Label file_test_mod2 as the solution

CHANGELOG.md

@@ -22,6 +22,8 @@
 
 * Point the `## VIASH START` blocks at files that exist. Several still referenced the openproblems-v2 monorepo layout or the pre-`normal/`-`swap/` resource layout, so running a script directly for debugging failed on the first read. Also added the missing `meta` to `knnr_r`'s block and replaced the borrowed `--id cxg_mouse_pancreas_atlas` in `run_test_local.sh` (PR #45).
 
+* `file_test_mod2`: Label this file "Solution" and say in the description that only the metrics and control methods receive it. It holds the ground truth, but read like just another input (PR #49).
+
 ## BUG FIXES
 
 * Fix the component paths, build paths and `rename_keys` separator in the helper scripts, which prevented `scripts/create_datasets/test_resources.sh` and both `run_test.sh` scripts from running at all (PR #22).

README.md

@@ -54,7 +54,7 @@ flowchart TB
   file_train_mod1("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-train-mod1'>Train mod1</a>")
   file_train_mod2("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-train-mod2'>Train mod2</a>")
   file_test_mod1("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-test-mod1'>Test mod1</a>")
-  file_test_mod2("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-test-mod2'>Test mod2</a>")
+  file_test_mod2("<a href='https://github.com/openproblems-bio/task_predict_modality#file-format-solution'>Solution</a>")
   comp_control_method[/"<a href='https://github.com/openproblems-bio/task_predict_modality#component-type-control-method'>Control method</a>"/]
   comp_method[/"<a href='https://github.com/openproblems-bio/task_predict_modality#component-type-method'>Method</a>"/]
   comp_method_predict[/"<a href='https://github.com/openproblems-bio/task_predict_modality#component-type-predict'>Predict</a>"/]
@@ -155,7 +155,7 @@ Arguments:
 | `--output_train_mod1` | `file` | (*Output*) The mod1 expression values of the train cells. |
 | `--output_train_mod2` | `file` | (*Output*) The mod2 expression values of the train cells. |
 | `--output_test_mod1` | `file` | (*Output*) The mod1 expression values of the test cells. |
-| `--output_test_mod2` | `file` | (*Output*) The mod2 expression values of the test cells. |
+| `--output_test_mod2` | `file` | (*Output*) The ground-truth mod2 expression values of the test cells. |
 
 </div>
 
@@ -293,13 +293,18 @@ Data structure:
 
 </div>
 
-## File format: Test mod2
+## File format: Solution
 
-The mod2 expression values of the test cells.
+The ground-truth mod2 expression values of the test cells.
 
 Example file:
 `resources_test/task_predict_modality/openproblems_neurips2021/bmmc_cite/swap/test_mod2.h5ad`
 
+Description:
+
+The ground truth against which predictions are scored. Only the metrics
+and the control methods receive this file; regular methods never see it.
+
 Format:
 
 <div class="small">
@@ -353,7 +358,7 @@ Arguments:
 | `--input_train_mod1` | `file` | The mod1 expression values of the train cells. |
 | `--input_train_mod2` | `file` | The mod2 expression values of the train cells. |
 | `--input_test_mod1` | `file` | The mod1 expression values of the test cells. |
-| `--input_test_mod2` | `file` | The mod2 expression values of the test cells. |
+| `--input_test_mod2` | `file` | The ground-truth mod2 expression values of the test cells. |
 | `--output` | `file` | (*Output*) A prediction of the mod2 expression values of the test cells. |
 
 </div>
@@ -421,7 +426,7 @@ Arguments:
 | Name | Type | Description |
 |:---|:---|:---|
 | `--input_prediction` | `file` | A prediction of the mod2 expression values of the test cells. |
-| `--input_test_mod2` | `file` | The mod2 expression values of the test cells. |
+| `--input_test_mod2` | `file` | The ground-truth mod2 expression values of the test cells. |
 | `--output` | `file` | (*Output*) Metric score file. |
 
 </div>

src/api/file_test_mod2.yaml

@@ -1,7 +1,10 @@
 type: file
 example: "resources_test/task_predict_modality/openproblems_neurips2021/bmmc_cite/swap/test_mod2.h5ad"
-label: "Test mod2"
-summary: "The mod2 expression values of the test cells."
+label: "Solution"
+summary: "The ground-truth mod2 expression values of the test cells."
+description: |
+  The ground truth against which predictions are scored. Only the metrics and the
+  control methods receive this file; regular methods never see it.
 info:
   format:
     type: h5ad