Adding option to generate ETL document as HTML or markdown

src/org/ohdsi/rabbitInAHat/ETLMarkupDocumentGenerator.java

@@ -0,0 +1,355 @@
+/*******************************************************************************
+ * Copyright 2019 Observational Health Data Sciences and Informatics
+ * 
+ * This file is part of WhiteRabbit
+ * 
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * 
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ ******************************************************************************/
+package org.ohdsi.rabbitInAHat;
+
+import java.awt.Color;
+import java.awt.image.BufferedImage;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.imageio.ImageIO;
+
+import org.apache.poi.openxml4j.exceptions.InvalidFormatException;
+import org.ohdsi.rabbitInAHat.dataModel.ETL;
+import org.ohdsi.rabbitInAHat.dataModel.ETL.FileFormat;
+import org.ohdsi.rabbitInAHat.dataModel.Field;
+import org.ohdsi.rabbitInAHat.dataModel.ItemToItemMap;
+import org.ohdsi.rabbitInAHat.dataModel.MappableItem;
+import org.ohdsi.rabbitInAHat.dataModel.Mapping;
+import org.ohdsi.rabbitInAHat.dataModel.Table;
+import org.ohdsi.utilities.StringUtilities;
+import org.ohdsi.utilities.files.Row;
+import org.ohdsi.utilities.files.WriteTextFile;
+
+public class ETLMarkupDocumentGenerator {
+
+	private MarkupDocument	document;
+	private ETL				etl;
+
+	public enum DocumentType {
+		MARKDOWN, HTML
+	};
+
+	public static void main(String[] args) {
+		ETL etl = ETL.fromFile("c:/temp/markdown/exampleEtl.json.gz", FileFormat.GzipJson);
+		ETLMarkupDocumentGenerator generator = new ETLMarkupDocumentGenerator(etl);
+		generator.generate("c:/temp/markdown/index.html", DocumentType.HTML);
+
+	}
+
+	public ETLMarkupDocumentGenerator(ETL etl) {
+		this.etl = etl;
+	}
+
+	public void generate(String fileName, DocumentType documentType) {
+		try {
+			if (documentType == DocumentType.HTML)
+				document = new HtmlDocument(fileName);
+			else
+				document = new MarkdownDocument(fileName);
+			addTableLevelSection();
+
+			for (Table targetTable : etl.getTargetDatabase().getTables())
+				addTargetTableSection(targetTable);
+
+			document.close();
+		} catch (FileNotFoundException e) {
+			e.printStackTrace();
+		} catch (IOException e) {
+			e.printStackTrace();
+		} catch (InvalidFormatException e) {
+			e.printStackTrace();
+		}
+	}
+
+	private void addTargetTableSection(Table targetTable) throws InvalidFormatException, IOException {
+		document.addHeader2("Table name: " + targetTable.getName());
+
+		for (ItemToItemMap tableToTableMap : etl.getTableToTableMapping().getSourceToTargetMaps())
+			if (tableToTableMap.getTargetItem() == targetTable) {
+				Table sourceTable = (Table) tableToTableMap.getSourceItem();
+				Mapping<Field> fieldtoFieldMapping = etl.getFieldToFieldMapping(sourceTable, targetTable);
+
+				document.addHeader3("Reading from " + tableToTableMap.getSourceItem());
+
+				if (!tableToTableMap.getLogic().equals("")) {
+					document.addParagraph(tableToTableMap.getLogic());
+				}
+
+				if (!tableToTableMap.getComment().equals("")) {
+					document.addParagraph(tableToTableMap.getComment());
+				}
+
+				// Add image of field to field mapping
+				MappingPanel mappingPanel = new MappingPanel(fieldtoFieldMapping);
+				mappingPanel.setShowOnlyConnectedItems(true);
+				int height = mappingPanel.getMinimumSize().height;
+				mappingPanel.setSize(800, height);
+				BufferedImage image = new BufferedImage(800, height, BufferedImage.TYPE_INT_ARGB);
+				image.getGraphics().setColor(Color.WHITE);
+				image.getGraphics().fillRect(0, 0, image.getWidth(), image.getHeight());
+				mappingPanel.paint(image.getGraphics());
+				document.addImage(image, "Field mapping");
+
+				// Add table of field to field mapping
+				List<Row> rows = new ArrayList<Row>();
+				for (MappableItem targetField : fieldtoFieldMapping.getTargetItems()) {
+					Row row = new Row();
+					row.add("Destination Field", targetField.getName());
+
+					StringBuilder source = new StringBuilder();
+					StringBuilder logic = new StringBuilder();
+					StringBuilder comment = new StringBuilder();
+					for (ItemToItemMap fieldToFieldMap : fieldtoFieldMapping.getSourceToTargetMaps()) {
+						if (fieldToFieldMap.getTargetItem() == targetField) {
+							if (source.length() != 0)
+								source.append("\n");
+							source.append(fieldToFieldMap.getSourceItem().getName().trim());
+
+							if (logic.length() != 0)
+								logic.append("\n");
+							logic.append(fieldToFieldMap.getLogic().trim());
+
+							if (comment.length() != 0)
+								comment.append("\n");
+							comment.append(fieldToFieldMap.getComment().trim());
+						}
+					}
+					row.add("Source field", source.toString().trim());
+					row.add("Logic", logic.toString().trim());
+					row.add("Comment field", comment.toString().trim());
+					rows.add(row);
+				}
+				document.addTable(rows);
+			}
+	}
+
+	private void addTableLevelSection() throws InvalidFormatException, IOException {
+		MappingPanel mappingPanel = new MappingPanel(etl.getTableToTableMapping());
+		mappingPanel.setShowOnlyConnectedItems(true);
+		int height = mappingPanel.getMinimumSize().height;
+		mappingPanel.setSize(800, height);
+
+		document.addHeader1(mappingPanel.getSourceDbName() + " Data Mapping Approach to " + mappingPanel.getTargetDbName());
+
+		BufferedImage image = new BufferedImage(800, height, BufferedImage.TYPE_INT_ARGB);
+		image.getGraphics().setColor(Color.WHITE);
+		image.getGraphics().fillRect(0, 0, image.getWidth(), image.getHeight());
+		mappingPanel.paint(image.getGraphics());
+		document.addImage(image, "Table mapping");
+	}
+
+	private interface MarkupDocument {
+		public void addHeader1(String header);
+
+		public void addHeader2(String header);
+
+		public void addHeader3(String header);
+
+		public void addParagraph(String text);
+
+		public void addImage(BufferedImage image, String alternative);
+
+		public void addTable(List<Row> rows);
+
+		public void close();
+	}
+
+	private class MarkdownDocument implements MarkupDocument {
+		private List<String>	lines		= new ArrayList<String>();
+		private int				imageIndex	= 0;
+		private String fileName;
+		private String filesFolder;
+		private String mainFolder;
+
+		/**
+		 * 
+		 * @param fileName  Full path of the markdown document to create
+		 */
+		public MarkdownDocument(String fileName) {
+			this.fileName = fileName;
+			mainFolder = new File(fileName).getParent();
+			filesFolder = new File(fileName).getName().replaceAll("(\\.md)|(\\.MD)", "_files");
+		}
+
+		@Override
+		public void addHeader1(String header) {
+			lines.add("# " + header);
+			lines.add("");
+		}
+
+		@Override
+		public void addHeader2(String header) {
+			lines.add("## " + header);
+			lines.add("");
+		}
+
+		@Override
+		public void addHeader3(String header) {
+			lines.add("### " + header);
+			lines.add("");
+		}
+
+		@Override
+		public void addParagraph(String text) {
+			lines.add(text);
+			lines.add("");
+		}
+
+		@Override
+		public void addImage(BufferedImage image, String alternative) {
+			if (imageIndex == 0) {
+				File folder = new File(mainFolder + "/"+ filesFolder);
+				if (!folder.exists())
+					folder.mkdirs();
+			}
+			imageIndex++;
+			String imageFile = filesFolder + "/image" + imageIndex + ".png";
+			try {
+				ImageIO.write(image, "png", new File(mainFolder + "/" + imageFile));
+			} catch (IOException e) {
+				throw new RuntimeException(e);
+			}
+			lines.add("![](" + imageFile + ")");
+			lines.add("");
+		}
+
+		@Override
+		public void close() {
+			WriteTextFile out = new WriteTextFile(fileName);
+			for (String line : lines)
+				out.writeln(line);
+			out.close();
+		}
+
+		@Override
+		public void addTable(List<Row> rows) {
+			if (rows.size() > 0) {
+				String header = "| " + StringUtilities.join(rows.get(0).getFieldNames(), " | ") + " |";
+				header = header.replaceAll("\n", "  ");
+				lines.add(header);
+				StringBuilder line = new StringBuilder();
+				for (int i = 0; i < rows.get(0).getFieldNames().size(); i++)
+					line.append("| --- ");
+				line.append("|");
+				lines.add(line.toString());
+
+				for (Row row : rows) {
+					line = new StringBuilder();
+					for (String value : row.getCells())
+						line.append("| " + value.replaceAll("\n", "  ") + " ");
+					line.append("|");
+					lines.add(line.toString());
+				}
+				lines.add("");
+			}
+		}
+	}
+
+	private class HtmlDocument implements MarkupDocument {
+		private List<String>	lines		= new ArrayList<String>();
+		private int				imageIndex	= 0;
+		private String fileName;
+		private String filesFolder;
+		private String mainFolder;
+
+		/**
+		 * 
+		 * @param fileName   Full path of the HTML file to create.
+		 */
+		public HtmlDocument(String fileName) {
+			this.fileName = fileName;
+			mainFolder = new File(fileName).getParent();
+			filesFolder = new File(fileName).getName().replaceAll("(\\.html?)|(\\.html?)", "_files");
+		}
+
+
+		@Override
+		public void addHeader1(String header) {
+			lines.add("<h1>" + header + "</h1>");
+			lines.add("");
+		}
+
+		@Override
+		public void addHeader2(String header) {
+			lines.add("<h2>" + header + "</h2>");
+			lines.add("");
+		}
+
+		@Override
+		public void addHeader3(String header) {
+			lines.add("<h3>" + header + "</h3>");
+			lines.add("");
+		}
+
+		@Override
+		public void addParagraph(String text) {
+			lines.add("<p>" + text + "</p>");
+			lines.add("");
+		}
+
+		@Override
+		public void addImage(BufferedImage image, String alternative) {
+			if (imageIndex == 0) {
+				File folder = new File(mainFolder + "/"+ filesFolder);
+				if (!folder.exists())
+					folder.mkdirs();
+			}
+			imageIndex++;
+			String imageFile = filesFolder + "/image" + imageIndex + ".png";
+			try {
+				ImageIO.write(image, "png", new File(mainFolder + "/" + imageFile));
+			} catch (IOException e) {
+				throw new RuntimeException(e);
+			}
+			lines.add("<img src=\"" + imageFile + "\" alt=\"" + alternative + "\">");
+			lines.add("");
+		}
+
+		@Override
+		public void close() {
+			WriteTextFile out = new WriteTextFile(fileName);
+			for (String line : lines)
+				out.writeln(line);
+			out.close();
+		}
+
+		@Override
+		public void addTable(List<Row> rows) {
+			if (rows.size() > 0) {
+				lines.add("<table>");
+				lines.add("\t<tr>");
+				for (String fieldName : rows.get(0).getFieldNames())
+					lines.add("\t\t<th>" + fieldName + "</th>");
+				lines.add("\t</tr>");
+
+				for (Row row : rows) {
+					lines.add("\t<tr>");
+					for (String cell : row.getCells())
+						lines.add("\t\t<td>" + cell + "</td>");
+					lines.add("\t</tr>");
+				}
+				lines.add("</table>");
+				lines.add("");
+			}
+		}
+	}
+}

src/org/ohdsi/rabbitInAHat/ETLDocumentGenerator.java → src/org/ohdsi/rabbitInAHat/ETLWordDocumentGenerator.java

@@ -39,7 +39,7 @@
 import org.ohdsi.rabbitInAHat.dataModel.Mapping;
 import org.ohdsi.rabbitInAHat.dataModel.Table;
 
-public class ETLDocumentGenerator {
+public class ETLWordDocumentGenerator {
 
 	public static void generate(ETL etl, String filename, boolean includeCounts) {
 		try {