From 441f50cd6ee3e8aab2be476dc89dac5e0a850834 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Thu, 29 Aug 2024 14:06:26 +0200
Subject: [PATCH] remove unused api

---
 src/api/file_spatialdata_processed.yaml | 96 -------------------------
 1 file changed, 96 deletions(-)
 delete mode 100644 src/api/file_spatialdata_processed.yaml

diff --git a/src/api/file_spatialdata_processed.yaml b/src/api/file_spatialdata_processed.yaml
deleted file mode 100644
index e5384bed..00000000
--- a/src/api/file_spatialdata_processed.yaml
+++ /dev/null
@@ -1,96 +0,0 @@
-type: file
-example: "resources_test/common/2023_10x_mouse_brain_xenium/dataset_preprocessed.zarr"
-label: "Preprocessed Dataset"
-summary: An unprocessed spatial imaging dataset stored as a zarr file.
-info:
-  format:
-    type: spatialdata_zarr
-    variables:
-      - name: replicate_id # rep1, rep2, rep3
-        type: string
-        description: The replicate identifier
-        required: true
-      - name: reference
-        type: str
-        description: Name of the reference dissociated dataset
-        required: true
-      - name: segm # cell, nucleus
-        type: string
-        description: Custom segmentation identifier
-        required: false
-      - name: patch
-        type: string
-        description: Expert segmentation image patch identifier
-        required: false
-    
-    images:
-      - type: DataTree[cyx]
-        dtype: int/float #TODO
-        name: "{rep}_image"
-        description: The raw image data
-        required: true
-      - type: DataTree[czyx]
-        dtype: int/float #TODO
-        name: "{rep}_image_3D"
-        description: The raw 3D image data
-        required: false
-      - type:
-        dtype:
-        name: "{rep}_he_image"
-        description: H&E image data
-        required: false 
-    labels:
-      - type: DataTree[yx]
-        dtype: int
-        name: "{rep}_{segm}"
-        description: Custom segmentation of the data
-        required: false
-      - type: DataTree[zyx]
-        dtype: int
-        name: "{rep}_{segm}_3D"
-        description: Custom segmentation of the 3D data
-        required: false
-      - type: DataTree[yx]
-        dtype: int
-        name: "{rep}_expert_segm_{patch}"
-        description: Expert segmentation of a patch of the data
-        required: false
-      - type: DataTree[zyx]
-        dtype: int
-        name: "{rep}_expert_segm_{patch}_3D"
-        description: Expert segmentation of a 3D patch of the data
-        required: false
-    points:
-      - type: DataFrame
-        dtype: str & float
-        name: "{rep}_transcripts"
-        description: Point cloud data of transcripts
-        required: true
-    shapes:
-      - type: GeoDataFrame
-        dtype: ???
-        name: "{rep}_{segm}_boundaries"
-        description: Cell polygons referring to "{rep}_{segm}"
-        required: false
-    tables:
-      - type: anndata
-        dtype: ???
-        name: "metadata"
-        description: Metadata of spatial dataset
-        required: true
-      - type: anndata
-        dtype: ???
-        name: "{reference}"
-        description: Map to define the reference cells to compare to for each rep
-        required: true
-      - type: anndata
-        dtype: ???
-        name: "{rep}_{segm}_table"
-        description: Count data referring to "{rep}_{segm}"
-        required: false
-    coordinate_systems:
-      - type: ???
-        dtype: ???
-        name: "{rep}_global"
-        description: Coordinate system of the replicate
-        required: true