Merge pull request #129 from ljwoodley/update_render_report_for_qmd

Update render report for qmd

report/render_report.R

@@ -18,43 +18,50 @@ if (!interactive()) {
     stop(sprintf("Specified file, %s, does not exist", script_name))
   }
 } else {
-  script_name <- "dummy.qmd"
-  stop(sprintf("Specified file, %s, does not exist", script_name))
+  script_name <- "report/sample_report.qmd"
+  if(!fs::file_exists(script_name)) {
+    stop(sprintf("Specified file, %s, does not exist", script_name))
+  }
 }
 
 report_name <- word(script_name, 1, sep = "\\.")
 report_type <- word(script_name, 2, sep = "\\.")
 
 script_run_time <- set_script_run_time()
-output_file <-
-  paste0(str_replace(report_name, ".*/", ""),
-         "_",
-         format(script_run_time, "%Y%m%d%H%M%S"),
-         if_else(report_type == "qmd", ".pdf", "")
-         )
+output_filename <-
+  paste0(
+    str_replace(report_name, ".*/", ""),
+    "_",
+    format(script_run_time, "%Y%m%d%H%M%S")
+  )
 
 if (report_type == "qmd") {
-  quarto::quarto_render(
+  full_path_to_output_file <- quarto::quarto_render(
     script_name,
-    output_file = output_file,
+    output_file = paste0(output_filename, ".pdf"),
     output_format = "pdf"
   )
+
+  attachment_object <- mime_part(paste0(output_filename, ".pdf"))
 } else {
-  render(
+  full_path_to_output_file <- render(
     script_name,
-    output_file = output_file
+    output_file = output_filename
   )
-}
 
-output_file_extension <- word(output_file, 2 , sep = "\\.")
-attachment_object <- mime_part(output_file, output_file)
+  attachment_object <- mime_part(
+    full_path_to_output_file,
+    basename(full_path_to_output_file)
+  )
+}
 
-email_subject <- paste(report_name, "|", script_run_time)
+email_subject <- paste(basename(report_name), "|", script_run_time)
 body <- "Please see the attached report."
 
 email_body <- list(body, attachment_object)
 
 # send the email with the attached output file
 send_email(email_body, email_subject)
 
+set_script_name("render_report")
 log_job_success(jsonlite::toJSON(script_name))

report/sample_report.qmd

@@ -0,0 +1,29 @@
+---
+title: "sample_report"
+format:
+  html:
+    toc: true
+  pdf:
+    toc: true
+---
+
+## Quarto
+
+Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
+
+## Running Code
+
+When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
+
+```{r}
+1 + 1
+```
+
+You can add options to executable code like this 
+
+```{r}
+#| echo: false
+2 * 2
+```
+
+The `echo: false` option disables the printing of code (only output is displayed).

study_template/report/render_report.R

@@ -18,43 +18,50 @@ if (!interactive()) {
     stop(sprintf("Specified file, %s, does not exist", script_name))
   }
 } else {
-  script_name <- "dummy.qmd"
-  stop(sprintf("Specified file, %s, does not exist", script_name))
+  script_name <- "report/sample_report.qmd"
+  if(!fs::file_exists(script_name)) {
+    stop(sprintf("Specified file, %s, does not exist", script_name))
+  }
 }
 
 report_name <- word(script_name, 1, sep = "\\.")
 report_type <- word(script_name, 2, sep = "\\.")
 
 script_run_time <- set_script_run_time()
-output_file <-
-  paste0(str_replace(report_name, ".*/", ""),
-         "_",
-         format(script_run_time, "%Y%m%d%H%M%S"),
-         if_else(report_type == "qmd", ".pdf", "")
-         )
+output_filename <-
+  paste0(
+    str_replace(report_name, ".*/", ""),
+    "_",
+    format(script_run_time, "%Y%m%d%H%M%S")
+  )
 
 if (report_type == "qmd") {
-  quarto::quarto_render(
+  full_path_to_output_file <- quarto::quarto_render(
     script_name,
-    output_file = output_file,
+    output_file = paste0(output_filename, ".pdf"),
     output_format = "pdf"
   )
+
+  attachment_object <- mime_part(paste0(output_filename, ".pdf"))
 } else {
-  render(
+  full_path_to_output_file <- render(
     script_name,
-    output_file = output_file
+    output_file = output_filename
   )
-}
 
-output_file_extension <- word(output_file, 2 , sep = "\\.")
-attachment_object <- mime_part(output_file, output_file)
+  attachment_object <- mime_part(
+    full_path_to_output_file,
+    basename(full_path_to_output_file)
+  )
+}
 
-email_subject <- paste(report_name, "|", script_run_time)
+email_subject <- paste(basename(report_name), "|", script_run_time)
 body <- "Please see the attached report."
 
 email_body <- list(body, attachment_object)
 
 # send the email with the attached output file
 send_email(email_body, email_subject)
 
+set_script_name("render_report")
 log_job_success(jsonlite::toJSON(script_name))

study_template/report/sample_report.qmd

@@ -0,0 +1,29 @@
+---
+title: "sample_report"
+format:
+  html:
+    toc: true
+  pdf:
+    toc: true
+---
+
+## Quarto
+
+Quarto enables you to weave together content and executable code into a finished document. To learn more about Quarto see <https://quarto.org>.
+
+## Running Code
+
+When you click the **Render** button a document will be generated that includes both content and the output of embedded code. You can embed code like this:
+
+```{r}
+1 + 1
+```
+
+You can add options to executable code like this 
+
+```{r}
+#| echo: false
+2 * 2
+```
+
+The `echo: false` option disables the printing of code (only output is displayed).