Update test_resources path

openproblems-bio · Sep 20, 2024 · 1b8f145 · 1b8f145
1 parent d49f215
commit 1b8f145
Show file tree

Hide file tree

Showing 18 changed files with 27 additions and 27 deletions.
diff --git a/_viash.yaml b/_viash.yaml
@@ -44,8 +44,8 @@ info:
   
   test_resources:
     - type: s3
-      path: s3://openproblems-data/resources_test/denoising/
-      dest: resources_test/denoising
+      path: s3://openproblems-data/resources_test/task_denoising/
+      dest: resources_test/task_denoising
     - type: s3
       path: s3://openproblems-data/resources_test/common/
       dest: resources_test/common

diff --git a/scripts/create_resources/test_resources.sh b/scripts/create_resources/test_resources.sh
@@ -9,7 +9,7 @@ cd "$REPO_ROOT"
 set -e
 
 RAW_DATA=resources_test/common
-DATASET_DIR=resources_test/denoising
+DATASET_DIR=resources_test/task_denoising
 
 mkdir -p $DATASET_DIR
 
@@ -41,5 +41,5 @@ HERE
 
 # only run this if you have access to the openproblems-data bucket
 aws s3 sync --profile OP \
-  "$DATASET_DIR" s3://openproblems-data/resources_test/denoising \
+  "$DATASET_DIR" s3://openproblems-data/resources_test/task_denoising \
   --delete --dryrun
diff --git a/scripts/run_benchmark/run_test_local.sh b/scripts/run_benchmark/run_test_local.sh
@@ -21,7 +21,7 @@ nextflow run . \
   -resume \
   -c common/nextflow_helpers/labels_ci.config \
   --id cxg_mouse_pancreas_atlas \
-  --input_train resources_test/denoising/cxg_mouse_pancreas_atlas/train.h5ad \
-  --input_test resources_test/denoising/cxg_mouse_pancreas_atlas/test.h5ad \
+  --input_train resources_test/task_denoising/cxg_mouse_pancreas_atlas/train.h5ad \
+  --input_test resources_test/task_denoising/cxg_mouse_pancreas_atlas/test.h5ad \
   --output_state state.yaml \
   --publish_dir "$publish_dir"
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/cxg_mouse_pancreas_atlas
-    dest: resources_test/denoising/cxg_mouse_pancreas_atlas
+  - path: /resources_test/task_denoising/cxg_mouse_pancreas_atlas
+    dest: resources_test/task_denoising/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/cxg_mouse_pancreas_atlas
-    dest: resources_test/denoising/cxg_mouse_pancreas_atlas
+  - path: /resources_test/task_denoising/cxg_mouse_pancreas_atlas
+    dest: resources_test/task_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/cxg_mouse_pancreas_atlas
-    dest: resources_test/denoising/cxg_mouse_pancreas_atlas
+  - path: /resources_test/task_denoising/cxg_mouse_pancreas_atlas
+    dest: resources_test/task_denoising/cxg_mouse_pancreas_atlas
diff --git a/src/api/file_prediction.yaml b/src/api/file_prediction.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/denoising/cxg_mouse_pancreas_atlas/denoised.h5ad"
+example: "resources_test/task_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/cxg_mouse_pancreas_atlas/score.h5ad
+example: resources_test/task_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/cxg_mouse_pancreas_atlas/test.h5ad"
+example: "resources_test/task_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/cxg_mouse_pancreas_atlas/train.h5ad"
+example: "resources_test/task_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/cxg_mouse_pancreas_atlas/train.h5ad',
-    'input_test': 'resources_test/denoising/cxg_mouse_pancreas_atlas/test.h5ad',
+    'input_train': 'resources_test/task_denoising/cxg_mouse_pancreas_atlas/train.h5ad',
+    'input_test': 'resources_test/task_denoising/cxg_mouse_pancreas_atlas/test.h5ad',
     'output': 'output_PD.h5ad',
 }
 meta = {

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/cxg_mouse_pancreas_atlas/train.h5ad",
+  input_train = "resources_test/task_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/cxg_mouse_pancreas_atlas/train.h5ad',
+    'input_train': 'resources_test/task_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/cxg_mouse_pancreas_atlas/train.h5ad',
+    'input_train': 'resources_test/task_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/cxg_mouse_pancreas_atlas/train.h5ad",
+    "input_train": "resources_test/task_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/cxg_mouse_pancreas_atlas/train.h5ad",
+  input_train = "resources_test/task_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/cxg_mouse_pancreas_atlas/test.h5ad',
-    'input_prediction': 'resources_test/denoising/cxg_mouse_pancreas_atlas/denoised.h5ad',
+    'input_test': 'resources_test/task_denoising/cxg_mouse_pancreas_atlas/test.h5ad',
+    'input_prediction': 'resources_test/task_denoising/cxg_mouse_pancreas_atlas/denoised.h5ad',
     'output': 'output_mse.h5ad'
 }
 meta = {

diff --git a/src/metrics/poisson/script.py b/src/metrics/poisson/script.py
@@ -4,8 +4,8 @@
 
 ## VIASH START
 par = {
-    'input_prediction': 'output_magic.h5ad',
-    'input_test': 'output_test.h5ad',
+    'input_test': 'resources_test/task_denoising/cxg_mouse_pancreas_atlas/test.h5ad',
+    'input_prediction': 'resources_test/task_denoising/cxg_mouse_pancreas_atlas/denoised.h5ad',
     'output': 'output_poisson.h5ad'
 }
 meta = {