diff --git a/plasmid/source/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.java b/plasmid/source/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.java
index e34d23b6d7781b06ac645571426bb9fea5095f67..68514657526f2688f701d8dcf12979bca9cd86e6 100644
--- a/plasmid/source/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.java
+++ b/plasmid/source/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.java
@@ -3,17 +3,17 @@ package ch.ethz.ssdm.eln;
import java.io.File;
import java.io.FileNotFoundException;
import java.net.URL;
-import java.util.ArrayList;
-import java.util.List;
-import org.apache.commons.httpclient.HttpClient;
-import org.apache.commons.httpclient.HttpStatus;
-import org.apache.commons.httpclient.methods.PostMethod;
-import org.apache.commons.httpclient.methods.multipart.FilePart;
-import org.apache.commons.httpclient.methods.multipart.MultipartRequestEntity;
-import org.apache.commons.httpclient.methods.multipart.Part;
-import org.apache.commons.httpclient.methods.multipart.StringPart;
import org.apache.commons.io.FileUtils;
+import org.eclipse.jetty.client.HttpClient;
+import org.eclipse.jetty.client.api.ContentProvider;
+import org.eclipse.jetty.client.api.ContentResponse;
+import org.eclipse.jetty.client.api.Request;
+import org.eclipse.jetty.client.util.StringContentProvider;
+import org.eclipse.jetty.http.HttpStatus;
+
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.http.JettyHttpClientFactory;
public class PlasmapperConnector
{
@@ -42,25 +42,21 @@ public class PlasmapperConnector
final String fastaInputFilePath,
final String svgOutputFilePath,
final String htmlOutputFilePath) {
-
-// System.out.println("Asking service " + serverURL + VECTOR_MAP_URL + " to generate the SVG file from " + fastaInputFile);
-
- PostMethod method = new PostMethod(serverURL + VECTOR_MAP_URL);
+ HttpClient client = JettyHttpClientFactory.getHttpClient();
+ Request requestEntity = client.newRequest(serverURL + VECTOR_MAP_URL).method("POST");
try {
- Part[] parts = getPlasmidFormOptions(fastaInputFilePath);
+ setPlasmidFormOptions(requestEntity, fastaInputFilePath);
+ ContentResponse contentResponse = requestEntity.send();
- MultipartRequestEntity requestEntity = new MultipartRequestEntity(parts, method.getParams());
- method.setRequestEntity(requestEntity);
- HttpClient client = new HttpClient();
- int statusCode = client.executeMethod(method);
-
- if (statusCode != HttpStatus.SC_OK)
+ int statusCode = contentResponse.getStatus();
+
+ if (statusCode != HttpStatus.Code.OK.getCode())
{
- throw new RuntimeException("Status Code was " + statusCode + " instead of " + HttpStatus.SC_OK);
+ throw new RuntimeException("Status Code was " + statusCode + " instead of " + HttpStatus.Code.OK.getCode());
}
- String svgFileURLPath = method.getResponseBodyAsString();
+ String svgFileURLPath = contentResponse.getContentAsString();
if (svgFileURLPath == null || !svgFileURLPath.contains("PlasMapper")) {
throw new RuntimeException("PlasMapper service failed returning incorrect path to file: " + svgFileURLPath);
} else if (svgFileURLPath.endsWith("\r\n"))
@@ -71,10 +67,6 @@ public class PlasmapperConnector
svgFileURLPath = svgFileURLPath.substring(0, svgFileURLPath.lastIndexOf("\n"));
}
// System.out.println("Downloading SVG file: " + serverURL + "/" + svgFileURLPath + " to " + svgOutputFile);
-
- if(svgFileURLPath.startsWith("/")) {
- svgFileURLPath = svgFileURLPath.substring(1, svgFileURLPath.length());
- }
URL svgFileURL = new URL(serverURL + "/" + svgFileURLPath);
File svgOutputFile = new File(svgOutputFilePath);
@@ -95,58 +87,67 @@ public class PlasmapperConnector
} catch(Exception ex) {
throw new RuntimeException(ex);
} finally {
- method.releaseConnection();
+
}
}
- private static Part[] getPlasmidFormOptions(final String fastaInputFile) throws FileNotFoundException
+ private static void setPlasmidFormOptions(final Request requestEntity, final String fastaInputFile) throws FileNotFoundException
{
- File fasta = new File(fastaInputFile);
- List<Part> parts = new ArrayList<Part>();
- parts.add(new FilePart("fastaFile", fasta));
- parts.add(new StringPart("vendor", "Amersham%20Pharmacia"));
- parts.add(new StringPart("showOption", "1"));
- parts.add(new StringPart("showOption", "2"));
- parts.add(new StringPart("showOption", "3"));
- parts.add(new StringPart("showOption", "4"));
- parts.add(new StringPart("showOption", "5"));
- parts.add(new StringPart("showOption", "6"));
- parts.add(new StringPart("showOption", "7"));
- parts.add(new StringPart("showOption", "8"));
- parts.add(new StringPart("showOption", "9"));
- parts.add(new StringPart("restriction", "1"));
- parts.add(new StringPart("orfLen", "200"));
- parts.add(new StringPart("strand", "1"));
- parts.add(new StringPart("strand", "2"));
- parts.add(new StringPart("dir1", "1"));
- parts.add(new StringPart("dir2", "1"));
- parts.add(new StringPart("dir3", "1"));
- parts.add(new StringPart("dir4", "1"));
- parts.add(new StringPart("dir5", "1"));
- parts.add(new StringPart("dir6", "1"));
- parts.add(new StringPart("category1", "origin_of_replication"));
- parts.add(new StringPart("category2", "origin_of_replication"));
- parts.add(new StringPart("category3", "origin_of_replication"));
- parts.add(new StringPart("category4", "origin_of_replication"));
- parts.add(new StringPart("category5", "origin_of_replication"));
- parts.add(new StringPart("category6", "origin_of_replication"));
- parts.add(new StringPart("scheme", "0"));
- parts.add(new StringPart("shading", "0"));
- parts.add(new StringPart("labColor", "0"));
- parts.add(new StringPart("labelBox", "1"));
- parts.add(new StringPart("labels", "0"));
- parts.add(new StringPart("innerLabels", "0"));
- parts.add(new StringPart("legend", "0"));
- parts.add(new StringPart("arrow", "0"));
- parts.add(new StringPart("tickMark", "0"));
- parts.add(new StringPart("mapTitle", ""));
- parts.add(new StringPart("comment", "Created using PlasMapper"));
- parts.add(new StringPart("imageFormat", "SVG"));
- parts.add(new StringPart("imageSize", "1000 x 1000"));
- parts.add(new StringPart("backbone", "medium"));
- parts.add(new StringPart("arc", "medium"));
- parts.add(new StringPart("biomoby", "true"));
- return parts.toArray(new Part[0]);
+ requestEntity.param("vendor", "Amersham%20Pharmacia");
+ requestEntity.param("showOption", "1");
+ requestEntity.param("showOption", "2");
+ requestEntity.param("showOption", "3");
+ requestEntity.param("showOption", "4");
+ requestEntity.param("showOption", "5");
+ requestEntity.param("showOption", "6");
+ requestEntity.param("showOption", "7");
+ requestEntity.param("showOption", "8");
+ requestEntity.param("showOption", "9");
+ requestEntity.param("restriction", "1");
+ requestEntity.param("orfLen", "200");
+ requestEntity.param("strand", "1");
+ requestEntity.param("strand", "2");
+ requestEntity.param("dir1", "1");
+ requestEntity.param("dir2", "1");
+ requestEntity.param("dir3", "1");
+ requestEntity.param("dir4", "1");
+ requestEntity.param("dir5", "1");
+ requestEntity.param("dir6", "1");
+ requestEntity.param("category1", "origin_of_replication");
+ requestEntity.param("category2", "origin_of_replication");
+ requestEntity.param("category3", "origin_of_replication");
+ requestEntity.param("category4", "origin_of_replication");
+ requestEntity.param("category5", "origin_of_replication");
+ requestEntity.param("category6", "origin_of_replication");
+ requestEntity.param("scheme", "0");
+ requestEntity.param("shading", "0");
+ requestEntity.param("labColor", "0");
+ requestEntity.param("labelBox", "1");
+ requestEntity.param("labels", "0");
+ requestEntity.param("innerLabels", "0");
+ requestEntity.param("legend", "0");
+ requestEntity.param("arrow", "0");
+ requestEntity.param("tickMark", "0");
+ requestEntity.param("mapTitle", "");
+ requestEntity.param("comment", "Created using PlasMapper");
+ requestEntity.param("imageFormat", "SVG");
+ requestEntity.param("imageSize", "1000 x 1000");
+ requestEntity.param("backbone", "medium");
+ requestEntity.param("arc", "medium");
+ requestEntity.param("biomoby", "true");
+
+ final String CRLF = "\r\n";
+ final String BOUNDARY = "MMMMM___MP_BOUNDARY___MMMMM";
+ final String FILE_PART_NAME = "fastaFile";
+
+ File fastaFile = new File(fastaInputFile);
+ String fileContent = FileUtilities.loadToString(fastaFile);
+ ContentProvider content = new StringContentProvider("--" + BOUNDARY + CRLF
+ + "Content-Disposition: form-data; name=\"" + FILE_PART_NAME + "\"; filename=\""
+ + fastaFile.getName() + "\"" + CRLF
+ + "Content-Type: application/octet-stream" + CRLF + CRLF
+ + fileContent + CRLF + "--" + BOUNDARY + "--" + CRLF);
+ requestEntity.content(content, "multipart/form-data; boundary=" + BOUNDARY);
}
}
diff --git a/plasmid/source/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper.jar b/plasmid/source/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper.jar
index 5e3c80c6258305700ad704ea30adc977d154f98d..02ced276c813bcdbe43183b72939d6667a62023c 100644
Binary files a/plasmid/source/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper.jar and b/plasmid/source/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper.jar differ