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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.
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
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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label = New Browser API
class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.jython.JythonIngestionService
script-path = script.py
openbis_standard_technologies/dist/core-plugins/eln-lims/1/dss/reporting-plugins/newbrowserapi/script.py deleted 100644 → 0
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#
# 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
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