Add formatter parameter to csv-report (#137)

* Add formatter * Finalize formatting Bootstrap-table initalization now via javascript * Expand help text for csv-report formatting parameter * Update CHANGELOG.md * Update doc link in help text for formatter parameter of csv-report * Remove unused context * Update CHANGELOG.md Co-authored-by: Johannes Köster <[email protected]>
rust-bio · Mar 10, 2021 · f4deedb · f4deedb
1 parent 2cb5a5b
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -2,6 +2,11 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [0.20.0] - 2021-03-10
+### Added
+- New parameter `--formatter` for `rbt csv-report`.
+- `--formatter` allows the specification of custom formatting functions for one or multiple columns of the given csv file.
+
 ## [0.19.7] - 2021-03-09
 ### Changed
 - Performance improvement for `rbt csv-report`.

diff --git a/src/bcf/report/mod.rs b/src/bcf/report/mod.rs
@@ -40,7 +40,6 @@ pub fn embed_js(
         ("report.js", include_str!("js/report.js")),
         ("gene-report.js", include_str!("js/gene-report.js")),
     ];
-    let csv_report_files = vec![("csv_report.js", include_str!("../../csv/csv_report.js"))];
     if vcf_report {
         files.extend(vcf_report_files.iter());
         if let Some(path) = custom_table_report_js {
@@ -54,8 +53,6 @@ pub fn embed_js(
         } else {
             files.push(("table-report.js", include_str!("js/table-report.js")))
         }
-    } else {
-        files.extend(csv_report_files.iter());
     }
     for (name, file) in files {
         let mut out_file = File::create(js_path.to_owned() + name)?;

diff --git a/src/cli.rs b/src/cli.rs
@@ -201,6 +201,11 @@ pub(crate) enum Command {
         #[structopt(long, short = "s", default_value = ",")]
         separator: char,
 
+        /// Configure a custom formatter function for each column by providing a file containing a javascript object with csv column title as the key and a format function as the value.
+        /// More information on the formatting functions and how to use them here: https://bootstrap-table.com/docs/api/column-options/#formatter.
+        #[structopt(long, short = "f")]
+        formatter: Option<String>,
+
         /// Relative output path for the report files. Default value is the current directory.
         #[structopt(default_value = ".")]
         output_path: String,

diff --git a/src/csv/csv_report.css b/src/csv/csv_report.css
@@ -2,3 +2,5 @@
 .table-container { display: none; }
 .loading { height: 100%; padding-top: 25%;}
 .active-row { background: lightgray !important; }
+th { white-space: nowrap; }
+#table { max-width: 90%; }
diff --git a/src/csv/csv_report.html.tera b/src/csv/csv_report.html.tera
@@ -59,30 +59,7 @@
             </div>
         </div>
         <div class="col-md-12 table-container" style="margin-top: 15px;">
-            <table id="table" class="table table-hover" data-toggle="table" data-height="510" style="max-width: 90%;">
-                <thead>
-                <tr>
-                    {% for title in titles %}
-                    <th style="white-space: nowrap;">{{ title }}
-                        <a class="sym" data-toggle="modal" data-target="#{{ title }}" onclick="vegaEmbed('#plot_{{ loop.index0 }}', plot_{{ loop.index0 }})">
-                            <svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-bar-chart-fill" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
-                                <rect width="4" height="5" x="1" y="10" rx="1"/>
-                                <rect width="4" height="9" x="6" y="6" rx="1"/>
-                                <rect width="4" height="14" x="11" y="1" rx="1"/>
-                            </svg>
-                        </a>
-                        <a class="sym" data-toggle="modal" data-target="#{{ title }}-search">
-                            <svg width="1em" height="1em" viewBox="0 0 16 16" class="bi bi-search" fill="currentColor" xmlns="http://www.w3.org/2000/svg">
-                                <path fill-rule="evenodd" d="M10.442 10.442a1 1 0 0 1 1.415 0l3.85 3.85a1 1 0 0 1-1.414 1.415l-3.85-3.85a1 1 0 0 1 0-1.415z"/>
-                                <path fill-rule="evenodd" d="M6.5 12a5.5 5.5 0 1 0 0-11 5.5 5.5 0 0 0 0 11zM13 6.5a6.5 6.5 0 1 1-13 0 6.5 6.5 0 0 1 13 0z"/>
-                            </svg>
-                        </a>
-                    </th>
-                    {% endfor %}
-                </tr>
-                </thead>
-                <tbody>
-                </tbody>
+            <table id="table" class="table table-hover">
             </table>
         </div>
     </div>

diff --git a/src/csv/csv_report.js b/src/csv/csv_report.js
diff --git a/src/csv/csv_report.js.tera b/src/csv/csv_report.js.tera
@@ -0,0 +1,41 @@
+$(document).ready(function() {
+    $('.table-container').show();
+    $('.loading').hide();
+    $('#table').bootstrapTable( 'resetView' , {height: window.innerHeight - 200} );
+    $('.modal').on('shown.bs.modal', function () {
+        window.dispatchEvent(new Event('resize'));
+    });
+    var decompressed = JSON.parse(LZString.decompressFromUTF16(data));
+
+    {% if formatter %}var format = {{ formatter }}{% endif %}
+
+    $('#table').bootstrapTable({
+        height: 510,
+        columns: [{% for title in titles %}{
+            field: '{{ title }}',
+            title: '{{ title }}\r\n                        <a class=\"sym\" data-toggle=\"modal\" data-target=\"#{{ title }}\" onclick=\"vegaEmbed(\'#plot_{{ loop.index0 }}\', plot_{{ loop.index0 }})\">\r\n                            <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-bar-chart-fill\" fill=\"currentColor\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\r\n                                <rect width=\"4\" height=\"5\" x=\"1\" y=\"10\" rx=\"1\"\/>\r\n                                <rect width=\"4\" height=\"9\" x=\"6\" y=\"6\" rx=\"1\"\/>\r\n                                <rect width=\"4\" height=\"14\" x=\"11\" y=\"1\" rx=\"1\"\/>\r\n                            <\/svg>\r\n                        <\/a>\r\n                        <a class=\"sym\" data-toggle=\"modal\" data-target=\"#{{ title }}-search\">\r\n                            <svg width=\"1em\" height=\"1em\" viewBox=\"0 0 16 16\" class=\"bi bi-search\" fill=\"currentColor\" xmlns=\"http:\/\/www.w3.org\/2000\/svg\">\r\n                                <path fill-rule=\"evenodd\" d=\"M10.442 10.442a1 1 0 0 1 1.415 0l3.85 3.85a1 1 0 0 1-1.414 1.415l-3.85-3.85a1 1 0 0 1 0-1.415z\"\/>\r\n                                <path fill-rule=\"evenodd\" d=\"M6.5 12a5.5 5.5 0 1 0 0-11 5.5 5.5 0 0 0 0 11zM13 6.5a6.5 6.5 0 1 1-13 0 6.5 6.5 0 0 1 13 0z\"\/>\r\n                            <\/svg>\r\n                        <\/a>'{% if formatter %},
+            formatter: format["{{ title }}"]{% endif %}
+        }{% if not loop.last %},{% endif %}{% endfor %}],
+        data: []
+    })
+
+    let columns = [{% for title in titles %}"{{ title }}"{% if not loop.last %},{% endif %}{% endfor %}];
+    var table_rows = [];
+    for (const r of decompressed) {
+        var i = 0;
+        row = {};
+        for (const el of r) {
+            row[columns[i]] = el;
+            i++;
+        }
+        table_rows.push(row);
+    }
+    $('#table').bootstrapTable('append', table_rows)
+    let to_be_highlighted = window.location.href.toString().split("highlight=").pop();
+    let rows = $("table > tbody > tr");
+    rows.each(function() {
+        if (this.dataset.index === to_be_highlighted) {
+            $(this).children().addClass('active-row');
+        }
+    });
+});
diff --git a/src/csv/report.rs b/src/csv/report.rs
@@ -10,7 +10,8 @@ use serde_json::json;
 use std::collections::{HashMap, HashSet};
 use std::convert::TryInto;
 use std::fs;
-use std::io::Write;
+use std::fs::File;
+use std::io::{Read, Write};
 use std::path::Path;
 use std::str::FromStr;
 use tera::{Context, Tera};
@@ -25,6 +26,7 @@ pub(crate) fn csv_report(
     separator: char,
     sort_column: Option<&str>,
     ascending: Option<bool>,
+    formatter: Option<&str>,
 ) -> Result<()> {
     let mut rdr = csv::ReaderBuilder::new()
         .delimiter(separator as u8)
@@ -293,6 +295,31 @@ pub(crate) fn csv_report(
         }
     }
 
+    let formatter_object = if let Some(f) = formatter {
+        let mut file_string = "".to_string();
+        let mut custom_file =
+            File::open(f).context("Unable to open given file for formatting colums")?;
+        custom_file
+            .read_to_string(&mut file_string)
+            .context("Unable to read string from formatting file")?;
+
+        Some(file_string)
+    } else {
+        None
+    };
+
+    let mut templates = Tera::default();
+    templates.add_raw_template("csv_report.js.tera", include_str!("csv_report.js.tera"))?;
+    let mut context = Context::new();
+    context.insert("titles", &titles);
+    context.insert("formatter", &formatter_object);
+
+    let js = templates.render("csv_report.js.tera", &context)?;
+
+    let file_path = output_path.to_owned() + "/js/csv_report.js";
+    let mut file = fs::File::create(file_path)?;
+    file.write_all(js.as_bytes())?;
+
     for (i, current_table) in table.chunks(rows_per_page).enumerate() {
         let page = i + 1;
 

diff --git a/src/main.rs b/src/main.rs
@@ -85,6 +85,7 @@ fn main() -> Result<()> {
             sort_column,
             sort_order,
             separator,
+            formatter,
             output_path,
         } => {
             if !Path::new(&output_path).exists() {
@@ -107,6 +108,7 @@ fn main() -> Result<()> {
                 separator,
                 sort_column.as_deref(),
                 order,
+                formatter.as_deref(),
             )?
         }
         VcfReport {