update components

src/reporting/get_dataset_info/config.vsh.yaml

@@ -6,20 +6,24 @@ arguments:
     type: file
     description: A yaml file
     required: true
-    example: resources_test/common/task_metadata/dataset_info.yaml
+    example: resources_test/openproblems/task_results_v3/raw/dataset_uns.yaml
   - name: --output
     type: file
     direction: output
     default: output.json
     description: Output json
+    info:
+      format:
+        type: json
+        # TODO: add schema
 resources:
   - type: r_script
     path: script.R
 test_resources:
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
-  - path: /resources_test/common/task_metadata
-    dest: resources_test/common/task_metadata
+  - path: /resources_test/openproblems/task_results_v3
+    dest: resources_test/openproblems/task_results_v3
 engines:
   - type: docker
     image: openproblems/base_r:1.0.0

src/reporting/get_dataset_info/script.R

@@ -20,7 +20,6 @@ outputs <- map(datasets, function(dataset) {
 
   # construct v1 format
   out <- list(
-    "task_id" = par$task_id,
     "dataset_id" = dataset$dataset_id,
     "dataset_name" = dataset$dataset_name,
     "dataset_summary" = dataset$dataset_summary,

src/reporting/get_method_info/config.vsh.yaml

@@ -6,20 +6,24 @@ arguments:
     type: file
     description: A yaml file
     required: true
-    example: resources_test/common/task_metadata/method_configs.yaml
+    example: resources_test/openproblems/task_results_v3/raw/method_configs.yaml
   - name: --output
     type: file
     direction: output
     default: output.json
     description: Output json
+    info:
+      format:
+        type: json
+        # TODO: add schema
 resources:
   - type: r_script
     path: script.R
 test_resources:
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
-  - path: /resources_test/common/task_metadata
-    dest: resources_test/common/task_metadata
+  - path: /resources_test/openproblems/task_results_v3
+    dest: resources_test/openproblems/task_results_v3
 engines:
   - type: docker
     image: openproblems/base_r:1.0.0

src/reporting/get_method_info/script.R

@@ -5,7 +5,7 @@ library(rlang, warn.conflicts = FALSE)
 
 ## VIASH START
 par <- list(
-  input = "output/temp/method_configs.yaml",
+  input = "resources_test/openproblems/task_results_v3/raw/method_configs.yaml",
   output = "output/test/method_info.json"
 )
 ## VIASH END
@@ -31,13 +31,17 @@ outputs <- map(configs, function(config) {
   info$task_id <- gsub("/.*", "", config$namespace)
   info$id <- config$name
   info$namespace <- config$namespace
+  info$label <- config$label %||% info$label
+  info$summary <- config$summary %||% info$summary
+  info$description <- config$description %||% info$description
   info$commit_sha <- build_info$git_commit %||% "missing-sha"
   info$code_version <- "missing-version"
-    info$implementation_url <- paste0(
-      build_info$git_remote, "/blob/",
-      build_info$git_commit, "/",
-      info$config_path
-    )
+  info$implementation_url <- paste0(
+    build_info$git_remote, "/blob/",
+    build_info$git_commit, "/",
+    info$config_path
+  )
+  info$type_info <- NULL
 
   # ↑ this could be used as the new format
 

src/reporting/get_metric_info/config.vsh.yaml

@@ -6,20 +6,24 @@ arguments:
     type: file
     description: A yaml file
     required: true
-    example: resources_test/common/task_metadata/metric_configs.yaml
+    example: resources_test/openproblems/task_results_v3/raw/metric_configs.yaml
   - name: --output
     type: file
     direction: output
     default: output.json
     description: Output json
+    info:
+      format:
+        type: json
+        # TODO: add schema
 resources:
   - type: r_script
     path: script.R
 test_resources:
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
-  - path: /resources_test/common/task_metadata
-    dest: resources_test/common/task_metadata
+  - path: /resources_test/openproblems/task_results_v3
+    dest: resources_test/openproblems/task_results_v3
 engines:
   - type: docker
     image: openproblems/base_r:1.0.0

src/reporting/get_metric_info/script.R

@@ -5,7 +5,7 @@ library(rlang, warn.conflicts = FALSE)
 
 ## VIASH START
 par <- list(
-  input = "output/temp/metric_configs.yaml",
+  input = "resources_test/openproblems/task_results_v3/raw/metric_configs.yaml",
   output = "output/metric_info.json"
 )
 ## VIASH END
@@ -31,6 +31,7 @@ outputs <- map(configs, function(config) {
       info$config_path <- gsub(".*/src/", "src/", build_info$config)
       info$task_id <- gsub("/.*", "", config$namespace)
       info$id <- info$name
+      info$name <- NULL
       info$component_id <- config$name
       info$namespace <- config$namespace
       info$commit_sha <- build_info$git_commit %||% "missing-sha"

src/reporting/get_results/config.vsh.yaml

@@ -1,49 +1,57 @@
 name: get_results
 namespace: reporting
 description: Extract execution info
-arguments:
-  - name: --task_id
-    type: string
-    description: Task id
-    example: batch_integration
-  - name: --input_scores
-    type: file
-    description: Scores file
-    example: score_uns.yaml
-  - name: --input_execution
-    type: file
-    description: Nextflow log file
-    example: trace.txt
-  - name: --input_dataset_info
-    type: file
-    description: Method info file
-    example: dataset_info.json
-  - name: --input_method_info
-    type: file
-    description: Method info file
-    example: method_info.json
-  - name: --input_metric_info
-    type: file
-    description: Metric info file
-    example: metric_info.json
-  - name: --output_results
-    type: file
-    direction: output
-    description: Output json
-    default: results.json
-  - name: --output_metric_execution_info
-    type: file
-    direction: output
-    description: Output metric execution info
-    default: metric_execution_info.json
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input_scores
+        type: file
+        description: Scores file
+        example: resources_test/openproblems/task_results_v3/raw/score_uns.yaml
+      - name: --input_execution
+        type: file
+        description: Nextflow log file
+        example: resources_test/openproblems/task_results_v3/raw/trace.txt
+      - name: --input_dataset_info
+        type: file
+        description: Method info file
+        example: resources_test/openproblems/task_results_v3/processed/dataset_info.json
+      - name: --input_method_info
+        type: file
+        description: Method info file
+        example: resources_test/openproblems/task_results_v3/processed/method_info.json
+      - name: --input_metric_info
+        type: file
+        description: Metric info file
+        example: resources_test/openproblems/task_results_v3/processed/metric_info.json
+  - name: Outputs
+    arguments:
+      - name: --output_results
+        type: file
+        direction: output
+        description: Output json
+        default: results.json
+        info:
+          format:
+            type: json
+            # TODO: add schema
+      - name: --output_metric_execution_info
+        type: file
+        direction: output
+        description: Output metric execution info
+        default: metric_execution_info.json
+        info:
+          format:
+            type: json
+            # TODO: add schema
 resources:
   - type: r_script
     path: script.R
 test_resources:
   - type: python_script
     path: /common/component_tests/run_and_check_output.py
-  - path: /resources_test/common/task_metadata
-    dest: resources_test/common/task_metadata
+  - path: /resources_test/openproblems/task_results_v3
+    dest: resources_test/openproblems/task_results_v3
 engines:
   - type: docker
     image: openproblems/base_r:1.0.0

src/reporting/get_results/script.R

@@ -11,7 +11,6 @@ library(rlang, warn.conflicts = FALSE)
 ## VIASH START
 dir <- "work/c1/6660ea0cc6155d7e13fa341d16057b/_viash_par"
 par <- list(
-  task_id = "task_1",
   input_scores = paste0(dir, "/input_scores_1/score_uns.yaml"),
   input_execution = paste0(dir, "/input_execution_1/trace.txt"),
   input_dataset_info = paste0(dir, "/input_dataset_info_1/output.json"),