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Add results to foundation models page (#376)
* update results * update task * update results * force rerender * make sure the resources get updated as well * don't filter resources by method * alternative approach * undo changes * update results * update results * update index qmd * update json * update results * update results * update results * Add resutls to foundation models page * Add foundation models data files * Fix foundation models task_info.json * Find commit_sha in foundation models task_info.json * Update label projection data * Update batch integration data * Touch label projection page to trigger rebuild * Fix typo in backticks * Update data files * Trigger preview page rebuild * Update foundation models data files * Fix missing values in foundation models data * Tidy results pages code * Add interpretation section to foundation models * Fix method counts on results pages Non-baseline controls moved back to methods section for foundation models * Fix error reasons for old results Assume exit code = 0 --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
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‎results/_include/_authors.qmd‎

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```{r authors}
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#| echo: false
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if (!is.null(task_info$authors) && length(task_info$authors) > 0) {
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lines <- map_chr(task_info$authors, function(author) {
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name <- author$name
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roles <- author$roles %>% paste(collapse = ", ")
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github <- author$info$github %||% NULL
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orcid <- author$info$orcid %||% NULL
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links <- c()
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if (!is.null(github)) {
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links <- c(links, glue::glue("[{{{{< fa brands github >}}}}](https://github.com/{github})"))
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}
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if (!is.null(orcid)) {
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links <- c(links, glue::glue("[{{{{< fa brands orcid >}}}}](https://orcid.org/{orcid})"))
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}
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links_label <-
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if (length(links) > 0) {
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glue::glue("{paste(links, collapse = ', ')}")
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} else {
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""
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}
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strip_margin(glue::glue("
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|* {name} ({roles}) {links_label}
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|"
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))
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})
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knitr::asis_output(paste(lines, collapse = "\n"))
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}
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```

‎results/_include/_baseline_descriptions.qmd‎

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@@ -1,63 +1,76 @@
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```{r baseline_descriptions}
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#| echo: false
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baselines <- method_info %>% filter(is_baseline)
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lines <- pmap_chr(baselines, function(method_name, method_summary, method_description, reference, code_url, implementation_url, ...) {
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rest <- list(...)
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image <- pluck(rest, "image", .default = NULL)
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documentation_url <- pluck(rest, "documentation_url", .default = NULL)
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code_version <- pluck(rest, "code_version", .default = NULL)
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references_doi <- pluck(rest, "references_doi", .default = NULL) |> na.omit()
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references_bibtex <- pluck(rest, "references_bibtex", .default = NULL) |> na.omit()
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ref <-
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if ("paper_reference" %in% names(rest)) {
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split_cite_fun(rest$paper_reference)
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} else {
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bibs <- c()
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if (!is.null(references_doi) && length(references_doi) != 0) {
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bibs <- get_bibtex_from_doi(references_doi)
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}
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if (!is.null(references_bibtex) && length(references_bibtex) != 0) {
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bibs <- c(bibs, references_bibtex)
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}
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# Write new entries to library.bib
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write_library(bibs)
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# Get bibtex references
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if (!is.null(bibs)) {
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get_bibtex_entries(bibs)
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baselines <- method_info %>%
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filter(is_baseline)
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lines <- pmap_chr(
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baselines,
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function(method_name, method_summary, method_description, reference, code_url, implementation_url, ...) {
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rest <- list(...)
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implementation_url <- if (is.na(implementation_url)) NULL else implementation_url
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code_url <- if (is.na(code_url)) NULL else code_url
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image <- pluck(rest, "image", .default = NULL) |> na.omit()
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documentation_url <- pluck(rest, "documentation_url", .default = NULL) |> na.omit()
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code_version <- pluck(rest, "code_version", .default = NULL) |> na.omit()
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references_doi <- pluck(rest, "references_doi", .default = NULL) |> na.omit()
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references_bibtex <- pluck(rest, "references_bibtex", .default = NULL) |> na.omit()
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ref <-
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if ("paper_reference" %in% names(rest)) {
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split_cite_fun(rest$paper_reference)
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} else {
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""
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bibs <- c()
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if (!is.null(references_doi) && length(references_doi) != 0) {
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bibs <- get_bibtex_from_doi(references_doi)
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}
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if (!is.null(references_bibtex) && length(references_bibtex) != 0) {
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bibs <- c(bibs, references_bibtex)
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}
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# Write new entries to library.bib
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write_library(bibs)
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# Get bibtex references
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if (!is.null(bibs)) {
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get_bibtex_entries(bibs)
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} else {
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""
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}
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}
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}
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if (ref != "") ref <- paste0(" ", ref)
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summ <- (method_summary %|% "Missing 'method_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
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method_meta <- tribble(
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~icon, ~value,
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"bi bi-book", if (!is.null(documentation_url)) paste0("[Documentation](", documentation_url, ")") else NULL,
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"bi bi-globe", if (!is.null(code_url)) paste0("[Repository](", code_url, ")") else NULL,
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"bi bi-file-earmark-code", if (!is.null(implementation_url)) paste0("[Source Code](", implementation_url, ")") else NULL,
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"bi bi-box-seam", if (!is.null(image)) paste0("[Container](", image, ")") else NULL,
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"bi bi-tag", if (!is.null(code_version) && !is.na(code_version)) code_version else NULL,
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) %>% filter(!sapply(value, is.null))
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meta_list <- paste(
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paste0("<i class=\"", method_meta$icon, "\"></i> ", method_meta$value),
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collapse = " · "
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)
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strip_margin(glue::glue("
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|### {method_name}
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|
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|{meta_list}
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|
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|{summ} {ref}
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|
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|{method_description %|% ''}
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|"
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))
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})
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if (ref != "") ref <- paste0(" ", ref)
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summ <- (method_summary %|% "Missing 'method_summary'") %>%
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str_replace_all("\\n", " ") %>%
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str_replace_all("\\. *$", "")
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method_meta <- tribble(
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~icon, ~value,
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"bi bi-book", if (!is.null(documentation_url)) paste0("[Documentation](", documentation_url, ")") else NULL,
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"bi bi-globe", if (!is.null(code_url)) paste0("[Repository](", code_url, ")") else NULL,
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"bi bi-file-earmark-code", if (!is.null(implementation_url)) paste0("[Source Code](", implementation_url, ")") else NULL,
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"bi bi-box-seam", if (!is.null(image)) paste0("[Container](", image, ")") else NULL,
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"bi bi-tag", if (!is.null(code_version) && !is.na(code_version)) code_version else NULL,
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) %>%
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filter(!sapply(value, is.null))
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meta_list <- paste(
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paste0("<i class=\"", method_meta$icon, "\"></i> ", method_meta$value),
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collapse = " · "
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)
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strip_margin(glue::glue("
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|### {method_name}
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|
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|{meta_list}
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|
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|{summ} {ref}
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|
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|{method_description %|% ''}
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|"
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))
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}
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)
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knitr::asis_output(paste(lines, collapse = "\n"))
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```
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```

‎results/_include/_dataset_descriptions.qmd‎

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@@ -19,7 +19,7 @@ lines <- pmap_chr(dataset_info, function(dataset_id, dataset_name, dataset_summa
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}
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if (ref != "") ref <- paste0(" ", ref)
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dataset_link <-
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if (!is.null(source_dataset_id) && dir.exists(paste0("../../datasets/", source_dataset_id))) {
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glue::glue("../../datasets/{source_dataset_id}")
@@ -49,14 +49,14 @@ lines <- pmap_chr(dataset_info, function(dataset_id, dataset_name, dataset_summa
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"bi bi-calendar", if(!is.null(date_created)) paste0(date_created) else NULL,
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"bi bi-file-earmark-text", file_size_str,
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) %>% filter(!sapply(value, is.null))
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meta_list <- paste(
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paste0("<i class=\"", dataset_meta$icon, "\"></i> ", dataset_meta$value),
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collapse = " · "
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)
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summ <- (dataset_summary %|% "Missing 'dataset_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
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strip_margin(glue::glue("
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|### {dataset_name}
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|
@@ -68,4 +68,4 @@ lines <- pmap_chr(dataset_info, function(dataset_id, dataset_name, dataset_summa
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|"))
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})
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knitr::asis_output(paste(lines, collapse = "\n"))
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```
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```

‎results/_include/_load_data.qmd‎

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```{r setup}
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#| include: false
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#| error: true
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library(tidyverse)
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library(funkyheatmap)
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library(kableExtra)
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# touch library.bib in data dir
@@ -28,7 +26,11 @@ method_info <- jsonlite::read_json(paste0(params$data_dir, "/method_info.json"),
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metric_info <- jsonlite::read_json(paste0(params$data_dir, "/metric_info.json"), simplifyVector = TRUE)
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dataset_info <- jsonlite::read_json(paste0(params$data_dir, "/dataset_info.json"), simplifyVector = TRUE)
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results <- jsonlite::read_json(paste0(params$data_dir, "/results.json"), simplifyVector = TRUE) %>% tibble()
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qc <- jsonlite::read_json(paste0(params$data_dir, "/quality_control.json"), simplifyVector = TRUE)
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qc <- if (file.exists(paste0(params$data_dir, "/quality_control.json"))) {
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jsonlite::read_json(paste0(params$data_dir, "/quality_control.json"), simplifyVector = TRUE)
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} else {
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NULL
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}
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# add missing columns
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for (col in c("method_summary", "method_description")) {
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split_cite_fun <- function(keys) {
4850
if (is.null(keys)) return("")
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5052
keys <- keys[!is.na(keys)]
5153
if (length(keys) == 0) return("")
5254
@@ -57,7 +59,6 @@ split_cite_fun <- function(keys) {
5759
paste0("[@", paste(refs, collapse = "; @"), "]")
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}
5961
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convert_to_bibtex <- function(refs) {
6263
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bibtexhandle <- curl::new_handle()
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8182
return(unlist(bibs))
8283
}
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get_bibtex_from_doi <- function(dois) {
8686
if (is.null(dois)) return("")
8787
@@ -137,16 +137,12 @@ get_bibtex_entries <- function(bibs) {
137137
return(ref_string)
138138
}
139139
140-
141-
142-
143140
aggregate_scores <- function(scaled_score) {
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mean(pmin(1, pmax(0, scaled_score)) %|% 0)
145142
}
146143
147-
148144
strip_margin <- function(text, symbol = "\\|") {
149-
str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1")
145+
str_replace_all(text, paste0("(\n?)[ \t]*", symbol), "\\1")
150146
}
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152148
ojs_define(
@@ -158,7 +154,6 @@ ojs_define(
158154
)
159155
```
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161-
162157
```{r overall_ranking}
163158
#| echo: false
164159
results_long <-
@@ -186,4 +181,4 @@ overall_ranking <- results_long %>%
186181
results_long$method_id <- factor(results_long$method_id, levels = rev(overall_ranking$method_id))
187182
results$method_id <- factor(results$method_id, levels = rev(overall_ranking$method_id))
188183
method_info$method_id <- factor(method_info$method_id, levels = rev(overall_ranking$method_id))
189-
```
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```

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