rule detail

ref #5
OuhscBbmc · Dec 30, 2021 · 82c55a6 · 82c55a6
1 parent 7c2233b
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diff --git a/inst/report-templates/rmarkdown-1/report-1.Rmd b/inst/report-templates/rmarkdown-1/report-1.Rmd
@@ -43,6 +43,8 @@ path_checks <-
 
 checkmate::assert_character(path_checks, any.missing = FALSE, len = 1)
 checkmate::assert_file_exists(path_checks, extension = "rds")
+
+palette_summary <- list(warm = "#fde0ef", hot = "#f1b6da", header = "#555") #http://colrd.com/palette/18841/
 ```
 
 <!-- Load the datasets.   -->
@@ -63,6 +65,45 @@ A *rule* is very exact.  Each record is examined, and determined if it passes ea
 Rule Summary
 -----------------------------
 ```{r table-rule-summary, echo = echo_chunks}
+ds_rule_summary <- checks$rules 
+
+ds_rule_summary |>
+  dplyr::select(
+    `Rule Name`           = .data$check_name,   
+    `Priority`            = .data$priority,   
+    `Error Message`       = .data$error_message,   
+    `Violation Count`     = .data$violation_count,  
+  ) |> 
+  knitr::kable(
+    align     = "lrlr",
+    escape    = FALSE,
+    format    = "html"
+  ) |>
+  kableExtra::kable_styling(
+    bootstrap_options = c("hover", "condensed", "responsive"), #"striped",
+    full_width        = FALSE,
+    position          = "left"
+  ) |>
+  kableExtra::row_spec(
+    row         = 0,
+    bold        = TRUE,
+    color       = "white",
+    background  = palette_summary$header
+  ) |>
+  kableExtra::row_spec(
+    row         = seq_len(nrow(ds_rule_summary)),
+    color       = "#555"
+  ) |>
+  kableExtra::row_spec(
+    row         = which(ds_rule_summary$violation_count > 0 & ds_rule_summary$priority == 1L),
+    bold        = TRUE,
+    background  = palette_summary$hot
+  ) |>
+  kableExtra::row_spec(
+    row         = which(ds_rule_summary$violation_count > 0 & ds_rule_summary$priority > 1L),
+    bold        = TRUE,
+    background  = palette_summary$warm
+  )
 ```
 
 Rule Detail
@@ -113,8 +154,6 @@ A *smell* test won't validate a specific record (like the rules above), but it w
 Smell Summary
 -----------------------------
 ```{r table-smell-summary, echo = echo_chunks}
-palette_summary <- list(warm = "#fde0ef", hot = "#f1b6da", header = "#555") #http://colrd.com/palette/18841/
-
 ds_smell_result_pretty <-
   checks$smells |>
   dplyr::transmute(

diff --git a/inst/report-templates/rmarkdown-1/report-1.html b/inst/report-templates/rmarkdown-1/report-1.html
diff --git a/inst/report-templates/rmarkdown-1/report-1.md b/inst/report-templates/rmarkdown-1/report-1.md
@@ -1,6 +1,6 @@
 ---
 title: Trawler Report
-date: "Date: 2021-12-30 15:10:26"
+date: "Date: 2021-12-30 15:30:11"
 output:
   html_document:
     keep_md: yes
@@ -35,14 +35,109 @@ A *rule* is very exact.  Each record is examined, and determined if it passes ea
 
 Rule Summary
 -----------------------------
-
+<table class="table table-hover table-condensed table-responsive" style="width: auto !important; ">
+ <thead>
+  <tr>
+   <th style="text-align:left;font-weight: bold;color: white !important;background-color: #555 !important;"> Rule Name </th>
+   <th style="text-align:right;font-weight: bold;color: white !important;background-color: #555 !important;"> Priority </th>
+   <th style="text-align:left;font-weight: bold;color: white !important;background-color: #555 !important;"> Error Message </th>
+   <th style="text-align:right;font-weight: bold;color: white !important;background-color: #555 !important;"> Violation Count </th>
+  </tr>
+ </thead>
+<tbody>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> baseline_prealbumin_levels </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Serum pre-albumin level of all enrolled patients do not meet the study criterion </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 10 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> missing_serum_marker_levels </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Relevant nutritional serum markers are missing </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 3 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> serum_prealbumin_levels_1 </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 15 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> serum_prealbumin_levels_2 </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> Baseline prealbumin levels and pre-albumin levels during the 1st visit are not missing however levels in the next reading are missing </td>
+   <td style="text-align:right;color: #555 !important;"> 0 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> serum_prealbumin_levels_completion_data </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> Baseline prealbumin levels are not missing however readings are not carefully monitored at completion </td>
+   <td style="text-align:right;color: #555 !important;"> 0 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> serum_prealbumin_levels_expectations </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> serum prealbumin levels are not missing however subsequent readings did not come as expected </td>
+   <td style="text-align:right;color: #555 !important;"> 0 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> baseline_first_visit_lab_parameters </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> Serum prealbumin levels are low and protein intake at baseline is less than optimal </td>
+   <td style="text-align:right;color: #555 !important;"> 0 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> daily_first_visit_lab_and_workup_parameters </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> In-addition to baseline &amp; visit lab protein parameters, blood work-up npcr levels are also low </td>
+   <td style="text-align:right;color: #555 !important;"> 0 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;"> daily_protein_intake </td>
+   <td style="text-align:right;color: #555 !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;"> npcr levels in study have not improved as intended </td>
+   <td style="text-align:right;color: #555 !important;"> 0 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> hospitalization_reason </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Patient was hospitalized but reason and the date of hospitalization is missing </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 2 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> optimal_daily_protein_intake </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> Daily protein intake is optimal but one of the nutritional marker is not within the normal range </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 7 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> recommended_npcr_range </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> NPCR values are not within the recommended range at completion </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 10 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> npcr </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> NPCR at completion is missing </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+  </tr>
+  <tr>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> npcr_comparison </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 1 </td>
+   <td style="text-align:left;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> NPCR at completion is not greater than npcr at baseline </td>
+   <td style="text-align:right;color: #555 !important;font-weight: bold;background-color: #f1b6da !important;"> 2 </td>
+  </tr>
+</tbody>
+</table>
 
 Rule Detail
 -----------------------------
 
 ```{=html}
-<div id="htmlwidget-461b53f3ee0ff6b457e0" style="width:100%;height:auto;" class="datatables html-widget"></div>
-<script type="application/json" data-for="htmlwidget-461b53f3ee0ff6b457e0">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"factor\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"width: 100%; display: none;\">\n      <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"[&quot;baseline_first_visit_lab_parameters&quot;,&quot;baseline_prealbumin_levels&quot;,&quot;daily_first_visit_lab_and_workup_parameters&quot;,&quot;daily_protein_intake&quot;,&quot;hospitalization_reason&quot;,&quot;missing_serum_marker_levels&quot;,&quot;npcr&quot;,&quot;npcr_comparison&quot;,&quot;optimal_daily_protein_intake&quot;,&quot;recommended_npcr_range&quot;,&quot;serum_prealbumin_levels_1&quot;,&quot;serum_prealbumin_levels_2&quot;,&quot;serum_prealbumin_levels_completion_data&quot;,&quot;serum_prealbumin_levels_expectations&quot;]\"><\/select>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"disabled\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","caption":"<caption>Violations at 2021-12-30 15:10:27<\/caption>","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14"],["baseline_prealbumin_levels","missing_serum_marker_levels","serum_prealbumin_levels_1","serum_prealbumin_levels_2","serum_prealbumin_levels_completion_data","serum_prealbumin_levels_expectations","baseline_first_visit_lab_parameters","daily_first_visit_lab_and_workup_parameters","daily_protein_intake","hospitalization_reason","optimal_daily_protein_intake","recommended_npcr_range","npcr","npcr_comparison"],["Serum pre-albumin level of all enrolled patients do not meet the study criterion","Relevant nutritional serum markers are missing","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels and pre-albumin levels during the 1st visit are not missing however levels in the next reading are missing","Baseline prealbumin levels are not missing however readings are not carefully monitored at completion","serum prealbumin levels are not missing however subsequent readings did not come as expected","Serum prealbumin levels are low and protein intake at baseline is less than optimal","In-addition to baseline & visit lab protein parameters, blood work-up npcr levels are also low","npcr levels in study have not improved as intended","Patient was hospitalized but reason and the date of hospitalization is missing","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","NPCR values are not within the recommended range at completion","NPCR at completion is missing","NPCR at completion is not greater than npcr at baseline"],[1,1,1,1,1,1,1,1,1,1,1,1,1,1]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>check name<\/th>\n      <th>error message<\/th>\n      <th>priority<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":30,"dom":"tip","initComplete":"function(settings, json) {\n$(this.api().table().header()).css({'background-color': '#555', 'color': '#fff'});\n}","columnDefs":[{"className":"dt-right","targets":3},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true,"lengthMenu":[10,25,30,50,100]}},"evals":["options.initComplete"],"jsHooks":[]}</script>
+<div id="htmlwidget-cffa4ac79791596b302f" style="width:100%;height:auto;" class="datatables html-widget"></div>
+<script type="application/json" data-for="htmlwidget-cffa4ac79791596b302f">{"x":{"filter":"top","vertical":false,"filterHTML":"<tr>\n  <td><\/td>\n  <td data-type=\"factor\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n    <div style=\"width: 100%; display: none;\">\n      <select multiple=\"multiple\" style=\"width: 100%;\" data-options=\"[&quot;baseline_first_visit_lab_parameters&quot;,&quot;baseline_prealbumin_levels&quot;,&quot;daily_first_visit_lab_and_workup_parameters&quot;,&quot;daily_protein_intake&quot;,&quot;hospitalization_reason&quot;,&quot;missing_serum_marker_levels&quot;,&quot;npcr&quot;,&quot;npcr_comparison&quot;,&quot;optimal_daily_protein_intake&quot;,&quot;recommended_npcr_range&quot;,&quot;serum_prealbumin_levels_1&quot;,&quot;serum_prealbumin_levels_2&quot;,&quot;serum_prealbumin_levels_completion_data&quot;,&quot;serum_prealbumin_levels_expectations&quot;]\"><\/select>\n    <\/div>\n  <\/td>\n  <td data-type=\"character\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n  <td data-type=\"disabled\" style=\"vertical-align: top;\">\n    <div class=\"form-group has-feedback\" style=\"margin-bottom: auto;\">\n      <input type=\"search\" placeholder=\"All\" class=\"form-control\" style=\"width: 100%;\"/>\n      <span class=\"glyphicon glyphicon-remove-circle form-control-feedback\"><\/span>\n    <\/div>\n  <\/td>\n<\/tr>","caption":"<caption>Violations at 2021-12-30 15:30:12<\/caption>","data":[["1","2","3","4","5","6","7","8","9","10","11","12","13","14"],["baseline_prealbumin_levels","missing_serum_marker_levels","serum_prealbumin_levels_1","serum_prealbumin_levels_2","serum_prealbumin_levels_completion_data","serum_prealbumin_levels_expectations","baseline_first_visit_lab_parameters","daily_first_visit_lab_and_workup_parameters","daily_protein_intake","hospitalization_reason","optimal_daily_protein_intake","recommended_npcr_range","npcr","npcr_comparison"],["Serum pre-albumin level of all enrolled patients do not meet the study criterion","Relevant nutritional serum markers are missing","Baseline prealbumin levels are not missing however levels were not carefully monitored in the subsequent visit","Baseline prealbumin levels and pre-albumin levels during the 1st visit are not missing however levels in the next reading are missing","Baseline prealbumin levels are not missing however readings are not carefully monitored at completion","serum prealbumin levels are not missing however subsequent readings did not come as expected","Serum prealbumin levels are low and protein intake at baseline is less than optimal","In-addition to baseline & visit lab protein parameters, blood work-up npcr levels are also low","npcr levels in study have not improved as intended","Patient was hospitalized but reason and the date of hospitalization is missing","Daily protein intake is optimal but one of the nutritional marker is not within the normal range","NPCR values are not within the recommended range at completion","NPCR at completion is missing","NPCR at completion is not greater than npcr at baseline"],[1,1,1,1,1,1,1,1,1,1,1,1,1,1]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th> <\/th>\n      <th>check name<\/th>\n      <th>error message<\/th>\n      <th>priority<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":30,"dom":"tip","initComplete":"function(settings, json) {\n$(this.api().table().header()).css({'background-color': '#555', 'color': '#fff'});\n}","columnDefs":[{"className":"dt-right","targets":3},{"orderable":false,"targets":0}],"order":[],"autoWidth":false,"orderClasses":false,"orderCellsTop":true,"lengthMenu":[10,25,30,50,100]}},"evals":["options.initComplete"],"jsHooks":[]}</script>
 ```
 
 Smells {.tabset .tabset-fade}