fix viash 0.9 refactoring

openproblems-bio · Oct 31, 2024 · 501a886 · 501a886
1 parent cb4543d
commit 501a886
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Showing 15 changed files with 22 additions and 22 deletions.
diff --git a/common b/common
diff --git a/src/control_methods/ground_truth/script.R b/src/control_methods/ground_truth/script.R
@@ -23,7 +23,7 @@ output <- anndata::AnnData(
   var = de_test_h5ad$var[, c()],
   uns = list(
     dataset_id = de_test_h5ad$uns$dataset_id,
-    method_id = meta$functionality_name
+    method_id = meta$name
   )
 )
 

diff --git a/src/control_methods/mean_across_celltypes/script.py b/src/control_methods/mean_across_celltypes/script.py
@@ -33,7 +33,7 @@
     var=pd.DataFrame(index=gene_names),
     uns={
       "dataset_id": de_train_h5ad.uns["dataset_id"],
-      "method_id": meta["functionality_name"]
+      "method_id": meta["name"]
     }
 )
 output.write_h5ad(par["output"], compression="gzip")
diff --git a/src/control_methods/mean_across_compounds/script.py b/src/control_methods/mean_across_compounds/script.py
@@ -32,7 +32,7 @@
     var=pd.DataFrame(index=gene_names),
     uns={
       "dataset_id": de_train_h5ad.uns["dataset_id"],
-      "method_id": meta["functionality_name"]
+      "method_id": meta["name"]
     }
 )
 output.write_h5ad(par["output"], compression="gzip")
diff --git a/src/control_methods/mean_outcome/script.py b/src/control_methods/mean_outcome/script.py
@@ -32,7 +32,7 @@
     var=pd.DataFrame(index=gene_names),
     uns={
       "dataset_id": de_train_h5ad.uns["dataset_id"],
-      "method_id": meta["functionality_name"]
+      "method_id": meta["name"]
     }
 )
 output.write_h5ad(par["output"], compression="gzip")
diff --git a/src/control_methods/sample/script.R b/src/control_methods/sample/script.R
@@ -9,7 +9,7 @@ par <- list(
   output = "resources/datasets/neurips-2023-data/output_identity.h5ad"
 )
 meta <- list(
-  functionality_name = "sample"
+  name = "sample"
 )
 ## VIASH END
 
@@ -35,7 +35,7 @@ output <- anndata::AnnData(
   shape = c(nrow(id_map), length(gene_names)),
   uns = list(
     dataset_id = de_train_h5ad$uns$dataset_id,
-    method_id = meta$functionality_name
+    method_id = meta$name
   )
 )
 

diff --git a/src/control_methods/zeros/script.py b/src/control_methods/zeros/script.py
@@ -25,7 +25,7 @@
     var=pd.DataFrame(index=gene_names),
     uns={
       "dataset_id": de_train_h5ad.uns["dataset_id"],
-      "method_id": meta["functionality_name"]
+      "method_id": meta["name"]
     }
 )
 output.write_h5ad(par["output"], compression="gzip")
diff --git a/src/methods/jn_ap_op2/script.py b/src/methods/jn_ap_op2/script.py
@@ -116,7 +116,7 @@
     var=pd.DataFrame(index=gene_names),
     uns={
       "dataset_id": de_train_h5ad.uns["dataset_id"],
-      "method_id": meta["functionality_name"]
+      "method_id": meta["name"]
     }
 )
 

diff --git a/src/methods/lgc_ensemble_helpers/predict.py b/src/methods/lgc_ensemble_helpers/predict.py
@@ -124,7 +124,7 @@ def predict(par, meta, paths):
         var=pd.DataFrame(index=gene_names),
         uns={
             "dataset_id": de_train_h5ad.uns["dataset_id"],
-            "method_id": meta["functionality_name"]
+            "method_id": meta["name"]
         }
     )
     print(output)

diff --git a/src/methods/lgc_ensemble_predict/script.py b/src/methods/lgc_ensemble_predict/script.py
@@ -145,7 +145,7 @@
 df_sub.reset_index(drop=True, inplace=True)
 
 # write output
-method_id = meta["functionality_name"].replace("_predict", "")
+method_id = meta["name"].replace("_predict", "")
 output = ad.AnnData(
     layers={"prediction": df_sub.to_numpy()},
     obs=pd.DataFrame(index=id_map["id"]),

diff --git a/src/methods/nn_retraining_with_pseudolabels/script.py b/src/methods/nn_retraining_with_pseudolabels/script.py
@@ -71,7 +71,7 @@
     var=pd.DataFrame(index=gene_names),
     uns={
       "dataset_id": de_train_h5ad.uns["dataset_id"],
-      "method_id": meta["functionality_name"]
+      "method_id": meta["name"]
     }
 )
 

diff --git a/src/methods/pyboost/script.py b/src/methods/pyboost/script.py
@@ -95,7 +95,7 @@
     var=pd.DataFrame(index=genes),
     uns={
       "dataset_id": de_train_h5ad.uns["dataset_id"],
-      "method_id": meta["functionality_name"]
+      "method_id": meta["name"]
     }
 )
 

diff --git a/src/methods/scape/script.py b/src/methods/scape/script.py
@@ -44,7 +44,7 @@ def write_predictions(df_submission_data, par, meta, de_train_h5ad, id_map):
 			var=pd.DataFrame(index=genes),
 			uns={
 				"dataset_id": de_train_h5ad.uns["dataset_id"],
-				"method_id": meta["functionality_name"]
+				"method_id": meta["name"]
 			}
 	)
 

diff --git a/src/methods/transformer_ensemble/script.py b/src/methods/transformer_ensemble/script.py
@@ -181,7 +181,7 @@
     var=pd.DataFrame(index=gene_names),
     uns={
       "dataset_id": de_train_h5ad.uns["dataset_id"],
-      "method_id": meta["functionality_name"]
+      "method_id": meta["name"]
     }
 )
 

diff --git a/src/workflows/run_benchmark/main.nf b/src/workflows/run_benchmark/main.nf
@@ -51,7 +51,7 @@ workflow run_wf {
           output: 'predictions/$id.$key.output.h5ad',
           output_model: null
         ]
-        if (comp.config.functionality.info.type == "control_method") {
+        if (comp.config.info.type == "control_method") {
           new_args.de_test_h5ad = state.de_test_h5ad
         }
         new_args
@@ -126,10 +126,10 @@ def run_benchmark_fun(args) {
   // add the key prefix to the method and metric names
   if (keyPrefix && keyPrefix != "") {
     methods_ = methods.collect{ method ->
-      method.run(key: keyPrefix + method.config.functionality.name)
+      method.run(key: keyPrefix + method.config.name)
     }
     metrics_ = metrics.collect{ metric ->
-      metric.run(key: keyPrefix + metric.config.functionality.name)
+      metric.run(key: keyPrefix + metric.config.name)
     }
   }
 
@@ -142,10 +142,10 @@ def run_benchmark_fun(args) {
       | runEach(
         components: methods_,
         filter: { id, state, comp ->
-          !state.method_ids || state.method_ids.contains(comp.config.functionality.name)
+          !state.method_ids || state.method_ids.contains(comp.config.name)
         },
         id: { id, state, comp ->
-          id + "." + comp.config.functionality.name
+          id + "." + comp.config.name
         },
         fromState: methodFromState,
         toState: methodToState,
@@ -156,10 +156,10 @@ def run_benchmark_fun(args) {
       | runEach(
         components: metrics_,
         filter: { id, state, comp ->
-          !state.metric_ids || state.metric_ids.contains(comp.config.functionality.name)
+          !state.metric_ids || state.metric_ids.contains(comp.config.name)
         },
         id: { id, state, comp ->
-          id + "." + comp.config.functionality.name
+          id + "." + comp.config.name
         },
         fromState: metricFromState,
         toState: metricToState,