From 66b39c1c90a692437874ada402964d43c20b0cb9 Mon Sep 17 00:00:00 2001
From: realbp <realbp@uw.edu>
Date: Thu, 11 Apr 2024 13:21:13 -0700
Subject: [PATCH 1/7] edited get metadata functions

---
 R/demo-population.R              |  2 ++
 R/get-metadata.R                 | 57 ++++++++++++++++++++++++++++----
 R/process-resp.R                 |  5 +--
 R/process_metadata.R             |  9 ++---
 man/extract_values.Rd            | 25 ++++++++++++++
 man/get_metadata.Rd              | 24 ++++++++++++++
 man/print.cancerprof_metadata.Rd |  2 +-
 man/print.cancerprof_tbl.Rd      |  4 +--
 8 files changed, 108 insertions(+), 20 deletions(-)
 create mode 100644 man/extract_values.Rd
 create mode 100644 man/get_metadata.Rd

diff --git a/R/demo-population.R b/R/demo-population.R
index c30dc2d..c87268d 100644
--- a/R/demo-population.R
+++ b/R/demo-population.R
@@ -122,4 +122,6 @@ demo_population <- function(area, areatype, population, race = NULL, sex = NULL)
       "Rank"
     )) %>%
     mutate(across(c("Percent", "People"), \(x) as.numeric(x)))
+  
+  process_metadata(resp)
 }
diff --git a/R/get-metadata.R b/R/get-metadata.R
index e93e546..6bbcddd 100644
--- a/R/get-metadata.R
+++ b/R/get-metadata.R
@@ -1,5 +1,17 @@
-
-#helper function to remove key from values
+#' Extract Values
+#'
+#' This function finds a string value that contains a key and removes the
+#' key from the value
+#'
+#' @param key A String value
+#' @param resp_metadaa A list of strings of metadata
+#' 
+#' @returns A string value without the key
+#' 
+#' @examples
+#' \dontrun{
+#' extract_values("Sorted by", resp_metadata)
+#' }
 extract_values <- function(key, resp_metadata) {
   values <- resp_metadata[grep(key, resp_metadata)]
   values <- gsub(paste0("^\\s*", key, ":?\\s*"), "", values)
@@ -9,7 +21,7 @@ extract_values <- function(key, resp_metadata) {
 #' Custom print function
 #'
 #' This custom print function processes the
-#' metadata output for a response object
+#' metadata output for easier readability
 #'
 #' @param x
 #'
@@ -17,7 +29,7 @@ extract_values <- function(key, resp_metadata) {
 print.cancerprof_metadata <- function(x, ...) {
 
   cat("\033[38;5;246m# Data Report: \033[39m", "\n")
-  cat(paste(x$data_report, '"\n', sep = "", collapse = " "), "\n")
+  cat(paste(x$data_report, '\n', sep = "", collapse = " "), "\n")
   
   cat("\033[38;5;246m# Sorted By: \033[39m", "\n")
   cat(x$sortedby, "\n")
@@ -37,11 +49,30 @@ print.cancerprof_metadata <- function(x, ...) {
   
   cat("\033[38;5;246m# Data Limitations: \033[39m", "\n")
   cat(x$data_limitations, "\n")
+  cat("\n")
+  
+  if (!is.null(x$additional_notes) && length(x$additional_notes) > 0) {
+    cat("\033[38;5;246m# Additional Notes: \033[39m", "\n")
+    cat(x$additional_notes, "\n")
+  }
   
   invisible(x)
 }
 
-
+#' Get Metadata
+#'
+#' This function assigns a list of metadata components and returns a string of
+#' processed metadata that is easily readable
+#'
+#' @param input_tbl A tibble object
+#' 
+#' @returns a string of metadata and an invisible metadata object as a list 
+#' of strings
+#' 
+#' @examples
+#' \dontrun{
+#' process_metadata(resp)
+#' }
 get_metadata <- function(input_tbl) {
   resp_metadata <- attr(input_tbl, "metadata")
   
@@ -51,20 +82,32 @@ get_metadata <- function(input_tbl) {
   sortedby <- extract_values("Sorted by", resp_metadata)
   createdby <- extract_values("Created by", resp_metadata)
   data_sources <- extract_values("Source", resp_metadata)
-  data_dictionary <- extract_values("For more information about", resp_metadata)
+  data_dictionary <- resp_metadata[grep("For more information", resp_metadata)]
   data_limitations <- extract_values("Data for", resp_metadata)
 
+  exclude_keywords <- c("Sorted by", "Created by", "Source", "For more information", "Data for")
 
+  additional_notes <- resp_metadata[!grepl(paste(exclude_keywords, collapse = "|"), resp_metadata, ignore.case = TRUE)]
+  
+  additional_notes <- additional_notes[!additional_notes %in% data_report]
+  
   demo_metadata_list <- list(
     data_report = data_report,
     sortedby = sortedby,
     createdby = createdby,
     data_sources = data_sources,
     data_dictionary = data_dictionary,
-    data_limitations = data_limitations
+    data_limitations = data_limitations,
+    additional_notes = additional_notes
   )
   
   class(demo_metadata_list) <- c("cancerprof_metadata", class(demo_metadata_list))
   
   print.cancerprof_metadata(demo_metadata_list)
 }
+
+get_raw_metadata <- function(input_tbl) {
+  resp_metadata <- attr(input_tbl, "metadata")
+  
+  return(resp_metadata)
+}
diff --git a/R/process-resp.R b/R/process-resp.R
index 6f2a642..6fb2ae8 100644
--- a/R/process-resp.R
+++ b/R/process-resp.R
@@ -82,10 +82,7 @@ process_resp <- function(resp, topic) {
     mutate_all(\(x) na_if(x, "data not available")) %>%
     mutate_all(\(x) na_if(x, "*")) %>% 
     as_tibble()
-  
-  #store metadata
-  
-  #return dataframe AND metadata
+
   resp_metadata <- c(
     resp_lines[1: (index_first_line_break - 1)], resp_lines[(index_second_line_break + 1): line_length]
   )
diff --git a/R/process_metadata.R b/R/process_metadata.R
index d813967..cc3d445 100644
--- a/R/process_metadata.R
+++ b/R/process_metadata.R
@@ -1,18 +1,15 @@
 #' Custom print function
 #'
-#' This custom print function processes the
-#' metadata output for a response object
+#' This custom print function edits the comment on the
+#' metadata tibble output for a response object
 #'
 #' @param x
 #'
 #' @export
 print.cancerprof_tbl <- function(x, ...) {
-  #cat("Metadata:", "\n")
   # we actually need to figure out how to use pillar here
   cat("\033[38;5;246m# Access metadata with `get_metadata()`\033[39m", "\n")
-  # for (i in seq_along(attr(x, "metadata"))) {
-  #   cat(names(attr(x, "metadata"))[i], attr(x, "metadata")[[i]], "\n")
-  # }
+
   NextMethod(x, ...)
 }
 
diff --git a/man/extract_values.Rd b/man/extract_values.Rd
new file mode 100644
index 0000000..6fd99e3
--- /dev/null
+++ b/man/extract_values.Rd
@@ -0,0 +1,25 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get-metadata.R
+\name{extract_values}
+\alias{extract_values}
+\title{Extract Values}
+\usage{
+extract_values(key, resp_metadata)
+}
+\arguments{
+\item{key}{A String value}
+
+\item{resp_metadaa}{A list of strings of metadata}
+}
+\value{
+A string value without the key
+}
+\description{
+This function finds a string value that contains a key and removes the
+key from the value
+}
+\examples{
+\dontrun{
+extract_values("Sorted by", resp_metadata)
+}
+}
diff --git a/man/get_metadata.Rd b/man/get_metadata.Rd
new file mode 100644
index 0000000..44c4666
--- /dev/null
+++ b/man/get_metadata.Rd
@@ -0,0 +1,24 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/get-metadata.R
+\name{get_metadata}
+\alias{get_metadata}
+\title{Get Metadata}
+\usage{
+get_metadata(input_tbl)
+}
+\arguments{
+\item{input_tbl}{A tibble object}
+}
+\value{
+a string of metadata and an invisible metadata object as a list
+of strings
+}
+\description{
+This function assigns a list of metadata components and returns a string of
+processed metadata that is easily readable
+}
+\examples{
+\dontrun{
+process_metadata(resp)
+}
+}
diff --git a/man/print.cancerprof_metadata.Rd b/man/print.cancerprof_metadata.Rd
index 8e63907..14a098b 100644
--- a/man/print.cancerprof_metadata.Rd
+++ b/man/print.cancerprof_metadata.Rd
@@ -11,5 +11,5 @@
 }
 \description{
 This custom print function processes the
-metadata output for a response object
+metadata output for easier readability
 }
diff --git a/man/print.cancerprof_tbl.Rd b/man/print.cancerprof_tbl.Rd
index 7e0a13b..fafd5c4 100644
--- a/man/print.cancerprof_tbl.Rd
+++ b/man/print.cancerprof_tbl.Rd
@@ -15,6 +15,6 @@
 This custom print function processes the
 metadata output for a response object
 
-This custom print function processes the
-metadata output for a response object
+This custom print function edits the comment on the
+metadata tibble output for a response object
 }

From b633c7d1af4d3377bd790b8a534f4c2b27b7c2a0 Mon Sep 17 00:00:00 2001
From: realbp <realbp@uw.edu>
Date: Fri, 12 Apr 2024 12:00:17 -0700
Subject: [PATCH 2/7] started url message

---
 R/demo-crowding.R       |  4 +++-
 R/demo-population.R     |  2 +-
 R/demo-svi.R            |  4 +++-
 R/get-metadata.R        | 34 ++++++++++++++++++----------------
 R/process_metadata.R    |  9 ++++++---
 man/process_metadata.Rd |  4 ++--
 6 files changed, 33 insertions(+), 24 deletions(-)

diff --git a/R/demo-crowding.R b/R/demo-crowding.R
index 7790bb7..5b2f09b 100644
--- a/R/demo-crowding.R
+++ b/R/demo-crowding.R
@@ -69,6 +69,8 @@ demo_crowding <- function(area, areatype, crowding, race) {
     ) %>%
     req_perform()
 
+  resp_url <- resp$url
+  
   resp <- process_resp(resp, "demographics")
   
   resp$data <- resp$data %>%
@@ -80,5 +82,5 @@ demo_crowding <- function(area, areatype, crowding, race) {
     )) %>%
     mutate(across(c("Percent", "Households"), \(x) as.numeric(x)))
 
-  process_metadata(resp)
+  process_metadata(resp, resp_url)
 }
diff --git a/R/demo-population.R b/R/demo-population.R
index c87268d..c115e95 100644
--- a/R/demo-population.R
+++ b/R/demo-population.R
@@ -114,7 +114,7 @@ demo_population <- function(area, areatype, population, race = NULL, sex = NULL)
 
   resp <- process_resp(resp, "demographics")
 
-  resp %>%
+  resp$data %>%
     setNames(c(
       get_area(areatype),
       "Percent",
diff --git a/R/demo-svi.R b/R/demo-svi.R
index 1d3b1e9..c9dcb43 100644
--- a/R/demo-svi.R
+++ b/R/demo-svi.R
@@ -56,7 +56,9 @@ demo_svi <- function(area, svi) {
 
   resp <- process_resp(resp, "demographics")
 
-  resp %>%
+  resp$data %>%
     setNames(c("County", "FIPS", "Score")) %>%
     mutate(across(c("Score"), \(x) as.numeric(x)))
+  
+  process_metadata(resp)
 }
diff --git a/R/get-metadata.R b/R/get-metadata.R
index 6bbcddd..c8d5d1b 100644
--- a/R/get-metadata.R
+++ b/R/get-metadata.R
@@ -27,29 +27,31 @@ extract_values <- function(key, resp_metadata) {
 #'
 #' @export
 print.cancerprof_metadata <- function(x, ...) {
+  
+  cli_h1("Metadata")
 
-  cat("\033[38;5;246m# Data Report: \033[39m", "\n")
+  cli_text("\033[38;5;246m# Data Report: \033[39m", "\n")
   cat(paste(x$data_report, '\n', sep = "", collapse = " "), "\n")
   
-  cat("\033[38;5;246m# Sorted By: \033[39m", "\n")
-  cat(x$sortedby, "\n")
-  cat("\n")
+  cli_text("\033[38;5;246m# Sorted By: \033[39m", "\n")
+  cli_text(x$sortedby, "\n")
+  cli_text("\n")
   
-  cat("\033[38;5;246m# Created By: \033[39m", "\n")
-  cat(x$createdby, "\n")
-  cat("\n")
+  cli_text("\033[38;5;246m# Created By: \033[39m", "\n")
+  cli_text(x$createdby, "\n")
+  cli_text("\n")
   
-  cat("\033[38;5;246m# Data Sources: \033[39m", "\n")
-  cat(x$data_sources, "\n")
-  cat("\n")
+  cli_text("\033[38;5;246m# Data Sources: \033[39m", "\n")
+  cli_text(x$data_sources, "\n")
+  cli_text("\n")
   
-  cat("\033[38;5;246m# Data Dictionary: \033[39m", "\n")
-  cat(x$data_dictionary, "\n")
-  cat("\n")
+  cli_text("\033[38;5;246m# Data Dictionary: \033[39m", "\n")
+  cli_text(x$data_dictionary, "\n")
+  cli_text("\n")
   
-  cat("\033[38;5;246m# Data Limitations: \033[39m", "\n")
-  cat(x$data_limitations, "\n")
-  cat("\n")
+  cli_text("\033[38;5;246m# Data Limitations: \033[39m", "\n")
+  cli_text(x$data_limitations, "\n")
+  cli_text("\n")
   
   if (!is.null(x$additional_notes) && length(x$additional_notes) > 0) {
     cat("\033[38;5;246m# Additional Notes: \033[39m", "\n")
diff --git a/R/process_metadata.R b/R/process_metadata.R
index cc3d445..286e1ed 100644
--- a/R/process_metadata.R
+++ b/R/process_metadata.R
@@ -8,7 +8,10 @@
 #' @export
 print.cancerprof_tbl <- function(x, ...) {
   # we actually need to figure out how to use pillar here
-  cat("\033[38;5;246m# Access metadata with `get_metadata()`\033[39m", "\n")
+  cli_par()
+  cli_text("\033[38;5;246m# Click to view the live data on State Cancer Profiles \033[39m", "\n")
+  cli_text("\033[38;5;246m# Access metadata with `get_metadata()`\033[39m", "\n")
+  cli_end()
 
   NextMethod(x, ...)
 }
@@ -26,7 +29,7 @@ print.cancerprof_tbl <- function(x, ...) {
 #' \dontrun{
 #' process_metadata(resp)
 #' }
-process_metadata <- function(resp) {
+process_metadata <- function(resp, resp_url) {
   
   resp_data <- resp$data
   resp_metadata <- resp$metadata
@@ -34,6 +37,6 @@ process_metadata <- function(resp) {
   class(resp_data) <- c("cancerprof_tbl", class(resp_data))
   attr(resp_data, "metadata") <- resp_metadata
   
-  #print(resp_metadata)
+  print(resp_metadata, resp_url = resp_url)
   return(resp_data)
 }
diff --git a/man/process_metadata.Rd b/man/process_metadata.Rd
index f728b58..0020a5d 100644
--- a/man/process_metadata.Rd
+++ b/man/process_metadata.Rd
@@ -4,9 +4,9 @@
 \alias{process_metadata}
 \title{Process Metadata}
 \usage{
-process_metadata(resp)
+process_metadata(resp, resp_url)
 
-process_metadata(resp)
+process_metadata(resp, resp_url)
 }
 \arguments{
 \item{resp}{A response object}

From 52d8a1e6e83833d62dac35d70441c2e4f27d8a68 Mon Sep 17 00:00:00 2001
From: realbp <realbp@uw.edu>
Date: Tue, 16 Apr 2024 10:41:29 -0700
Subject: [PATCH 3/7] completed hyperlink function

---
 R/browse-trend.R        | 42 +++++++++++++++++++++++++++++++++++++++++
 R/demo-crowding.R       |  2 +-
 R/get-metadata.R        | 12 +++++++++++-
 R/process_metadata.R    | 21 +++++++++++++++------
 man/process_metadata.Rd |  4 ++--
 5 files changed, 71 insertions(+), 10 deletions(-)
 create mode 100644 R/browse-trend.R

diff --git a/R/browse-trend.R b/R/browse-trend.R
new file mode 100644
index 0000000..519bd92
--- /dev/null
+++ b/R/browse-trend.R
@@ -0,0 +1,42 @@
+https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1#results
+
+req_url_query(https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6) %>% 
+  req_perform()
+
+browseURL(paste0(https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1#results))
+                 
+                 
+                 
+req <- "https://statecancerprofiles.cancer.gov/historicaltrend/index.php"
+ 
+api_arguments <- "0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6"
+ 
+ resp <- req %>%
+   req_url_query(
+     stateFIPS = fips_scp(area),
+     areatype = tolower(areatype),
+     topic = "crowd",
+     demo = handle_crowding(crowding),
+     race = handle_race(race),
+     type = "manyareacensus",
+     sortVariableName = "value",
+     sortOrder = "default",
+     output = 1
+   ) %>%
+   req_perform()
+ 
+ 
+ test_ur_fail <- "https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6"
+ req <- "https://statecancerprofiles.cancer.gov/historicaltrend/data.php/historicaltrend.csv?0&9953&999&7599&136&071&07&2&0&0&1&1&1&1&6"
+ req <- request("https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6")
+ 
+resp <- req %>%
+  req_perform() %>% 
+  resp_body_string()
+
+
+if (httr2::resp_content_type(resp) != "text/csv") {
+  cli_abort("Invalid input, please check documentation for valid arguments.")
+}
+ 
+ 
\ No newline at end of file
diff --git a/R/demo-crowding.R b/R/demo-crowding.R
index 5b2f09b..8402460 100644
--- a/R/demo-crowding.R
+++ b/R/demo-crowding.R
@@ -82,5 +82,5 @@ demo_crowding <- function(area, areatype, crowding, race) {
     )) %>%
     mutate(across(c("Percent", "Households"), \(x) as.numeric(x)))
 
-  process_metadata(resp, resp_url)
+  process_metadata(resp, "demographics", resp_url)
 }
diff --git a/R/get-metadata.R b/R/get-metadata.R
index c8d5d1b..ed480f2 100644
--- a/R/get-metadata.R
+++ b/R/get-metadata.R
@@ -31,7 +31,10 @@ print.cancerprof_metadata <- function(x, ...) {
   cli_h1("Metadata")
 
   cli_text("\033[38;5;246m# Data Report: \033[39m", "\n")
-  cat(paste(x$data_report, '\n', sep = "", collapse = " "), "\n")
+  for (i in seq_along(x$data_report)) {
+    cli_text(x$data_report[i], "\n")
+  }
+  cli_text("\n")
   
   cli_text("\033[38;5;246m# Sorted By: \033[39m", "\n")
   cli_text(x$sortedby, "\n")
@@ -76,6 +79,13 @@ print.cancerprof_metadata <- function(x, ...) {
 #' process_metadata(resp)
 #' }
 get_metadata <- function(input_tbl) {
+  
+  #check data topic somehow
+  data_topic <- attributes(input_tbl)$data_topic
+  
+  # do some conditionals to filter data topic
+  
+  
   resp_metadata <- attr(input_tbl, "metadata")
   
   resp_metadata <- gsub("\\\"", "", resp_metadata)
diff --git a/R/process_metadata.R b/R/process_metadata.R
index 286e1ed..cddeeca 100644
--- a/R/process_metadata.R
+++ b/R/process_metadata.R
@@ -7,12 +7,19 @@
 #'
 #' @export
 print.cancerprof_tbl <- function(x, ...) {
-  # we actually need to figure out how to use pillar here
+  original_url <- attributes(x)$url
+  modified_url <- gsub("&output=1", "#results", original_url)
+  
+  cli_div(theme = list(
+    span.cancerprof_class = list(color = "darkgray")))
+  
   cli_par()
-  cli_text("\033[38;5;246m# Click to view the live data on State Cancer Profiles \033[39m", "\n")
-  cli_text("\033[38;5;246m# Access metadata with `get_metadata()`\033[39m", "\n")
+  cli_text(
+    "{.href [# Click to view this query on State Cancer Profiles](", modified_url, ")}"
+  )
+  cli_text("{.cancerprof_class # Access metadata with `get_metadata()`}")
   cli_end()
-
+  
   NextMethod(x, ...)
 }
 
@@ -29,7 +36,7 @@ print.cancerprof_tbl <- function(x, ...) {
 #' \dontrun{
 #' process_metadata(resp)
 #' }
-process_metadata <- function(resp, resp_url) {
+process_metadata <- function(resp, data_topic, resp_url) {
   
   resp_data <- resp$data
   resp_metadata <- resp$metadata
@@ -37,6 +44,8 @@ process_metadata <- function(resp, resp_url) {
   class(resp_data) <- c("cancerprof_tbl", class(resp_data))
   attr(resp_data, "metadata") <- resp_metadata
   
-  print(resp_metadata, resp_url = resp_url)
+  attr(resp_data, "data_topic") <- data_topic
+  
+  attr(resp_data, "url") <- resp_url
   return(resp_data)
 }
diff --git a/man/process_metadata.Rd b/man/process_metadata.Rd
index 0020a5d..3fb7dd8 100644
--- a/man/process_metadata.Rd
+++ b/man/process_metadata.Rd
@@ -4,9 +4,9 @@
 \alias{process_metadata}
 \title{Process Metadata}
 \usage{
-process_metadata(resp, resp_url)
+process_metadata(resp, data_topic, resp_url)
 
-process_metadata(resp, resp_url)
+process_metadata(resp, data_topic, resp_url)
 }
 \arguments{
 \item{resp}{A response object}

From 6ac68e08ee3646b9cec580e23291bcef94d0dcad Mon Sep 17 00:00:00 2001
From: realbp <realbp@uw.edu>
Date: Wed, 17 Apr 2024 10:52:48 -0700
Subject: [PATCH 4/7] started risk metadata

---
 R/browse-trend.R              | 80 +++++++++++++++++------------------
 R/demo-education.R            |  4 +-
 R/get-metadata.R              | 22 ++++++----
 R/risk-colorectal-screening.R |  8 +++-
 4 files changed, 62 insertions(+), 52 deletions(-)

diff --git a/R/browse-trend.R b/R/browse-trend.R
index 519bd92..100a52e 100644
--- a/R/browse-trend.R
+++ b/R/browse-trend.R
@@ -1,42 +1,42 @@
-https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1#results
-
-req_url_query(https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6) %>% 
-  req_perform()
-
-browseURL(paste0(https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1#results))
-                 
-                 
-                 
-req <- "https://statecancerprofiles.cancer.gov/historicaltrend/index.php"
- 
-api_arguments <- "0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6"
- 
- resp <- req %>%
-   req_url_query(
-     stateFIPS = fips_scp(area),
-     areatype = tolower(areatype),
-     topic = "crowd",
-     demo = handle_crowding(crowding),
-     race = handle_race(race),
-     type = "manyareacensus",
-     sortVariableName = "value",
-     sortOrder = "default",
-     output = 1
-   ) %>%
-   req_perform()
- 
- 
- test_ur_fail <- "https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6"
- req <- "https://statecancerprofiles.cancer.gov/historicaltrend/data.php/historicaltrend.csv?0&9953&999&7599&136&071&07&2&0&0&1&1&1&1&6"
- req <- request("https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6")
- 
-resp <- req %>%
-  req_perform() %>% 
-  resp_body_string()
-
-
-if (httr2::resp_content_type(resp) != "text/csv") {
-  cli_abort("Invalid input, please check documentation for valid arguments.")
-}
+# https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1#results
+# 
+# req_url_query(https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6) %>% 
+#   req_perform()
+# 
+# browseURL(paste0(https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1#results))
+#                  
+#                  
+#                  
+# req <- "https://statecancerprofiles.cancer.gov/historicaltrend/index.php"
+#  
+# api_arguments <- "0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6"
+#  
+#  resp <- req %>%
+#    req_url_query(
+#      stateFIPS = fips_scp(area),
+#      areatype = tolower(areatype),
+#      topic = "crowd",
+#      demo = handle_crowding(crowding),
+#      race = handle_race(race),
+#      type = "manyareacensus",
+#      sortVariableName = "value",
+#      sortOrder = "default",
+#      output = 1
+#    ) %>%
+#    req_perform()
+#  
+#  
+#  test_ur_fail <- "https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6"
+#  req <- "https://statecancerprofiles.cancer.gov/historicaltrend/data.php/historicaltrend.csv?0&9953&999&7599&136&071&07&2&0&0&1&1&1&1&6"
+#  req <- request("https://statecancerprofiles.cancer.gov/historicaltrend/index.php?0&9953&999&7599&136&071&48&2&0&0&1&1&1&1&6")
+#  
+# resp <- req %>%
+#   req_perform() %>% 
+#   resp_body_string()
+# 
+# 
+# if (httr2::resp_content_type(resp) != "text/csv") {
+#   cli_abort("Invalid input, please check documentation for valid arguments.")
+# }
  
  
\ No newline at end of file
diff --git a/R/demo-education.R b/R/demo-education.R
index 931769a..f1ab15e 100644
--- a/R/demo-education.R
+++ b/R/demo-education.R
@@ -88,6 +88,8 @@ demo_education <- function(area, areatype, education, sex = NULL, race = NULL) {
 
   resp <- resp %>%
     req_perform()
+  
+  resp_url <- resp$url
 
   resp <- process_resp(resp, "demographics")
   
@@ -100,6 +102,6 @@ demo_education <- function(area, areatype, education, sex = NULL, race = NULL) {
     )) %>%
     mutate(across(c("Percent", "Households"), \(x) as.numeric(x)))
   
-  process_metadata(resp)
+  process_metadata(resp, "demographics", resp_url)
 
 }
diff --git a/R/get-metadata.R b/R/get-metadata.R
index ed480f2..f1a0ca8 100644
--- a/R/get-metadata.R
+++ b/R/get-metadata.R
@@ -29,36 +29,40 @@ extract_values <- function(key, resp_metadata) {
 print.cancerprof_metadata <- function(x, ...) {
   
   cli_h1("Metadata")
-
-  cli_text("\033[38;5;246m# Data Report: \033[39m", "\n")
+  cli_text("\n")
+  
+  cli_div(theme = list(
+    span.cancerprof_class = list(color = "darkgray")))
+  
+  cli_text("{.cancerprof_class # Data Report:}")
   for (i in seq_along(x$data_report)) {
     cli_text(x$data_report[i], "\n")
   }
   cli_text("\n")
   
-  cli_text("\033[38;5;246m# Sorted By: \033[39m", "\n")
+  cli_text("{.cancerprof_class # Sorted By:}")
   cli_text(x$sortedby, "\n")
   cli_text("\n")
   
-  cli_text("\033[38;5;246m# Created By: \033[39m", "\n")
+  cli_text("{.cancerprof_class # Created By:}")
   cli_text(x$createdby, "\n")
   cli_text("\n")
   
-  cli_text("\033[38;5;246m# Data Sources: \033[39m", "\n")
+  cli_text("{.cancerprof_class # Data Sources:}")
   cli_text(x$data_sources, "\n")
   cli_text("\n")
   
-  cli_text("\033[38;5;246m# Data Dictionary: \033[39m", "\n")
+  cli_text("{.cancerprof_class # Data Dictionary:}")
   cli_text(x$data_dictionary, "\n")
   cli_text("\n")
   
-  cli_text("\033[38;5;246m# Data Limitations: \033[39m", "\n")
+  cli_text("{.cancerprof_class # Data Limitations:}")
   cli_text(x$data_limitations, "\n")
   cli_text("\n")
   
   if (!is.null(x$additional_notes) && length(x$additional_notes) > 0) {
-    cat("\033[38;5;246m# Additional Notes: \033[39m", "\n")
-    cat(x$additional_notes, "\n")
+    cli_text("{.cancerprof_class # Additional Notes:}", "\n")
+    cli_text(x$additional_notes, "\n")
   }
   
   invisible(x)
diff --git a/R/risk-colorectal-screening.R b/R/risk-colorectal-screening.R
index ceca7e4..324376d 100644
--- a/R/risk-colorectal-screening.R
+++ b/R/risk-colorectal-screening.R
@@ -96,11 +96,13 @@ risk_colorectal_screening <- function(screening, race = NULL, sex = NULL, area =
 
   resp <- resp %>%
     req_perform()
+  
+  resp_url <- resp$url
 
   resp <- process_resp(resp, "risks")
 
   if (screening %in% screening_type_1) {
-    resp %>%
+    resp$data <- resp$data %>%
       setNames(c(
         "State",
         "FIPS",
@@ -116,7 +118,7 @@ risk_colorectal_screening <- function(screening, race = NULL, sex = NULL, area =
         "Number_of_Respondents"
       ), \(x) as.numeric(x)))
   } else if (screening %in% screening_type_2) {
-    resp %>%
+    resp$data <- resp$data %>%
       setNames(c(
         "County",
         "FIPS",
@@ -130,4 +132,6 @@ risk_colorectal_screening <- function(screening, race = NULL, sex = NULL, area =
         "Upper_95%_CI"
       ), \(x) as.numeric(x)))
   }
+  
+  process_metadata(resp, "risks", resp_url)
 }

From d0187ed9b57d42de6a23123855ab26b65c05ed44 Mon Sep 17 00:00:00 2001
From: realbp <realbp@uw.edu>
Date: Thu, 18 Apr 2024 11:50:56 -0700
Subject: [PATCH 5/7] removed new lines in metadata

---
 R/get-metadata.R       | 74 +++++++++++++++++++++++++++---------------
 R/incidence-cancer.R   |  8 +++--
 R/mortality-cancer.R   |  6 +++-
 R/process-resp.R       |  2 +-
 R/process_metadata.R   |  3 ++
 R/risk-diet-exercise.R |  8 +++--
 6 files changed, 69 insertions(+), 32 deletions(-)

diff --git a/R/get-metadata.R b/R/get-metadata.R
index f1a0ca8..af0a945 100644
--- a/R/get-metadata.R
+++ b/R/get-metadata.R
@@ -84,38 +84,60 @@ print.cancerprof_metadata <- function(x, ...) {
 #' }
 get_metadata <- function(input_tbl) {
   
+  resp_metadata <- attr(input_tbl, "metadata")
+  
+  resp_metadata <- gsub("\\\"", "", resp_metadata)
+  
   #check data topic somehow
   data_topic <- attributes(input_tbl)$data_topic
   
   # do some conditionals to filter data topic
+  if (data_topic == "demographics") {
+    data_report <- c(resp_metadata[1], resp_metadata[2], resp_metadata[3], resp_metadata[4])
+    sortedby <- extract_values("Sorted by", resp_metadata)
+    createdby <- extract_values("Created by", resp_metadata)
+    data_sources <- extract_values("Source", resp_metadata)
+    data_dictionary <- resp_metadata[grep("For more information", resp_metadata)]
+    data_limitations <- extract_values("Data for", resp_metadata)
+    
+    exclude_keywords <- c("Sorted by", "Created by", "Source", "For more information", "Data for")
+    
+    additional_notes <- resp_metadata[!grepl(paste(exclude_keywords, collapse = "|"), resp_metadata, ignore.case = TRUE)]
+    
+    additional_notes <- additional_notes[!additional_notes %in% data_report]
+    
+    demo_metadata_list <- list(
+      data_report = data_report,
+      sortedby = sortedby,
+      createdby = createdby,
+      data_sources = data_sources,
+      data_dictionary = data_dictionary,
+      data_limitations = data_limitations,
+      additional_notes = additional_notes
+    )
+  } else if (data_topic == "risks") {
+    
+  } else if (data_topic == "incidence") {
+    data_report <- c(resp_metadata[1], resp_metadata[2], resp_metadata[3])
+    sortedby <- extract_values("Sorted by", resp_metadata)
+    createdby <- extract_values("Created by", resp_metadata)
+    trend <- extract_values("Trend", resp_metadata)
+    rate_note <- extract_values("rate note", resp_metadata)
+    stage_note <- extract_values("^ ", resp_metadata)
+    rank_note <- extract_values("rank note", resp_metadata)
+    data_not_available <- extract_values("Data not available", resp_metadata)
+    
+    
+  } else if (data_topic == "mortality") {
+    data_report <- c(resp_metadata[1], resp_metadata[2], resp_metadata[3])
+    sortedby <- extract_values("Sorted by", resp_metadata)
+    createdby <- extract_values("Created by", resp_metadata)
+  } else {
+    cli_abort("Incorrect data topic argument, please ensure that it is correct.")
+  }
   
-  
-  resp_metadata <- attr(input_tbl, "metadata")
-  
-  resp_metadata <- gsub("\\\"", "", resp_metadata)
 
-  data_report <- c(resp_metadata[1], resp_metadata[2], resp_metadata[3], resp_metadata[4])
-  sortedby <- extract_values("Sorted by", resp_metadata)
-  createdby <- extract_values("Created by", resp_metadata)
-  data_sources <- extract_values("Source", resp_metadata)
-  data_dictionary <- resp_metadata[grep("For more information", resp_metadata)]
-  data_limitations <- extract_values("Data for", resp_metadata)
-
-  exclude_keywords <- c("Sorted by", "Created by", "Source", "For more information", "Data for")
-
-  additional_notes <- resp_metadata[!grepl(paste(exclude_keywords, collapse = "|"), resp_metadata, ignore.case = TRUE)]
-  
-  additional_notes <- additional_notes[!additional_notes %in% data_report]
-  
-  demo_metadata_list <- list(
-    data_report = data_report,
-    sortedby = sortedby,
-    createdby = createdby,
-    data_sources = data_sources,
-    data_dictionary = data_dictionary,
-    data_limitations = data_limitations,
-    additional_notes = additional_notes
-  )
+  
   
   class(demo_metadata_list) <- c("cancerprof_metadata", class(demo_metadata_list))
   
diff --git a/R/incidence-cancer.R b/R/incidence-cancer.R
index df2535e..9d3b8c3 100644
--- a/R/incidence-cancer.R
+++ b/R/incidence-cancer.R
@@ -166,6 +166,8 @@ incidence_cancer <- function(area, areatype, cancer, race, sex, age, stage, year
 
   resp <- resp %>%
     req_perform()
+  
+  resp_url <- resp$url
 
   resp <- process_resp(resp, "incidence")
 
@@ -179,7 +181,7 @@ incidence_cancer <- function(area, areatype, cancer, race, sex, age, stage, year
   )
 
   if (stage == "all stages") {
-    resp %>%
+    resp$data <- resp$data %>%
       setNames(c(
         get_area(areatype),
         shared_names_to_numeric,
@@ -196,7 +198,7 @@ incidence_cancer <- function(area, areatype, cancer, race, sex, age, stage, year
         "Trend_Upper_95%_CI"
       ), \(x) as.numeric(x)))
   } else if (stage == "late stage (regional & distant)") {
-    resp %>%
+    resp$data <- resp$data %>%
       setNames(c(
         get_area(areatype),
         shared_names_to_numeric,
@@ -208,4 +210,6 @@ incidence_cancer <- function(area, areatype, cancer, race, sex, age, stage, year
         "Percentage_of_Cases_with_Late_Stage"
       ), \(x) as.numeric(x)))
   }
+  
+  process_metadata(resp, "risks", resp_url)
 }
diff --git a/R/mortality-cancer.R b/R/mortality-cancer.R
index dbb08c4..0f30bf8 100644
--- a/R/mortality-cancer.R
+++ b/R/mortality-cancer.R
@@ -147,6 +147,8 @@ mortality_cancer <- function(area, areatype, cancer, race, sex, age, year) {
   resp <- resp %>%
     req_perform()
 
+  resp_url <- resp$url
+  
   resp <- process_resp(resp, "mortality")
 
   names_to_numeric <- c(
@@ -158,7 +160,7 @@ mortality_cancer <- function(area, areatype, cancer, race, sex, age, year) {
     "Upper_CI_Rank"
   )
 
-  resp %>%
+  resp$data <- resp$data %>%
     setNames(c(
       get_area(areatype),
       "Met Healthy People Objective of ***?",
@@ -180,4 +182,6 @@ mortality_cancer <- function(area, areatype, cancer, race, sex, age, year) {
       "Lower_95%_CI_Trend",
       "Upper_95%_CI_Trend"
     ), \(x) as.numeric(x)))
+  
+  process_metadata(resp, "risks", resp_url)
 }
diff --git a/R/process-resp.R b/R/process-resp.R
index 6fb2ae8..011f731 100644
--- a/R/process-resp.R
+++ b/R/process-resp.R
@@ -48,7 +48,7 @@ process_resp <- function(resp, topic) {
     index_first_line_break <- which(resp_lines == "")[4]
     index_second_line_break <- which(resp_lines == "")[5]
   } else {
-    cli_abort("Incorrect topic argument, please ensure that correct.")
+    cli_abort("Incorrect topic argument, please ensure that it is correct.")
   }
 
   resp <- resp_lines[
diff --git a/R/process_metadata.R b/R/process_metadata.R
index cddeeca..c33ac82 100644
--- a/R/process_metadata.R
+++ b/R/process_metadata.R
@@ -41,6 +41,9 @@ process_metadata <- function(resp, data_topic, resp_url) {
   resp_data <- resp$data
   resp_metadata <- resp$metadata
   
+  #remove new lines
+  resp_metadata <- resp_metadata[!grepl("^\\s*$", resp_metadata)]
+  
   class(resp_data) <- c("cancerprof_tbl", class(resp_data))
   attr(resp_data, "metadata") <- resp_metadata
   
diff --git a/R/risk-diet-exercise.R b/R/risk-diet-exercise.R
index c2000b8..47b632c 100644
--- a/R/risk-diet-exercise.R
+++ b/R/risk-diet-exercise.R
@@ -60,6 +60,8 @@ risk_diet_exercise <- function(diet_exercise, race, sex) {
       output = 1
     ) %>%
     req_perform()
+  
+  resp_url <- resp$url
 
   resp <- process_resp(resp, "risks")
 
@@ -69,7 +71,7 @@ risk_diet_exercise <- function(diet_exercise, race, sex) {
   )
 
   if (diet_exercise %in% diet_exercise_type1) {
-    resp %>%
+    resp$data <- resp$data %>%
       setNames(c(
         "State",
         "FIPS",
@@ -83,7 +85,7 @@ risk_diet_exercise <- function(diet_exercise, race, sex) {
         "Upper_95%_CI"
       ), \(x) as.numeric(x)))
   } else {
-    resp %>%
+    resp$data <- resp$data %>%
       setNames(c(
         "State",
         "FIPS",
@@ -99,4 +101,6 @@ risk_diet_exercise <- function(diet_exercise, race, sex) {
         "Number_of_Respondents"
       ), \(x) as.numeric(x)))
   }
+  
+  process_metadata(resp, "risks", resp_url)
 }

From 35e8f76c389096d59cff2c9d4c6807f69764b879 Mon Sep 17 00:00:00 2001
From: realbp <realbp@uw.edu>
Date: Thu, 18 Apr 2024 16:07:50 -0700
Subject: [PATCH 6/7] completed incd and mortality metadata

---
 R/get-metadata.R     | 184 +++++++++++++++++++++++++++++++++----------
 R/incidence-cancer.R |   2 +-
 R/mortality-cancer.R |   2 +-
 3 files changed, 143 insertions(+), 45 deletions(-)

diff --git a/R/get-metadata.R b/R/get-metadata.R
index af0a945..2f42c8a 100644
--- a/R/get-metadata.R
+++ b/R/get-metadata.R
@@ -34,36 +34,113 @@ print.cancerprof_metadata <- function(x, ...) {
   cli_div(theme = list(
     span.cancerprof_class = list(color = "darkgray")))
   
-  cli_text("{.cancerprof_class # Data Report:}")
-  for (i in seq_along(x$data_report)) {
-    cli_text(x$data_report[i], "\n")
-  }
-  cli_text("\n")
-  
-  cli_text("{.cancerprof_class # Sorted By:}")
-  cli_text(x$sortedby, "\n")
-  cli_text("\n")
+  data_topic <- attributes(x)$data_topic
   
-  cli_text("{.cancerprof_class # Created By:}")
-  cli_text(x$createdby, "\n")
-  cli_text("\n")
-  
-  cli_text("{.cancerprof_class # Data Sources:}")
-  cli_text(x$data_sources, "\n")
-  cli_text("\n")
-  
-  cli_text("{.cancerprof_class # Data Dictionary:}")
-  cli_text(x$data_dictionary, "\n")
-  cli_text("\n")
+  # do some conditionals to filter data topic
+  if (data_topic == "demographics") {
+    cli_text("{.cancerprof_class # Data Report:}")
+    for (i in seq_along(x$data_report)) {
+      cli_text(x$data_report[i], "\n")
+    }
+    cli_text("\n")
+    
+    cli_text("{.cancerprof_class # Sorted By:}")
+    cli_text(x$sortedby, "\n")
+    cli_text("\n")
+    
+    cli_text("{.cancerprof_class # Created By:}")
+    cli_text(x$createdby, "\n")
+    cli_text("\n")
+    
+    cli_text("{.cancerprof_class # Data Sources:}")
+    cli_text(x$data_sources, "\n")
+    cli_text("\n")
+    
+    cli_text("{.cancerprof_class # Data Dictionary:}")
+    cli_text(x$data_dictionary, "\n")
+    cli_text("\n")
+    
+    cli_text("{.cancerprof_class # Data Limitations:}")
+    cli_text(x$data_limitations, "\n")
+    cli_text("\n")
+    
+    if (!is.null(x$additional_notes) && length(x$additional_notes) > 0) {
+      cli_text("{.cancerprof_class # Additional Notes:}", "\n")
+      cli_text(x$additional_notes, "\n")
+    }
+  } else if (data_topic == "risks") {
+    
+  } else if (data_topic == "incidence" || data_topic == "mortality") {
+    cli_text("{.cancerprof_class # Data Report:}")
+    
+    for (i in seq_along(x$data_report)) {
+      cli_text(x$data_report[i], "\n")
+    }
+    cli_text("\n")
+    
+    cli_text("{.cancerprof_class # Sorted By:}")
+    cli_text(x$sortedby, "\n")
+    cli_text("\n")
+    
+    cli_text("{.cancerprof_class # Created By:}")
+    cli_text(x$createdby, "\n")
+    cli_text("\n")
+    
+    if (!is.null(x$trend) && length(x$x$trend) > 0) {
+      cli_text("{.cancerprof_class # Trend:}", "\n")
+      cli_text(x$x$trend, "\n")
+      cli_text("\n")
+    }
+    
+    if (!is.null(x$trend_note) && length(x$trend_note) > 0) {
+      cli_text("{.cancerprof_class # Trend Note:}", "\n")
+      cli_text(x$trend_note, "\n")
+      cli_text("\n")
+    }
+    
+    if (!is.null(x$rate_note) && length(x$rate_note) > 0) {
+      cli_text("{.cancerprof_class # Rate Note:}", "\n")
+      cli_text(x$rate_note, "\n")
+      cli_text("\n")
+    }
+    
+    if (!is.null(x$stage_note) && length(x$stage_note) > 0) {
+      cli_text("{.cancerprof_class # Stage Note:}", "\n")
+      cli_text(x$stage_note, "\n")
+      cli_text("\n")
+    }
+    
+    if (!is.null(x$rank_note) && length(x$rank_note) > 0) {
+      cli_text("{.cancerprof_class # Rank Note:}", "\n")
+      cli_text(x$rank_note, "\n")
+      cli_text("\n")
+    }
+    
+    if (!is.null(x$data_not_available) && length(x$data_not_available) > 0) {
+      cli_text("{.cancerprof_class # Data not available:}", "\n")
+      cli_text(x$data_not_available, "\n")
+      cli_text("\n")
+    }
+    
+    if (!is.null(x$data_sources) && length(x$data_sources) > 0) {
+      cli_text("{.cancerprof_class # Data sources:}", "\n")
+      cli_text(x$data_sources, "\n")
+      cli_text("\n")
+    }
+    
+    if (!is.null(x$data_limitations) && length(x$data_limitations) > 0) {
+      cli_text("{.cancerprof_class # Data limitations:}", "\n")
+      cli_text(x$data_limitations, "\n")
+      cli_text("\n")
+    }
+    
+    if (!is.null(x$additional_notes) && length(x$additional_notes) > 0) {
+      cli_text("{.cancerprof_class # Additional Notes:}", "\n")
+      cli_text(x$additional_notes, "\n")
+    }
+  }
   
-  cli_text("{.cancerprof_class # Data Limitations:}")
-  cli_text(x$data_limitations, "\n")
-  cli_text("\n")
   
-  if (!is.null(x$additional_notes) && length(x$additional_notes) > 0) {
-    cli_text("{.cancerprof_class # Additional Notes:}", "\n")
-    cli_text(x$additional_notes, "\n")
-  }
   
   invisible(x)
 }
@@ -88,7 +165,7 @@ get_metadata <- function(input_tbl) {
   
   resp_metadata <- gsub("\\\"", "", resp_metadata)
   
-  #check data topic somehow
+  #check data topic
   data_topic <- attributes(input_tbl)$data_topic
   
   # do some conditionals to filter data topic
@@ -98,15 +175,14 @@ get_metadata <- function(input_tbl) {
     createdby <- extract_values("Created by", resp_metadata)
     data_sources <- extract_values("Source", resp_metadata)
     data_dictionary <- resp_metadata[grep("For more information", resp_metadata)]
-    data_limitations <- extract_values("Data for", resp_metadata)
+    data_limitations <- resp_metadata[grep("Data for", resp_metadata)]
     
     exclude_keywords <- c("Sorted by", "Created by", "Source", "For more information", "Data for")
     
     additional_notes <- resp_metadata[!grepl(paste(exclude_keywords, collapse = "|"), resp_metadata, ignore.case = TRUE)]
-    
     additional_notes <- additional_notes[!additional_notes %in% data_report]
     
-    demo_metadata_list <- list(
+    output_metadata_list <- list(
       data_report = data_report,
       sortedby = sortedby,
       createdby = createdby,
@@ -115,33 +191,55 @@ get_metadata <- function(input_tbl) {
       data_limitations = data_limitations,
       additional_notes = additional_notes
     )
+    
   } else if (data_topic == "risks") {
     
-  } else if (data_topic == "incidence") {
+  } else if (data_topic == "incidence" || data_topic == "mortality") {
     data_report <- c(resp_metadata[1], resp_metadata[2], resp_metadata[3])
     sortedby <- extract_values("Sorted by", resp_metadata)
     createdby <- extract_values("Created by", resp_metadata)
-    trend <- extract_values("Trend", resp_metadata)
+    trend <- extract_values("^ ", resp_metadata)
+    trend_note <- extract_values("trend note", resp_metadata)
     rate_note <- extract_values("rate note", resp_metadata)
-    stage_note <- extract_values("^ ", resp_metadata)
+    stage_note <- extract_values("Stage ", resp_metadata)
     rank_note <- extract_values("rank note", resp_metadata)
-    data_not_available <- extract_values("Data not available", resp_metadata)
+    data_not_available <- resp_metadata[grep("Data not available", resp_metadata)]
+    data_sources <- extract_values("Source:", resp_metadata)
+    data_limitations <- resp_metadata[grep("Data for", resp_metadata)]
     
+    exclude_keywords <- c("Sorted by", "Created by", "^ ", "trend note", 
+                          "rate note", "Stage ", "rank note", 
+                          "Data not available",  "Source", "Data for")
+    
+    additional_notes <- resp_metadata[!grepl(paste(exclude_keywords, collapse = "|"), resp_metadata, ignore.case = TRUE)]
+    additional_notes <- additional_notes[!additional_notes %in% data_report]
+    
+    output_metadata_list <- list(
+      data_report = data_report,
+      sortedby = sortedby,
+      createdby = createdby,
+      trend = trend,
+      trend_note = trend_note,
+      rate_note = rate_note,
+      stage_note = stage_note,
+      rank_note = rank_note,
+      data_not_available = data_not_available,
+      data_sources = data_sources,
+      data_limitations = data_limitations,
+      additional_notes = additional_notes
+    )
     
-  } else if (data_topic == "mortality") {
-    data_report <- c(resp_metadata[1], resp_metadata[2], resp_metadata[3])
-    sortedby <- extract_values("Sorted by", resp_metadata)
-    createdby <- extract_values("Created by", resp_metadata)
   } else {
     cli_abort("Incorrect data topic argument, please ensure that it is correct.")
   }
   
-
-  
+  #add attribute to list
+  attr(output_metadata_list, "data_topic") <- data_topic
   
-  class(demo_metadata_list) <- c("cancerprof_metadata", class(demo_metadata_list))
+  #add custom print
+  class(output_metadata_list) <- c("cancerprof_metadata", class(output_metadata_list))
   
-  print.cancerprof_metadata(demo_metadata_list)
+  print.cancerprof_metadata(output_metadata_list)
 }
 
 get_raw_metadata <- function(input_tbl) {
diff --git a/R/incidence-cancer.R b/R/incidence-cancer.R
index 9d3b8c3..1da161a 100644
--- a/R/incidence-cancer.R
+++ b/R/incidence-cancer.R
@@ -211,5 +211,5 @@ incidence_cancer <- function(area, areatype, cancer, race, sex, age, stage, year
       ), \(x) as.numeric(x)))
   }
   
-  process_metadata(resp, "risks", resp_url)
+  process_metadata(resp, "incidence", resp_url)
 }
diff --git a/R/mortality-cancer.R b/R/mortality-cancer.R
index 0f30bf8..91457d9 100644
--- a/R/mortality-cancer.R
+++ b/R/mortality-cancer.R
@@ -183,5 +183,5 @@ mortality_cancer <- function(area, areatype, cancer, race, sex, age, year) {
       "Upper_95%_CI_Trend"
     ), \(x) as.numeric(x)))
   
-  process_metadata(resp, "risks", resp_url)
+  process_metadata(resp, "mortality", resp_url)
 }

From 03c527c2388ca51f368e3cbe2d560ae3f2730570 Mon Sep 17 00:00:00 2001
From: realbp <realbp@uw.edu>
Date: Fri, 19 Apr 2024 14:01:19 -0700
Subject: [PATCH 7/7] completed get-metadata-function

---
 R/get-metadata.R | 41 ++++++++++++++++++++++++++---------------
 1 file changed, 26 insertions(+), 15 deletions(-)

diff --git a/R/get-metadata.R b/R/get-metadata.R
index 2f42c8a..e66b84d 100644
--- a/R/get-metadata.R
+++ b/R/get-metadata.R
@@ -37,7 +37,7 @@ print.cancerprof_metadata <- function(x, ...) {
   data_topic <- attributes(x)$data_topic
   
   # do some conditionals to filter data topic
-  if (data_topic == "demographics") {
+  if (data_topic == "demographics" || data_topic == "risks") {
     cli_text("{.cancerprof_class # Data Report:}")
     for (i in seq_along(x$data_report)) {
       cli_text(x$data_report[i], "\n")
@@ -52,23 +52,34 @@ print.cancerprof_metadata <- function(x, ...) {
     cli_text(x$createdby, "\n")
     cli_text("\n")
     
-    cli_text("{.cancerprof_class # Data Sources:}")
-    cli_text(x$data_sources, "\n")
-    cli_text("\n")
+    if (!is.null(x$data_sources) && length(x$data_sources) > 0) {
+      cli_text("{.cancerprof_class # Data Sources:}", "\n")
+      cli_text(x$data_sources, "\n")
+      cli_text("\n")
+    }
     
-    cli_text("{.cancerprof_class # Data Dictionary:}")
-    cli_text(x$data_dictionary, "\n")
-    cli_text("\n")
+    if (!is.null(x$data_dictionary) && length(x$data_dictionary) > 0) {
+      cli_text("{.cancerprof_class # Data Dictionary:}", "\n")
+      cli_text(x$data_dictionary, "\n")
+      cli_text("\n")
+    }
     
-    cli_text("{.cancerprof_class # Data Limitations:}")
-    cli_text(x$data_limitations, "\n")
-    cli_text("\n")
+    if (!is.null(x$data_limitations) && length(x$data_limitations) > 0) {
+      cli_text("{.cancerprof_class # Data Limitations:}", "\n")
+      cli_text(x$data_limitations, "\n")
+      cli_text("\n")
+    }
+    
+    if (!is.null(x$name_change) && length(x$name_change) > 0) {
+      cli_text("{.cancerprof_class # Name Change:}", "\n")
+      cli_text(x$name_change, "\n")
+      cli_text("\n")
+    }
     
     if (!is.null(x$additional_notes) && length(x$additional_notes) > 0) {
       cli_text("{.cancerprof_class # Additional Notes:}", "\n")
       cli_text(x$additional_notes, "\n")
     }
-  } else if (data_topic == "risks") {
     
   } else if (data_topic == "incidence" || data_topic == "mortality") {
     cli_text("{.cancerprof_class # Data Report:}")
@@ -169,7 +180,7 @@ get_metadata <- function(input_tbl) {
   data_topic <- attributes(input_tbl)$data_topic
   
   # do some conditionals to filter data topic
-  if (data_topic == "demographics") {
+  if (data_topic == "demographics" || data_topic == "risks") {
     data_report <- c(resp_metadata[1], resp_metadata[2], resp_metadata[3], resp_metadata[4])
     sortedby <- extract_values("Sorted by", resp_metadata)
     createdby <- extract_values("Created by", resp_metadata)
@@ -177,7 +188,9 @@ get_metadata <- function(input_tbl) {
     data_dictionary <- resp_metadata[grep("For more information", resp_metadata)]
     data_limitations <- resp_metadata[grep("Data for", resp_metadata)]
     
-    exclude_keywords <- c("Sorted by", "Created by", "Source", "For more information", "Data for")
+    name_change <- extract_values("Name Change:", resp_metadata)
+    
+    exclude_keywords <- c("Sorted by", "Created by", "Source", "For more information", "Data for", "Name Change")
     
     additional_notes <- resp_metadata[!grepl(paste(exclude_keywords, collapse = "|"), resp_metadata, ignore.case = TRUE)]
     additional_notes <- additional_notes[!additional_notes %in% data_report]
@@ -192,8 +205,6 @@ get_metadata <- function(input_tbl) {
       additional_notes = additional_notes
     )
     
-  } else if (data_topic == "risks") {
-    
   } else if (data_topic == "incidence" || data_topic == "mortality") {
     data_report <- c(resp_metadata[1], resp_metadata[2], resp_metadata[3])
     sortedby <- extract_values("Sorted by", resp_metadata)