openproblems-bio · rcannood · Dec 20, 2023 · Oct 30, 2023 · Nov 10, 2023 · Nov 10, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -15,6 +15,13 @@
   - Simplify footer
   - Update openproblems-v2 submodule
 
+* Updates to the way tasks are rendered (PR #296):
+
+  - Show task motivation, if present.
+  - Allow multiple citations for datasets, methods, and metrics.
+  - Render dataset name instead of dataset id in figures and tables.
+  - Change the way bibliographic references are rendered.
+
 ## BUG FIXES
 
 * Updated the `openproblems-v2` submodule (PR #295). This fixes a deprecation error due to an update in ruamel.yaml.

diff --git a/_openproblems-v2 b/_openproblems-v2
diff --git a/bibliography/library.bib b/bibliography/library.bib
diff --git a/results/_generate_task_pages.py b/results/_generate_task_pages.py
@@ -19,8 +19,10 @@
 title: "{task_name}"
 subtitle: "{task_summary}"
 engine: knitr
-image: featured.png
+image: thumbnail.svg
 page-layout: full
+css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{{r}}

diff --git a/results/_include/_baseline_descriptions.qmd b/results/_include/_baseline_descriptions.qmd
@@ -1,8 +1,8 @@
-```{r}
+```{r baseline_descriptions}
 #| echo: false
 baselines <- method_info %>% filter(is_baseline)
 lines <- pmap_chr(baselines, function(method_name, method_summary, reference, code_url, ...) {
-  summ <- (method_summary %|% "Missing 'method_summary'") %>% str_replace_all("\\. *$", "")
+  summ <- (method_summary %|% "Missing 'method_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
   glue::glue("* **{method_name}**: {summ}.")
 })
 knitr::asis_output(paste(lines, collapse = "\n"))

diff --git a/results/_include/_dataset_descriptions.qmd b/results/_include/_dataset_descriptions.qmd
@@ -1,13 +1,9 @@
-```{r}
+```{r dataset_description}
 #| echo: false
 lines <- pmap_chr(dataset_info, function(dataset_name, dataset_summary, data_reference, ...) {
-  ref <- 
-    if (!is.na(data_reference)) {
-      paste0("<sup>", cite_fun(data_reference, "html"), "</sup>")
-    } else {
-      ""
-    }
-  summ <- (dataset_summary %|% "Missing 'dataset_summary'") %>% str_replace_all("\\. *$", "")
+  ref <- split_cite_fun(data_reference)
+  if (ref != "") ref <- paste0(" ", ref)
+  summ <- (dataset_summary %|% "Missing 'dataset_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
   glue::glue("* **{dataset_name}**{ref}: {summ}.")
 })
 knitr::asis_output(paste(lines, collapse = "\n"))

diff --git a/results/_include/_load_data.qmd b/results/_include/_load_data.qmd
@@ -10,7 +10,10 @@ library(kableExtra)
 
 # read task info
 task_info <- jsonlite::read_json(paste0(params$data_dir, "/task_info.json"))
+
+# add missing data
 task_info$task_description <- task_info$task_description %||% NA_character_
+task_info$task_motivation <- task_info$task_motivation %||% NA_character_
 
 `%|%` <- function(x, y) {
   ifelse(is.na(x), y, x)
@@ -22,43 +25,37 @@ dataset_info <- jsonlite::read_json(paste0(params$data_dir, "/dataset_info.json"
 results <- jsonlite::read_json(paste0(params$data_dir, "/results.json"), simplifyVector = TRUE)
 qc <- jsonlite::read_json(paste0(params$data_dir, "/quality_control.json"), simplifyVector = TRUE)
 
+# add missing columns
 for (col in c("method_summary")) {
   method_info[[col]] <- method_info[[col]] %||% NA_character_
 }
 for (col in c("metric_summary")) {
   metric_info[[col]] <- metric_info[[col]] %||% NA_character_
 }
-for (col in c("dataset_summary")) {
+for (col in c("dataset_summary", "dataset_name")) {
   dataset_info[[col]] <- dataset_info[[col]] %||% NA_character_
 }
 
+# fill missing data
+dataset_info$dataset_name <- dataset_info$dataset_name %|% dataset_info$dataset_id
+
 num_methods <- sum(!method_info$is_baseline)
 num_baselines <- sum(method_info$is_baseline)
 num_datasets <- nrow(dataset_info)
 num_metrics <- nrow(metric_info)
 
+split_cite_fun <- function(keys) {
+  if (is.null(keys)) return("")
+
+  keys <- keys[!is.na(keys)]
+  if (length(keys) == 0) return("")
 
-link_fun <- function(label, url, format = "markdown") {
-  if (format == "markdown") {
-    paste0("[", label, "](", url, ")")
-  } else {
-    paste0("<a href=\"", url, "\" target=\"_blank\">", label, "</a>")
-  }
+  refs <- unlist(stringr::str_split(keys, ", *"))
+  # inner_str <- sapply(refs, function(ref) cite_fun(ref, format = format))
+  # paste0("<sup>", paste(inner_str, collapse = ", "), "</sup>")
+  # paste0("[", paste(inner_str, collapse = ", "), "]")
+  paste0("[@", paste(refs, collapse = "; @"), "]")
 }
-cite_map <- list()
-cite_fun <- function(key, format = "markdown") {
-  # if (is.null(options("citation_map"))) {
-  #   options("citation_map" = list())
-  # }
-  # cm <- options("citation_map")
-  if (!key %in% names(cite_map)) {
-    cite_map[[key]] <<- length(cite_map) + 1
-    # options("citation_map" = cm)
-  }
-  num <- cite_map[[key]]
-  link_fun(num, paste0("/bibliography/#", key), format = format)
-}
-
 ```
 
 

diff --git a/results/_include/_method_descriptions.qmd b/results/_include/_method_descriptions.qmd
@@ -1,25 +1,27 @@
-```{r}
+```{r method_description}
 #| echo: false
 # show each method just once
 lines <- pmap_chr(method_info, function(method_name, method_summary, paper_reference, code_url, code_version, ...) {
+
   links <- c()
   if (!is.na(code_url)) {
     links <- c(links, glue::glue(" [Docs]({code_url})"))
   }
   version_label <- 
-    if (!is.na(code_version)) {
+    if (!is.na(code_version) && code_version != "missing-version") {
       glue::glue(" Software version {code_version}.")
     } else {
       ""
     }
-  ref <- 
-    if (!is.na(paper_reference)) {
-      paste0("<sup>", cite_fun(paper_reference, "html"), "</sup>")
+  ref <- split_cite_fun(paper_reference)
+  if (ref != "") ref <- paste0(" ", ref)
+  links_label <-
+    if (length(links) > 0) {
+      glue::glue(" Links: {paste(links, collapse = ', ')}.")
     } else {
       ""
     }
-  links_label <- glue::glue(" Links: {paste(links, collapse = ', ')}.")
-  summ <- (method_summary %|% "Missing 'method_summary'") %>% str_replace_all("\\. *$", "")
+  summ <- (method_summary %|% "Missing 'method_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "")
   glue::glue("* **{method_name}**{ref}: {summ}.{version_label}{links_label}")
 })
 knitr::asis_output(paste(lines, collapse = "\n"))

diff --git a/results/_include/_metric_descriptions.qmd b/results/_include/_metric_descriptions.qmd
@@ -1,13 +1,9 @@
 ```{r}
 #| echo: false
 lines <- pmap_chr(metric_info, function(metric_name, metric_summary, paper_reference, ...) {
-  ref <- 
-    if (!is.na(paper_reference)) {
-      paste0("<sup>", cite_fun(paper_reference, "html"), "</sup>")
-    } else {
-      ""
-    }
-  summ <- (metric_summary %|% "Missing 'metric_summary'") %>% str_replace_all("\\. *$", "")
+  ref <- split_cite_fun(paper_reference)
+  if (ref != "") ref <- paste0(" ", ref)
+  summ <- (metric_summary %|% "Missing 'metric_summary'") %>% str_replace_all("\\n", " ") %>% str_replace_all("\\. *$", "") 
   glue::glue("* **{metric_name}**{ref}: {summ}.")
 })
 knitr::asis_output(paste(lines, collapse = "\n"))

diff --git a/results/_include/_results_table.qmd b/results/_include/_results_table.qmd
@@ -3,7 +3,7 @@ Results table of the scores per method, dataset and metric (after scaling). Use
 ```{r resultstable}
 #| echo: false
 res_tib0 <- results %>%
-  unnest(scaled_scores) %>%
+  unnest(metric_values) %>%
   unnest(resources) %>%
   left_join(method_info %>% select(-commit_sha, -code_version, -task_id), by = "method_id") %>%
   filter(!is_baseline) %>%
@@ -14,7 +14,7 @@ mean_na_zero <- function(x) {
 }
 
 res_tib1 <- res_tib0 %>% 
-  group_by(method_id, method_name, paper_reference, code_url, code_version) %>%
+  group_by(method_id, method_name, paper_reference, code_url) %>%
   summarise_if(is.numeric, mean_na_zero) %>%
   ungroup() %>%
   mutate(
@@ -27,16 +27,12 @@ res_tib <- res_tib1 %>%
   arrange(desc(mean_score)) %>%
   rowwise() %>%
   mutate(
-    method_label = ifelse(is.na(paper_reference), method_name, glue::glue("{method_name} <sup>{cite_fun(paper_reference, format = 'html')}</sup>")),
-    dataset_label = ifelse(is.na(data_reference), dataset_name, glue::glue("{dataset_name} <sup>{cite_fun(data_reference, format = 'html')}</sup>")),
-    # method_label = method_name,
-    # dataset_label = dataset_name,
     peak_memory_gb = peak_memory_mb / 1024
   ) %>%
   ungroup() %>%
   select(
-    method_label,
-    dataset_label,
+    method_name,
+    dataset_name,
     mean_score,
     any_of(metric_info$metric_id),
     duration_sec,

diff --git a/results/_include/_summary_figure.qmd b/results/_include/_summary_figure.qmd
@@ -95,10 +95,12 @@ palettes <- list(
 #   column_info = column_info %>% filter(id %in% colnames(summary_all)),
 #   column_groups = column_groups,
 #   palettes = palettes,
-#   # determine xmax expand heuristically
-#   expand = c(xmax = max(str_length(tail(column_info$name, 4))) / 5),
-#   # determine offset heuristically
-#   col_annot_offset = max(str_length(column_info$name)) / 5,
+#   position_args = position_arguments(
+#     # determine xmax expand heuristically
+#     expand_xmax = max(str_length(tail(column_info$name, 4))) / 5,
+#     # determine offset heuristically
+#     col_annot_offset = max(str_length(column_info$name)) / 5
+#   ),
 #   add_abc = FALSE,
 #   scale_column = FALSE
 # )

diff --git a/results/_include/_task_template.qmd b/results/_include/_task_template.qmd
@@ -5,8 +5,17 @@
 `r num_methods` methods • `r num_metrics` metrics • `r num_datasets` datasets
 :::
 
-## Description 
-`r task_info$task_description %|% "Missing 'task_description'"`
+Data:
+<a href="data/task_info.json" class="btn btn-secondary">Task info</a>
+<a href="data/method_info.json" class="btn btn-secondary">Method info</a>
+<a href="data/metric_info.json" class="btn btn-secondary">Metric info</a>
+<a href="data/dataset_info.json" class="btn btn-secondary">Dataset info</a>
+<a href="data/results.json" class="btn btn-secondary">Results</a>
+<a href="data/quality_control.json" class="btn btn-secondary">Quality control</a>
+
+`r task_info$task_motivation %|% ""`
+
+`r task_info$task_description %|% ""`
 
 ## Summary
 
@@ -40,19 +49,6 @@
 
 </details>
 
-
-<details><summary>Download raw data</summary>
-
-<a href="data/task_info.json" class="btn btn-secondary">Task info</a>
-<a href="data/method_info.json" class="btn btn-secondary">Method info</a>
-<a href="data/metric_info.json" class="btn btn-secondary">Metric info</a>
-<a href="data/dataset_info.json" class="btn btn-secondary">Dataset info</a>
-<a href="data/results.json" class="btn btn-secondary">Results</a>
-<a href="data/quality_control.json" class="btn btn-secondary">Quality control</a>
-
-</details>
-
-
 <details><summary>Quality control results</summary>
 
 {{< include ../_include/_qc_table.qmd >}}

diff --git a/results/batch_integration_embed/index.qmd b/results/batch_integration_embed/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
 image: thumbnail.svg
 page-layout: full
 css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{r}

diff --git a/results/batch_integration_feature/index.qmd b/results/batch_integration_feature/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
 image: thumbnail.svg
 page-layout: full
 css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{r}

diff --git a/results/batch_integration_graph/index.qmd b/results/batch_integration_graph/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
 image: thumbnail.svg
 page-layout: full
 css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{r}

diff --git a/results/cell_cell_communication_ligand_target/index.qmd b/results/cell_cell_communication_ligand_target/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
 image: thumbnail.svg
 page-layout: full
 css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{r}

diff --git a/results/cell_cell_communication_source_target/index.qmd b/results/cell_cell_communication_source_target/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
 image: thumbnail.svg
 page-layout: full
 css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{r}

diff --git a/results/denoising/index.qmd b/results/denoising/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
 image: thumbnail.svg
 page-layout: full
 css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{r}

diff --git a/results/dimensionality_reduction/index.qmd b/results/dimensionality_reduction/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
 image: thumbnail.svg
 page-layout: full
 css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{r}

diff --git a/results/label_projection/index.qmd b/results/label_projection/index.qmd
@@ -5,6 +5,7 @@ engine: knitr
 image: thumbnail.svg
 page-layout: full
 css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{r}

diff --git a/results/matching_modalities/index.qmd b/results/matching_modalities/index.qmd
@@ -1,10 +1,11 @@
 ---
-title: "Matching modalities"
+title: "Multimodal Data Integration"
 subtitle: "Alignment of cellular profiles from two different modalities"
 engine: knitr
 image: thumbnail.svg
 page-layout: full
 css: ../task_template.css
+bibliography: ../../bibliography/library.bib
 ---
 
 ```{r}