diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/htmlcleaner-2.16-licence.txt b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/htmlcleaner-2.16-licence.txt
deleted file mode 100644
index 1d32e8f74036682eaca4fb76c452c9476e9d53ef..0000000000000000000000000000000000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/htmlcleaner-2.16-licence.txt
+++ /dev/null
@@ -1,35 +0,0 @@
-Copyright (c) 2006-2015, the HTMLCleaner project
-All rights reserved.
-
-Redistribution and use of this software in source and binary forms,
-with or without modification, are permitted provided that the following
-conditions are met:
-
-* Redistributions of source code must retain the above
- copyright notice, this list of conditions and the
- following disclaimer.
-
-* Redistributions in binary form must reproduce the above
- copyright notice, this list of conditions and the
- following disclaimer in the documentation and/or other
- materials provided with the distribution.
-
-* The name of HtmlCleaner may not be used to endorse or promote
- products derived from this software without specific prior
- written permission.
-
-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
-POSSIBILITY OF SUCH DAMAGE.
-
-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
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/htmlcleaner-2.16.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/htmlcleaner-2.16.jar
deleted file mode 100644
index 75dc35f17775a145698b459f692bab681817908d..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/htmlcleaner-2.16.jar and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/FRP1955.fasta b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/FRP1955.fasta
deleted file mode 100644
index 190e2431671ab6769c9d1564b5594ec25a1d5514..0000000000000000000000000000000000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/FRP1955.fasta
+++ /dev/null
@@ -1,72 +0,0 @@
->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
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.java b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.java
deleted file mode 100644
index 48a414552f0b3909ec3761dadca53f8023534a79..0000000000000000000000000000000000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.java
+++ /dev/null
@@ -1,157 +0,0 @@
-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);
- }
-}
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.sh b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.sh
deleted file mode 100644
index 205ac254ff1b7f4b8506300150b8cb34726fc8e4..0000000000000000000000000000000000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper-source/PlasmapperConnector.sh
+++ /dev/null
@@ -1,60 +0,0 @@
-#!/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
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper.jar
deleted file mode 100644
index 3bad25f84b433c18e7c55f0be129ac4ed62feea8..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/plasmapper.jar and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/zip4j_1.3.2.jar b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/zip4j_1.3.2.jar
deleted file mode 100644
index 66a19e49a2a29b39b76ade1b619de9db0a8fdcaa..0000000000000000000000000000000000000000
Binary files a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/lib/zip4j_1.3.2.jar and /dev/null differ
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/plugin.properties b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/plugin.properties
deleted file mode 100644
index d6fb4fb3f27907bf877efc1699a0750f8c75122d..0000000000000000000000000000000000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/plugin.properties
+++ /dev/null
@@ -1,3 +0,0 @@
-label = New Browser API
-class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
-script-path = script.py
diff --git a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/script.py b/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/script.py
deleted file mode 100644
index 85ae413c113471d54f8768434e53903b71b2c52e..0000000000000000000000000000000000000000
--- a/openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/script.py
+++ /dev/null
@@ -1,947 +0,0 @@
-#
-# Copyright 2014 ETH Zuerich, Scientific IT Services
-#
-# 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.
-#
-
-# IDataSetRegistrationTransactionV2 Class
-from ch.systemsx.cisd.openbis.dss.client.api.v1 import DssComponentFactory
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto import SearchCriteria
-from ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria import MatchClause, SearchOperator, MatchClauseAttribute
-from ch.systemsx.cisd.openbis.generic.shared.basic.dto import DataTypeCode;
-
-from java.util import ArrayList
-from java.util import Date;
-from java.text import SimpleDateFormat;
-
-from ch.systemsx.cisd.common.spring import HttpInvokerUtils;
-from org.apache.commons.io import IOUtils
-from java.io import File
-from java.io import FileOutputStream
-from java.lang import System
-from net.lingala.zip4j.core import ZipFile
-from ch.systemsx.cisd.common.exceptions import UserFailureException
-
-from ch.ethz.ssdm.eln import PlasmapperConnector
-
-import time
-import subprocess
-import os.path
-import re
-
-from java.io import StringWriter
-from org.htmlcleaner import HtmlCleaner
-from org.htmlcleaner import SimpleHtmlSerializer
-from org.htmlcleaner import CleanerProperties
-
-#AS API
-from ch.systemsx.cisd.openbis.generic.shared.api.v1 import IGeneralInformationService;
-
-#For Screeening API
-from ch.systemsx.cisd.openbis.common.api.client import ServiceFinder;
-from java.util import Arrays;
-
-from ch.ethz.sis.openbis.generic.asapi.v3 import IApplicationServerApi
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.fetchoptions import SampleFetchOptions;
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.search import SampleSearchCriteria;
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.common.search import SearchResult;
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id import SampleIdentifier;
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id import SamplePermId
-from ch.ethz.sis.openbis.generic.asapi.v3.dto.experiment.id import ExperimentIdentifier;
-from ch.ethz.sis.openbis.generic.server.sharedapi.v3.json import GenericObjectMapper;
-from ch.systemsx.cisd.openbis.dss.generic.server import DataStoreServer
-from ch.systemsx.cisd.common.shared.basic.string import StringUtils
-
-#from ch.systemsx.cisd.common.ssl import SslCertificateHelper;
-
-#Plasmapper server used
-PLASMAPPER_BASE_URL = "http://wishart.biology.ualberta.ca"
-OPENBISURL = DataStoreServer.getConfigParameters().getServerURL() + "/openbis/openbis"
-def getConfigParameterAsString(propertyKey):
- properties = DataStoreServer.getConfigParameters().getProperties();
- property = properties.getProperty(propertyKey);
- if StringUtils.isBlank(property):
- return None;
- else:
- return property;
-
-def getDirectLinkURL():
- ftpServerEnable = getConfigParameterAsString("ftp.server.enable");
-
- ftpServerUseSsl = getConfigParameterAsString("ftp.server.use-ssl");
- useSsl = getConfigParameterAsString("use-ssl");
-
- ftpPortLegacy = getConfigParameterAsString("ftp.server.port");
- ftpPort = getConfigParameterAsString("ftp.server.ftp-port");
-
- sftpPort = getConfigParameterAsString("ftp.server.sftp-port");
-
-
- protocol = None;
- port = None;
- if (ftpServerEnable == "true") and (sftpPort is not None):
- protocol = "sftp";
- elif (ftpServerEnable == "true") and ((ftpPort is not None) or (ftpPortLegacy is not None)) and (ftpServerUseSsl == "true" or useSsl == "true"):
- protocol = "ftps";
-
- if protocol is not None:
- if sftpPort is not None:
- port = sftpPort;
- elif ftpPort is not None:
- port = ftpPort;
- elif ftpPortLegacy is not None:
- port = ftpPortLegacy;
-
- directLinkURL = None;
- if protocol is not None:
- directLinkURL = protocol + "://$URL:" + str(port) + "/";
-
- return getJsonForData(directLinkURL);
-
-def getProperties(tr, parameters):
- sessionToken = parameters.get("sessionToken");
- servFinder = ServiceFinder("openbis", IGeneralInformationService.SERVICE_URL);
- infService = servFinder.createService(IGeneralInformationService, OPENBISURL);
- properties = infService.listPropertyTypes(sessionToken, False);
- return properties
-
-def isPropertyRichText(properties, propertyCode):
- for property in properties:
- if property.getCode() == propertyCode and property.getCode() != "FREEFORM_TABLE_STATE":
- return property.getDataType() == DataTypeCode.MULTILINE_VARCHAR;
- return None;
-
-def updateIfIsPropertyRichText(properties, propertyCode, propertyValue):
- if isPropertyRichText(properties, propertyCode):
- if propertyValue is not None:
- cleanerProperties = CleanerProperties();
- cleanerProperties.setPruneTags("meta, link, script");
- cleaner = HtmlCleaner(cleanerProperties);
- htmlSerializer = SimpleHtmlSerializer(cleanerProperties);
- propertytagNode = cleaner.clean(propertyValue);
- return htmlSerializer.getAsString(propertytagNode);
- return propertyValue;
-
-def getSampleByIdentifierForUpdate(tr, identifier):
- space = identifier.split("/")[1];
- code = identifier.split("/")[2];
-
- criteria = SearchCriteria();
- criteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.SPACE, space));
- criteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, code));
- criteria.setOperator(SearchOperator.MATCH_ALL_CLAUSES);
-
- searchService = tr.getSearchService();
- found = list(searchService.searchForSamples(criteria));
- if len(found) == 1:
- return tr.makeSampleMutable(found[0]);
- else:
- raise UserFailureException(identifier + " Not found by search service.");
-
-def username(sessiontoken):
- m = re.compile('(.*)-[^-]*').match(sessiontoken)
- if m:
- return m.group(1)
-
-def process(tr, parameters, tableBuilder):
- method = parameters.get("method");
-
- isOk = False;
- result = None;
- # Obtain the user using the dropbox
- sessionToken = parameters.get("sessionToken"); #String
- sessionId = username(sessionToken); #String
- if sessionId == userId:
- tr.setUserId(userId);
- else:
- print "[SECURITY] User " + userId + " tried to execute the eln-lims dropbox using " + sessionId + " account.";
- raise UserFailureException("[SECURITY] User " + userId + " tried to use " + sessionId + " account, this will be communicated to the admin.");
-
- if method == "init":
- isOk = init(tr, parameters, tableBuilder);
- if method == "searchSamples":
- result = searchSamples(tr, parameters, tableBuilder, sessionId);
- isOk = True;
- if method == "registerUserPassword":
- isOk = registerUserPassword(tr, parameters, tableBuilder);
- if method == "getDirectLinkURL":
- result = getDirectLinkURL();
- isOk = True;
-
- if method == "copyAndLinkAsParent":
- isOk = copyAndLinkAsParent(tr, parameters, tableBuilder);
-
- if method == "batchOperation":
- isOk = batchOperation(tr, parameters, tableBuilder);
-
- if method == "insertProject":
- isOk = insertUpdateProject(tr, parameters, tableBuilder);
- if method == "updateProject":
- isOk = insertUpdateProject(tr, parameters, tableBuilder);
-
- if method == "insertExperiment":
- isOk = insertUpdateExperiment(tr, parameters, tableBuilder);
- if method == "updateExperiment":
- isOk = insertUpdateExperiment(tr, parameters, tableBuilder);
-
- if method == "copySample":
- isOk = copySample(tr, parameters, tableBuilder);
- if method == "insertSample":
- isOk = insertUpdateSample(tr, parameters, tableBuilder);
- if method == "updateSample":
- isOk = insertUpdateSample(tr, parameters, tableBuilder);
- if method == "moveSample":
- isOk = moveSample(tr, parameters, tableBuilder);
- if method == "insertDataSet":
- isOk = insertDataSet(tr, parameters, tableBuilder);
- if method == "updateDataSet":
- isOk = updateDataSet(tr, parameters, tableBuilder);
-
- if method == "listFeatureVectorDatasetsPermIds":
- result = listFeatureVectorDatasetsPermIds(tr, parameters, tableBuilder);
- isOk = True;
- if method == "listAvailableFeatures":
- result = listAvailableFeatures(tr, parameters, tableBuilder);
- isOk = True;
- if method == "getFeaturesFromFeatureVector":
- result = getFeaturesFromFeatureVector(tr, parameters, tableBuilder);
- isOk = True;
-
- if isOk:
- tableBuilder.addHeader("STATUS");
- tableBuilder.addHeader("MESSAGE");
- tableBuilder.addHeader("RESULT");
- row = tableBuilder.addRow();
- row.setCell("STATUS","OK");
- row.setCell("MESSAGE", "Operation Successful");
- row.setCell("RESULT", result);
- else :
- tableBuilder.addHeader("STATUS");
- tableBuilder.addHeader("MESSAGE");
- row = tableBuilder.addRow();
- row.setCell("STATUS","FAIL");
- row.setCell("MESSAGE", "Operation Failed");
-
-def listFeatureVectorDatasets(sessionToken, samplePlatePermId):
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1 import IScreeningApiServer;
- from ch.systemsx.cisd.openbis.dss.screening.shared.api.v1 import IDssServiceRpcScreening;
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import PlateIdentifier;
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import FeatureVectorDatasetReference;
-
- screeningFinder = ServiceFinder("openbis", IScreeningApiServer.SERVICE_URL);
- screeningServiceAS = screeningFinder.createService(IScreeningApiServer, OPENBISURL);
-
- plateIdentifier = PlateIdentifier.createFromPermId(samplePlatePermId);
- featureVectorDatasets = screeningServiceAS.listFeatureVectorDatasets(sessionToken, Arrays.asList(plateIdentifier));
- return featureVectorDatasets;
-
-def getJsonForData(data):
- objectMapper = GenericObjectMapper();
- jsonValue = objectMapper.writeValueAsString(data);
- return jsonValue;
-
-def listFeatureVectorDatasetsPermIds(tr, parameters, tableBuilder):
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1 import IScreeningApiServer;
- from ch.systemsx.cisd.openbis.dss.screening.shared.api.v1 import IDssServiceRpcScreening;
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import PlateIdentifier;
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import FeatureVectorDatasetReference;
-
- sessionToken = parameters.get("sessionToken");
- samplePlatePermId = parameters.get("samplePlatePermId");
-
- featureVectorDatasets = listFeatureVectorDatasets(sessionToken, samplePlatePermId);
- featureVectorDatasetCodes = [];
- for featureVectorDataset in featureVectorDatasets:
- featureVectorDatasetCodes.append(featureVectorDataset.getDatasetCode());
-
- return getJsonForData(featureVectorDatasetCodes);
-
-def listAvailableFeatures(tr, parameters, tableBuilder):
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1 import IScreeningApiServer;
- from ch.systemsx.cisd.openbis.dss.screening.shared.api.v1 import IDssServiceRpcScreening;
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import PlateIdentifier;
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import FeatureVectorDatasetReference;
-
- sessionToken = parameters.get("sessionToken");
- samplePlatePermId = parameters.get("samplePlatePermId");
- featureVectorDatasetPermId = parameters.get("featureVectorDatasetPermId");
-
- featureVectorDataset = None;
- featureVectorDatasets = listFeatureVectorDatasets(sessionToken, samplePlatePermId);
- for featureVectorDataset in featureVectorDatasets:
- if featureVectorDataset.getDatasetCode() == featureVectorDatasetPermId:
- featureVectorDataset = featureVectorDataset;
-
- from ch.systemsx.cisd.openbis.dss.generic.server import DssScreeningApplicationContext
- screeningServiceDSS = DssScreeningApplicationContext.getInstance().getBean("data-store-rpc-service-screening-logic-target")
-
- featureInformationList = screeningServiceDSS.listAvailableFeatures(sessionToken, [featureVectorDataset]);
- features = {};
- for featureInformation in featureInformationList:
- features[featureInformation.getCode()] = featureInformation.getLabel();
-
- return getJsonForData(features);
-
-def getFeaturesFromFeatureVector(tr, parameters, tableBuilder):
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1 import IScreeningApiServer;
- from ch.systemsx.cisd.openbis.dss.screening.shared.api.v1 import IDssServiceRpcScreening;
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import PlateIdentifier;
- from ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto import FeatureVectorDatasetReference;
-
- sessionToken = parameters.get("sessionToken");
- samplePlatePermId = parameters.get("samplePlatePermId");
- featureVectorDatasetPermId = parameters.get("featureVectorDatasetPermId");
- featuresCodesFromFeatureVector = parameters.get("featuresCodesFromFeatureVector");
-
- featureVectorDataset = None;
- featureVectorDatasets = listFeatureVectorDatasets(sessionToken, samplePlatePermId);
- for featureVectorDatasetAux in featureVectorDatasets:
- if featureVectorDatasetAux.getDatasetCode() == featureVectorDatasetPermId:
- featureVectorDataset = featureVectorDatasetAux;
-
- from ch.systemsx.cisd.openbis.dss.generic.server import DssScreeningApplicationContext
- screeningServiceDSS = DssScreeningApplicationContext.getInstance().getBean("data-store-rpc-service-screening-logic-target")
-
- featuresFromFeatureVector = screeningServiceDSS.loadFeatures(sessionToken, [featureVectorDataset], featuresCodesFromFeatureVector);
- return getJsonForData(featuresFromFeatureVector);
-
-def init(tr, parameters, tableBuilder):
- inventorySpace = tr.getSpace("DEFAULT_LAB_NOTEBOOK");
- if inventorySpace == None:
- elnTypes = tr.getVocabularyForUpdate("ELN_TYPES_METADATA");
- if elnTypes is not None: # We can only create the data if the ELN metadata is present, this is not true on highly customized systems.
- tr.createNewSpace("MATERIALS", None);
-
- tr.createNewProject("/MATERIALS/REAGENTS");
- tr.createNewExperiment("/MATERIALS/REAGENTS/ANTIBODY_COLLECTION", "MATERIALS");
- tr.createNewExperiment("/MATERIALS/REAGENTS/CHEMICAL_COLLECTION", "MATERIALS");
- tr.createNewExperiment("/MATERIALS/REAGENTS/ENZYME_COLLECTION", "MATERIALS");
- tr.createNewExperiment("/MATERIALS/REAGENTS/MEDIA_COLLECTION", "MATERIALS");
- tr.createNewExperiment("/MATERIALS/REAGENTS/SOLUTION_BUFFER_COLLECTION", "MATERIALS");
-
- tr.createNewProject("/MATERIALS/BACTERIA");
- tr.createNewExperiment("/MATERIALS/BACTERIA/BACTERIA_COLLECTION_1", "MATERIALS");
- tr.createNewProject("/MATERIALS/CELL_LINES");
- tr.createNewExperiment("/MATERIALS/CELL_LINES/CELL_LINE_COLLECTION_1", "MATERIALS");
- tr.createNewProject("/MATERIALS/FLIES");
- tr.createNewExperiment("/MATERIALS/FLIES/FLY_COLLECTION_1", "MATERIALS");
- tr.createNewProject("/MATERIALS/YEASTS");
- tr.createNewExperiment("/MATERIALS/YEASTS/YEAST_COLLECTION_1", "MATERIALS");
- tr.createNewProject("/MATERIALS/PLASMIDS");
- tr.createNewExperiment("/MATERIALS/PLASMIDS/PLASMID_COLLECTION_1", "MATERIALS");
- tr.createNewProject("/MATERIALS/POLYNUCLEOTIDES");
- tr.createNewExperiment("/MATERIALS/POLYNUCLEOTIDES/OLIGO_COLLECTION_1", "MATERIALS");
- tr.createNewExperiment("/MATERIALS/POLYNUCLEOTIDES/RNA_COLLECTION_1", "MATERIALS");
-
- tr.createNewSpace("METHODS", None);
-
- tr.createNewProject("/METHODS/PROTOCOLS");
- tr.createNewExperiment("/METHODS/PROTOCOLS/GENERAL_PROTOCOLS", "METHODS");
- tr.createNewExperiment("/METHODS/PROTOCOLS/PCR_PROTOCOLS", "METHODS");
- tr.createNewExperiment("/METHODS/PROTOCOLS/WESTERN_BLOTTING_PROTOCOLS", "METHODS");
-
- tr.createNewSpace("DEFAULT_LAB_NOTEBOOK", None);
-
- tr.createNewProject("/DEFAULT_LAB_NOTEBOOK/DEFAULT_PROJECT");
- tr.createNewExperiment("/DEFAULT_LAB_NOTEBOOK/DEFAULT_PROJECT/DEFAULT_EXPERIMENT", "DEFAULT_EXPERIMENT");
-
- return True;
-
-def registerUserPassword(tr, parameters, tableBuilder):
- userId = parameters.get("userId"); #String
- password = parameters.get("password"); #String
- path = '../openBIS-server/jetty/bin/passwd.sh';
- if os.path.isfile(path):
- subprocess.call([path, 'add', userId, '-p', password]) #Adds the user, if the user exists, will fail
- subprocess.call([path, 'change', userId, '-p', password]) #Changes the user pass, works always
- return True;
- else:
- return False;
-
-def getThreadProperties(transaction):
- threadPropertyDict = {}
- threadProperties = transaction.getGlobalState().getThreadParameters().getThreadProperties()
- for key in threadProperties:
- try:
- threadPropertyDict[key] = threadProperties.getProperty(key)
- except:
- pass
- return threadPropertyDict
-
-def insertUpdateProject(tr, parameters, tableBuilder):
- method = parameters.get("method"); #String
- projectIdentifier = parameters.get("projectIdentifier"); #String
- projectDescription = parameters.get("projectDescription"); #String
-
- project = None;
- if method == "insertProject":
- project = tr.createNewProject(projectIdentifier);
- if method == "updateProject":
- project = tr.getProjectForUpdate(projectIdentifier);
-
- project.setDescription(projectDescription);
-
- #Return from the call
- return True;
-
-def updateDataSet(tr, parameters, tableBuilder):
- dataSetCode = parameters.get("dataSetCode"); #String
- metadata = parameters.get("metadata"); #java.util.LinkedHashMap<String, String> where the key is the name
- dataSet = tr.getDataSetForUpdate(dataSetCode);
- properties = getProperties(tr, parameters);
- #Hack - Fix Sample Lost bug from openBIS, remove when SSDM-1979 is fix
- #Found in S211: In new openBIS versions if you set the already existing sample when doing a dataset update is deleted
- #sampleIdentifier = parameters.get("sampleIdentifier"); #String
- #dataSetSample = getSampleByIdentifierForUpdate(tr, sampleIdentifier);
- #dataSet.setSample(dataSetSample);
- #Assign Data Set properties
- for key in metadata.keySet():
- propertyValue = unicode(metadata[key]);
- if propertyValue == "":
- propertyValue = None;
- else:
- propertyValue = updateIfIsPropertyRichText(properties, key, propertyValue);
- dataSet.setPropertyValue(key,propertyValue);
-
- #Return from the call
- return True;
-
-def insertDataSet(tr, parameters, tableBuilder):
- #Mandatory parameters
- sampleIdentifier = parameters.get("sampleIdentifier"); #String
- dataSetType = parameters.get("dataSetType"); #String
- folderName = parameters.get("folderName"); #String
- fileNames = parameters.get("filenames"); #List<String>
- isZipDirectoryUpload = parameters.get("isZipDirectoryUpload"); #String
- metadata = parameters.get("metadata"); #java.util.LinkedHashMap<String, String> where the key is the name
- properties = getProperties(tr, parameters);
-
- #Create Dataset
- dataSetSample = getSampleByIdentifierForUpdate(tr, sampleIdentifier);
- dataSet = tr.createNewDataSet(dataSetType);
- dataSet.setSample(dataSetSample);
-
- #Assign Data Set properties
- for key in metadata.keySet():
- propertyValue = unicode(metadata[key]);
- if propertyValue == "":
- propertyValue = None;
- else:
- propertyValue = updateIfIsPropertyRichText(properties, key, propertyValue);
- dataSet.setPropertyValue(key,propertyValue);
-
- #Move All Files using a tmp directory close to the datastore
- threadProperties = getThreadProperties(tr);
- tempDir = threadProperties[u'incoming-dir'] + "/tmp_eln/" + str(time.time());
- tempDirFile = File(tempDir);
- tempDirFile.mkdirs();
-
- #tempDir = System.getProperty("java.io.tmpdir");
- dss_component = DssComponentFactory.tryCreate(parameters.get("sessionID"), OPENBISURL);
-
- for fileName in fileNames:
- folderFile = File(tempDir + "/" + folderName);
- folderFile.mkdir();
- temFile = File(tempDir + "/" + folderName + "/" + fileName);
- inputStream = dss_component.getFileFromSessionWorkspace(fileName);
- outputStream = FileOutputStream(temFile);
- IOUtils.copyLarge(inputStream, outputStream);
- IOUtils.closeQuietly(inputStream);
- IOUtils.closeQuietly(outputStream);
-
- #CASE - 1: Only one file as zip, uncompressed on the folder
- if fileNames.size() == 1 and isZipDirectoryUpload:
- temFile = File(tempDir + "/" + folderName + "/" + fileNames.get(0));
- tempFolder = tempDir + "/" + folderName;
- zipFile = ZipFile(temFile.getAbsolutePath());
- zipFile.extractAll(tempFolder);
- temFile.delete();
- tr.moveFile(tempFolder, dataSet);
- elif fileNames.size() > 1: #CASE - 2: Multiple files on the folder
- temFile = File(tempDir + "/"+ folderName);
- tr.moveFile(temFile.getAbsolutePath(), dataSet);
- else: #CASE - 3: One file only
- temFile = File(tempDir + "/" + folderName + "/" + fileNames.get(0));
- if temFile.getName().endswith(".fasta") and dataSetType == "SEQ_FILE" and PLASMAPPER_BASE_URL != None:
- futureSVG = File(tempDir + "/" + folderName + "/generated/" + temFile.getName().replace(".fasta", ".svg"));
- futureHTML = File(tempDir + "/" + folderName + "/generated/" + temFile.getName().replace(".fasta", ".html"));
- try:
- PlasmapperConnector.downloadPlasmidMap(
- PLASMAPPER_BASE_URL,
- tempDir + "/" + folderName + "/" + temFile.getName(),
- tempDir + "/" + folderName + "/generated/" + temFile.getName().replace(".fasta", ".svg"),
- tempDir + "/" + folderName + "/generated/" + temFile.getName().replace(".fasta", ".html")
- );
- except:
- raise UserFailureException("Plasmapper service unavailable, try to upload your dataset later.");
- tr.moveFile(temFile.getParentFile().getAbsolutePath(), dataSet);
- else:
- tr.moveFile(temFile.getAbsolutePath(), dataSet);
- #Clean Files from workspace
- for fileName in fileNames:
- dss_component.deleteSessionWorkspaceFile(fileName);
-
- #Return from the call
- return True;
-
-def copyAndLinkAsParent(tr, parameters, tableBuilder):
- newSampleIdentifier = parameters.get("newSampleIdentifier"); #String
- sampleIdentifierToCopyAndLinkAsParent = parameters.get("sampleIdentifierToCopyAndLinkAsParent"); #String
- experimentIdentifierToAssignToCopy = parameters.get("experimentIdentifierToAssignToCopy"); #String
-
- #Create new Sample
- sampleToCopyAndLinkAsParent = getSampleByIdentifierForUpdate(tr, sampleIdentifierToCopyAndLinkAsParent); #Retrieve Sample
- newSample = tr.createNewSample(newSampleIdentifier, sampleToCopyAndLinkAsParent.getSampleType()); #Create Sample given his id
-
- #Assign Parent
- newSample.setParentSampleIdentifiers([sampleIdentifierToCopyAndLinkAsParent]);
-
- #Assign properties
- propertiesDefinitions = searchService.listPropertiesDefinitionsForSampleType(sampleToCopyAndLinkAsParent.getSampleType());
- for propertyDefinition in propertiesDefinitions:
- propCode = propertyDefinition.getPropertyTypeCode();
- propValue = sampleToCopyAndLinkAsParent.getPropertyValue(propCode);
- if propValue is not None:
- newSample.setPropertyValue(propCode, propValue);
-
- #Assign Experiment
- experimentToAssignToCopy = tr.getExperiment(experimentIdentifierToAssignToCopy);
- newSample.setExperiment(experimentToAssignToCopy);
-
- return True;
-
-def copySample(tr, parameters, tableBuilder):
- #Store Children to copy later
- sampleSpace = parameters.get("sampleSpace"); #String
- sampleCode = parameters.get("sampleCode"); #String
- sampleIdentifier = '/' + sampleSpace + '/' + sampleCode;
-
- sampleChildren = parameters.get("sampleChildren"); #List<String> Identifiers are in SPACE/CODE format
- parameters.put("sampleChildren", []); #List<String> Identifiers are in SPACE/CODE format
-
- #Create new Sample
- parameters.put("method", "insertSample"); #List<String> Identifiers are in SPACE/CODE format
- insertUpdateSample(tr, parameters, tableBuilder);
-
- #Copy children and attach to Sample
- if sampleChildren != None:
- for sampleChildIdentifier in sampleChildren:
- child = getSampleByIdentifierForUpdate(tr, sampleChildIdentifier); #Retrieve Sample child to copy
-
- copyChildCode = None
- try: #For autogenerated children that have the code as sufix
- indexFromCopiedChildrenParentCode = child.getCode().index('_')
- copyChildCode = parameters.get("sampleCode") + child.getCode()[indexFromCopiedChildrenParentCode:];
- except: #For all other children
- copyChildCode = parameters.get("sampleCode") + "_" + child.getCode();
-
- copyChildIdentifier = "/" + parameters.get("sampleSpace") + "/" + copyChildCode;
-
- # Create new sample children
- childCopy = tr.createNewSample(copyChildIdentifier, child.getSampleType()); #Create Sample given his id
- childParents = childCopy.getParentSampleIdentifiers();
- childParents.add(sampleIdentifier);
- childCopy.setParentSampleIdentifiers(childParents);
- if(child.getExperiment() is not None):
- childCopy.setExperiment(child.getExperiment());
- searchService = tr.getSearchService();
- propertiesDefinitions = searchService.listPropertiesDefinitionsForSampleType(child.getSampleType());
- for propertyDefinition in propertiesDefinitions:
- propCode = propertyDefinition.getPropertyTypeCode();
- propValue = getCopySampleChildrenPropertyValue(
- propCode,
- child.getPropertyValue(propCode),
- parameters.get("notCopyProperties"),
- parameters.get("defaultBenchPropertyList"),
- parameters.get("defaultBenchProperties")
- );
- if propValue != None:
- childCopy.setPropertyValue(propCode, propValue);
-
- return True;
-
-#This method is used to return the properties, deleting the storage ones and setting the default storage
-def getCopySampleChildrenPropertyValue(propCode, propValue, notCopyProperties, defaultBenchPropertyList, defaultBenchProperties):
- isPropertyToSkip = any(propCode == s for s in notCopyProperties);
- isDefaultBenchProperty = any(propCode == s for s in defaultBenchPropertyList);
- if isPropertyToSkip:
- return None;
- elif isDefaultBenchProperty:
- return str(defaultBenchProperties[propCode]);
- else:
- return propValue;
-
-def batchOperation(tr, parameters, tableBuilder):
- for operationParameters in parameters.get("operations"):
- if operationParameters.get("method") == "updateSample":
- operationParameters["sessionToken"] = parameters.get("sessionToken");
- insertUpdateSample(tr, operationParameters, tableBuilder);
- return True;
-
-def insertUpdateSample(tr, parameters, tableBuilder):
-
- #Mandatory parameters
- sampleSpace = parameters.get("sampleSpace"); #String
- sampleProject = parameters.get("sampleProject"); #String
- sampleExperiment = parameters.get("sampleExperiment"); #String
- sampleCode = parameters.get("sampleCode"); #String
- sampleType = parameters.get("sampleType"); #String
- sampleProperties = parameters.get("sampleProperties"); #java.util.LinkedHashMap<String, String> where the key is the name
- changesToDo = parameters.get("changesToDo");
-
- #Optional parameters
- sampleParents = parameters.get("sampleParents"); #List<String> Identifiers are in SPACE/CODE format
- sampleChildrenNew = parameters.get("sampleChildrenNew"); #List<java.util.LinkedHashMap<String, String>>
- sampleChildren = parameters.get("sampleChildren"); #List<String> Identifiers are in SPACE/CODE format
- sampleChildrenRemoved = parameters.get("sampleChildrenRemoved"); #List<String> Identifiers are in SPACE/CODE format
-
- #Create/Get for update sample
- sampleIdentifier = '/' + sampleSpace + '/' + sampleCode;
-
- method = parameters.get("method");
- if method == "insertSample":
- sample = tr.createNewSample(sampleIdentifier, sampleType); #Create Sample given his id
-
- if method == "updateSample":
- sample = getSampleByIdentifierForUpdate(tr, sampleIdentifier); #Retrieve Sample
-
- #Obtain space
- space = None;
- if sampleSpace != None:
- space = tr.getSpace(sampleSpace);
- if space == None:
- space = tr.createNewSpace(sampleSpace, None);
-
- #Obtain experiment
- experiment = None;
- if sampleSpace != None and sampleProject != None and sampleExperiment != None:
- experimentIdentifier = "/" + sampleSpace + "/" + sampleProject + "/" + sampleExperiment;
- experiment = tr.getExperiment(experimentIdentifier);
-
- #Assign experiment
- if experiment != None:
- sample.setExperiment(experiment);
- #Assign sample properties
- if sampleProperties != None:
- properties = getProperties(tr, parameters);
- for key in sampleProperties.keySet():
- propertyValue = sampleProperties[key];
- if propertyValue == "":
- propertyValue = None;
- else:
- propertyValue = updateIfIsPropertyRichText(properties, key, propertyValue);
- sample.setPropertyValue(key, unicode(propertyValue));
- #Add sample parents
- if sampleParents != None:
- sample.setParentSampleIdentifiers(sampleParents);
-
- #Create new sample children
- sampleChildrenNewIdentifiers = [];
- if sampleChildrenNew != None:
- for newSampleChild in sampleChildrenNew:
- child = tr.createNewSample(newSampleChild["identifier"], newSampleChild["sampleTypeCode"]); #Create Sample given his id
- sampleChildrenNewIdentifiers.append(newSampleChild["identifier"]);
- child.setParentSampleIdentifiers([sampleIdentifier]);
- if experiment != None:
- child.setExperiment(experiment);
- for key in newSampleChild["properties"].keySet():
- propertyValue = unicode(newSampleChild["properties"][key]);
- if propertyValue == "":
- propertyValue = None;
-
- child.setPropertyValue(key,propertyValue);
-
- #Add sample children that are not newly created
- if sampleChildren != None:
- for sampleChildIdentifier in sampleChildren:
- if sampleChildIdentifier not in sampleChildrenNewIdentifiers:
- child = getSampleByIdentifierForUpdate(tr, sampleChildIdentifier); #Retrieve Sample
- childParents = child.getParentSampleIdentifiers();
- childParents.add(sampleIdentifier);
- child.setParentSampleIdentifiers(childParents);
-
- #Remove sample children
- if sampleChildrenRemoved != None:
- for sampleChildIdentifier in sampleChildrenRemoved:
- child = getSampleByIdentifierForUpdate(tr, sampleChildIdentifier); #Retrieve Sample
- if child != None: #The new created ones will not be found
- childParents = child.getParentSampleIdentifiers();
- childParents.remove(sampleIdentifier);
- child.setParentSampleIdentifiers(childParents);
-
- #Changes to do
- if changesToDo is not None:
- for change in changesToDo:
- sampleWithChanges = getSampleByIdentifierForUpdate(tr, change["identifier"]); #Retrieve Sample
- for key in change["properties"].keySet():
- propertyValue = unicode(change["properties"][key]);
- if propertyValue == "":
- propertyValue = None;
- sampleWithChanges.setPropertyValue(key,propertyValue);
-
- #Return from the call
- return True;
-
-def moveSample(tr, parameters, tableBuilder):
- sampleIdentifier = parameters.get("sampleIdentifier"); #String
- experimentIdentifier = parameters.get("experimentIdentifier"); #String
- experimentType = parameters.get("experimentType"); #String
-
- sample = getSampleByIdentifierForUpdate(tr, sampleIdentifier); #Retrieve Sample
- experiment = tr.getExperiment(experimentIdentifier); #Retrieve Experiment
-
- if experiment is None:
- experiment = tr.createNewExperiment(experimentIdentifier, experimentType);
-
- sample.setExperiment(experiment);
- return True
-
-def insertUpdateExperiment(tr, parameters, tableBuilder):
-
- #Mandatory parameters
- experimentType = parameters.get("experimentType"); #String
- experimentIdentifier = parameters.get("experimentIdentifier"); #String
- experimentProperties = parameters.get("experimentProperties"); #java.util.LinkedHashMap<String, String> where the key is the name
- properties = getProperties(tr, parameters);
-
- experiment = None;
- method = parameters.get("method");
- if method == "insertExperiment":
- experiment = tr.createNewExperiment(experimentIdentifier, experimentType); #Create Experiment given his id
- if method == "updateExperiment":
- experiment = tr.getExperimentForUpdate(experimentIdentifier); #Retrieve Experiment
-
- for key in experimentProperties.keySet():
- propertyValue = unicode(experimentProperties[key]);
- if propertyValue == "":
- propertyValue = None;
- else:
- propertyValue = updateIfIsPropertyRichText(properties, key, propertyValue);
- experiment.setPropertyValue(key,propertyValue);
-
- return True;
-
-def searchSamples(tr, parameters, tableBuilder, sessionId):
- v3 = HttpInvokerUtils.createServiceStub(IApplicationServerApi, OPENBISURL + IApplicationServerApi.SERVICE_URL, 30 * 1000);
-
- ###############
- ############### V3 Search
- ###############
- fechOptions = parameters;
-
- # FreeText
- anyFieldContains = fechOptions.get("anyFieldContains");
-
- # Attributes
- samplePermId = fechOptions.get("samplePermId");
- withExperimentWithProjectPermId = fechOptions.get("withExperimentWithProjectPermId");
- sampleIdentifier = fechOptions.get("sampleIdentifier");
- sampleCode = fechOptions.get("sampleCode");
- sampleTypeCode = fechOptions.get("sampleTypeCode");
- registrationDate = fechOptions.get("registrationDate");
- modificationDate = fechOptions.get("modificationDate");
-
- # Properties
- properyKeyValueList = fechOptions.get("properyKeyValueList");
-
- # Sub Queries
- sampleExperimentIdentifier = fechOptions.get("sampleExperimentIdentifier");
- sampleContainerPermId = fechOptions.get("sampleContainerPermId");
-
- # Hierarchy Options
- withProperties = fechOptions.get("withProperties");
- withParents = fechOptions.get("withParents");
- withChildren = fechOptions.get("withChildren");
- withAncestors = fechOptions.get("withAncestors");
- withDescendants = fechOptions.get("withDescendants");
-
- #Search Setup
- criterion = SampleSearchCriteria();
- criterion.withAndOperator();
- fetchOptions = SampleFetchOptions();
-
- #Free Text
- if anyFieldContains is not None:
- words = anyFieldContains.split();
- for word in words:
- if (word != None) and (word != ""):
- criterion.withAnyField().thatContains(word);
-
- #Attributes
- if samplePermId is not None:
- criterion.withPermId().thatEquals(samplePermId);
- if withExperimentWithProjectPermId is not None:
- criterion.withExperiment().withProject().withPermId().thatEquals(withExperimentWithProjectPermId);
- if sampleIdentifier is not None:
- criterion.withId().thatEquals(SampleIdentifier(sampleIdentifier));
- if sampleCode is not None:
- criterion.withCode().thatEquals(sampleCode);
- if sampleTypeCode is not None:
- criterion.withType().withCode().thatEquals(sampleTypeCode);
- if registrationDate is not None:
- formatter = SimpleDateFormat("yyyy-MM-dd");
- registrationDateObject = formatter.parse(registrationDate);
- criterion.withRegistrationDate().thatEquals(registrationDateObject);
- if modificationDate is not None:
- formatter = SimpleDateFormat("yyyy-MM-dd");
- modificationDateObject = formatter.parse(modificationDate);
- criterion.withModificationDate().thatEquals(modificationDateObject);
-
- #Properties
- if properyKeyValueList is not None:
- for keyValuePair in properyKeyValueList:
- for propertyTypeCode in keyValuePair.keySet():
- propertyValue = keyValuePair.get(propertyTypeCode);
- criterion.withProperty(propertyTypeCode).thatEquals(propertyValue);
-
- #Sub queries
- if sampleExperimentIdentifier is not None:
- criterion.withExperiment().withId().thatEquals(ExperimentIdentifier(sampleExperimentIdentifier));
- if sampleContainerPermId is not None:
- criterion.withContainer().withPermId().thatEquals(sampleContainerPermId);
-
- #Hierarchy Fetch Options
- if withProperties:
- fetchOptions.withProperties();
- if withParents:
- fetchOptionsParents = SampleFetchOptions();
- fetchOptionsParents.withProperties();
- fetchOptionsParents.withType();
- fetchOptionsParents.withSpace();
- fetchOptionsParents.withExperiment();
- fetchOptionsParents.withRegistrator();
- fetchOptionsParents.withModifier();
- fetchOptions.withParentsUsing(fetchOptionsParents);
- if withChildren:
- fetchOptionsChildren = SampleFetchOptions();
- fetchOptionsChildren.withProperties();
- fetchOptionsChildren.withType();
- fetchOptionsChildren.withSpace();
- fetchOptionsChildren.withExperiment();
- fetchOptionsChildren.withRegistrator();
- fetchOptionsChildren.withModifier();
- fetchOptions.withChildrenUsing(fetchOptionsChildren);
- if withAncestors:
- fetchOptionsAncestors = SampleFetchOptions();
- fetchOptionsAncestors.withProperties();
- fetchOptionsAncestors.withType();
- fetchOptionsAncestors.withSpace();
- fetchOptionsAncestors.withExperiment();
- fetchOptionsAncestors.withRegistrator();
- fetchOptionsAncestors.withModifier();
- fetchOptionsAncestors.withParentsUsing(fetchOptionsAncestors);
- fetchOptions.withParentsUsing(fetchOptionsAncestors);
- if withDescendants:
- fetchOptionsDescendants = SampleFetchOptions();
- fetchOptionsDescendants.withProperties();
- fetchOptionsDescendants.withType();
- fetchOptionsDescendants.withSpace();
- fetchOptionsDescendants.withExperiment();
- fetchOptionsDescendants.withRegistrator();
- fetchOptionsDescendants.withModifier();
- fetchOptionsDescendants.withChildrenUsing(fetchOptionsDescendants);
- fetchOptions.withChildrenUsing(fetchOptionsDescendants);
-
- #Standard Fetch Options, always use
- fetchOptions.withType();
- fetchOptions.withSpace();
- fetchOptions.withExperiment();
- fetchOptions.withRegistrator();
- fetchOptions.withModifier();
-
- ###############
- ###############
- ###############
-
-
- ##
- ## Custom (Interceptor to modify standard results)
- ##
- result = None;
-
- isCustom = parameters.get("custom"); #Boolean
- if isCustom:
- result = searchSamplesCustom(tr, parameters, tableBuilder, v3, criterion, fetchOptions);
- else:
- result = v3.searchSamples(parameters.get("sessionToken"), criterion, fetchOptions);
-
- ##
- ##
- ##
-
- ###
- ### Json Conversion
- ###
- objectMapper = GenericObjectMapper();
- resultAsString = objectMapper.writeValueAsString(result);
- return resultAsString;
-
-def searchSamplesCustom(tr, parameters, tableBuilder, v3, criterion, fetchOptions):
- # SEARCH CUSTOM PLACEHOLDER START
- return [];
- # SEARCH CUSTOM PLACEHOLDER END
-
-def searchSamplesNexus(tr, parameters, tableBuilder, v3, criterion, fetchOptions):
-
- toReturnPermIds = []; #
- #Right Givers: The sample with all his descendants
- #1. Request user search with all right givers
- descendantsFetchOptions = SampleFetchOptions();
- descendantsFetchOptions.withChildrenUsing(descendantsFetchOptions);
- requestedResults = v3.searchSamples(tr.getOpenBisServiceSessionToken(), criterion, descendantsFetchOptions);
-
- if requestedResults.getTotalCount() > 0:
- #Prepare data structures for the rights givers to accelerate the process
- requestedToRigthsGivers = {};
- allRightsGivers = set();
- for requestedResult in requestedResults.getObjects():
- rigthsGivers = getDescendantsTreePermIdsStringSet([requestedResult]);
- allRightsGivers = allRightsGivers | rigthsGivers;
- requestedToRigthsGivers[requestedResult.getPermId().getPermId()] = rigthsGivers;
-
- #2. Search for the visible right givers
-
- visibleRightGivers = v3.getSamples(parameters.get("sessionToken"), getSamplePermIdsObjFromPermIdStrings(allRightsGivers), SampleFetchOptions());
- visibleRightGiversPermIds = getDescendantsTreePermIdsStringSet(visibleRightGivers.values());
- #3. Intersect what the user wants and is available to see and keep matches
- for requestedResultPermIdString in requestedToRigthsGivers:
- rigthsGiversPermIds = requestedToRigthsGivers[requestedResultPermIdString];
- intersection = rigthsGiversPermIds & visibleRightGiversPermIds;
- if len(intersection) > 0:
- toReturnPermIds.append(SamplePermId(requestedResultPermIdString));
-
- #Now we complete those permIds with all information available for them using a search by the ETL server
- systemResultAsMap = v3.getSamples(tr.getOpenBisServiceSessionToken(), toReturnPermIds, fetchOptions);
- systemResult = ArrayList(systemResultAsMap.values());
- systemSearchResult = SearchResult(systemResult, systemResult.size());
-
- return systemSearchResult
-
-def getSamplePermIdsObjFromPermIdStrings(samplePermIds):
- values = [];
- for samplePermId in samplePermIds:
- values.append(SamplePermId(samplePermId));
- return values;
-
-def getDescendantsTreePermIdsStringSet(samples):
- descendantsPermIds = set();
- for sample in samples:
- descendantsQueue = [sample];
- while len(descendantsQueue) > 0:
- queueSample = descendantsQueue.pop();
- if queueSample.getPermId().getPermId() not in descendantsPermIds:
- descendantsPermIds.add(queueSample.getPermId().getPermId());
- if queueSample.getFetchOptions().hasChildren():
- for child in queueSample.getChildren():
- descendantsQueue.append(child);
- return descendantsPermIds;
\ No newline at end of file