diff --git a/INSTALL.md b/INSTALL.md index 10bf4d2..e97c762 100644 --- a/INSTALL.md +++ b/INSTALL.md @@ -151,7 +151,7 @@ zcat *fastq.gz | fastqc stdin:my_results If you want to run FastQC as part of a sequencing pipeline you may wish to change the formatting of the report to add in your own branding or to include extra information. -In the Templates directory you will find a file called `header_template.html` which +In the Templates directory you will find a file called `fastqc.css` which you can edit to change the look of the report. This file contains all of the header for the report file, including the CSS section and you can alter this however you see fit. diff --git a/Templates/header_template.html b/Templates/fastqc.css similarity index 100% rename from Templates/header_template.html rename to Templates/fastqc.css diff --git a/Templates/module_wrapper.html b/Templates/module_wrapper.html new file mode 100644 index 0000000..4d071bb --- /dev/null +++ b/Templates/module_wrapper.html @@ -0,0 +1,6 @@ +
+

+ {{ALT}}{{MODULE_NAME}} +

+{{MODULE_CONTENT}} +
diff --git a/Templates/report_template.html b/Templates/report_template.html new file mode 100644 index 0000000..ebcd91d --- /dev/null +++ b/Templates/report_template.html @@ -0,0 +1,31 @@ + + + + {{TITLE}} FastQC Report + + + +
+
+ FastQCFastQC Report +
+
+ {{DATE}}
{{FILENAME}} +
+
+
+

Summary

+ +
+
+{{MODULE_CONTENT}} +
+
+ Produced by FastQC (version {{VERSION}}) +
+ + diff --git a/Templates/sidebar_item.html b/Templates/sidebar_item.html new file mode 100644 index 0000000..1eb5bca --- /dev/null +++ b/Templates/sidebar_item.html @@ -0,0 +1,4 @@ +
  • + {{ALT}} + {{MODULE_NAME}} +
    • diff --git a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java index 334eda5..bc1f399 100644 --- a/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java +++ b/uk/ac/babraham/FastQC/Report/HTMLReportArchive.java @@ -66,90 +66,58 @@ public class HTMLReportArchive { private byte [] buffer = new byte[1024]; private File htmlFile; private File zipFile; + private final String reportTemplate; + private final String sidebarItemTemplate; + private final String moduleWrapperTemplate; + private final String cssContent; 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(); + this.reportTemplate = loadTemplate("/Templates/report_template.html"); + this.sidebarItemTemplate = loadTemplate("/Templates/sidebar_item.html"); + this.moduleWrapperTemplate = loadTemplate("/Templates/module_wrapper.html"); + this.cssContent = loadResource("/Templates/fastqc.css"); + XMLOutputFactory xmlfactory = XMLOutputFactory.newInstance(); - this.xhtml= xmlfactory.createXMLStreamWriter(htmlStr); + this.xhtml= xmlfactory.createXMLStreamWriter(new StringWriter()); zip = new ZipOutputStream(new FileOutputStream(zipFile)); zip.putNextEntry(new ZipEntry(folderName()+"/")); zip.putNextEntry(new ZipEntry(folderName()+"/Icons/")); zip.putNextEntry(new ZipEntry(folderName()+"/Images/")); - startDocument(); - 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(); - } - closeDocument(); - - zip.putNextEntry(new ZipEntry(folderName()+"/fastqc_report.html")); + data.append("##FastQC\t"); + data.append(FastQCApplication.VERSION); + data.append("\n"); + addIconsToZip(); + + String moduleContent = generateModuleContent(); xhtml.flush(); xhtml.close(); - zip.write(htmlStr.toString().getBytes()); + + String finalHtml = generateHtmlFromTemplate(moduleContent); + + 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(); - + + zip.putNextEntry(new ZipEntry(folderName()+"/summary.txt")); + zip.write(generateSummaryText().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) { @@ -176,7 +144,7 @@ else if (modules[m].raisesWarning()) { PrintWriter pr = new PrintWriter(new FileWriter(htmlFile)); - pr.print(htmlStr.toString()); + pr.print(finalHtml); pr.close(); @@ -238,15 +206,7 @@ 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"); - - // Add in the icon files for pass/fail/warn + private void addIconsToZip() throws IOException { for(String icnName:new String[]{ "fastqc_icon.png", "warning.png", @@ -263,121 +223,172 @@ 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"); + private String loadResource(String resourcePath) throws IOException { + InputStream in = getClass().getResourceAsStream(resourcePath); + if (in == null) { + throw new IOException("Resource not found: " + resourcePath); + } - 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 - } + StringWriter writer = new StringWriter(); + byte[] readBuffer = new byte[1024]; + int nRead; + while ((nRead = in.read(readBuffer)) != -1) { + writer.write(new String(readBuffer, 0, nRead)); + } + in.close(); + return writer.toString(); + } - - - - xhtml.writeEndElement();//head - - xhtml.writeStartElement("body"); - - xhtml.writeStartElement("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.writeCharacters(df.format(new Date())); - xhtml.writeEmptyElement("br"); - xhtml.writeCharacters(sequenceFile.name()); - 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 { + return loadResource(templatePath).stripTrailing(); + } + + private String escapeXml(String s) { + return s.replace("&", "&").replace("<", "<").replace(">", ">"); + } + + private String generateSummaryItems() throws IOException { + StringBuffer summaryItems = new StringBuffer(); + + 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"); + + modules[m].makeReport(this); + data.append(">>END_MODULE\n"); + + moduleXhtml.flush(); + moduleXhtml.close(); + + this.xhtml = originalXhtml; + + String icon; + String alt; + if (modules[m].raisesError()) { + icon = base64ForIcon("Icons/error.png"); + alt = "[FAIL]"; + } + else if (modules[m].raisesWarning()) { + icon = base64ForIcon("Icons/warning.png"); + alt = "[WARN]"; + } + else { + icon = base64ForIcon("Icons/tick.png"); + alt = "[OK]"; + } + + String moduleWrapper = moduleWrapperTemplate + .replace("{{MODULE_INDEX}}", String.valueOf(m)) + .replace("{{ICON}}", icon) + .replace("{{ALT}}", alt) + .replace("{{MODULE_NAME}}", escapeXml(modules[m].name())) + .replace("{{MODULE_CONTENT}}", moduleBodyWriter.toString()); + + allModulesContent.append(moduleWrapper); + } + + return allModulesContent.toString(); } - + + private String generateHtmlFromTemplate(String moduleContent) throws IOException { + SimpleDateFormat df = new SimpleDateFormat("EEE d MMM yyyy"); + + return reportTemplate + .replace("{{TITLE}}", escapeXml(sequenceFile.name())) + .replace("{{CSS_CONTENT}}", escapeXml(cssContent)) + .replace("{{FASTQC_ICON}}", base64ForIcon("Icons/fastqc_icon.png")) + .replace("{{DATE}}", escapeXml(df.format(new Date()))) + .replace("{{FILENAME}}", escapeXml(sequenceFile.name())) + .replace("{{SUMMARY_ITEMS}}", generateSummaryItems()) + .replace("{{MODULE_CONTENT}}", moduleContent) + .replace("{{VERSION}}", FastQCApplication.VERSION); + } + private String base64ForIcon (String path) { try { BufferedImage b = ImageIO.read(ClassLoader.getSystemResource("Templates/"+path)); @@ -388,25 +399,4 @@ private String base64ForIcon (String path) { return "Failed"; } } - - private void closeDocument () throws XMLStreamException - { - xhtml.writeEndElement();//div - xhtml.writeStartElement("div"); - xhtml.writeAttribute("class", "footer"); - xhtml.writeCharacters("Produced by "); - xhtml.writeStartElement("a"); - xhtml.writeAttribute("href", "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/"); - xhtml.writeCharacters("FastQC"); - xhtml.writeEndElement();//a - xhtml.writeCharacters(" (version "+FastQCApplication.VERSION+")"); - xhtml.writeEndElement();//div - - xhtml.writeEndElement();//body - xhtml.writeEndElement();//html - } - - - - }