Set up API directory

_viash.yaml

@@ -18,7 +18,7 @@ links:
 
 # Step 4: Update the label, summary and description.
 # A unique, human-readable, short label. Used for creating summary tables and visualisations.
-label: Template
+label: Spatial Segmentation
 summary: A one sentence summary of purpose and methodology. Used for creating an overview tables.
 description: |
   Provide a clear and concise description of your task, detailing the specific problem it aims
@@ -48,6 +48,12 @@ references:
 info:
   image: The name of the image file to use for the component on the website.
   test_resources:
+    - type: s3
+      path: s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium_rep1/
+      dest: resources_test/common/2023_10x_mouse_brain_xenium_rep1/
+    - type: s3
+      path: s3://openproblems-data/resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/
+      dest: resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/
     - type: s3
       path: s3://openproblems-data/resources_test/task_spatial_segmentation/
       dest: resources_test/task_spatial_segmentation

scripts/create_test_resources/mouse_brain_combined.sh

@@ -16,12 +16,12 @@ fi
 # we can just copy them for now
 
 aws s3 sync --profile op \
-  s3://openproblems-data/resources_test/task_ist_preprocessing/mouse_brain_combined/raw_ist.zarr \
-  resources_test/task_spatial_segmentation/mouse_brain_combined/raw_ist.zarr
+  s3://openproblems-data/resources_test/common/2023_10x_mouse_brain_xenium_rep1/dataset.zarr \
+  resources_test/task_spatial_segmentation/mouse_brain_combined/common_ist.zarr
 
 aws s3 cp --profile op \
-  s3://openproblems-data/resources_test/task_ist_preprocessing/mouse_brain_combined/scrnaseq_reference.h5ad \
-  resources_test/task_spatial_segmentation/mouse_brain_combined/scrnaseq_reference.h5ad
+  s3://openproblems-data/resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2/dataset.h5ad \
+  resources_test/task_spatial_segmentation/mouse_brain_combined/common_scrnaseq.h5ad
 
 # ...additional preprocessing if needed ...
 

scripts/run_benchmark/run_test_local.sh

@@ -29,8 +29,8 @@ nextflow run . \
   -resume \
   -c common/nextflow_helpers/labels_ci.config \
   --id cxg_mouse_pancreas_atlas \
-  --input_train resources_test/task_template/cxg_mouse_pancreas_atlas/train.h5ad \
-  --input_test resources_test/task_template/cxg_mouse_pancreas_atlas/test.h5ad \
-  --input_solution resources_test/task_template/cxg_mouse_pancreas_atlas/solution.h5ad \
+  --input_train resources_test/task_spatial_segmentation/mouse_brain_combined/train.h5ad \
+  --input_test resources_test/task_spatial_segmentation/mouse_brain_combined/test.h5ad \
+  --input_solution resources_test/task_spatial_segmentation/mouse_brain_combined/solution.h5ad \
   --output_state state.yaml \
   --publish_dir "$publish_dir"

src/api/comp_control_method.yaml

@@ -12,16 +12,12 @@ info:
       the task, and also as a quality control for the metrics defined
       in the task.
 arguments:
-  - name: --input_train
-    __merge__: file_train.yaml
+  - name: --input
+    __merge__: file_spatial_dataset.yaml
     required: true
     direction: input
-  - name: --input_test
-    __merge__: file_test.yaml
-    required: true
-    direction: input
-  - name: "--input_solution"
-    __merge__: file_solution.yaml
+  - name: "--input_scrnaseq_reference"
+    __merge__: file_scrnaseq_reference.yaml
     direction: input
     required: true
   - name: --output
@@ -33,5 +29,5 @@ test_resources:
     path: /common/component_tests/run_and_check_output.py
   - type: python_script
     path: /common/component_tests/check_config.py
-  - path: /resources_test/task_template/cxg_mouse_pancreas_atlas
-    dest: resources_test/task_template/cxg_mouse_pancreas_atlas
+  - path: /resources_test/task_spatial_segmentation/mouse_brain_combined
+    dest: resources_test/task_spatial_segmentation/mouse_brain_combined

src/api/comp_data_processor.yaml

@@ -6,26 +6,32 @@ info:
     summary: A data processor.
     description: |
       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
-    direction: output
-    required: true
-  - name: "--output_solution"
-    __merge__: file_solution.yaml
-    direction: output
-    required: true
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: "--input_sp"
+        __merge__: file_common_ist.yaml
+        required: true
+        direction: input
+      - name: "--input_sc"
+        __merge__: file_common_scrnaseq.yaml
+        required: true
+        direction: input
+  - name: Outputs
+    arguments:
+      - name: "--output_spatial_dataset"
+        __merge__: file_spatial_dataset.yaml
+        direction: output
+        required: true
+      - name: "--output_scrnaseq_reference"
+        __merge__: file_scrnaseq_reference.yaml
+        direction: output
+        required: true
 test_resources:
-  - path: /resources_test/common/cxg_mouse_pancreas_atlas
-    dest: resources_test/common/cxg_mouse_pancreas_atlas
+  - path: /resources_test/common/2023_10x_mouse_brain_xenium_rep1
+    dest: resources_test/common/2023_10x_mouse_brain_xenium_rep1
+  - path: /resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2
+    dest: resources_test/common/2023_yao_mouse_brain_scrnaseq_10xv2
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
 

src/api/comp_method.yaml

@@ -7,14 +7,10 @@ info:
     description: |
       A method to predict the task effects.
 arguments:
-  - name: --input_train
-    __merge__: file_train.yaml
+  - name: --input
+    __merge__: file_spatial_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
@@ -24,5 +20,5 @@ test_resources:
     path: /common/component_tests/run_and_check_output.py
   - type: python_script
     path: /common/component_tests/check_config.py
-  - path: /resources_test/task_template/cxg_mouse_pancreas_atlas
-    dest: resources_test/task_template/cxg_mouse_pancreas_atlas
+  - path: /resources_test/task_spatial_segmentation/mouse_brain_combined
+    dest: resources_test/task_spatial_segmentation/mouse_brain_combined

src/api/comp_metric.yaml

@@ -7,14 +7,14 @@ info:
     description: |
       A metric for evaluating method predictions.
 arguments:
-  - name: "--input_solution"
-    __merge__: file_solution.yaml
-    direction: input
-    required: true
   - name: "--input_prediction"
     __merge__: file_prediction.yaml
     direction: input
     required: true
+  - name: "--input_scrnaseq_reference"
+    __merge__: file_scrnaseq_reference.yaml
+    direction: input
+    required: true
   - name: "--output"
     __merge__: file_score.yaml
     direction: output
@@ -24,5 +24,5 @@ test_resources:
     path: /common/component_tests/run_and_check_output.py
   - type: python_script
     path: /common/component_tests/check_config.py
-  - path: /resources_test/task_template/cxg_mouse_pancreas_atlas
-    dest: resources_test/task_template/cxg_mouse_pancreas_atlas
+  - path: /resources_test/task_spatial_segmentation/mouse_brain_combined
+    dest: resources_test/task_spatial_segmentation/mouse_brain_combined