diff --git a/datastore_server/build.gradle b/datastore_server/build.gradle
index a5cd41854c738fdc62757c184c4fcc835740aa03..1501e6205d54c6bfa2e1a33ebc90927f7c4ca0ca 100644
--- a/datastore_server/build.gradle
+++ b/datastore_server/build.gradle
@@ -32,6 +32,9 @@ dependencies {
'cisd:cisd-image-readers:r1553067167',
'hjg:pngj:0.62',
'apache:commons-fileupload:1.3.3',
+ 'docx4j:docx4j:6.1.2',
+ 'freva:ascii-table:1.2.0',
+ 'jsoup:jsoup:1.14.2',
'dspace:xoai-data-provider:4.2.0'
runtime 'bioformats:bioformats:6.5.1'
diff --git a/datastore_server/source/java/ch/ethz/sis/DOCXBuilder.java b/datastore_server/source/java/ch/ethz/sis/DOCXBuilder.java
new file mode 100644
index 0000000000000000000000000000000000000000..6c0f4185b58ad39b7a78f1a606281f2d2592a8f3
--- /dev/null
+++ b/datastore_server/source/java/ch/ethz/sis/DOCXBuilder.java
@@ -0,0 +1,256 @@
+package ch.ethz.sis;
+
+import java.io.ByteArrayOutputStream;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.util.Base64;
+
+import org.docx4j.jaxb.Context;
+import org.docx4j.openpackaging.contenttype.ContentType;
+import org.docx4j.openpackaging.packages.WordprocessingMLPackage;
+import org.docx4j.openpackaging.parts.PartName;
+import org.docx4j.openpackaging.parts.WordprocessingML.AlternativeFormatInputPart;
+import org.docx4j.relationships.Relationship;
+import org.docx4j.wml.CTAltChunk;
+import org.eclipse.jetty.client.HttpClient;
+import org.eclipse.jetty.client.api.ContentResponse;
+import org.eclipse.jetty.client.api.Request;
+import org.jsoup.Jsoup;
+import org.jsoup.nodes.Document;
+import org.jsoup.nodes.Element;
+import org.jsoup.select.Elements;
+
+import ch.systemsx.cisd.common.http.JettyHttpClientFactory;
+import com.github.freva.asciitable.AsciiTable;
+
+public class DOCXBuilder
+{
+ public static void main(String[] args) throws Exception
+ {
+ DOCXBuilder docx = new DOCXBuilder();
+ docx.addTitle("TitleA");
+ docx.addHeader("MetaA");
+ docx.addProperty("PropertyA", "ValueA");
+ docx.addProperty("PropertyB", "ValueB");
+ docx.addProperty("PropertyC",
+ "<p>I am normal</p><p style=\"color:red;\">I am red</p><p style=\"color:blue;\">I am blue</p><p style=\"font-size:36px;\">I am big</p>");
+
+ FileOutputStream out = new FileOutputStream(new File("wordFromHTML.docx"));
+ out.write(docx.getDocBytes());
+ out.close();
+ }
+
+ private static final String START_RICH_TEXT = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<html><head></head><body>";
+
+ private static final String END_RICH_TEXT = "</body></html>";
+
+ private StringBuffer doc;
+
+ private String closedDoc;
+
+ private boolean closed;
+
+ public DOCXBuilder()
+ {
+ System.setProperty("javax.xml.transform.TransformerFactory", "com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl");
+ closed = false;
+ doc = new StringBuffer();
+ startDoc();
+ }
+
+ public void setDocument(String doc)
+ {
+ this.doc = new StringBuffer(doc);
+ closed = true;
+ }
+
+ private void startDoc()
+ {
+ if (!closed)
+ {
+ doc.append("<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Strict//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd\">");
+ doc.append("<html xmlns=\"http://www.w3.org/1999/xhtml\">");
+ doc.append("<head></head>");
+ doc.append("<body>");
+ }
+ }
+
+ private void endDoc()
+ {
+ if (!closed)
+ {
+ doc.append("</body>");
+ doc.append("</html>");
+ closed = true;
+ closedDoc = fixImages(doc);
+ }
+ }
+
+ public void addProperty(String key, String value)
+ {
+ if (!closed)
+ {
+ doc.append("<p>").append("<b>").append(key).append(": ").append("</b>").append("</p>");
+ addParagraph(value);
+ }
+ }
+
+ public void addParagraph(String value)
+ {
+ if (!closed)
+ {
+ value = cleanXMLEnvelope(value);
+ doc.append("<p>").append(value).append("</p>");
+ }
+ }
+
+ public void addTitle(String title)
+ {
+ if (!closed)
+ {
+ doc.append("<h1>").append(title).append("</h1>");
+ }
+ }
+
+ public void addHeader(String header)
+ {
+ if (!closed)
+ {
+ doc.append("<h2>").append(header).append("</h2>");
+ }
+ }
+
+ public byte[] getHTMLBytes() throws Exception
+ {
+ if (!closed)
+ {
+ endDoc();
+ }
+ return closedDoc.getBytes();
+ }
+
+ public byte[] getDocBytes() throws Exception
+ {
+ // .. Finish Document
+ if (!closed)
+ {
+ endDoc();
+ }
+
+ // .. HTML Code
+ WordprocessingMLPackage wordMLPackage = WordprocessingMLPackage.createPackage();
+ AlternativeFormatInputPart afiPart = new AlternativeFormatInputPart(new PartName("/hw.html"));
+ afiPart.setBinaryData(closedDoc.getBytes());
+ afiPart.setContentType(new ContentType("text/html"));
+ Relationship altChunkRel = wordMLPackage.getMainDocumentPart().addTargetPart(afiPart);
+
+ // .. the bit in document body
+ CTAltChunk ac = Context.getWmlObjectFactory().createCTAltChunk();
+ ac.setId(altChunkRel.getId());
+ wordMLPackage.getMainDocumentPart().addObject(ac);
+
+ // .. content type
+ wordMLPackage.getContentTypeManager().addDefaultContentType("html", "text/html");
+ ByteArrayOutputStream outStream = new ByteArrayOutputStream();
+ wordMLPackage.save(outStream);
+
+ return outStream.toByteArray();
+ }
+
+ private String cleanXMLEnvelope(String value)
+ {
+ if (value.startsWith(START_RICH_TEXT) && value.endsWith(END_RICH_TEXT))
+ {
+ value = value.substring(START_RICH_TEXT.length(), value.length() - END_RICH_TEXT.length());
+ }
+ return value;
+ }
+
+ private String fixImages(StringBuffer buffer)
+ {
+ Document jsoupDoc = Jsoup.parse(buffer.toString());
+ jsoupDoc.outputSettings().syntax(Document.OutputSettings.Syntax.xml);
+ Elements elements = jsoupDoc.select("img");
+
+ // Fixes images sizes
+ for (Element element : elements)
+ {
+ String style = element.attr("style");
+ if (style != null)
+ {
+ String[] rules = style.split(";");
+ if (rules != null)
+ {
+ for (int rIdx = 0; rIdx < rules.length; rIdx++)
+ {
+ String rule = rules[rIdx];
+ String[] ruleElements = rule.split(":");
+ if (ruleElements != null && ruleElements.length == 2)
+ {
+ String ruleKey = ruleElements[0].trim();
+ String ruleValue = ruleElements[1].trim();
+ if ((ruleKey.toLowerCase().equals("width") || ruleKey.toLowerCase().equals("height"))
+ && ruleValue.endsWith("px"))
+ {
+ element.attr(ruleKey, ruleValue.substring(0, ruleValue.length() - 2));
+ }
+ }
+ }
+ }
+ }
+
+ // Converts to Base64
+ String src = element.attr("src");
+ try
+ {
+ element.attr("src", getDataUriFromUri(src));
+ } catch (Exception ex)
+ {
+
+ }
+ }
+
+ return jsoupDoc.html();
+ }
+
+ // private String encodeImgAsBase64(String value) {
+ // Document doc = Jsoup.parse(value);
+ // doc.outputSettings().syntax(Document.OutputSettings.Syntax.xml);
+ // Elements elements = doc.select("img");
+ //
+ // for (Element element : elements) {
+ // String src = element.attr("src");
+ // try {
+ // element.attr("src", getDataUriFromUri(src));
+ // } catch(Exception ex) {
+ //
+ // }
+ // }
+ //
+ // return doc.html();
+ // }
+
+ private static String getDataUriFromUri(String url) throws Exception
+ {
+ HttpClient client = JettyHttpClientFactory.getHttpClient();
+ Request requestEntity = client.newRequest(url).method("GET");
+ ContentResponse contentResponse = requestEntity.send();
+ return "data:" + contentResponse.getMediaType() + ";base64," + Base64.getEncoder().encodeToString(contentResponse.getContent());
+ }
+
+ // public static String convertJsonToText(final String jsonString) {
+ // return AsciiTable.getTable(null, jsonStringToArray(jsonString));
+ // }
+ //
+ // private static String[] jsonStringToArray(final String jsonString) {
+ // final ArrayList<String> stringList = new ArrayList<String>();
+ //
+ // final JSONArray jsonArray = new JSONArray(jsonString);
+ //
+ // for (int i = 0; i < jsonArray.length(); i++) {
+ // stringList.add(jsonArray.getString(i));
+ // }
+ //
+ // return stringList.toArray();
+ // }
+}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/docxbuilder-source/DOCXBuilder.java b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/docxbuilder-source/DOCXBuilder.java
deleted file mode 100644
index 1543daad5c20b9c1826ec530b4c5cf19e4872b34..0000000000000000000000000000000000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/docxbuilder-source/DOCXBuilder.java
+++ /dev/null
@@ -1,225 +0,0 @@
-package ch.ethz.sis;
-import java.io.ByteArrayOutputStream;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.util.Base64;
-
-import org.docx4j.jaxb.Context;
-import org.docx4j.openpackaging.contenttype.ContentType;
-import org.docx4j.openpackaging.packages.WordprocessingMLPackage;
-import org.docx4j.openpackaging.parts.PartName;
-import org.docx4j.openpackaging.parts.WordprocessingML.AlternativeFormatInputPart;
-import org.docx4j.relationships.Relationship;
-import org.docx4j.wml.CTAltChunk;
-import org.eclipse.jetty.client.HttpClient;
-import org.eclipse.jetty.client.api.ContentResponse;
-import org.eclipse.jetty.client.api.Request;
-import org.jsoup.Jsoup;
-import org.jsoup.nodes.Document;
-import org.jsoup.nodes.Element;
-import org.jsoup.select.Elements;
-
-import ch.systemsx.cisd.common.http.JettyHttpClientFactory;
-import com.github.freva.asciitable.AsciiTable;
-
-public class DOCXBuilder {
- public static void main(String[] args) throws Exception {
- DOCXBuilder docx = new DOCXBuilder();
- docx.addTitle("TitleA");
- docx.addHeader("MetaA");
- docx.addProperty("PropertyA", "ValueA");
- docx.addProperty("PropertyB", "ValueB");
- docx.addProperty("PropertyC",
- "<p>I am normal</p><p style=\"color:red;\">I am red</p><p style=\"color:blue;\">I am blue</p><p style=\"font-size:36px;\">I am big</p>");
-
- FileOutputStream out = new FileOutputStream(new File("wordFromHTML.docx"));
- out.write(docx.getDocBytes());
- out.close();
- }
-
- private static final String START_RICH_TEXT = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>\n<html><head></head><body>";
-
- private static final String END_RICH_TEXT = "</body></html>";
-
- private StringBuffer doc;
-
- private String closedDoc;
-
- private boolean closed;
-
- public DOCXBuilder() {
- System.setProperty("javax.xml.transform.TransformerFactory", "com.sun.org.apache.xalan.internal.xsltc.trax.TransformerFactoryImpl");
- closed = false;
- doc = new StringBuffer();
- startDoc();
- }
-
- public void setDocument(String doc) {
- this.doc = new StringBuffer(doc);
- closed = true;
- }
-
- private void startDoc() {
- if (!closed) {
- doc.append("<!DOCTYPE html PUBLIC \"-//W3C//DTD XHTML 1.0 Strict//EN\" \"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd\">");
- doc.append("<html xmlns=\"http://www.w3.org/1999/xhtml\">");
- doc.append("<head></head>");
- doc.append("<body>");
- }
- }
-
- private void endDoc() {
- if (!closed) {
- doc.append("</body>");
- doc.append("</html>");
- closed = true;
- closedDoc = fixImages(doc);
- }
- }
-
- public void addProperty(String key, String value) {
- if (!closed) {
- doc.append("<p>").append("<b>").append(key).append(": ").append("</b>").append("</p>");
- addParagraph(value);
- }
- }
-
- public void addParagraph(String value)
- {
- if (!closed)
- {
- value = cleanXMLEnvelope(value);
- doc.append("<p>").append(value).append("</p>");
- }
- }
-
- public void addTitle(String title) {
- if (!closed) {
- doc.append("<h1>").append(title).append("</h1>");
- }
- }
-
- public void addHeader(String header) {
- if (!closed) {
- doc.append("<h2>").append(header).append("</h2>");
- }
- }
-
- public byte[] getHTMLBytes() throws Exception {
- if (!closed) {
- endDoc();
- }
- return closedDoc.getBytes();
- }
-
- public byte[] getDocBytes() throws Exception {
- // .. Finish Document
- if (!closed) {
- endDoc();
- }
-
- // .. HTML Code
- WordprocessingMLPackage wordMLPackage = WordprocessingMLPackage.createPackage();
- AlternativeFormatInputPart afiPart = new AlternativeFormatInputPart(new PartName("/hw.html"));
- afiPart.setBinaryData(closedDoc.getBytes());
- afiPart.setContentType(new ContentType("text/html"));
- Relationship altChunkRel = wordMLPackage.getMainDocumentPart().addTargetPart(afiPart);
-
- // .. the bit in document body
- CTAltChunk ac = Context.getWmlObjectFactory().createCTAltChunk();
- ac.setId(altChunkRel.getId());
- wordMLPackage.getMainDocumentPart().addObject(ac);
-
- // .. content type
- wordMLPackage.getContentTypeManager().addDefaultContentType("html", "text/html");
- ByteArrayOutputStream outStream = new ByteArrayOutputStream();
- wordMLPackage.save(outStream);
-
- return outStream.toByteArray();
- }
-
- private String cleanXMLEnvelope(String value) {
- if (value.startsWith(START_RICH_TEXT) && value.endsWith(END_RICH_TEXT)) {
- value = value.substring(START_RICH_TEXT.length() + 3, value.length() - END_RICH_TEXT.length());
- }
- return value;
- }
-
- private String fixImages(StringBuffer buffer) {
- Document jsoupDoc = Jsoup.parse(buffer.toString());
- jsoupDoc.outputSettings().syntax(Document.OutputSettings.Syntax.xml);
- Elements elements = jsoupDoc.select("img");
-
- // Fixes images sizes
- for (Element element : elements) {
- String style = element.attr("style");
- if (style != null) {
- String[] rules = style.split(";");
- if(rules != null) {
- for (int rIdx = 0; rIdx < rules.length; rIdx++) {
- String rule = rules[rIdx];
- String[] ruleElements = rule.split(":");
- if (ruleElements != null && ruleElements.length == 2) {
- String ruleKey = ruleElements[0].trim();
- String ruleValue = ruleElements[1].trim();
- if ((ruleKey.toLowerCase().equals("width") || ruleKey.toLowerCase().equals("height"))
- && ruleValue.endsWith("px")) {
- element.attr(ruleKey, ruleValue.substring(0, ruleValue.length() - 2));
- }
- }
- }
- }
- }
-
- // Converts to Base64
- String src = element.attr("src");
- try {
- element.attr("src", getDataUriFromUri(src));
- } catch(Exception ex) {
-
- }
- }
-
- return jsoupDoc.html();
- }
-
-// private String encodeImgAsBase64(String value) {
-// Document doc = Jsoup.parse(value);
-// doc.outputSettings().syntax(Document.OutputSettings.Syntax.xml);
-// Elements elements = doc.select("img");
-//
-// for (Element element : elements) {
-// String src = element.attr("src");
-// try {
-// element.attr("src", getDataUriFromUri(src));
-// } catch(Exception ex) {
-//
-// }
-// }
-//
-// return doc.html();
-// }
-
- private static String getDataUriFromUri(String url) throws Exception {
- HttpClient client = JettyHttpClientFactory.getHttpClient();
- Request requestEntity = client.newRequest(url).method("GET");
- ContentResponse contentResponse = requestEntity.send();
- return "data:"+contentResponse.getMediaType()+";base64,"+Base64.getEncoder().encodeToString(contentResponse.getContent());
- }
-
-// public static String convertJsonToText(final String jsonString) {
-// return AsciiTable.getTable(null, jsonStringToArray(jsonString));
-// }
-//
-// private static String[] jsonStringToArray(final String jsonString) {
-// final ArrayList<String> stringList = new ArrayList<String>();
-//
-// final JSONArray jsonArray = new JSONArray(jsonString);
-//
-// for (int i = 0; i < jsonArray.length(); i++) {
-// stringList.add(jsonArray.getString(i));
-// }
-//
-// return stringList.toArray();
-// }
-}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/generalExports.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/generalExports.py
index 085255914b26c92a1a7e76bc3bbe29c4acab1a33..b8e43ee8ee5170f8b32362913f1defe636a17206 100644
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/generalExports.py
+++ b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/generalExports.py
@@ -97,6 +97,10 @@ def generateZipFile(entities, includeRoot, sessionToken, tempDirPath, tempZipFil
try:
generateFilesInZip(zos, entities, includeRoot, sessionToken, tempDirPath)
+ except BaseException as e:
+ operationLog.error("Error occurred: %s" % e)
+ except Throwable as e:
+ operationLog.error("Error occurred: %s" % e, e)
finally:
zos.close()
fos.close()
\ No newline at end of file
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/ascii-table-1.1.0.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/ascii-table-1.1.0.jar
deleted file mode 100644
index df2fd3bcc3372019cb319f49eb267b5d9a06391d..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/ascii-table-1.1.0.jar and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docx4j-3.3.3.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docx4j-3.3.3.jar
deleted file mode 100644
index d7baf6c21d8bc639542552e0f0f42185b15786f2..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docx4j-3.3.3.jar and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docxbuilder.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docxbuilder.jar
deleted file mode 100644
index d74f90a27a688fb2c5025ff99c782a733566b315..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/docxbuilder.jar and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/jsoup-1.11.3.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/jsoup-1.11.3.jar
deleted file mode 100644
index 80c0ca8252a0a00f0ea7156d7aed058b1ce876b4..0000000000000000000000000000000000000000
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diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/serializer-2.7.2.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/serializer-2.7.2.jar
deleted file mode 100644
index 10c881c100ebd5ecd9ffb5ba912711f667169a76..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/serializer-2.7.2.jar and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/slf4j-api-1.7.21.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/slf4j-api-1.7.21.jar
deleted file mode 100644
index 2a5c33ec55491e5b4be53525d8d7242e53e020c0..0000000000000000000000000000000000000000
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diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/xalan-2.7.2.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/exports-api/lib/xalan-2.7.2.jar
deleted file mode 100644
index abdabe33ec1368f910ac7012f081ad2ae9e4897b..0000000000000000000000000000000000000000
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