From ce8a25d1ac5103e7b749e369035184d304dda40a Mon Sep 17 00:00:00 2001
From: Nikolay Akhmetov <nick.akhmetov@gmail.com>
Date: Mon, 14 Aug 2023 11:41:55 -0400
Subject: [PATCH] Add `create_coordination_values` helper util

---
 .../builders/scatterplot_builders.py          | 36 +++++--------------
 .../builders/sprm_builders.py                 | 15 +++-----
 src/portal_visualization/utils.py             |  7 ++++
 3 files changed, 20 insertions(+), 38 deletions(-)

diff --git a/src/portal_visualization/builders/scatterplot_builders.py b/src/portal_visualization/builders/scatterplot_builders.py
index 304f15d..8b6d981 100644
--- a/src/portal_visualization/builders/scatterplot_builders.py
+++ b/src/portal_visualization/builders/scatterplot_builders.py
@@ -5,7 +5,7 @@
 )
 
 
-from ..utils import get_conf_cells
+from ..utils import create_coordination_values, get_conf_cells
 from ..paths import SCRNA_SEQ_DIR, SCATAC_SEQ_DIR
 from .base_builders import ViewConfBuilder
 
@@ -54,31 +54,22 @@ def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
             {
                 "rel_path": f"{SCRNA_SEQ_DIR}.cells.json",
                 "file_type": ft.OBS_SEGMENTATIONS_CELLS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                },
+                "coordination_values": create_coordination_values(),
             },
             {
                 "rel_path": f"{SCRNA_SEQ_DIR}.cells.json",
                 "file_type": ft.OBS_LOCATIONS_CELLS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                },
+                "coordination_values": create_coordination_values()
             },
             {
                 "rel_path": f"{SCRNA_SEQ_DIR}.cells.json",
                 "file_type": ft.OBS_EMBEDDING_CELLS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                    "embeddingType": "UMAP",
-                },
+                "coordination_values": create_coordination_values(embeddingType="UMAP")
             },
             {
                 "rel_path": f"{SCRNA_SEQ_DIR}.cell-sets.json",
                 "file_type": ft.OBS_SETS_CELL_SETS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                },
+                "coordination_values": create_coordination_values()
             },
         ]
 
@@ -98,33 +89,24 @@ def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
                 "rel_path": SCATAC_SEQ_DIR
                 + "/umap_coords_clusters.cells.json",
                 "file_type": ft.OBS_SEGMENTATIONS_CELLS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                },
+                "coordination_values": create_coordination_values()
             },
             {
                 "rel_path": SCATAC_SEQ_DIR
                 + "/umap_coords_clusters.cells.json",
                 "file_type": ft.OBS_LOCATIONS_CELLS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                },
+                "coordination_values": create_coordination_values()
             },
             {
                 "rel_path": SCATAC_SEQ_DIR
                 + "/umap_coords_clusters.cells.json",
                 "file_type": ft.OBS_EMBEDDING_CELLS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                    "embeddingType": "UMAP",
-                },
+                "coordination_values": create_coordination_values(embeddingType="UMAP")
             },
             {
                 "rel_path": SCATAC_SEQ_DIR
                 + "/umap_coords_clusters.cell-sets.json",
                 "file_type": ft.OBS_SETS_CELL_SETS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                },
+                "coordination_values": create_coordination_values()
             },
         ]
diff --git a/src/portal_visualization/builders/sprm_builders.py b/src/portal_visualization/builders/sprm_builders.py
index e8cd67f..e7df177 100644
--- a/src/portal_visualization/builders/sprm_builders.py
+++ b/src/portal_visualization/builders/sprm_builders.py
@@ -12,7 +12,7 @@
 )
 
 from .base_builders import ViewConfBuilder
-from ..utils import get_matches, get_conf_cells
+from ..utils import create_coordination_values, get_matches, get_conf_cells
 from ..paths import (
     SPRM_JSON_DIR, STITCHED_REGEX, CODEX_TILE_DIR,
     TILE_REGEX, STITCHED_IMAGE_DIR, SPRM_PYRAMID_SUBDIR, IMAGE_PYRAMID_DIR
@@ -93,25 +93,18 @@ def __init__(self, entity, groups_token, assets_endpoint, **kwargs):
             {
                 "rel_path": f"{SPRM_JSON_DIR}/" + f"{self._base_name}.cells.json",
                 "file_type": ft.CELLS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                },
+                "coordination_values": create_coordination_values()
             },
             {
                 "rel_path": f"{SPRM_JSON_DIR}/" + f"{self._base_name}.cell-sets.json",
                 "file_type": ft.CELL_SETS_JSON,
-                "coordination_values": {
-                    "obsType": "cell",
-                },
+                "coordination_values": create_coordination_values()
 
             },
             {
                 "rel_path": f"{SPRM_JSON_DIR}/" + f"{self._base_name}.clusters.json",
                 "file_type": "clusters.json",
-                "coordination_values": {
-                    "obsType": "cell",
-                },
-
+                "coordination_values": create_coordination_values()
             },
         ]
 
diff --git a/src/portal_visualization/utils.py b/src/portal_visualization/utils.py
index c09fb97..a8261e9 100644
--- a/src/portal_visualization/utils.py
+++ b/src/portal_visualization/utils.py
@@ -16,6 +16,13 @@ def get_matches(files, regex):
     )
 
 
+def create_coordination_values(obs_type='cell', **kwargs):
+    return {
+        'obsType': obs_type,
+        **kwargs
+    }
+
+
 def _get_path_name(file):
     return Path(file).name