From ecc35df0992872103a6cdf17141877e459fefa54 Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Tue, 17 Sep 2024 22:47:30 +0200
Subject: [PATCH] fix api

---
 README.md                        | 16 +++++++++-------
 src/api/comp_control_method.yaml |  6 +++++-
 src/api/comp_method.yaml         |  2 +-
 src/api/comp_metric.yaml         |  9 ++++-----
 4 files changed, 19 insertions(+), 14 deletions(-)

diff --git a/README.md b/README.md
index 5ada19a..9cc10c9 100644
--- a/README.md
+++ b/README.md
@@ -64,7 +64,7 @@ flowchart LR
   file_solution("Solution")
   comp_control_method[/"Control method"/]
   comp_method[/"Method"/]
-  comp_metric[/"Metric (embedding)"/]
+  comp_metric[/"Metric"/]
   file_integrated("Integrated Dataset")
   file_score("Score")
   file_common_dataset---comp_process_dataset
@@ -72,6 +72,7 @@ flowchart LR
   comp_process_dataset-->file_solution
   file_dataset---comp_control_method
   file_dataset---comp_method
+  file_solution---comp_control_method
   file_solution---comp_metric
   comp_control_method-->file_integrated
   comp_method-->file_integrated
@@ -249,10 +250,11 @@ Arguments:
 
 <div class="small">
 
-| Name       | Type   | Description                               |
-|:-----------|:-------|:------------------------------------------|
-| `--input`  | `file` | Unintegrated AnnData HDF5 file.           |
-| `--output` | `file` | (*Output*) An integrated AnnData dataset. |
+| Name               | Type   | Description                                    |
+|:-------------------|:-------|:-----------------------------------------------|
+| `--input_dataset`  | `file` | Unintegrated AnnData HDF5 file.                |
+| `--input_solution` | `file` | Uncensored dataset containing the true labels. |
+| `--output`         | `file` | (*Output*) An integrated AnnData dataset.      |
 
 </div>
 
@@ -271,9 +273,9 @@ Arguments:
 
 </div>
 
-## Component type: Metric (embedding)
+## Component type: Metric
 
-A batch integration embedding metric.
+A metric for evaluating batch integration methods.
 
 Arguments:
 
diff --git a/src/api/comp_control_method.yaml b/src/api/comp_control_method.yaml
index 1d9bb7a..f3f4435 100644
--- a/src/api/comp_control_method.yaml
+++ b/src/api/comp_control_method.yaml
@@ -7,10 +7,14 @@ info:
     description: |
       A control method for the batch integration task.
 arguments:
-  - name: --input
+  - name: --input_dataset
     __merge__: file_dataset.yaml
     direction: input
     required: true
+  - name: --input_solution
+    __merge__: file_solution.yaml
+    direction: input
+    required: true
   - name: --output
     direction: output
     __merge__: file_integrated.yaml
diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml
index 8110618..22972ce 100644
--- a/src/api/comp_method.yaml
+++ b/src/api/comp_method.yaml
@@ -1,4 +1,4 @@
-namespace: batch_integration/methods
+namespace: methods
 info:
   type: method
   type_info:
diff --git a/src/api/comp_metric.yaml b/src/api/comp_metric.yaml
index e5a4ce8..844e9c9 100644
--- a/src/api/comp_metric.yaml
+++ b/src/api/comp_metric.yaml
@@ -1,12 +1,11 @@
-namespace: batch_integration/metrics
+namespace: metrics
 info:
   type: metric
-  subtype: embedding
   type_info:
-    label: Metric (embedding)
-    summary: A batch integration embedding metric.
+    label: Metric
+    summary: A metric for evaluating batch integration methods.
     description: |
-      A metric for evaluating batch corrected embeddings.
+      A metric for evaluating batch integration methods.
 arguments:
   - name: --input_integrated
     __merge__: file_integrated.yaml