Update reporting components to include all links (#915)

* update get_method_info * update get_task_info * update get_metric_info * simplify gsub code * fix implementation url * fix typo * update touch url * add name to image * change image order * update task info output * add code version * update changelog * fix image url * Add image link for nextflow method * flatten references * update references output * fix method references output --------- Co-authored-by: Robrecht Cannoodt <[email protected]>
openproblems-bio · Nov 26, 2024 · f52c8c4 · f52c8c4
1 parent 927b5a6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -28,10 +28,14 @@
 
 - Update `dataset_id` for `tenx_visium`, `zenodo_spatial`, `zenodo_spatial_slidetags` datasets and use `mouse_brain_coronal` as a test resource in the `spatially_variable_genes` task (PR #908).
 
+- Update `get_task_info`, `get_method_info` and `get_metrics_info` reporting components with more info and extend output (PR #915).
+
 ## Bug fixes
 
 - Fix extracting metadata from anndata files in the `extract_metadata` component (PR #914).
 
+- Fix path in `touch` cmd in `reporting/process_task_results/run_test.sh` (PR #915).
+
 # openproblems v2.0.0
 
 A major update to the OpenProblems framework, switching from a Python-based framework to a Viash + Nextflow-based framework. This update features the same concepts as the previous version, but with a new implementation that is more flexible, scalable, and maintainable.

diff --git a/src/reporting/get_method_info/script.R b/src/reporting/get_method_info/script.R
@@ -5,7 +5,7 @@ library(rlang, warn.conflicts = FALSE)
 
 ## VIASH START
 par <- list(
-  input = "resources_test/openproblems/task_results_v3/raw/method_configs.yaml",
+  input = "method_configs.yaml",
   output = "resources_test/openproblems/task_results_v3/processed/method_info.json"
 )
 ## VIASH END
@@ -27,22 +27,57 @@ outputs <- map(configs, function(config) {
   info <- config$info
 
   # add extra info
-  info$config_path <- gsub(".*/src/", "src/", build_info$config)
+  info$comp_path <- gsub(".*/src/", "src/", build_info$config) %>% gsub("/config.vsh.yaml", "", .)
   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$code_version <- config$version
+  info$code_url <- config$links$repository
+  info$documentation_url <- config$links$documentation
+  # Check if the method has a docker container to create an image url. If it does not have a docker it will be a nextflow component consisting of different components that will have a docker image.
+  engines <- config$engines
+  has_docker <- any(map_lgl(engines, ~ .x$type == "docker"))
+  if (has_docker) {
+    info$image <- paste0(
+      "https://",
+      config$links$docker_registry, "/",
+      config$package_config$organization, "/",
+      config$package_config$name, "/",
+      gsub("src/", "", info$comp_path),
+      ":",
+      info$code_version
+    )
+  }  else {
+    info$image <- paste0(
+      "https://github.com/orgs/openproblems-bio/packages?repo_name=",
+      config$package_config$name,
+      "&q=",
+      gsub("src/", "", info$comp_path)
+    )
+  }
   info$implementation_url <- paste0(
     build_info$git_remote, "/blob/",
     build_info$git_commit, "/",
-    info$config_path
+    info$comp_path
   )
   info$type_info <- NULL
 
+  # Flatten references
+  if (!is.null(config$references) && config$references != "") {
+    info <- imap(config$references, function(value, key) {
+      info[[paste0("references_", key)]] <- value
+      return(info)
+    })[[1]]
+  }
+  info$references <- NULL
+
+  print(info)
+
+
   # ↑ this could be used as the new format
 
   # construct v1 format
@@ -53,10 +88,13 @@ outputs <- map(configs, function(config) {
     method_summary = info$summary,
     method_description = info$description,
     is_baseline = grepl("control", info$type),
-    paper_reference = info$reference %||% NA_character_,
-    code_url = info$repository_url %||% NA_character_,
+    references_doi = info$references_doi %||% NA_character_,
+    references_bibtex = info$references_bibtex %||% NA_character_,
+    code_url = info$code_url %||% NA_character_,
+    documentation_url = info$documentation_url %||% NA_character_,
+    image = info$image %||% NA_character_,
     implementation_url = info$implementation_url %||% NA_character_,
-    code_version = NA_character_,
+    code_version = info$code_version %||% NA_character_,
     commit_sha = info$commit_sha
   )
 

diff --git a/src/reporting/get_metric_info/script.R b/src/reporting/get_metric_info/script.R
@@ -28,19 +28,36 @@ outputs <- map(configs, function(config) {
     config$info$metrics,
     function(info) {
       # add extra info
-      info$config_path <- gsub(".*/src/", "src/", build_info$config)
+      info$comp_path <- gsub(".*/src/", "src/", build_info$config) %>% gsub("/config.vsh.yaml", "", .)
       info$task_id <- gsub("/.*", "", config$namespace)
       info$id <- info$name
       info$name <- NULL
       info$component_name <- config$name
       info$namespace <- config$namespace
       info$commit_sha <- build_info$git_commit %||% "missing-sha"
-      info$code_version <- "missing-version"
+      info$code_version <- config$version %||% "missing-version"
+      info$image_url <- paste0(
+        "https://",
+        config$links$docker_registry, "/",
+        config$package_config$organization, "/",
+        config$package_config$name, "/",
+        gsub("src/", "", info$comp_path),
+        ":",
+        info$code_version
+      )
       info$implementation_url <- paste0(
         build_info$git_remote, "/blob/",
         build_info$git_commit, "/",
-        info$config_path
+        info$comp_path
       )
+      # Flatten references
+      if (!is.null(info$references) && info$references != "") {
+        info <- imap(info$references, function(value, key) {
+          info[[paste0("references_", key)]] <- value
+          return(info)
+        })[[1]]
+      }
+      info$references <- NULL
 
       # ↑ this could be used as the new format
 
@@ -52,9 +69,11 @@ outputs <- map(configs, function(config) {
         metric_name = info$label,
         metric_summary = info$summary,
         metric_description = info$description,
-        paper_reference = info$reference %||% NA_character_,
+        references_doi = info$references_doi %||% NA_character_,
+        references_bibtex = info$references_bibtex %||% NA_character_,
         implementation_url = info$implementation_url %||% NA_character_,
-        code_version = NA_character_,
+        image = info$image_url %||% NA_character_,
+        code_version = info$code_version %||% NA_character_,
         commit_sha = info$commit_sha,
         maximize = info$maximize
       )

diff --git a/src/reporting/get_task_info/script.R b/src/reporting/get_task_info/script.R
@@ -15,7 +15,9 @@ info <- yaml::yaml.load_file(par$input)
 
 # construct v1 format
 repo <-
-  if ("name" %in% names(info) && "organization" %in% names(info)) {
+  if ("links" %in% names(info) && "repository" %in% names(info$links)) {
+    info$links$repository
+  } else if ("name" %in% names(info) && "organization" %in% names(info)) {
     paste0(info$organization, "/", info$name)
   } else {
     "openproblems-bio/openproblems"
@@ -33,7 +35,10 @@ out <- list(
   task_summary = info$summary,
   task_description = description,
   repo = repo,
-  authors = info$authors
+  issue_tracker = info$links$issue_tracker %||% NA_character_,
+  authors = info$authors,
+  version = info$version,
+  license = info$license %||% NA_character_
 )
 
 # show warning when certain data is missing and return null?