design API for spatial TI

Author: seohyonkim

src/api/comp_control_method.yaml

@@ -3,7 +3,7 @@ info:
   type: control_method
   type_info:
     label: Control Method
-    summary: Quality control methods for verifying the pipeline.
+    summary: Quality control methods for verifying the pipeline of the spatial TI task.
     description: |
       This folder contains control components for the task. 
       These components have the same interface as the regular methods
@@ -12,12 +12,8 @@ info:
       the task, and also as a quality control for the metrics defined
       in the task.
 arguments:
-  - name: --input_train
-    __merge__: file_train.yaml
-    required: true
-    direction: input
-  - name: --input_test
-    __merge__: file_test.yaml
+  - name: --dataset
+    __merge__: file_dataset.yaml
     required: true
     direction: input
   - name: "--input_solution"

src/api/comp_data_processor.yaml

@@ -3,20 +3,16 @@ info:
   type: data_processor
   type_info:
     label: Data processor
-    summary: A data processor.
-    description: |
+    summary: A data processor for the spatial TI task.
+    description: | # better description TODO
       A component for processing a Common Dataset into a task-specific dataset.
 arguments:
   - name: "--input"
     __merge__: file_common_dataset.yaml
     direction: input
     required: true
-  - name: "--output_train"
-    __merge__: file_train.yaml
-    direction: output
-    required: true
-  - name: "--output_test"
-    __merge__: file_test.yaml
+  - name: "--output"
+    __merge__: file_dataset.yaml
     direction: output
     required: true
   - name: "--output_solution"

src/api/comp_method.yaml

@@ -5,16 +5,12 @@ info:
     label: Method
     summary: A method.
     description: |
-      A method to predict the task effects.
+      A method for the spatial TI task.
 arguments:
-  - name: --input_train
-    __merge__: file_train.yaml
+  - name: --input
+    __merge__: file_dataset.yaml
     required: true
     direction: input
-  - name: "--input_test"
-    __merge__: file_test.yaml
-    direction: input
-    required: true
   - name: --output
     __merge__: file_prediction.yaml
     required: true

src/api/comp_metric.yaml

@@ -3,9 +3,9 @@ info:
   type: metric
   type_info:
     label: Metric
-    summary: A task template metric.
+    summary: A metric for spatial TI task.
     description: |
-      A metric for evaluating method predictions.
+      A metric for evaluating spatial TI method predictions.
 arguments:
   - name: "--input_solution"
     __merge__: file_solution.yaml

src/api/file_train.yaml src/api/file_dataset.yamlsrc/api/file_train.yaml renamed to src/api/file_dataset.yaml

@@ -1,8 +1,8 @@
 #TODO: Change to the required and/or optional fields of the anndata
 type: file
-example: "resources_test/task_template/cxg_mouse_pancreas_atlas/train.h5ad"
-label: "Training data"
-summary: "The training data in h5ad format"
+example: "resources_test/task_template/cxg_mouse_pancreas_atlas/train.h5ad" # maybe adjust this after syncing resources
+label: "Input data"
+summary: "The input data for the spatial TI task"
 info:
   format:
     type: h5ad