Add create_coordination_values helper util

hubmapconsortium · Aug 14, 2023 · ce8a25d · ce8a25d
1 parent 1a55416
commit ce8a25d
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Showing 3 changed files with 20 additions and 38 deletions.
diff --git 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
@@ -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
@@ -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