From ff5ea1c5b02a61e03b6a6a55b55d0b9a65666d02 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 13 Aug 2025 00:27:19 +0200 Subject: [PATCH 01/27] Material design SVG icons instead of PNG --- .../FastQC/Report/HTMLReportArchive.java | 53 +++++++++++-------- 1 file changed, 31 insertions(+), 22 deletions(-) diff --git a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java index 334eda5..2e93497 100644 --- a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java +++ b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java @@ -93,24 +93,29 @@ public HTMLReportArchive (SequenceFile sequenceFile, QCModule [] modules, File h // Add an icon before the module name + xhtml.writeStartElement("svg"); + xhtml.writeAttribute("xmlns", "http://www.w3.org/2000/svg"); + xhtml.writeAttribute("width", "24"); + xhtml.writeAttribute("height", "24"); + xhtml.writeAttribute("viewBox", "0 0 24 24"); + xhtml.writeStartElement("path"); if (modules[m].raisesError()) { - xhtml.writeEmptyElement("img"); - xhtml.writeAttribute("src",base64ForIcon("Icons/error.png")); - xhtml.writeAttribute("alt","[FAIL]"); + xhtml.writeAttribute("fill", "#d65d3e"); + xhtml.writeAttribute("d", "M12 2c5.53 0 10 4.47 10 10s-4.47 10-10 10S2 17.53 2 12S6.47 2 12 2m3.59 5L12 10.59L8.41 7L7 8.41L10.59 12L7 15.59L8.41 17L12 13.41L15.59 17L17 15.59L13.41 12L17 8.41z"); } - + else if (modules[m].raisesWarning()) { - xhtml.writeEmptyElement("img"); - xhtml.writeAttribute("src",base64ForIcon("Icons/warning.png")); - xhtml.writeAttribute("alt","[WARN]"); + xhtml.writeAttribute("fill", "#eab30d"); + xhtml.writeAttribute("d", "M13 14h-2V9h2m0 9h-2v-2h2M1 21h22L12 2z"); } else { - xhtml.writeEmptyElement("img"); - xhtml.writeAttribute("src",base64ForIcon("Icons/tick.png")); - xhtml.writeAttribute("alt","[OK]"); + xhtml.writeAttribute("fill", "#4ba359"); + xhtml.writeAttribute("d", "M12 2C6.5 2 2 6.5 2 12s4.5 10 10 10s10-4.5 10-10S17.5 2 12 2m-2 15l-5-5l1.41-1.41L10 14.17l7.59-7.59L19 8z"); } + xhtml.writeEndElement(); // path + xhtml.writeEndElement(); // svg xhtml.writeCharacters(modules[m].name()); @@ -248,10 +253,7 @@ private void startDocument () throws IOException,XMLStreamException // Add in the icon files for pass/fail/warn for(String icnName:new String[]{ - "fastqc_icon.png", - "warning.png", - "error.png", - "tick.png"}) + "fastqc_icon.png"}) { InputStream in =getClass().getResourceAsStream("/Templates/Icons/"+icnName); if(in==null) continue; @@ -336,22 +338,29 @@ private void startDocument () throws IOException,XMLStreamException continue; } xhtml.writeStartElement("li"); - xhtml.writeEmptyElement("img"); + xhtml.writeStartElement("svg"); + xhtml.writeAttribute("xmlns", "http://www.w3.org/2000/svg"); + xhtml.writeAttribute("width", "24"); + xhtml.writeAttribute("height", "24"); + xhtml.writeAttribute("viewBox", "0 0 24 24"); + xhtml.writeStartElement("path"); if (modules[m].raisesError()) { - xhtml.writeAttribute("src", base64ForIcon("Icons/error.png")); - xhtml.writeAttribute("alt", "[FAIL]"); + xhtml.writeAttribute("fill", "#d65d3e"); + xhtml.writeAttribute("d", "M12 2c5.53 0 10 4.47 10 10s-4.47 10-10 10S2 17.53 2 12S6.47 2 12 2m3.59 5L12 10.59L8.41 7L7 8.41L10.59 12L7 15.59L8.41 17L12 13.41L15.59 17L17 15.59L13.41 12L17 8.41z"); summaryText.append("FAIL"); } else if (modules[m].raisesWarning()) { - xhtml.writeAttribute("src", base64ForIcon("Icons/warning.png")); - xhtml.writeAttribute("alt", "[WARNING]"); + xhtml.writeAttribute("fill", "#eab30d"); + xhtml.writeAttribute("d", "M13 14h-2V9h2m0 9h-2v-2h2M1 21h22L12 2z"); summaryText.append("WARN"); } else { - xhtml.writeAttribute("src", base64ForIcon("Icons/tick.png")); - xhtml.writeAttribute("alt", "[PASS]"); + xhtml.writeAttribute("fill", "#4ba359"); + xhtml.writeAttribute("d", "M12 2C6.5 2 2 6.5 2 12s4.5 10 10 10s10-4.5 10-10S17.5 2 12 2m-2 15l-5-5l1.41-1.41L10 14.17l7.59-7.59L19 8z"); summaryText.append("PASS"); } + xhtml.writeEndElement(); // path + xhtml.writeEndElement(); // svg summaryText.append("\t"); summaryText.append(modules[m].name()); summaryText.append("\t"); @@ -409,4 +418,4 @@ private void closeDocument () throws XMLStreamException -} +} \ No newline at end of file From dd99dd52cacde39d5e12eb72040310de41a175ad Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Wed, 13 Aug 2025 01:22:04 +0200 Subject: [PATCH 02/27] Playing with refreshed sidebar style --- Templates/header_template.html | 66 +++++++++++++++---- .../FastQC/Report/HTMLReportArchive.java | 55 ++++++++-------- 2 files changed, 83 insertions(+), 38 deletions(-) diff --git a/Templates/header_template.html b/Templates/header_template.html index 7ffb43b..01451ea 100644 --- a/Templates/header_template.html +++ b/Templates/header_template.html @@ -1,10 +1,10 @@ @media screen { div.summary { - width: 18em; position:fixed; top: 3em; - margin:1em 0 0 1em; + margin-top:1em; + width: 18em; } div.main { @@ -29,7 +29,6 @@ margin:0; padding: 0.5em; font-size: 200%; - font-weight: bold; position:fixed; width:100%; top:0; @@ -85,7 +84,6 @@ margin:0; padding: 0.5em; font-size: 200%; - font-weight: bold; width:100%; } @@ -93,6 +91,7 @@ display:inline-block; float:left; clear:left; + font-weight: bold; } #header_filename { display:inline-block; @@ -102,22 +101,23 @@ margin-right:2em; text-align: right; } + #header_filename p { + margin: 0; + } div.header h3 { font-size: 50%; margin-bottom: 0; } - + + div.summary h2 { + margin-left: 1rem; + } div.summary ul { padding-left:0; list-style-type:none; } - - div.summary ul li img { - margin-bottom:-0.5em; - margin-top:0.5em; - } - + div.main { background-color: white; } @@ -184,3 +184,47 @@ padding-top: 0; margin-top: 0; } + + .summary li { + padding: 0.2rem 1rem; + border-bottom: 1px solid #CCC; + } + .summary li:last-child { + border-bottom: none; + } + .summary li a { + text-decoration: none; + color: #000; + font-size: 0.9rem; + } + .summary li span { + display: inline-block; + border: 2px solid; + border-radius: 0.2rem; + font-size: 0.7rem; + padding: 0.1rem 0.2rem; + margin-right: 0.4rem; + text-align: center; + width: 3rem; + text-transform: uppercase; + } + .sidebar-error { + background-color: #f0c6bc; + color: #862a13; + border-color: #862a13; + } + .sidebar-warning { + background-color: #e8d28f; + color: #8d6c08; + border-color: #8d6c08; + } + .sidebar-pass { + background-color: #afe0b7; + color: #2f6638; + border-color: #2f6638; + } + + h2 svg { + vertical-align: -0.1rem; + margin-right: 0.2rem; + } diff --git a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java index 2e93497..e518946 100644 --- a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java +++ b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java @@ -259,9 +259,9 @@ private void startDocument () throws IOException,XMLStreamException if(in==null) continue; zip.putNextEntry(new ZipEntry(folderName()+"/Icons/"+icnName)); int len; - while ((len = in.read(buffer)) > 0) { - zip.write(buffer, 0, len); - } + while ((len = in.read(buffer)) > 0) { + zip.write(buffer, 0, len); + } in.close(); zip.closeEntry(); } @@ -299,7 +299,7 @@ private void startDocument () throws IOException,XMLStreamException xhtml.writeStartElement("body"); - xhtml.writeStartElement("div"); + xhtml.wrxiteStartElement("div"); xhtml.writeAttribute("class", "header"); xhtml.writeStartElement("div"); @@ -313,9 +313,14 @@ private void startDocument () throws IOException,XMLStreamException xhtml.writeStartElement("div"); xhtml.writeAttribute("id", "header_filename"); + xhtml.writeStartElement("p"); xhtml.writeCharacters(df.format(new Date())); - xhtml.writeEmptyElement("br"); + xhtml.writeEndElement();//p + xhtml.writeStartElement("p"); + xhtml.writeStartElement("strong"); xhtml.writeCharacters(sequenceFile.name()); + xhtml.writeEndElement();//strong + xhtml.writeEndElement();//p xhtml.writeEndElement();//div xhtml.writeEndElement();//div @@ -338,42 +343,38 @@ private void startDocument () throws IOException,XMLStreamException continue; } xhtml.writeStartElement("li"); - xhtml.writeStartElement("svg"); - xhtml.writeAttribute("xmlns", "http://www.w3.org/2000/svg"); - xhtml.writeAttribute("width", "24"); - xhtml.writeAttribute("height", "24"); - xhtml.writeAttribute("viewBox", "0 0 24 24"); - xhtml.writeStartElement("path"); + xhtml.writeStartElement("a"); + xhtml.writeAttribute("href", "#M"+m); + + xhtml.writeStartElement("span"); if (modules[m].raisesError()) { - xhtml.writeAttribute("fill", "#d65d3e"); - xhtml.writeAttribute("d", "M12 2c5.53 0 10 4.47 10 10s-4.47 10-10 10S2 17.53 2 12S6.47 2 12 2m3.59 5L12 10.59L8.41 7L7 8.41L10.59 12L7 15.59L8.41 17L12 13.41L15.59 17L17 15.59L13.41 12L17 8.41z"); + xhtml.writeAttribute("class", "sidebar-error"); + xhtml.writeCharacters("Error"); summaryText.append("FAIL"); } else if (modules[m].raisesWarning()) { - xhtml.writeAttribute("fill", "#eab30d"); - xhtml.writeAttribute("d", "M13 14h-2V9h2m0 9h-2v-2h2M1 21h22L12 2z"); + xhtml.writeAttribute("class", "sidebar-warning"); + xhtml.writeCharacters("Warn"); summaryText.append("WARN"); } else { - xhtml.writeAttribute("fill", "#4ba359"); - xhtml.writeAttribute("d", "M12 2C6.5 2 2 6.5 2 12s4.5 10 10 10s10-4.5 10-10S17.5 2 12 2m-2 15l-5-5l1.41-1.41L10 14.17l7.59-7.59L19 8z"); + xhtml.writeAttribute("class", "sidebar-pass"); + xhtml.writeCharacters("Pass"); summaryText.append("PASS"); } - xhtml.writeEndElement(); // path - xhtml.writeEndElement(); // svg + xhtml.writeEndElement(); // span + + xhtml.writeCharacters(modules[m].name()); + xhtml.writeEndElement();//a + xhtml.writeEndElement();//li + summaryText.append("\t"); summaryText.append(modules[m].name()); summaryText.append("\t"); summaryText.append(sequenceFile.name()); summaryText.append(FastQCConfig.getInstance().lineSeparator); - - xhtml.writeStartElement("a"); - xhtml.writeAttribute("href", "#M"+m); - xhtml.writeCharacters(modules[m].name()); - xhtml.writeEndElement();//a - xhtml.writeEndElement();//li - - + + } xhtml.writeEndElement();//ul xhtml.writeEndElement();//div From 8a77c3270682ba9500f38b4dbafca6354294b115 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sat, 23 Aug 2025 23:40:47 +0200 Subject: [PATCH 03/27] Rename header template to .CSS, create new scaffold HTML template --- .../{header_template.html => fastqc.css} | 2 +- Templates/report_template.html | 35 ++ .../FastQC/Report/HTMLReportArchive.java | 302 ++++++++---------- 3 files changed, 173 insertions(+), 166 deletions(-) rename Templates/{header_template.html => fastqc.css} (99%) create mode 100644 Templates/report_template.html diff --git a/Templates/header_template.html b/Templates/fastqc.css similarity index 99% rename from Templates/header_template.html rename to Templates/fastqc.css index 01451ea..f52cd07 100644 --- a/Templates/header_template.html +++ b/Templates/fastqc.css @@ -1,5 +1,5 @@ - @media screen { +@media screen { div.summary { position:fixed; top: 3em; diff --git a/Templates/report_template.html b/Templates/report_template.html new file mode 100644 index 0000000..90be960 --- /dev/null +++ b/Templates/report_template.html @@ -0,0 +1,35 @@ + + + + {{TITLE}} + + + +
+
+ FastQCFastQC Report +
+
+

{{DATE}}

+

{{FILENAME}}

+
+
+ +
+

Summary

+
    +{{SUMMARY_ITEMS}} +
+
+ +
+{{MODULE_CONTENT}} +
+ +
+ Produced by FastQC (version {{VERSION}}) +
+ + diff --git a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java index e518946..32e7e20 100644 --- a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java +++ b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java @@ -66,32 +66,47 @@ public class HTMLReportArchive { private byte [] buffer = new byte[1024]; private File htmlFile; private File zipFile; + private StringWriter moduleContentWriter; + private String htmlTemplate; public HTMLReportArchive (SequenceFile sequenceFile, QCModule [] modules, File htmlFile) throws IOException, XMLStreamException { this.sequenceFile = sequenceFile; this.modules = modules; this.htmlFile = htmlFile; this.zipFile = new File(htmlFile.getAbsoluteFile().toString().replaceAll("\\.html$", "")+".zip"); - StringWriter htmlStr = new StringWriter(); + + // Load the HTML template + this.htmlTemplate = loadTemplate("/Templates/report_template.html"); + + // Create XMLStreamWriter for module content + this.moduleContentWriter = new StringWriter(); XMLOutputFactory xmlfactory = XMLOutputFactory.newInstance(); - this.xhtml= xmlfactory.createXMLStreamWriter(htmlStr); - - + this.xhtml= xmlfactory.createXMLStreamWriter(moduleContentWriter); + + zip = new ZipOutputStream(new FileOutputStream(zipFile)); zip.putNextEntry(new ZipEntry(folderName()+"/")); zip.putNextEntry(new ZipEntry(folderName()+"/Icons/")); zip.putNextEntry(new ZipEntry(folderName()+"/Images/")); - startDocument(); + + // Initialize data document + data.append("##FastQC\t"); + data.append(FastQCApplication.VERSION); + data.append("\n"); + + // Add icon files to zip + addIconsToZip(); + + // Generate module content for (int m=0;m>"); data.append(modules[m].name()); @@ -135,26 +149,36 @@ else if (modules[m].raisesWarning()) { xhtml.writeEndElement(); modules[m].makeReport(this); data.append(">>END_MODULE\n"); - + xhtml.writeEndElement(); } - closeDocument(); - - zip.putNextEntry(new ZipEntry(folderName()+"/fastqc_report.html")); + + // Close XMLStreamWriter and generate final HTML xhtml.flush(); xhtml.close(); - zip.write(htmlStr.toString().getBytes()); + + // Generate final HTML from template + String finalHtml = generateHtmlFromTemplate(); + + zip.putNextEntry(new ZipEntry(folderName()+"/fastqc_report.html")); + zip.write(finalHtml.getBytes()); zip.closeEntry(); zip.putNextEntry(new ZipEntry(folderName()+"/fastqc_data.txt")); zip.write(data.toString().getBytes()); zip.closeEntry(); - + + // Generate summary.txt + String summaryText = generateSummaryText(); + zip.putNextEntry(new ZipEntry(folderName()+"/summary.txt")); + zip.write(summaryText.getBytes()); + zip.closeEntry(); + //XSL-FO try { DocumentBuilderFactory domFactory=DocumentBuilderFactory.newInstance(); domFactory.setNamespaceAware(false); DocumentBuilder builder=domFactory.newDocumentBuilder(); - Document src=builder.parse(new InputSource( new StringReader(htmlStr.toString()))); + Document src=builder.parse(new InputSource( new StringReader(finalHtml))); InputStream rsrc=getClass().getResourceAsStream("/Templates/fastqc2fo.xsl"); if(rsrc!=null) { @@ -162,7 +186,7 @@ else if (modules[m].raisesWarning()) { builder=domFactory.newDocumentBuilder(); Document html2fo=builder.parse(rsrc); rsrc.close(); - + TransformerFactory tf=TransformerFactory.newInstance(); Templates templates=tf.newTemplates(new DOMSource(html2fo)); zip.putNextEntry(new ZipEntry(folderName()+"/fastqc.fo")); @@ -173,19 +197,19 @@ else if (modules[m].raisesWarning()) { catch (Exception e) { e.printStackTrace(); } - - + + zip.close(); - + // Save the HTML file at the same level as the zip file - + PrintWriter pr = new PrintWriter(new FileWriter(htmlFile)); - - pr.print(htmlStr.toString()); - + + pr.print(finalHtml); + pr.close(); - + if (FastQCConfig.getInstance().do_unzip) { unzipZipFile(zipFile); if (FastQCConfig.getInstance().delete_after_unzip) { @@ -193,18 +217,18 @@ else if (modules[m].raisesWarning()) { } } } - + private void unzipZipFile (File file) throws IOException { ZipFile zipFile = new ZipFile(file); Enumeration entries = zipFile.entries(); int size; byte [] buffer = new byte[1024]; - + while (entries.hasMoreElements()) { ZipEntry entry = entries.nextElement(); - + // System.out.println("Going to extract '"+entry.getName()+"'"); - + if (entry.isDirectory()) { File dir = new File(file.getParent()+"/"+entry.getName()); if (dir.exists() && dir.isDirectory()) continue; // Don't need to do anything @@ -222,7 +246,7 @@ private void unzipZipFile (File file) throws IOException { bos.close(); bis.close(); } - + zipFile.close(); } @@ -230,27 +254,20 @@ public XMLStreamWriter xhtmlStream () { return this.xhtml; } - + public StringBuffer dataDocument() { return data; } - + public String folderName () { return htmlFile.getName().replaceAll("\\.html$", ""); } - + public ZipOutputStream zipFile () { return zip; } - - private void startDocument () throws IOException,XMLStreamException - { - - // Just put the fastQC version at the start of the text report - data.append("##FastQC\t"); - data.append(FastQCApplication.VERSION); - data.append("\n"); - + + private void addIconsToZip() throws IOException { // Add in the icon files for pass/fail/warn for(String icnName:new String[]{ "fastqc_icon.png"}) @@ -265,129 +282,99 @@ private void startDocument () throws IOException,XMLStreamException in.close(); zip.closeEntry(); } - - + } - SimpleDateFormat df = new SimpleDateFormat("EEE d MMM yyyy"); - - xhtml.writeDTD(""); - xhtml.writeStartElement("html"); - xhtml.writeStartElement("head"); - - xhtml.writeStartElement("title"); - xhtml.writeCharacters(sequenceFile.name()); - xhtml.writeCharacters(" FastQC Report"); - xhtml.writeEndElement();//title - - InputStream rsrc=getClass().getResourceAsStream("/Templates/header_template.html"); - if(rsrc!=null) - { - xhtml.writeStartElement("style"); - xhtml.writeAttribute("type", "text/css"); - - byte array[]=new byte[128]; - int nRead; - while((nRead=rsrc.read(array))!=-1) { xhtml.writeCharacters(new String(array,0,nRead));} - rsrc.close(); - xhtml.writeEndElement();//style - } - - - - - xhtml.writeEndElement();//head - - xhtml.writeStartElement("body"); - - xhtml.wrxiteStartElement("div"); - xhtml.writeAttribute("class", "header"); - - xhtml.writeStartElement("div"); - xhtml.writeAttribute("id", "header_title"); - - xhtml.writeEmptyElement("img"); - xhtml.writeAttribute("src", base64ForIcon("Icons/fastqc_icon.png")); - xhtml.writeAttribute("alt", "FastQC"); - xhtml.writeCharacters("FastQC Report"); - xhtml.writeEndElement();//div - - xhtml.writeStartElement("div"); - xhtml.writeAttribute("id", "header_filename"); - xhtml.writeStartElement("p"); - xhtml.writeCharacters(df.format(new Date())); - xhtml.writeEndElement();//p - xhtml.writeStartElement("p"); - xhtml.writeStartElement("strong"); - xhtml.writeCharacters(sequenceFile.name()); - xhtml.writeEndElement();//strong - xhtml.writeEndElement();//p - xhtml.writeEndElement();//div - xhtml.writeEndElement();//div - - - xhtml.writeStartElement("div"); - xhtml.writeAttribute("class", "summary"); - - xhtml.writeStartElement("h2"); - xhtml.writeCharacters("Summary"); - xhtml.writeEndElement();//h2 - - - xhtml.writeStartElement("ul"); - + private String loadTemplate(String templatePath) throws IOException { + InputStream templateStream = getClass().getResourceAsStream(templatePath); + if (templateStream == null) { + throw new IOException("Template not found: " + templatePath); + } + + StringWriter templateWriter = new StringWriter(); + byte[] buffer = new byte[1024]; + int nRead; + while ((nRead = templateStream.read(buffer)) != -1) { + templateWriter.write(new String(buffer, 0, nRead)); + } + templateStream.close(); + return templateWriter.toString(); + } + + private String loadCss() throws IOException { + return loadTemplate("/Templates/fastqc.css"); + } + + private String generateSummaryItems() { + StringBuffer summaryItems = new StringBuffer(); + + for (int m=0;m\n"); + summaryItems.append(" \n"); + summaryItems.append(" Error"); + } else if (modules[m].raisesWarning()) { + summaryItems.append("sidebar-warning\">Warn"); + } else { + summaryItems.append("sidebar-pass\">Pass"); + } + + summaryItems.append(""); + summaryItems.append(modules[m].name()); + summaryItems.append("\n \n"); + summaryItems.append(" \n"); + } + + return summaryItems.toString(); + } + + private String generateSummaryText() { StringBuffer summaryText = new StringBuffer(); - + for (int m=0;m Date: Sat, 23 Aug 2025 23:53:29 +0200 Subject: [PATCH 04/27] Move more HTML out of the .java file and into file fragments --- Templates/Icons/error.svg | 3 + Templates/Icons/pass.svg | 3 + Templates/Icons/warning.svg | 3 + Templates/module_wrapper.html | 6 + Templates/report_template.html | 2 +- Templates/sidebar_item.html | 5 + .../FastQC/Report/HTMLReportArchive.java | 154 ++++++++++-------- 7 files changed, 104 insertions(+), 72 deletions(-) create mode 100644 Templates/Icons/error.svg create mode 100644 Templates/Icons/pass.svg create mode 100644 Templates/Icons/warning.svg create mode 100644 Templates/module_wrapper.html create mode 100644 Templates/sidebar_item.html diff --git a/Templates/Icons/error.svg b/Templates/Icons/error.svg new file mode 100644 index 0000000..e0adc44 --- /dev/null +++ b/Templates/Icons/error.svg @@ -0,0 +1,3 @@ + + + diff --git a/Templates/Icons/pass.svg b/Templates/Icons/pass.svg new file mode 100644 index 0000000..39f109f --- /dev/null +++ b/Templates/Icons/pass.svg @@ -0,0 +1,3 @@ + + + diff --git a/Templates/Icons/warning.svg b/Templates/Icons/warning.svg new file mode 100644 index 0000000..3023ec0 --- /dev/null +++ b/Templates/Icons/warning.svg @@ -0,0 +1,3 @@ + + + diff --git a/Templates/module_wrapper.html b/Templates/module_wrapper.html new file mode 100644 index 0000000..26dda66 --- /dev/null +++ b/Templates/module_wrapper.html @@ -0,0 +1,6 @@ +
+

+ {{STATUS_ICON}}{{MODULE_NAME}} +

+{{MODULE_CONTENT}} +
diff --git a/Templates/report_template.html b/Templates/report_template.html index 90be960..4b58f94 100644 --- a/Templates/report_template.html +++ b/Templates/report_template.html @@ -9,7 +9,7 @@
- FastQCFastQC Report + FastQCFastQC Report

{{DATE}}

diff --git a/Templates/sidebar_item.html b/Templates/sidebar_item.html new file mode 100644 index 0000000..0f7b354 --- /dev/null +++ b/Templates/sidebar_item.html @@ -0,0 +1,5 @@ +
  • + + {{STATUS_TEXT}}{{MODULE_NAME}} + +
    • diff --git a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java index 32e7e20..0328dac 100644 --- a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java +++ b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java @@ -97,68 +97,15 @@ public HTMLReportArchive (SequenceFile sequenceFile, QCModule [] modules, File h // Add icon files to zip addIconsToZip(); - // Generate module content - for (int m=0;m>"); - data.append(modules[m].name()); - data.append("\t"); - if (modules[m].raisesError()) { - data.append("fail"); - } - else if (modules[m].raisesWarning()) { - data.append("warn"); - } - else { - data.append("pass"); - } - data.append("\n"); - xhtml.writeEndElement(); - modules[m].makeReport(this); - data.append(">>END_MODULE\n"); - - xhtml.writeEndElement(); - } - - // Close XMLStreamWriter and generate final HTML + // Close XMLStreamWriter (no longer needed for main content) xhtml.flush(); xhtml.close(); // Generate final HTML from template - String finalHtml = generateHtmlFromTemplate(); + String finalHtml = generateHtmlFromTemplate(moduleContent); zip.putNextEntry(new ZipEntry(folderName()+"/fastqc_report.html")); zip.write(finalHtml.getBytes()); @@ -300,34 +247,35 @@ private String loadTemplate(String templatePath) throws IOException { return templateWriter.toString(); } - private String loadCss() throws IOException { + private String loadCss() throws IOException { return loadTemplate("/Templates/fastqc.css"); } - private String generateSummaryItems() { + private String generateSummaryItems() throws IOException { StringBuffer summaryItems = new StringBuffer(); + String sidebarItemTemplate = loadTemplate("/Templates/sidebar_item.html"); for (int m=0;m\n"); - summaryItems.append(" \n"); - summaryItems.append(" Error"); + item = item.replace("{{STATUS_CLASS}}", "sidebar-error"); + item = item.replace("{{STATUS_TEXT}}", "Error"); } else if (modules[m].raisesWarning()) { - summaryItems.append("sidebar-warning\">Warn"); + item = item.replace("{{STATUS_CLASS}}", "sidebar-warning"); + item = item.replace("{{STATUS_TEXT}}", "Warn"); } else { - summaryItems.append("sidebar-pass\">Pass"); + item = item.replace("{{STATUS_CLASS}}", "sidebar-pass"); + item = item.replace("{{STATUS_TEXT}}", "Pass"); } - summaryItems.append(""); - summaryItems.append(modules[m].name()); - summaryItems.append("\n \n"); - summaryItems.append(" \n"); + summaryItems.append(item).append("\n"); } return summaryItems.toString(); @@ -359,7 +307,71 @@ private String generateSummaryText() { return summaryText.toString(); } - private String generateHtmlFromTemplate() throws IOException { + private String getStatusIcon(QCModule module) throws IOException { + if (module.raisesError()) { + return loadTemplate("/Templates/Icons/error.svg"); + } else if (module.raisesWarning()) { + return loadTemplate("/Templates/Icons/warning.svg"); + } else { + return loadTemplate("/Templates/Icons/pass.svg"); + } + } + + private String generateModuleContent() throws IOException, XMLStreamException { + StringBuffer allModulesContent = new StringBuffer(); + String moduleWrapperTemplate = loadTemplate("/Templates/module_wrapper.html"); + + // Generate content for each module + for (int m=0;m>"); + data.append(modules[m].name()); + data.append("\t"); + if (modules[m].raisesError()) { + data.append("fail"); + } else if (modules[m].raisesWarning()) { + data.append("warn"); + } else { + data.append("pass"); + } + data.append("\n"); + + // Let the module generate its content + modules[m].makeReport(this); + data.append(">>END_MODULE\n"); + + // Close the module's XMLStreamWriter + moduleXhtml.flush(); + moduleXhtml.close(); + + // Restore the original XMLStreamWriter + this.xhtml = originalXhtml; + + // Apply the module wrapper template + String moduleWrapper = moduleWrapperTemplate; + moduleWrapper = moduleWrapper.replace("{{MODULE_INDEX}}", String.valueOf(m)); + moduleWrapper = moduleWrapper.replace("{{MODULE_NAME}}", modules[m].name()); + moduleWrapper = moduleWrapper.replace("{{STATUS_ICON}}", getStatusIcon(modules[m])); + moduleWrapper = moduleWrapper.replace("{{MODULE_CONTENT}}", moduleBodyWriter.toString()); + + allModulesContent.append(moduleWrapper).append("\n"); + } + + return allModulesContent.toString(); + } + + private String generateHtmlFromTemplate(String moduleContent) throws IOException { SimpleDateFormat df = new SimpleDateFormat("EEE d MMM yyyy"); String html = htmlTemplate; @@ -369,7 +381,7 @@ private String generateHtmlFromTemplate() throws IOException { html = html.replace("{{FILENAME}}", sequenceFile.name()); html = html.replace("{{FASTQC_ICON_BASE64}}", base64ForIcon("Icons/fastqc_icon.png")); html = html.replace("{{SUMMARY_ITEMS}}", generateSummaryItems()); - html = html.replace("{{MODULE_CONTENT}}", moduleContentWriter.toString()); + html = html.replace("{{MODULE_CONTENT}}", moduleContent); html = html.replace("{{VERSION}}", FastQCApplication.VERSION); return html; From 897ecc74e8a0edf52cd96e582ced874df202b5e9 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sun, 24 Aug 2025 00:01:01 +0200 Subject: [PATCH 05/27] Clean up CSS file, remove @screen stuff and remove duplicates --- Templates/fastqc.css | 310 ++++++++++++++++++++----------------------- 1 file changed, 146 insertions(+), 164 deletions(-) diff --git a/Templates/fastqc.css b/Templates/fastqc.css index f52cd07..859d729 100644 --- a/Templates/fastqc.css +++ b/Templates/fastqc.css @@ -1,62 +1,4 @@ - -@media screen { - div.summary { - position:fixed; - top: 3em; - margin-top:1em; - width: 18em; - } - - div.main { - display:block; - position:absolute; - overflow:auto; - height:auto; - width:auto; - top:4.5em; - bottom:2.3em; - left:18em; - right:0; - border-left: 1px solid #CCC; - padding:0 0 0 1em; - background-color: white; - z-index:1; - } - - div.header { - background-color: #EEE; - border:0; - margin:0; - padding: 0.5em; - font-size: 200%; - position:fixed; - width:100%; - top:0; - left:0; - z-index:2; - } - - div.footer { - background-color: #EEE; - border:0; - margin:0; - padding:0.5em; - height: 1.3em; - overflow:hidden; - font-size: 100%; - font-weight: bold; - position:fixed; - bottom:0; - width:100%; - z-index:2; - } - - img.indented { - margin-left: 3em; - } - } - - @media print { +@media print { img { max-width:100% !important; page-break-inside: avoid; @@ -67,164 +9,204 @@ div.header { background-color: #FFF; } - - } - - body { - font-family: sans-serif; - color: #000; + +} + +body { + font-family: sans-serif; + color: #000; background-color: #FFF; border: 0; margin: 0; padding: 0; - } - - div.header { +} + +div.summary { + position:fixed; + top: 3em; + margin-top:1em; + width: 18em; +} + +div.summary h2 { + margin-left: 1rem; +} + +div.summary ul { + padding-left:0; + list-style-type:none; +} + +div.main { + display:block; + position:absolute; + overflow:auto; + height:auto; + width:auto; + top:4.5em; + bottom:2.3em; + left:18em; + right:0; + border-left: 1px solid #CCC; + padding:0 0 0 1em; + background-color: white; + z-index:1; +} + +div.module { + padding-bottom:1.5em; + padding-top:1.5em; +} + +div.header { + background-color: #EEE; border:0; margin:0; padding: 0.5em; font-size: 200%; + position:fixed; width:100%; - } - - #header_title { + top:0; + left:0; + z-index:2; +} + +#header_title { display:inline-block; float:left; clear:left; font-weight: bold; - } - #header_filename { +} + +#header_filename { display:inline-block; float:right; clear:right; font-size: 50%; margin-right:2em; text-align: right; - } - #header_filename p { - margin: 0; - } +} - div.header h3 { +#header_filename p { + margin: 0; +} + +div.header h3 { font-size: 50%; margin-bottom: 0; - } +} - div.summary h2 { - margin-left: 1rem; - } - div.summary ul { - padding-left:0; - list-style-type:none; - } - - div.main { - background-color: white; - } - - div.module { - padding-bottom:1.5em; - padding-top:1.5em; - } - - div.footer { +div.footer { background-color: #EEE; border:0; margin:0; - padding: 0.5em; + padding:0.5em; + height: 1.3em; + overflow:hidden; font-size: 100%; font-weight: bold; + position:fixed; + bottom:0; width:100%; - } + z-index:2; +} +img.indented { + margin-left: 3em; +} - a { +a { color: #000080; - } +} - a:hover { +a:hover { color: #800000; - } - - h2 { +} + +h2 { color: #800000; padding-bottom: 0; margin-bottom: 0; clear:left; - } +} - table { +table { margin-left: 3em; text-align: center; - } - - th { +} + +th { text-align: center; background-color: #000080; color: #FFF; padding: 0.4em; - } - - td { - font-family: monospace; +} + +td { + font-family: monospace; text-align: left; background-color: #EEE; color: #000; padding: 0.4em; - } +} - img { +img { padding-top: 0; margin-top: 0; border-top: 0; - } +} - - p { +p { padding-top: 0; margin-top: 0; - } - - .summary li { - padding: 0.2rem 1rem; - border-bottom: 1px solid #CCC; - } - .summary li:last-child { - border-bottom: none; - } - .summary li a { - text-decoration: none; - color: #000; - font-size: 0.9rem; - } - .summary li span { - display: inline-block; - border: 2px solid; - border-radius: 0.2rem; - font-size: 0.7rem; - padding: 0.1rem 0.2rem; - margin-right: 0.4rem; - text-align: center; - width: 3rem; - text-transform: uppercase; - } - .sidebar-error { - background-color: #f0c6bc; - color: #862a13; - border-color: #862a13; - } - .sidebar-warning { - background-color: #e8d28f; - color: #8d6c08; - border-color: #8d6c08; - } - .sidebar-pass { - background-color: #afe0b7; - color: #2f6638; - border-color: #2f6638; - } - - h2 svg { - vertical-align: -0.1rem; - margin-right: 0.2rem; - } +} + +.summary li { + padding: 0.2rem 1rem; + border-bottom: 1px solid #CCC; +} + +.summary li:last-child { + border-bottom: none; +} + +.summary li a { + text-decoration: none; + color: #000; + font-size: 0.9rem; +} + +.summary li span { + display: inline-block; + border: 2px solid; + border-radius: 0.2rem; + font-size: 0.7rem; + padding: 0.1rem 0.2rem; + margin-right: 0.4rem; + text-align: center; + width: 3rem; + text-transform: uppercase; +} + +.sidebar-error { + background-color: #f0c6bc; + color: #862a13; + border-color: #862a13; +} + +.sidebar-warning { + background-color: #e8d28f; + color: #8d6c08; + border-color: #8d6c08; +} + +.sidebar-pass { + background-color: #afe0b7; + color: #2f6638; + border-color: #2f6638; +} + +h2 svg { + vertical-align: -0.1rem; + margin-right: 0.2rem; +} From d58129337aa168e97ca5deca25b2dd70551779b6 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sun, 24 Aug 2025 00:38:57 +0200 Subject: [PATCH 06/27] Restructure report * No fixed navbar + sidebar * Updated sidebar with nav and details * Mobile responsive design, using CSS-only approach --- Templates/fastqc.css | 489 +++++++++++++++++++++++++-------- Templates/report_template.html | 56 ++-- 2 files changed, 408 insertions(+), 137 deletions(-) diff --git a/Templates/fastqc.css b/Templates/fastqc.css index 859d729..761ade1 100644 --- a/Templates/fastqc.css +++ b/Templates/fastqc.css @@ -1,15 +1,30 @@ @media print { - img { - max-width:100% !important; - page-break-inside: avoid; - } - h2, h3 { - page-break-after: avoid; - } - div.header { - background-color: #FFF; - } + img { + max-width:100% !important; + page-break-inside: avoid; + } + h2, h3 { + page-break-after: avoid; + } + .sidebar-header { + background-color: #FFF; + } + .mobile-nav { + display: none !important; + } + .sidebar { + position: static !important; + transform: none !important; + width: auto !important; + } + .container { + flex-direction: column !important; + } +} +/* Reset and base styles */ +* { + box-sizing: border-box; } body { @@ -19,173 +34,188 @@ body { border: 0; margin: 0; padding: 0; + line-height: 1.4; } -div.summary { - position:fixed; - top: 3em; - margin-top:1em; - width: 18em; +/* Mobile navigation bar */ +.mobile-nav { + display: none; + background-color: #EEE; + padding: 0.75rem 1rem; + border-bottom: 1px solid #CCC; + position: fixed; + top: 0; + left: 0; + right: 0; + z-index: 1000; + align-items: center; + justify-content: space-between; } -div.summary h2 { - margin-left: 1rem; +.menu-toggle-input { + display: none; } -div.summary ul { - padding-left:0; - list-style-type:none; +.menu-toggle { + cursor: pointer; + padding: 0.25rem; + display: flex; + flex-direction: column; + gap: 3px; + background: none; + border: none; } -div.main { - display:block; - position:absolute; - overflow:auto; - height:auto; - width:auto; - top:4.5em; - bottom:2.3em; - left:18em; - right:0; - border-left: 1px solid #CCC; - padding:0 0 0 1em; - background-color: white; - z-index:1; +.hamburger { + width: 20px; + height: 2px; + background-color: #333; + transition: all 0.3s ease; } -div.module { - padding-bottom:1.5em; - padding-top:1.5em; +.mobile-title { + font-size: 1rem; + display: flex; + align-items: center; + justify-content: flex-end; + gap: 0.25rem; + flex: 1; + min-width: 0; /* Allow shrinking */ + margin-right: 1rem; + text-align: right; } -div.header { - background-color: #EEE; - border:0; - margin:0; - padding: 0.5em; - font-size: 200%; - position:fixed; - width:100%; - top:0; - left:0; - z-index:2; -} - -#header_title { - display:inline-block; - float:left; - clear:left; +.mobile-title-app { font-weight: bold; + flex-shrink: 0; /* Don't shrink the "FastQC:" part */ } -#header_filename { - display:inline-block; - float:right; - clear:right; - font-size: 50%; - margin-right:2em; - text-align: right; +.mobile-title-filename { + font-weight: normal; + font-size: 0.9rem; + color: #666; + overflow: hidden; + text-overflow: ellipsis; + white-space: nowrap; + min-width: 0; /* Allow shrinking */ } -#header_filename p { - margin: 0; +.mobile-icon { + height: 20px; + width: 20px; + flex-shrink: 0; + margin: 0 !important; } -div.header h3 { - font-size: 50%; - margin-bottom: 0; +/* Main container */ +.container { + display: flex; + min-height: 100vh; } -div.footer { - background-color: #EEE; - border:0; - margin:0; - padding:0.5em; - height: 1.3em; - overflow:hidden; - font-size: 100%; - font-weight: bold; - position:fixed; - bottom:0; - width:100%; - z-index:2; +/* Sidebar */ +.sidebar { + width: 300px; + background-color: #F8F8F8; + border-right: 1px solid #CCC; + display: flex; + flex-direction: column; + position: fixed; + top: 0; + left: 0; + bottom: 0; + overflow-y: auto; } -img.indented { - margin-left: 3em; +.sidebar-header { + background-color: #EEE; + padding: 1rem; + border-bottom: 1px solid #CCC; } - -a { - color: #000080; +.sidebar-header a { + text-decoration: none; + color: #000; } -a:hover { - color: #800000; +.header-title { + font-weight: bold; + font-size: 1.25rem; + margin-bottom: 0.5rem; + display: flex; + align-items: center; + gap: 0.5rem; } -h2 { - color: #800000; - padding-bottom: 0; - margin-bottom: 0; - clear:left; +.header-title img { + height: 24px; + width: auto; + margin: 0; } -table { - margin-left: 3em; - text-align: center; +.header-filename { + font-size: 0.85rem; + color: #666; } -th { - text-align: center; - background-color: #000080; - color: #FFF; - padding: 0.4em; +.header-filename p { + margin: 0.25rem 0; } -td { - font-family: monospace; - text-align: left; - background-color: #EEE; +.header-filename strong { color: #000; - padding: 0.4em; } -img { - padding-top: 0; - margin-top: 0; - border-top: 0; +/* Navigation */ +.navigation { + flex: 1; + padding: 1rem 0; } -p { - padding-top: 0; - margin-top: 0; +.navigation h2 { + margin: 0 0 1rem 1rem; + color: #800000; + font-size: 1.1rem; } -.summary li { - padding: 0.2rem 1rem; - border-bottom: 1px solid #CCC; +.navigation ul { + padding: 0; + margin: 0; + list-style-type: none; +} + +.navigation li { + padding: 0.5rem 1rem; + border-bottom: 1px solid #DDD; + transition: background-color 0.2s ease; } -.summary li:last-child { +.navigation li:last-child { border-bottom: none; } -.summary li a { +.navigation li:hover { + background-color: #F0F0F0; +} + +.navigation li a { text-decoration: none; color: #000; font-size: 0.9rem; + display: flex; + align-items: center; + gap: 0.5rem; } -.summary li span { +.navigation li span { display: inline-block; border: 2px solid; border-radius: 0.2rem; font-size: 0.7rem; - padding: 0.1rem 0.2rem; - margin-right: 0.4rem; + padding: 0.1rem 0.3rem; text-align: center; - width: 3rem; + min-width: 3.5rem; text-transform: uppercase; + font-weight: bold; } .sidebar-error { @@ -206,7 +236,224 @@ p { border-color: #2f6638; } +/* Main content area */ +.main { + flex: 1; + margin-left: 300px; + padding: 2rem; + background-color: white; + min-height: 100vh; +} + +.module { + padding-bottom: 2rem; + padding-top: 1rem; + overflow-x: auto; +} + +/* Footer */ +.footer { + margin-top: 3rem; + padding: 1.5rem 0; + border-top: 1px solid #EEE; + font-size: 0.9rem; + color: #666; + text-align: center; +} + +/* Content styling */ +h2 { + color: #800000; + padding-bottom: 0.5rem; + margin-bottom: 1rem; + border-bottom: 2px solid #800000; + display: flex; + align-items: center; + gap: 0.5rem; +} + h2 svg { vertical-align: -0.1rem; - margin-right: 0.2rem; +} + +/* Table wrapper for horizontal scrolling */ + +table { + margin: 1rem 0; + border-collapse: collapse; + width: 100%; + max-width: 100%; + min-width: 600px; /* Ensure tables don't get too cramped */ +} + +th { + text-align: center; + background-color: #000080; + color: #FFF; + padding: 0.75rem 0.5rem; + font-weight: bold; +} + +td { + font-family: monospace; + text-align: left; + background-color: #F5F5F5; + color: #000; + padding: 0.5rem; + border-bottom: 1px solid #DDD; +} + +tr:nth-child(even) td { + background-color: #EEE; +} + +img { + max-width: 100%; + height: auto; + padding-top: 0; + margin-top: 0; + border-top: 0; + display: block; + margin-left: auto; + margin-right: auto; +} + +img.indented { + margin-left: 2rem; +} + +p { + padding-top: 0; + margin: 1rem 0; +} + +a { + color: #000080; + transition: color 0.2s ease; +} + +a:hover { + color: #800000; +} + +/* Mobile responsive styles */ +@media (max-width: 768px) { + .mobile-nav { + display: flex; + } + + .container { + padding-top: 60px; /* Account for fixed mobile nav */ + } + + .sidebar { + position: fixed; + top: 48px; + left: 0; + bottom: 0; + right: 0; + width: 100%; + height: calc(100% - 48px); + transform: translateX(-100%); + transition: transform 0.3s ease; + z-index: 999; + box-shadow: none; + } + + /* CSS-only toggle for mobile sidebar */ + .menu-toggle-input:checked ~ .container .sidebar { + transform: translateX(0); + } + + /* Hide entire sidebar header on mobile */ + .sidebar-header { + display: none; + } + + /* Hamburger animation when menu is open */ + .menu-toggle-input:checked ~ .mobile-nav .hamburger:nth-child(1) { + transform: rotate(45deg) translate(3px, 3px); + } + + .menu-toggle-input:checked ~ .mobile-nav .hamburger:nth-child(2) { + opacity: 0; + } + + .menu-toggle-input:checked ~ .mobile-nav .hamburger:nth-child(3) { + transform: rotate(-45deg) translate(4px, -4px); + } + + .main { + width: 100%; + margin-left: 0; + padding: 1rem; + overflow-x: hidden; /* Prevent main content horizontal scroll */ + } + + .module { + padding-bottom: 1.5rem; + padding-left: 0; + padding-right: 0; + } + + table { + font-size: 0.85rem; + min-width: 500px; /* Smaller minimum width for mobile */ + } + + th, td { + padding: 0.5rem 0.25rem; + } + + /* Ensure images don't cause horizontal scroll */ + img { + max-width: 100% !important; + height: auto !important; + } + + /* Remove left margin from indented images on mobile */ + img.indented { + margin-left: 0 !important; + margin-right: 0 !important; + } +} + +@media (max-width: 480px) { + .main { + padding: 0.75rem; + padding-left: 0.5rem; + padding-right: 0.5rem; + } + + .sidebar { + width: 100%; + } + + .sidebar-header { + padding: 0.75rem; + } + + .header-title { + font-size: 1.1rem; + } + + table { + font-size: 0.8rem; + min-width: 400px; /* Even smaller for very small screens */ + } + + .navigation li { + padding: 0.4rem 0.75rem; + } + + .module { + padding-left: 0; + padding-right: 0; + } + + /* Remove left margin from indented images on small mobile */ + img.indented { + margin-left: 0 !important; + margin-right: 0 !important; + } } diff --git a/Templates/report_template.html b/Templates/report_template.html index 4b58f94..6ae00c1 100644 --- a/Templates/report_template.html +++ b/Templates/report_template.html @@ -2,34 +2,58 @@ {{TITLE}} + -
    -
    - FastQCFastQC Report -
    -
    -

    {{DATE}}

    -

    {{FILENAME}}

    + + + + +
    + +
    + FastQC + FastQC: + {{FILENAME}}
    -
    -

    Summary

    - + + -
    + +
    {{MODULE_CONTENT}} -
    -
    - Produced by FastQC (version {{VERSION}}) +
    + Produced by FastQC (version {{VERSION}}) +
    +
    From df973cf0777f4bba81ab9b4f9afbdeae7c4aa0de Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Sun, 24 Aug 2025 21:19:21 +0200 Subject: [PATCH 07/27] Basic stats - look like a definition list (CSS only) --- Templates/fastqc.css | 55 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 55 insertions(+) diff --git a/Templates/fastqc.css b/Templates/fastqc.css index 761ade1..758cb0b 100644 --- a/Templates/fastqc.css +++ b/Templates/fastqc.css @@ -307,6 +307,61 @@ tr:nth-child(even) td { background-color: #EEE; } +/* Style Basic Statistics table (first module) to look like a definition list */ +.module:first-of-type table { + border-collapse: separate; + border-spacing: 0; + min-width: auto; + margin: 1rem 0; + width: auto; + max-width: 600px; +} + +.module:first-of-type table thead { + display: none; /* Hide the table headers */ +} + +.module:first-of-type table tbody tr { + display: block; + margin-bottom: 1.5rem; + border: none; + background: none; +} + +.module:first-of-type table tbody td:first-child { + /* Style like definition list title (label above) */ + display: block; + font-weight: normal; + font-family: sans-serif; + background-color: transparent; + padding: 0; + border: none; + color: #666; + text-transform: uppercase; + font-size: 0.75rem; + letter-spacing: 0.8px; + margin-bottom: 0.25rem; + line-height: 1.2; +} + +.module:first-of-type table tbody td:last-child { + /* Style like definition list value (below label) */ + display: block; + font-family: sans-serif; + font-weight: normal; + background-color: transparent; + padding: 0; + margin: 0; + border: none; + color: #000; + font-size: 1.1rem; + line-height: 1.3; +} + +.module:first-of-type table tbody tr:nth-child(even) td { + background-color: transparent; +} + img { max-width: 100%; height: auto; From cebd4d4a81534f156d9b7cee2b58091c92c67b42 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 25 Aug 2025 07:36:14 +0200 Subject: [PATCH 08/27] Basic stats: revert to table, but keep clean styling --- Templates/fastqc.css | 45 ++++++++++---------------------------------- 1 file changed, 10 insertions(+), 35 deletions(-) diff --git a/Templates/fastqc.css b/Templates/fastqc.css index 758cb0b..be9e5b9 100644 --- a/Templates/fastqc.css +++ b/Templates/fastqc.css @@ -258,7 +258,6 @@ body { border-top: 1px solid #EEE; font-size: 0.9rem; color: #666; - text-align: center; } /* Content styling */ @@ -309,12 +308,8 @@ tr:nth-child(even) td { /* Style Basic Statistics table (first module) to look like a definition list */ .module:first-of-type table { - border-collapse: separate; - border-spacing: 0; min-width: auto; - margin: 1rem 0; - width: auto; - max-width: 600px; + max-width: 100%; } .module:first-of-type table thead { @@ -322,44 +317,24 @@ tr:nth-child(even) td { } .module:first-of-type table tbody tr { - display: block; - margin-bottom: 1.5rem; - border: none; background: none; } - -.module:first-of-type table tbody td:first-child { - /* Style like definition list title (label above) */ - display: block; - font-weight: normal; +.module:first-of-type table td { font-family: sans-serif; background-color: transparent; - padding: 0; - border: none; - color: #666; - text-transform: uppercase; - font-size: 0.75rem; - letter-spacing: 0.8px; - margin-bottom: 0.25rem; - line-height: 1.2; } +.module:first-of-type table tbody td:first-child { + font-weight: bold; + color: #333; + text-align: right; + width: 12rem; +} .module:first-of-type table tbody td:last-child { - /* Style like definition list value (below label) */ - display: block; - font-family: sans-serif; - font-weight: normal; - background-color: transparent; - padding: 0; - margin: 0; - border: none; color: #000; - font-size: 1.1rem; - line-height: 1.3; } - -.module:first-of-type table tbody tr:nth-child(even) td { - background-color: transparent; +.module:first-of-type table tbody tr:last-child td { + border-bottom: none; } img { From e7f36622460e455cedaf28ec61877a7d63a22e7e Mon Sep 17 00:00:00 2001 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uedy`>U`v-vw@*z4Mi|h#VNS&8|6^;qw^?byyPA0nK;Y@>=d#Wzp$PyomPE?{ literal 0 HcmV?d00001 From 90c8a270a888429c939585da4628c13b84d8ecb6 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Mon, 25 Aug 2025 10:37:16 +0200 Subject: [PATCH 10/27] Use SVG icon instead of PNG --- Templates/Icons/fastqc_icon.svg | 47 +++++++++++++++++++ Templates/fastqc.css | 6 ++- Templates/report_template.html | 4 +- .../FastQC/Report/HTMLReportArchive.java | 47 +++++-------------- 4 files changed, 65 insertions(+), 39 deletions(-) create mode 100644 Templates/Icons/fastqc_icon.svg diff --git a/Templates/Icons/fastqc_icon.svg b/Templates/Icons/fastqc_icon.svg new file mode 100644 index 0000000..618ccb4 --- /dev/null +++ b/Templates/Icons/fastqc_icon.svg @@ -0,0 +1,47 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/Templates/fastqc.css b/Templates/fastqc.css index be9e5b9..8c7a7e5 100644 --- a/Templates/fastqc.css +++ b/Templates/fastqc.css @@ -100,7 +100,8 @@ body { min-width: 0; /* Allow shrinking */ } -.mobile-icon { +.mobile-icon, +.mobile-title svg { height: 20px; width: 20px; flex-shrink: 0; @@ -146,7 +147,8 @@ body { gap: 0.5rem; } -.header-title img { +.header-title img, +.header-title svg { height: 24px; width: auto; margin: 0; diff --git a/Templates/report_template.html b/Templates/report_template.html index 6ae00c1..0e0e545 100644 --- a/Templates/report_template.html +++ b/Templates/report_template.html @@ -19,7 +19,7 @@
    - FastQC + {{FASTQC_ICON_SVG_MOBILE}} FastQC: {{FILENAME}}
    @@ -30,7 +30,7 @@