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Commit 03251d39 authored by juanf's avatar juanf
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Rename legacy name from the reporting plugin api 

SVN: 36431
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openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/htmlcleaner-2.16-licence.txt deleted 100644 → 0
+ 0
− 35
View file @ faa3bcf2
Copyright (c) 2006-2015, the HTMLCleaner project
All rights reserved.
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with or without modification, are permitted provided that the following
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* Redistributions of source code must retain the above
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following disclaimer.
* Redistributions in binary form must reproduce the above
copyright notice, this list of conditions and the
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* The name of HtmlCleaner may not be used to endorse or promote
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
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You can contact Vladimir Nikic by sending e-mail to
nikic_vladimir@yahoo.com. Please include the word "HtmlCleaner" in the
subject line.
\ No newline at end of file
openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/FRP1955.fasta deleted 100644 → 0
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>Act1_mkokappa (5632 bp)
GACGTCGAAAGAACGCGGCATTAGCAACATTTGCGAAGCGAACGATTTTGCGAACTGCTATTAATTAActctGGCGCGcc
actactttttggaactcttgttgttctttggagttcaatgcgtccatctttacagtcctgtcttattgttcttgatttgt
gccccgtaaaatactgttacttggttctggcgaggtattggatagttcctttttataaaggccatgaagGtttttctttc
caattttttttttttcgtcattatagaaatcattacgaccgagattcccggCATATGGTAATAACTGATATAATTAAATT
GAAGCTCTAATTTGTGAGTTTAGTATACATGCATTTACTTATAATACAGTTTTTTAGTTTTGCTGGCCGCATCTTCTCAA
ATATGCTTCCCAGCCTGCTTTTCTGTAACGTTCACCCTCTACCTTAGCATCCCTTCCCTTTGCAAATAGTCCTCTTCCAA
CAATAATAATGTCAGATCCTGTAGAGACCACATCATCCACGGTTCTATACTGTTGACCCAATGCGTCTCCCTTGTCATCT
AAACCCACACCGGGTGTCATAATCAACCAATCGTAACCTTCATCTCTTCCACCCATGTCTCTTTGAGCAATAAAGCCGAT
AACAAAATCTTTGTCGCTCTTCGCAATGTCAACAGTACCCTTAGTATATTCTCCAGTAGCTAGGGAGCCCTTGCATGACA
ATTCTGCTAACATCAAAAGGCCTCTAGGTTCCTTTGTTACTTCTTCCGCCGCCTGCTTCAAACCGCTAACAATACCTGGG
CCCACCACACCGTGTGCATTCGTAATGTCTGCCCATTCTGCTATTCTGTATACACACGCAGAGTACTGCAATTTGACTGT
ATTACCAATGTCAGCAAATTTTCTGTCTTCGAAGAGTAAAAAATTGTACTTGGCGGATAATGCCTTTAGCGGCTTAACTG
TGCCCTCCATGGAAAAATCAGTCAAGAGATCCACATGTGTTTTTAGTAAACAAATTTTGGGACCTAATGCTTCAACTAAC
TCCAGTAATTCCTTGGTGGTACGAACATCCAATGAAGCACACAAGTTTGTTTGCTTTTCGTGCATGATATTAAATAGCTT
GGCAGCAACAGGACTAGGATGAGTAGCAGCACGTTCCTTATATGTAGCTTTCGACATGATTTATCTTCGTTTCCTGCACG
TTTTTGTTCTGTGCAGTTGGGTTAAGAATACTGGGCAATTTCATGTTTCTTCAACACCACCTATGCGTATATATACCAAT
CTAAGTCTGTGCTCCTTCCTTCGTTCTTCCTTCTGCTCGGAGATTACCGAATCAAAAAAATTTCAAAGAAACCGGAATCA
AAAAAAAGAACAAAAAAAAAAAAGATGAATGAAAAGCGATCGGATGTGCTGCAAGGCGATTAAGTTGGGTAACGCCAGGG
TTTTCCCAGTCACGACGTTGTAAAACGACGGCCAGTGAATTGTAATACGACTCACTATAGGGCGAATTGGAGAAACAGAA
TAATATATAAACCTGTATAATATAACCTTGAAGACTATATTTCTTTTCGCGGCCGCCTATAGGGCGAATTGGAGCTCCAC
CGCGGTGGCGGCCGCTCTAGAGAAGCGGGTAAGCTGCCACAGCAATTAATGCACAACATTTAACCTACATTCTTCCTTAT
CGGATCgTCAAAACCCTTAAAAAgATATGCCTCACCCTAACATATTTTCCAATTAACCCTCAATATTTCTCTGTCACCCG
GCCTCTATTTTCCATTTTCTTCTTTACCCGCCACGCGTTTTTTTCTTTCAAATTTTTTTCTTCCTTCTTCTTTTTCTTCC
ACGTCCTCTTGCATAAATAAATAAACCGTTTTGAAACCAAACTCGCCTCTCTCTCTCCTTTTTGAAATATTTTTGGGTTT
GTTTGATCCTTTCCTTCCCAATCTCTCTTGTTTAATATATATTCATTTATATCACGCTCTCTTTTTATCTTCCTTTTTTT
CCTCTCTCTTGTATTCTTCCTTCCCCTTTCTACTCAAACCAAGAAGAAAAAGAAAAGGTCAATCTTTGTTAAAGAATAGG
ATCTTCTACTACATCAGCTTTTAGATTTTTCACGCTTACTGCTTTTTTCTTCCCAAGATCGAAAATTTACTGAATTAACA
ACTAGTGGATCCCCCGGGCTGCAGGAATTCGATATCAagctTATGAGATCTGTTTCTGTTATTAAGCCAGAAATGAAGAT
GAGATATTACATGGATGGTTCTGTTAATGGTCATGAATTTACTATTGAAGGTGAAGGTACTGGTAGACCATATGAAGGTC
ATCAAGAAATGACTTTGAGAGTTACTATGGCTGAAGGTGGTCCAATGCCATTTGCTTTTGATTTGGTTTCTCATGTTTTT
TGTTACGGTCATAGAGTTTTTACAAAGTACCCAGAAGAAATTCCAGATTACTTTAAGCAAGCATTTCCAGAAGGTTTGTC
TTGGGAAAGATCATTGGAATTTGAAGATGGTGGTTCTGCTTCTGTTTCTGCTCATATTTCTTTGAGAGGTAACACTTTTT
ACCATAAGTCTAAGTTTACTGGTGTTAATTTTCCAGCTGATGGTCCAATTATGCAAAATCAATCTGTTGATTGGGAACCA
TCTACTGAAAAGATTACTGCTTCTGATGGTGTTTTGAAAGGTGATGTTACAATGTACTTGAAATTGGAAGGTGGTGGTAA
TCATAAATGTCAATTCAAGACTACTTATAAAGCTGCTGAAAAGATTTTGGAAATGCCAGGTGATCATTATATTGGTCATA
GATTGGTTAGAAAGACTGAAGGTAACATTACTGAACAAGTTGAAGATGCTGTTGCTCATTCTGGATCCTAGCtcgaGACA
GGCCCCTTTTCCTTTGTCtATATCATGTAATTAGTTATGTCACGCTTACATTCACGCCCTCCTCCCACATCCGCTCTAAC
CGAAAAGGAAGGAGTTAGACAACCTGAAGTCTAGGTCCCTATTTATTTTTTTTAATAGTTATGTTAGTATTAAGAACGTT
ATTTATATTTCAAATTTTTCTTTTTTTTCTGTACAAACGCGTGTACGCATGTAACATTATACTGAAAACCTTGCTTGAGA
AGGTTTTGGGACGCTCGAAGGCTTTAATTTGCAAGgTTCGCAGTTTACACTCTCATCGTCGCTCTCATCATCGCTTCCGT
TGTTGTTTTCCTTAGTAGCGTCTGCTTGGTACCCAGCTTCGGCCGTATTTACAGATAACGATGTCGTTATTATATATATA
TATATATATTGTCACTTGTACCCAGCTTTTGTTCCCTTTAGTGAGGGTTAATTTCGAGCTTGGCGTAATCATGGTCATAG
CTGTTTCCTGTGTGAAATTGTTATCCGCTCACAACAGCTGgatgaattgaaTagctttatggaccctgaaaccacagcca
cattaaccttctttgatggtcaaaacttatccttcaccataaatatgcctcgcaaaaaaggtaattaacatatatagaat
tacattatttatgaaatatcatcactatctcttagcatctttaatccttttctacatcagataacttcggtttgttatca
tcgtctgtattgtcatcaattggCGCGCCtctcCCTGCAGGCATTAATGAATCGGCCAACGCGCGGGGAGAGGCGGTTTG
CGTATTGGGCGCTCTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCGGCTGCGGCGAGCGGTATCAGCTCA
CTCAAAGGCGGTAATACGGTTATCCACAGAATCAGGGGATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGG
CCAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGCATCACAAAAATCGACGC
TCAAGTCAGAGGTGGCGAAACCCGACAGGACTATAAAGATACCAGGCGTTTCCCCCTGGAAGCTCCCTCGTGCGCTCTCC
TGTTCCGACCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACGCT
GTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCGCTGC
GCCTTATCCGGTAACTATCGTCTTGAGTCCAACCCGGTAAGACACGACTTATCGCCACTGGCAGCAGCCACTGGTAACAG
GATTAGCAGAGCGAGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTAACTACGGCTACACTAGAAGAACAG
TATTTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACAAACCACC
GCTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCCTTTGATCTT
TTGTTTAAACCTACGGGGTCTGACGCTCAGTGGAACGAAAACTCACGTTAAGGGATTTTGGTCATGAGATTATCAAAAAG
GATCTTCACCTAGATCCTTTTAAATTAAAAATGAAGTTTTAAATCAATCTAAAGTATATATGAGTAAACTTGGTCTGACA
GTTACCAATGCTTAATCAGTGAGGCACCTATCTCAGCGATCTGTCTATTTCGTTCATCCATAGTTGCCTGACTCCCCGTC
GTGTAGATAACTACGATACGGGAGGGCTTACCATCTGGCCCCAGTGCTGCAATGATACCGCGAGACCCACGCTCACCGGC
TCCAGATTTATCAGCAATAAACCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACTTTATCCGCCTCCATCC
AGTCTATTAATTGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTTTGCGCAACGTTGTTGCCATTGCTACA
GGCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGTTACATGATC
CCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTCGGTCCTCCGATGGTTGTCAGAAGTAAGTTGGCCGCAGTGTTATCAC
TCATGGTTATGGCAGCACTGCATAATTCTCTTACTGTCATGCCATCCGTAAGATGCTTTTCTGTGACTGGTGAGTACTCA
ACCAAGTCATTCTGAGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCCCGGCGTCAATACGGGATAATACCGCGCCACA
TAGCAGAACTTTAAAAGTGCTCATCATTGGAAAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGTTGAGAT
CCAGTTCGATGTAACCCACTCGTGCACCCAACTGATCTTCAGCATCTTTTACTTTCACCAGCGTTTCTGGGTGAGCAAAA
ACAGGAAGGCAAAATGCCGCAAAAAAGGGAATAAGGGCGACACGGAAATGTTGAATACTCATACTCTTCCTTTTTCAATA
TTATTGAAGCATTTATCAGGGTTATTGTCTCATGAGCGGATACATATTTGAATGTATTTAGAAAAATAAACAAATAGGGG
TTCCGCGCACATTTCCCCGAAAAGTGCCACCT
openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.java deleted 100644 → 0
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package ch.ethz.ssdm.eln;
import java.io.File;
import java.io.FileNotFoundException;
import java.net.URL;
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
{
public static void main(String[] args) throws Exception {
//URL to the server without the dash '/'
String serverURL = "http://wishart.biology.ualberta.ca";
//Path to input fasta file
String fastaInputFilePath = "FRP1955.fasta";
//Path to output svg file
String svgOutputFilePath = "FRP1955.svg";
//Path to output html file
String htmlOutputFilePath = "FRP1955.html";
downloadPlasmidMap(
serverURL,
fastaInputFilePath,
svgOutputFilePath,
htmlOutputFilePath);
}
private static final String VECTOR_MAP_URL = "/PlasMapper/servlet/DrawVectorMap";
public static void downloadPlasmidMap(
final String serverURL,
final String fastaInputFilePath,
final String svgOutputFilePath,
final String htmlOutputFilePath) {
HttpClient client = JettyHttpClientFactory.getHttpClient();
Request requestEntity = client.newRequest(serverURL + VECTOR_MAP_URL).method("POST");
try {
setPlasmidFormOptions(requestEntity, fastaInputFilePath);
ContentResponse contentResponse = requestEntity.send();
int statusCode = contentResponse.getStatus();
if (statusCode != HttpStatus.Code.OK.getCode())
{
throw new RuntimeException("Status Code was " + statusCode + " instead of " + HttpStatus.Code.OK.getCode());
}
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"))
{
svgFileURLPath = svgFileURLPath.substring(0, svgFileURLPath.lastIndexOf("\r\n"));
} else if (svgFileURLPath.endsWith("\n"))
{
svgFileURLPath = svgFileURLPath.substring(0, svgFileURLPath.lastIndexOf("\n"));
}
// System.out.println("Downloading SVG file: " + serverURL + "/" + svgFileURLPath + " to " + svgOutputFile);
if(svgFileURLPath.startsWith("/")) {
svgFileURLPath = svgFileURLPath.substring(1);
}
URL svgFileURL = new URL(serverURL + "/" + svgFileURLPath);
File svgOutputFile = new File(svgOutputFilePath);
FileUtils.copyURLToFile(svgFileURL, svgOutputFile);
// System.out.println("Generating HTML file: " + htmlOutputFile);
String htmlFileContents = "<html>"
+ "<head>"
+ "<meta http-equiv=\"content-type\" content=\"text/html; charset=ISO-8859-1\">"
+ "<title>PlasMapper - Graphic Map</title>"
+ "</head>"
+ "<body>"
+ "<embed src=\"" + svgOutputFile.getName() + "\" type=\"image/svg+xml\" pluginspage=\"http://www.adobe.com/svg/viewer/install/\" id=\"Panel\" height=\"1010\" width=\"1010\">"
+ "<br>"
+ "<a href=\"" + svgOutputFile.getName() + "\" target=\"_blank\">Download Link</a>"
+ "</body>"
+ "</html>";
FileUtils.writeStringToFile(new File(htmlOutputFilePath), htmlFileContents, "UTF-8");
} catch(Exception ex) {
throw new RuntimeException(ex);
} finally {
}
}
private static void setPlasmidFormOptions(final Request requestEntity, final String fastaInputFile) throws FileNotFoundException
{
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);
}
}
openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.sh deleted 100644 → 0
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#!/bin/bash
#URL to the server without the dash '/'
serverURL=http://wishart.biology.ualberta.ca
#Path to input fasta file
fastaInputFile=FRP1955.fasta
#Path to output svg file
svgOutputFile=FRP1955.svg
#Path to output html file
htmlOutputFile=FRP1955.html
echo Asking service $serverURL/PlasMapper/servlet/DrawVectorMap to generate the SVG file
imageURL=$(curl -k -F "fastaFile=@$fastaInputFile;type=application/octet-stream" \
-F "vendor=Amersham%20Pharmacia" \
-F "Submit=Graphic Map" \
-F "showOption=1" \
-F "showOption=2" \
-F "showOption=3" \
-F "showOption=4" \
-F "showOption=5" \
-F "showOption=6" \
-F "showOption=7" \
-F "showOption=8" \
-F "showOption=9" \
-F "restriction=1" \
-F "orfLen=200" \
-F "strand=1" \
-F "strand=2" \
-F "dir1=1" \
-F "dir2=1" \
-F "dir3=1" \
-F "dir4=1" \
-F "dir5=1" \
-F "dir6=1" \
-F "category1=origin_of_replication" \
-F "category2=origin_of_replication" \
-F "category3=origin_of_replication" \
-F "category4=origin_of_replication" \
-F "category5=origin_of_replication" \
-F "category6=origin_of_replication" \
-F "scheme=0" \
-F "shading=0" \
-F "labColor=0" \
-F "labelBox=1" \
-F "labels=0" \
-F "innerLabels=0" \
-F "legend=0" \
-F "arrow=0" \
-F "tickMark=0" \
-F "comment=Created using PlasMapper" \
-F "imageFormat=SVG" \
-F "imageSize=1000 x 1000" \
-F "backbone=medium" \
-F "arc=medium" \
-F "biomoby=true" \
$serverURL/PlasMapper/servlet/DrawVectorMap
)
echo Downloading SVG file: $serverURL/$imageURL
curl -o $svgOutputFile $serverURL/$imageURL
echo Generating HTML file: $htmlOutputFile
echo "<html><head><meta http-equiv=\"content-type\" content=\"text/html; charset=ISO-8859-1\"><title>PlasMapper - Graphic Map</title></head><body><embed src=\"$svgOutputFile\" type=\"image/svg+xml\" pluginspage=\"http://www.adobe.com/svg/viewer/install/\" id=\"Panel\" height=\"1010\" width=\"1010\"><br><a href=\"$svgOutputFile\" target=\"_blank\">Download Link</a></body></html>" > $htmlOutputFile
\ No newline at end of file
openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/plugin.properties deleted 100644 → 0
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View file @ faa3bcf2
label = New Browser API
class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
script-path = script.py
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