Update test_resources path (#375)

openproblems-bio · Feb 14, 2024 · e2cc44f · e2cc44f
1 parent fe7b02e
commit e2cc44f
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Showing 10 changed files with 13 additions and 12 deletions.
diff --git a/src/tasks/predict_modality/api/comp_control_method.yaml b/src/tasks/predict_modality/api/comp_control_method.yaml
@@ -38,5 +38,5 @@ functionality:
       path: /src/common/comp_tests/check_method_config.py
     - type: python_script
       path: /src/common/comp_tests/run_and_check_adata.py
-    - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite
-      dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite
+    - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT
+      dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT
diff --git a/src/tasks/predict_modality/api/comp_method.yaml b/src/tasks/predict_modality/api/comp_method.yaml
@@ -30,6 +30,6 @@ functionality:
       path: /src/common/comp_tests/check_method_config.py
     - type: python_script
       path: /src/common/comp_tests/run_and_check_adata.py
-    - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite
-      dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite
+    - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT
+      dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT
     - path: /src/common/library.bib
diff --git a/src/tasks/predict_modality/api/comp_metric.yaml b/src/tasks/predict_modality/api/comp_metric.yaml
@@ -25,6 +25,6 @@ functionality:
       path: /src/common/comp_tests/check_metric_config.py
     - type: python_script
       path: /src/common/comp_tests/run_and_check_adata.py
-    - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite
-      dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite
+    - path: /resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT
+      dest: resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT
     - path: /src/common/library.bib
diff --git a/src/tasks/predict_modality/api/file_prediction.yaml b/src/tasks/predict_modality/api/file_prediction.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/prediction.h5ad"
+example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/prediction.h5ad"
 info:
   label: "Prediction"
   summary: "A prediction of the mod2 expression values of the test cells"

diff --git a/src/tasks/predict_modality/api/file_score.yaml b/src/tasks/predict_modality/api/file_score.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/score.h5ad"
+example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/score.h5ad"
 info:
   label: "Score"
   summary: "Metric score file"

diff --git a/src/tasks/predict_modality/api/file_test_mod1.yaml b/src/tasks/predict_modality/api/file_test_mod1.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod1.h5ad"
+example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/test_mod1.h5ad"
 info:
   label: "Test mod1"
   summary: "The mod1 expression values of the test cells."

diff --git a/src/tasks/predict_modality/api/file_test_mod2.yaml b/src/tasks/predict_modality/api/file_test_mod2.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/test_mod2.h5ad"
+example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/test_mod2.h5ad"
 info:
   label: "Test mod2"
   summary: "The mod2 expression values of the test cells."

diff --git a/src/tasks/predict_modality/api/file_train_mod1.yaml b/src/tasks/predict_modality/api/file_train_mod1.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod1.h5ad"
+example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod1.h5ad"
 info:
   label: "Train mod1"
   summary: "The mod1 expression values of the train cells."

diff --git a/src/tasks/predict_modality/api/file_train_mod2.yaml b/src/tasks/predict_modality/api/file_train_mod2.yaml
@@ -1,5 +1,5 @@
 type: file
-example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite/train_mod2.h5ad"
+example: "resources_test/predict_modality/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod2.h5ad"
 info:
   label: "Train mod2"
   summary: "The mod2 expression values of the train cells."

diff --git a/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh b/src/tasks/predict_modality/resources_test_scripts/neurips2021_bmmc.sh
@@ -38,6 +38,7 @@ nextflow run . \
   --output_state '$id/state.yaml'
 
 echo "Run one method"
+
 viash run src/tasks/predict_modality/methods/knnr_py/config.vsh.yaml -- \
   --input_train_mod1 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod1.h5ad \
   --input_train_mod2 $OUTPUT_DIR/openproblems_neurips2021/bmmc_cite_GEX2ADT/train_mod2.h5ad \