update test resources used

openproblems-bio · Sep 20, 2024 · 176bca1 · 176bca1
1 parent bfa6075
commit 176bca1
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Showing 17 changed files with 23 additions and 23 deletions.
diff --git a/src/api/comp_control_method.yaml b/src/api/comp_control_method.yaml
@@ -29,5 +29,5 @@ test_resources:
   - type: python_script
     path: /common/component_tests/check_config.py
   - path: /common/library.bib
-  - path: /resources_test/denoising/pancreas
-    dest: resources_test/denoising/pancreas
+  - path: /resources_test/denoising/cxg_mouse_pancreas_atlas
+    dest: resources_test/denoising/cxg_mouse_pancreas_atlas
diff --git a/src/api/comp_data_processor.yaml b/src/api/comp_data_processor.yaml
@@ -22,5 +22,5 @@ arguments:
 test_resources:
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
-  - path: /resources_test/common/pancreas
-    dest: resources_test/common/pancreas
+  - path: /resources_test/common/cxg_mouse_pancreas_atlas
+    dest: resources_test/common/cxg_mouse_pancreas_atlas
diff --git a/src/api/comp_method.yaml b/src/api/comp_method.yaml
@@ -21,5 +21,5 @@ test_resources:
   - type: python_script
     path: /common/component_tests/check_config.py
   - path: /common/library.bib
-  - path: /resources_test/denoising/pancreas
-    dest: resources_test/denoising/pancreas
+  - path: /resources_test/denoising/cxg_mouse_pancreas_atlas
+    dest: resources_test/denoising/cxg_mouse_pancreas_atlas
diff --git a/src/api/comp_metric.yaml b/src/api/comp_metric.yaml
@@ -25,5 +25,5 @@ test_resources:
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
   - path: /common/library.bib
-  - path: /resources_test/denoising/pancreas
-    dest: resources_test/denoising/pancreas
+  - path: /resources_test/denoising/cxg_mouse_pancreas_atlas
+    dest: resources_test/denoising/cxg_mouse_pancreas_atlas
diff --git a/src/api/file_common_dataset.yaml b/src/api/file_common_dataset.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/common/pancreas/dataset.h5ad"
+example: "resources_test/common/cxg_mouse_pancreas_atlas/dataset.h5ad"
 label: "Common Dataset"
 summary: A subset of the common dataset.
 info:

diff --git a/src/api/file_prediction.yaml b/src/api/file_prediction.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/denoising/pancreas/denoised.h5ad"
+example: "resources_test/denoising/cxg_mouse_pancreas_atlas/denoised.h5ad"
 label: "Denoised data"
 summary: A denoised dataset as output by a method.
 info:

diff --git a/src/api/file_score.yaml b/src/api/file_score.yaml
@@ -1,5 +1,5 @@
 type: file
-example: resources_test/denoising/pancreas/score.h5ad
+example: resources_test/denoising/cxg_mouse_pancreas_atlas/score.h5ad
 label: Score
 summary: "File indicating the score of a metric."
 info:

diff --git a/src/api/file_test.yaml b/src/api/file_test.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/denoising/pancreas/test.h5ad"
+example: "resources_test/denoising/cxg_mouse_pancreas_atlas/test.h5ad"
 label: "Test data"
 summary: The subset of molecules used for the test dataset
 info:

diff --git a/src/api/file_train.yaml b/src/api/file_train.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/denoising/pancreas/train.h5ad"
+example: "resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad"
 label: "Training data"
 summary: The subset of molecules used for the training dataset
 info:

diff --git a/src/control_methods/perfect_denoising/script.py b/src/control_methods/perfect_denoising/script.py
@@ -2,8 +2,8 @@
 
 ## VIASH START
 par = {
-    'input_train': 'resources_test/denoising/pancreas/train.h5ad',
-    'input_test': 'resources_test/denoising/pancreas/test.h5ad',
+    'input_train': 'resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad',
+    'input_test': 'resources_test/denoising/cxg_mouse_pancreas_atlas/test.h5ad',
     'output': 'output_PD.h5ad',
 }
 meta = {

diff --git a/src/data_processors/process_dataset/script.py b/src/data_processors/process_dataset/script.py
@@ -5,7 +5,7 @@
 
 ## VIASH START
 par = {
-    'input': "resources_test/common/pancreas/dataset.h5ad",
+    'input': "resources_test/common/cxg_mouse_pancreas_atlas/dataset.h5ad",
     'output_train': "train.h5ad",
     'output_test': "test.h5ad",
     'train_frac': 0.9,

diff --git a/src/methods/alra/script.R b/src/methods/alra/script.R
@@ -4,7 +4,7 @@ library(ALRA, warn.conflicts = FALSE)
 
 ## VIASH START
 par <- list(
-  input_train = "resources_test/denoising/pancreas/train.h5ad",
+  input_train = "resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad",
   norm = "log",
   output = "output.h5ad"
 )

diff --git a/src/methods/dca/script.py b/src/methods/dca/script.py
@@ -3,7 +3,7 @@
 
 ## VIASH START
 par = {
-    'input_train': 'resources_test/denoising/pancreas/train.h5ad',
+    'input_train': 'resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad',
     'output': 'output_dca.h5ad',
     'epochs': 300,
 }

diff --git a/src/methods/knn_smoothing/script.py b/src/methods/knn_smoothing/script.py
@@ -3,7 +3,7 @@
 
 ## VIASH START
 par = {
-    'input_train': 'resources_test/denoising/pancreas/train.h5ad',
+    'input_train': 'resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad',
     'output': 'output_knn.h5ad',
 }
 meta = {

diff --git a/src/methods/magic/script.py b/src/methods/magic/script.py
@@ -7,7 +7,7 @@
 
 ## VIASH START
 par = {
-    "input_train": "resources_test/denoising/pancreas/train.h5ad",
+    "input_train": "resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad",
     "output": "output_magic.h5ad",
     "solver": "exact",
     "norm": "sqrt",

diff --git a/src/methods/saver/script.R b/src/methods/saver/script.R
@@ -5,7 +5,7 @@ library(Matrix, warn.conflicts = FALSE)
 
 ## VIASH START
 par <- list(
-  input_train = "resources_test/denoising/pancreas/train.h5ad",
+  input_train = "resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad",
   norm = "log",
   output = "output.h5ad"
 )

diff --git a/src/metrics/mse/script.py b/src/metrics/mse/script.py
@@ -5,8 +5,8 @@
 
 ## VIASH START
 par = {
-    'input_test': 'resources_test/denoising/pancreas/test.h5ad',
-    'input_prediction': 'resources_test/denoising/pancreas/denoised.h5ad',
+    'input_test': 'resources_test/denoising/cxg_mouse_pancreas_atlas/test.h5ad',
+    'input_prediction': 'resources_test/denoising/cxg_mouse_pancreas_atlas/denoised.h5ad',
     'output': 'output_mse.h5ad'
 }
 meta = {