 ++
 4 files changed, 33 insertions(+), 9 deletions(-)

diff --git a/doc/index.rst b/doc/index.rst
index 300acaa4..df62a863 100644
--- a/doc/index.rst
+++ b/doc/index.rst
@@ -16,3 +16,4 @@ Widgets
    widgets/score_genes
    widgets/score_cells
    widgets/dot_matrix
+   widgets/spatial_autocorrelation
diff --git a/doc/widgets.json b/doc/widgets.json
index 83731152..1869815e 100644
--- a/doc/widgets.json
+++ b/doc/widgets.json
@@ -75,6 +75,13 @@
     "icon": "../orangecontrib/single_cell/widgets/icons/DotMatrix.svg",
     "background": "light-blue",
     "keywords": []
+   },
+   {
+    "text": "Spatial Autocorrelation Scorer",
+    "doc": "widgets/spatial_autocorrelation.md",
+    "icon": "../orangecontrib/single_cell/widgets/icons/SpatialAutocorrelation.svg",
+    "background": "light-blue",
+    "keywords": []
    }
   ]
  ]
diff --git a/orangecontrib/single_cell/widgets/load_data.py b/orangecontrib/single_cell/widgets/load_data.py
index 60183822..80a642d2 100644
--- a/orangecontrib/single_cell/widgets/load_data.py
+++ b/orangecontrib/single_cell/widgets/load_data.py
@@ -488,12 +488,18 @@ def leading_cols(self, value):
 
     def _set_annotation_files(self):
         dir_name, _ = os.path.split(self._file_name)
-        genes_path = os.path.join(dir_name, "genes.tsv")
-        if os.path.isfile(genes_path):
-            self.col_annotation_file = RecentPath.create(genes_path, [])
-        barcodes_path = os.path.join(dir_name, "barcodes.tsv")
-        if os.path.isfile(barcodes_path):
-            self.row_annotation_file = RecentPath.create(barcodes_path, [])
+        genes_paths = ['genes.tsv', 'features.tsv', 'genes.tsv.gz', 'features.tsv.gz']
+        for genes_path in genes_paths:
+            genes_path = os.path.join(dir_name, genes_path)
+            if os.path.isfile(genes_path):
+                self.col_annotation_file = RecentPath.create(genes_path, [])
+                break
+        barcodes_paths = ['barcodes.tsv', 'barcodes.tsv.gz']
+        for barcodes_path in barcodes_paths:
+            barcodes_path = os.path.join(dir_name, barcodes_path)
+            if os.path.isfile(barcodes_path):
+                self.row_annotation_file = RecentPath.create(barcodes_path, [])
+                break
 
     def _set_enable_annotations(self):
         # 10x gene-barcode matrix
@@ -756,13 +762,21 @@ def key(var):
                             metas=sorted(metas, key=key))
             concat_data_t = concat_data.transform(domain)
             data_t = data.transform(domain)
-            source_var.values + (source_name, )
+
+            new_values = source_var.values + (source_name,)
+            new_source_var = DiscreteVariable(source_var.name, values=new_values)
+            new_metas = tuple(var if var.name != source_var.name else new_source_var for var in domain.metas)
+            new_domain = Domain(domain.attributes, metas=new_metas)
+            concat_data_t = concat_data_t.transform(new_domain)
+            data_t = data_t.transform(new_domain)
+            source_var_index = new_source_var.values.index(source_name)
             # metas can be unlocked, source_var added to metas by append_source_name
             with data_t.unlocked(data_t.metas):
-                data_t[:, source_var] = np.full(
-                    (len(data), 1), len(source_var.values) - 1, dtype=object
+                data_t[:, new_source_var] = np.full(
+                    (len(data_t), 1), source_var_index, dtype=object
                 )
             concat_data = Table.concatenate((concat_data_t, data_t), axis=0)
+            source_var = new_source_var # Update source_var for the next iteration
         return concat_data
 
     @staticmethod
diff --git a/orangecontrib/single_cell/widgets/owloaddata.py b/orangecontrib/single_cell/widgets/owloaddata.py
index db82f205..ab38d6a3 100644
--- a/orangecontrib/single_cell/widgets/owloaddata.py
+++ b/orangecontrib/single_cell/widgets/owloaddata.py
@@ -613,6 +613,7 @@ def browse_row_annotations(self):
             pathitem = RecentPath.create(filename, [])
             index = insert_recent_path(m, pathitem)
             self.row_annotations_combo.setCurrentIndex(index)
+            self._row_annotations_combo_changed()
             self._invalidate()
 
     @Slot()
@@ -632,6 +633,7 @@ def browse_col_annotations(self):
             pathitem = RecentPath.create(filename, [])
             index = insert_recent_path(m, pathitem)
             self.col_annotations_combo.setCurrentIndex(index)
+            self._col_annotations_combo_changed()
             self._invalidate()
 
     def _invalidate(self):