diff --git a/CHANGELOG.md b/CHANGELOG.md index 1bc18c9..ed6f811 100644 --- a/CHANGELOG.md +++ b/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). diff --git a/README.md b/README.md index 20227a4..223c017 100644 --- a/README.md +++ b/README.md @@ -54,7 +54,7 @@ flowchart TB file_train_mod1("Train mod1") file_train_mod2("Train mod2") file_test_mod1("Test mod1") - file_test_mod2("Test mod2") + file_test_mod2("Solution") comp_control_method[/"Control method"/] comp_method[/"Method"/] comp_method_predict[/"Predict"/] @@ -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. | @@ -293,13 +293,18 @@ Data structure: -## 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:
@@ -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. |
@@ -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. | diff --git a/src/api/file_test_mod2.yaml b/src/api/file_test_mod2.yaml index c41889c..dc6417d 100644 --- a/src/api/file_test_mod2.yaml +++ b/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