testfile.ftl and TestFileController.java: modifications for calling a script instead of directly calling Harvester
This commit is contained in:
mbarbier
parent
bcdc7ee981
commit
09daaa58ac
2 changed files with 315 additions and 464 deletions
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@ -1,35 +1,64 @@
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<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
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<script type="text/javascript">
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var alreadyDone = false;
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var harvestProgressResponse;
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function doFunStuff()
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{
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if(!alreadyDone)
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{
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alreadyDone = true;
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document.getElementById("progress").style.visibility = "visible"
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document.getElementById("progressUploading").style.visibility = "visible"
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window.setTimeout(uploadingSuccess, 2000);
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doHarvest();
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}
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function doHarvest()
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{
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var request = createRequest();
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request.onreadystatechange=function() {
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if(request.readyState == 4 && request.status == 200) {
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harvestProgressResponse = request.responseText;
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window.setTimeout(continueHarvest, 1000);
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}
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}
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request.open("POST", "/vivo/harvester/testfile", true);
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request.setRequestHeader("content-type","application/x-www-form-urlencoded");
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request.send("${paramIsHarvestClick}=true");
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}
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function continueHarvest()
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{
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var response = harvestProgressResponse;
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var json = eval("(" + response + ")");
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if(!json.finished) {
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var logAppend = json.progressSinceLastCheck;
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var progressTextArea = document.getElementById("progressTextArea");
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progressTextArea.innerHTML = progressTextArea.innerHTML + logAppend;
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progressTextArea.scrollTop = progressTextArea.scrollHeight;
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var request = createRequest();
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request.onreadystatechange=function() {
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if(request.readyState == 4 && request.status == 200) {
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harvestProgressResponse = request.responseText;
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window.setTimeout(continueHarvest, 1000);
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}
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}
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request.open("POST", "/vivo/harvester/testfile", true);
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request.setRequestHeader("Content-type","application/x-www-form-urlencoded");
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request.send("${paramIsHarvestClick}=false");
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}
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}
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function uploadingSuccess()
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{
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document.getElementById("progressUploadingSuccess").style.visibility = "visible"
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document.getElementById("progressGenerating").style.visibility = "visible"
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window.setTimeout(generatingSuccess, 2000);
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}
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function generatingSuccess()
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{
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document.getElementById("progressGeneratingSuccess").style.visibility = "visible"
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document.getElementById("progressExecuting").style.visibility = "visible"
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window.setTimeout(executingSuccess, 2000);
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}
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function executingSuccess()
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{
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document.getElementById("progressExecutingSuccess").style.visibility = "visible"
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document.getElementById("results").style.visibility = "visible"
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}
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function createRequest() {
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var request;
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if (window.XMLHttpRequest) {
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request = new XMLHttpRequest();
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} else {
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request = new ActiveXObject("Microsoft.XMLHTTP");
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}
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return request;
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}
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function toggleCollapsibleDiv(divName)
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{
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@ -72,6 +101,7 @@
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function init()
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{
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document.getElementById("${paramFirstUpload}").value = "true";
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document.getElementById("fileUploadForm").onsubmit = function()
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{
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document.getElementById("fileUploadForm").target = "uploadTarget";
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@ -168,270 +198,14 @@
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</div>
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<div class="clearBothDiv" />
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</div>
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<div id="step5" class="testfile-step">
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<h3 class="testfile-step-header">Step 5</h3>
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<div id="step5-inner" class="testfile-step-body">
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<h4 class="testfile-step-subheader">View results</h4>
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<div id="progress" style="visibility:hidden">
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<ul>
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<li id="progressUploading" style="visibility:hidden">Validating files... <span id="progressUploadingSuccess" style="visibility:hidden">success</span></li>
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<li id="progressGenerating" style="visibility:hidden">Generating script... <span id="progressGeneratingSuccess" style="visibility:hidden">success</span></li>
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<li id="progressExecuting" style="visibility:hidden">Executing script... <span id="progressExecutingSuccess" style="visibility:hidden">success</span></li>
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</ul>
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</div>
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<div style="height:30px"></div>
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<div id="results" style="visibility:hidden">
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<h3>Results</h3>
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<span style="color:green;font-weight:bold">Harvest successful.</span>
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<h4>Script used for harvest</h4>
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<div><input type="button" value="Save" style="margin-bottom:10px" /></div>
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<textarea cols="100" rows="50" readonly="readonly"><#noparse>#!/bin/bash
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# Copyright (c) 2010 Christopher Haines, Dale Scheppler, Nicholas Skaggs, Stephen V. Williams, Michael Barbieri.
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# All rights reserved. This program and the accompanying materials
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# are made available under the terms of the new BSD license
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# which accompanies this distribution, and is available at
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# http://www.opensource.org/licenses/bsd-license.html
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#
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# Contributors:
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# Christopher Haines, Dale Scheppler, Nicholas Skaggs, Stephen V. Williams, Michael Barbieri - initial API and implementation
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#KNOWN ISSUE: Seems to tie in matches that were originally in VIVO into the input model, so that if the input model is cleaned out of VIVO,
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# then those matches will be removed. Actually they remain, hidden, but much of their data including their rdf:type is gone. An
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# RDF export will show this.
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# Exit on first error
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set -e
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# Set working directory
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HARVESTERDIR=`dirname "$(cd "${0%/*}" 2>/dev/null; echo "$PWD"/"${0##*/}")"`
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HARVESTERDIR=$(cd $HARVESTERDIR; cd ..; pwd)
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HARVESTER_TASK=mods
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if [ -f scripts/env ]; then
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. scripts/env
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else
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exit 1
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fi
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echo "Full Logging in $HARVESTER_TASK_DATE.log"
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BASEDIR=harvested-data/$HARVESTER_TASK
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BIBINDIR=$BASEDIR/rh-bibutils-in
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BIBOUTDIR=$BASEDIR/rh-bibutils-out
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RAWRHDIR=$BASEDIR/rh-raw
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RAWRHDBURL=jdbc:h2:$RAWRHDIR/store
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RDFRHDIR=$BASEDIR/rh-rdf
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RDFRHDBURL=jdbc:h2:$RDFRHDIR/store
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MODELDIR=$BASEDIR/model
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MODELDBURL=jdbc:h2:$MODELDIR/store
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MODELNAME=modsTempTransfer
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SCOREDATADIR=$BASEDIR/score-data
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SCOREDATADBURL=jdbc:h2:$SCOREDATADIR/store
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SCOREDATANAME=modsScoreData
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TEMPCOPYDIR=$BASEDIR/temp-copy
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MATCHEDDIR=$BASEDIR/matched
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MATCHEDDBURL=jdbc:h2:$MATCHEDDIR/store
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MATCHEDNAME=matchedData
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#scoring algorithms
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EQTEST="org.vivoweb.harvester.score.algorithm.EqualityTest"
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LEVDIFF="org.vivoweb.harvester.score.algorithm.NormalizedLevenshteinDifference"
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#matching properties
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CWEMAIL="http://vivoweb.org/ontology/core#workEmail"
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SWEMAIL="http://vivoweb.org/ontology/score#workEmail"
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FFNAME="http://xmlns.com/foaf/0.1/firstName"
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SFNAME="http://vivoweb.org/ontology/score#foreName"
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FLNAME="http://xmlns.com/foaf/0.1/lastName"
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CMNAME="http://vivoweb.org/ontology/core#middleName"
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BPMID="http://purl.org/ontology/bibo/pmid"
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CTITLE="http://vivoweb.org/ontology/core#title"
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BISSN="http://purl.org/ontology/bibo/ISSN"
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PVENUEFOR="http://vivoweb.org/ontology/core#publicationVenueFor"
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LINKAUTH="http://vivoweb.org/ontology/core#linkedAuthor"
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LINKINFORES="http://vivoweb.org/ontology/core#linkedInformationResource"
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AUTHINAUTH="http://vivoweb.org/ontology/core#authorInAuthorship"
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RDFTYPE="http://www.w3.org/1999/02/22-rdf-syntax-ns#type"
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RDFSLABEL="http://www.w3.org/2000/01/rdf-schema#label"
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BASEURI="http://vivoweb.org/harvest/mods/"
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#BIBUTILSBASE="lib/bibutils/bibutils_4.12_x86_64"
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BIBUTILSBASE="lib/bibutils/bibutils_4.12_i386"
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BIBUTILSINPUTFORMAT="med"
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#clear old fetches
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rm -rf $BIBINDIR
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# Execute Fetch for Pubmed
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$PubmedFetch -X config/tasks/ufl.pubmedfetch.xml -o $TFRH -OfileDir=$BIBINDIR
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# clear old bibutils runs
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rm -rf $BIBOUTDIR
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# run bibutils
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$RunBibutils -b $BIBUTILSBASE -m $BIBUTILSINPUTFORMAT -i $TFRH -IfileDir=$BIBINDIR -o $TFRH -OfileDir=$BIBOUTDIR
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# clear old sanitizes
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rm -rf $RAWRHDIR
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# Sanitize data
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$SanitizeMODSXML -i $TFRH -IfileDir=$BIBOUTDIR -o $TFRH -OfileDir=$RAWRHDIR
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# clear old translates
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rm -rf $RDFRHDIR
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# Execute Translate using the mods-to-vivo.xsl file
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$XSLTranslator -i $TFRH -IfileDir=$RAWRHDIR -o $H2RH -OdbUrl=$RDFRHDBURL -x config/datamaps/mods-to-vivo.xsl -f
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# backup translate
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BACKRDF="rdf"
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backup-path $RDFRHDIR $BACKRDF
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# uncomment to restore previous translate
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#restore-path $RDFRHDIR $BACKRDF
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# Clear old H2 transfer model
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rm -rf $MODELDIR
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# Execute Transfer to import from record handler into local temp model
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$Transfer -o $H2MODEL -OmodelName=$MODELNAME -OcheckEmpty=$CHECKEMPTY -OdbUrl=$MODELDBURL -h $H2RH -HdbUrl=$RDFRHDBURL
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# backup H2 transfer Model
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BACKMODEL="model"
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backup-path $MODELDIR $BACKMODEL
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# uncomment to restore previous H2 transfer Model
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#restore-path $MODELDIR $BACKMODEL
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# Clear old H2 score data
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rm -rf $SCOREDATADIR
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# Clear old H2 match data
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rm -rf $MATCHEDDIR
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# Clear old H2 temp copy
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rm -rf $TEMPCOPYDIR
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# Score variables for cleaner lines
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SCOREINPUT="-i $H2MODEL -ImodelName=$MODELNAME -IdbUrl=$MODELDBURL -IcheckEmpty=$CHECKEMPTY"
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SCOREDATA="-s $H2MODEL -SmodelName=$SCOREDATANAME -SdbUrl=$SCOREDATADBURL -ScheckEmpty=$CHECKEMPTY"
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MATCHOUTPUT="-o $H2MODEL -OmodelName=$MATCHEDNAME -OdbUrl=$MATCHEDDBURL -OcheckEmpty=$CHECKEMPTY"
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MATCHEDINPUT="-i $H2MODEL -ImodelName=$MATCHEDNAME -IdbUrl=$MATCHEDDBURL -IcheckEmpty=$CHECKEMPTY"
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SCOREMODELS="$SCOREINPUT -v $VIVOCONFIG -VcheckEmpty=$CHECKEMPTY $SCOREDATA -t $TEMPCOPYDIR -b $SCOREBATCHSIZE"
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# Execute Score to disambiguate data in "scoring" JENA model
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TITLE="-Atitle=$EQTEST -Ftitle=$RDFSLABEL -Wtitle=1.0 -Ptitle=$RDFSLABEL"
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$Score $SCOREMODELS $TITLE -n ${BASEURI}pub/
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$Match $SCOREINPUT $SCOREDATA -t 0.7 -r
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# clear H2 score data Model
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rm -rf $SCOREDATADIR
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#Author, Organization, Geographic Location, Journal match
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LNAME="-AlName=$LEVDIFF -FlName=$FLNAME -WlName=0.5 -PlName=$FLNAME"
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FNAME="-AfName=$LEVDIFF -FfName=$FFNAME -WfName=0.3 -PfName=$FFNAME"
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RDFSLABELSCORE="-ArdfsLabel=$LEVDIFF -FrdfsLabel=$RDFSLABEL -WrdfsLabel=1.0 -PrdfsLabel=$RDFSLABEL"
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$Score $SCOREMODELS $FNAME $LNAME -n ${BASEURI}author/
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$Score $SCOREMODELS $RDFSLABELSCORE -n ${BASEURI}org/
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$Score $SCOREMODELS $RDFSLABELSCORE -n ${BASEURI}geo/
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$Score $SCOREMODELS $RDFSLABELSCORE -n ${BASEURI}journal/
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$Match $SCOREINPUT $SCOREDATA -t 0.7 -r
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# clear H2 score data Model
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rm -rf $SCOREDATADIR
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# Clear old H2 temp copy of input (URI here is hardcoded in Score)
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$JenaConnect -Jtype=tdb -JdbDir=$TEMPCOPYDIR -JmodelName=http://vivoweb.org/harvester/model/scoring#inputClone -t
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#Authorship match
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AUTHPUB="-Aauthpub=$EQTEST -Fauthpub=$LINKINFORES -Wauthpub=0.5 -Pauthpub=$LINKINFORES"
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AUTHAUTH="-Aauthauth=$EQTEST -Fauthauth=$LINKAUTH -Wauthauth=0.5 -Pauthauth=$LINKAUTH"
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$Score $SCOREMODELS $AUTHPUB $AUTHAUTH -n ${BASEURI}authorship/
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$Match $SCOREINPUT $SCOREDATA -t 0.7 -r
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# backup H2 score data Model
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BACKSCOREDATA="scoredata-auths"
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backup-path $SCOREDATADIR $BACKSCOREDATA
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# uncomment to restore previous H2 matched Model
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#restore-path $SCOREDATADIR $BACKSCOREDATA
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# clear H2 score data Model
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rm -rf $SCOREDATADIR
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# Clear old H2 temp copy
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rm -rf $TEMPCOPYDIR
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# Execute ChangeNamespace lines: the -o flag value is determined by the XSLT used to translate the data
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CNFLAGS="$SCOREINPUT -v $VIVOCONFIG -VcheckEmpty=$CHECKEMPTY -n $NAMESPACE"
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# Execute ChangeNamespace to get unmatched Publications into current namespace
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$ChangeNamespace $CNFLAGS -u ${BASEURI}pub/
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# Execute ChangeNamespace to get unmatched Authorships into current namespace
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$ChangeNamespace $CNFLAGS -u ${BASEURI}authorship/
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# Execute ChangeNamespace to get unmatched Authors into current namespace
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$ChangeNamespace $CNFLAGS -u ${BASEURI}author/
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# Execute ChangeNamespace to get unmatched Organizations into current namespace
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$ChangeNamespace $CNFLAGS -u ${BASEURI}org/
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# Execute ChangeNamespace to get unmatched Geographic Locations into current namespace
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$ChangeNamespace $CNFLAGS -u ${BASEURI}geo/
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# Execute ChangeNamespace to get unmatched Journals into current namespace
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$ChangeNamespace $CNFLAGS -u ${BASEURI}journal/
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# Backup pretransfer vivo database, symlink latest to latest.sql
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BACKPREDB="pretransfer"
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backup-mysqldb $BACKPREDB
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# uncomment to restore pretransfer vivo database
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#restore-mysqldb $BACKPREDB
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PREVHARVESTMODEL="http://vivoweb.org/ingest/mods"
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ADDFILE="$BASEDIR/additions.rdf.xml"
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SUBFILE="$BASEDIR/subtractions.rdf.xml"
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# Find Subtractions
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$Diff -m $VIVOCONFIG -MmodelName=$PREVHARVESTMODEL -McheckEmpty=$CHECKEMPTY -s $H2MODEL -ScheckEmpty=$CHECKEMPTY -SdbUrl=$MODELDBURL -SmodelName=$MODELNAME -d $SUBFILE
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# Find Additions
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$Diff -m $H2MODEL -McheckEmpty=$CHECKEMPTY -MdbUrl=$MODELDBURL -MmodelName=$MODELNAME -s $VIVOCONFIG -ScheckEmpty=$CHECKEMPTY -SmodelName=$PREVHARVESTMODEL -d $ADDFILE
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PREVHARVESTMODELINPUT="-i $VIVOCONFIG -ImodelName=$PREVHARVESTMODEL -IcheckEmpty=$CHECKEMPTY"
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# Backup adds and subs
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backup-file $ADDFILE adds.rdf.xml
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backup-file $SUBFILE subs.rdf.xml
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# Apply Subtractions to Previous model
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$Transfer -o $H2MODEL -OdbUrl=${PREVHARVDBURLBASE}${HARVESTER_TASK}/store -OcheckEmpty=$CHECKEMPTY -OmodelName=$PREVHARVESTMODEL -r $SUBFILE -m
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# Apply Additions to Previous model
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$Transfer -o $H2MODEL -OdbUrl=${PREVHARVDBURLBASE}${HARVESTER_TASK}/store -OcheckEmpty=$CHECKEMPTY -OmodelName=$PREVHARVESTMODEL -r $ADDFILE
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# Apply Subtractions to VIVO
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$Transfer -o $VIVOCONFIG -OcheckEmpty=$CHECKEMPTY -r $SUBFILE -m
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# Apply Additions to VIVO
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$Transfer -o $VIVOCONFIG -OcheckEmpty=$CHECKEMPTY -r $ADDFILE
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#Restart Tomcat
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#Tomcat must be restarted in order for the harvested data to appear in VIVO
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echo $HARVESTER_TASK ' completed successfully'
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/etc/init.d/tomcat stop
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/etc/init.d/apache2 reload
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/etc/init.d/tomcat start</#noparse></textarea>
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<div id="progress">
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<textarea cols="100" rows="50" readonly="readonly" id="progressTextArea"></textarea>
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</div>
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</div>
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<div class="clearBothDiv" />
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@ -1,21 +1,24 @@
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.vitro.webapp.controller.harvester;
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package edu.cornell.mannlib.vitro.webapp.controller.harvester;
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import java.io.BufferedReader;
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import java.io.File;
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import java.io.FileReader;
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import java.io.FileWriter;
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import java.io.IOException;
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import java.io.InputStreamReader;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.Hashtable;
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import java.util.List;
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import java.util.Map;
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import javax.servlet.ServletContext;
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import javax.servlet.ServletException;
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import javax.servlet.http.HttpServletRequest;
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import javax.servlet.http.HttpServletResponse;
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import org.apache.commons.fileupload.FileItem;
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import org.apache.commons.fileupload.servlet.ServletFileUpload;
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import org.apache.commons.logging.Log;
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import org.apache.commons.logging.LogFactory;
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import org.json.JSONException;
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@ -39,6 +42,7 @@ public class TestFileController extends FreemarkerHttpServlet {
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private static final String PARAMETER_FIRST_UPLOAD = "firstUpload";
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private static final String PARAMETER_UPLOADED_FILE = "uploadedFile";
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private static final String PARAMETER_IS_HARVEST_CLICK = "isHarvestClick";
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@Override
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protected ResponseValues processRequest(VitroRequest vreq) {
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@ -47,6 +51,7 @@ public class TestFileController extends FreemarkerHttpServlet {
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//body.put("uploadPostback", "false");
|
||||
body.put("paramFirstUpload", PARAMETER_FIRST_UPLOAD);
|
||||
body.put("paramUploadedFile", PARAMETER_UPLOADED_FILE);
|
||||
body.put("paramIsHarvestClick", PARAMETER_IS_HARVEST_CLICK);
|
||||
return new TemplateResponseValues(TEMPLATE_DEFAULT, body);
|
||||
} catch (Throwable e) {
|
||||
log.error(e, e);
|
||||
|
|
@ -65,7 +70,8 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
*/
|
||||
public static String getHarvesterPath()
|
||||
{
|
||||
String harvesterPath = "/usr/share/vivo/harvester/"; //todo: hack
|
||||
//String harvesterPath = "/usr/share/vivo/harvester/"; //todo: hack
|
||||
String harvesterPath = "/home/mbarbieri/workspace/HarvesterDevTomcat2/";
|
||||
return harvesterPath;
|
||||
}
|
||||
|
||||
|
|
@ -75,7 +81,7 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
* @return the base directory for file harvest uploads
|
||||
* @throws Exception if the Vitro home directory could not be found
|
||||
*/
|
||||
private String getUploadPathBase(ServletContext context) throws Exception
|
||||
private static String getUploadPathBase(ServletContext context) throws Exception
|
||||
{
|
||||
String vitroHomeDirectoryName = ConfigurationProperties.getBean(context).getProperty(FileStorageSetup.PROPERTY_VITRO_HOME_DIR);
|
||||
if (vitroHomeDirectoryName == null) {
|
||||
|
|
@ -89,35 +95,66 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
/**
|
||||
* Gets the FileHarvestJob implementation that is needed to handle the specified request. This
|
||||
* will depend on the type of harvest being performed (CSV, RefWorks, etc.)
|
||||
* @param request the request from the browser
|
||||
* @param vreq the request from the browser
|
||||
* @return the FileHarvestJob that will provide harvest-type-specific services for this request
|
||||
*/
|
||||
private FileHarvestJob getJob(HttpServletRequest request)
|
||||
private FileHarvestJob getJob(VitroRequest vreq)
|
||||
{
|
||||
String namespace = vreq.getWebappDaoFactory().getDefaultNamespace();
|
||||
|
||||
//todo: complete
|
||||
return new CsvHarvestJob("persontemplate.csv");
|
||||
return new CsvHarvestJob(vreq, "granttemplate.csv", namespace);
|
||||
}
|
||||
|
||||
public static String getUploadPath(VitroRequest vreq) {
|
||||
try {
|
||||
String path = getUploadPathBase(vreq.getSession().getServletContext()) + getSessionId(vreq) + "/";
|
||||
return path;
|
||||
} catch(Exception e) {
|
||||
log.error(e, e);
|
||||
throw new RuntimeException(e);
|
||||
}
|
||||
}
|
||||
|
||||
@Override
|
||||
public void doPost(HttpServletRequest request, HttpServletResponse response)
|
||||
throws IOException, ServletException {
|
||||
|
||||
log.error("this is a post.");
|
||||
|
||||
try {
|
||||
boolean isMultipart = ServletFileUpload.isMultipartContent(request);
|
||||
if(isMultipart)
|
||||
doFileUploadPost(request, response);
|
||||
else if(request.getParameter(PARAMETER_IS_HARVEST_CLICK).toLowerCase().equals("true"))
|
||||
doHarvestPost(request, response);
|
||||
else
|
||||
doCheckHarvestStatusPost(request, response);
|
||||
} catch(Exception e) {
|
||||
log.error(e, e);
|
||||
}
|
||||
}
|
||||
|
||||
private void doFileUploadPost(HttpServletRequest request, HttpServletResponse response)
|
||||
throws IOException, ServletException {
|
||||
|
||||
log.error("file upload post.");
|
||||
JSONObject json = new JSONObject();
|
||||
try {
|
||||
|
||||
String path = getUploadPathBase(request.getSession().getServletContext()) + getSessionId(request) + "/";
|
||||
File directory = new File(path);
|
||||
|
||||
VitroRequest vreq = new VitroRequest(request);
|
||||
|
||||
int maxFileSize = 1024 * 1024;
|
||||
FileUploadServletRequest req = FileUploadServletRequest.parseRequest(request, maxFileSize);
|
||||
FileUploadServletRequest req = FileUploadServletRequest.parseRequest(vreq, maxFileSize);
|
||||
if(req.hasFileUploadException()) {
|
||||
Exception e = req.getFileUploadException();
|
||||
new ExceptionVisibleToUser(e);
|
||||
}
|
||||
|
||||
String path = getUploadPath(vreq);
|
||||
File directory = new File(path);
|
||||
|
||||
String firstUpload = req.getParameter(PARAMETER_FIRST_UPLOAD); //clear directory on first upload
|
||||
log.error(firstUpload);
|
||||
if(firstUpload.toLowerCase().equals("true")) {
|
||||
if(directory.exists()) {
|
||||
File[] children = directory.listFiles();
|
||||
|
|
@ -130,7 +167,7 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
if(!directory.exists())
|
||||
directory.mkdirs();
|
||||
|
||||
FileHarvestJob job = getJob(req);
|
||||
FileHarvestJob job = getJob(vreq);
|
||||
|
||||
Map<String, List<FileItem>> fileStreams = req.getFiles();
|
||||
if(fileStreams.get(PARAMETER_UPLOADED_FILE) != null && fileStreams.get(PARAMETER_UPLOADED_FILE).size() > 0) {
|
||||
|
|
@ -140,7 +177,7 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
File file = new File(path + name);
|
||||
try {
|
||||
csvStream.write(file);
|
||||
} finally {
|
||||
} finally {
|
||||
csvStream.delete();
|
||||
}
|
||||
|
||||
|
|
@ -194,6 +231,96 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
response.getWriter().write(json.toString());
|
||||
}
|
||||
|
||||
private void doHarvestPost(HttpServletRequest request, HttpServletResponse response) {
|
||||
|
||||
log.error("harvest post.");
|
||||
try {
|
||||
VitroRequest vreq = new VitroRequest(request);
|
||||
FileHarvestJob job = getJob(vreq);
|
||||
|
||||
//String path = getUploadPath(vreq);
|
||||
|
||||
String script = job.getScript();
|
||||
log.error("start harvest");
|
||||
runScript(getSessionId(request), script);
|
||||
log.error("end harvest");
|
||||
|
||||
JSONObject json = new JSONObject();
|
||||
json.put("progressSinceLastCheck", "");
|
||||
json.put("finished", false);
|
||||
|
||||
response.getWriter().write(json.toString());
|
||||
|
||||
} catch(Exception e) {
|
||||
log.error(e, e);
|
||||
}
|
||||
}
|
||||
|
||||
private void doCheckHarvestStatusPost(HttpServletRequest request, HttpServletResponse response) {
|
||||
|
||||
log.error("check harvest status post.");
|
||||
|
||||
try {
|
||||
String newline = "\n";
|
||||
|
||||
String sessionId = getSessionId(request);
|
||||
|
||||
ArrayList<String> unsentLogLinesList = sessionIdToUnsentLogLines.get(sessionId);
|
||||
String[] unsentLogLines;
|
||||
if(unsentLogLinesList != null) {
|
||||
synchronized (unsentLogLinesList) {
|
||||
unsentLogLines = unsentLogLinesList.toArray(new String[unsentLogLinesList.size()]);
|
||||
unsentLogLinesList.clear();
|
||||
}
|
||||
|
||||
String progressSinceLastCheck = "";
|
||||
for(int i = 0; i < unsentLogLines.length; i++) {
|
||||
progressSinceLastCheck += unsentLogLines[i] + newline;
|
||||
}
|
||||
|
||||
boolean finished = !sessionIdToHarvestThread.containsKey(sessionId);
|
||||
|
||||
JSONObject json = new JSONObject();
|
||||
json.put("progressSinceLastCheck", progressSinceLastCheck);
|
||||
json.put("finished", finished);
|
||||
|
||||
response.getWriter().write(json.toString());
|
||||
}
|
||||
} catch(Exception e) {
|
||||
log.error(e, e);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
private File createScriptFile(String script) throws IOException {
|
||||
File scriptDirectory = new File(getHarvesterPath() + "scripts/temp");
|
||||
if(!scriptDirectory.exists()) {
|
||||
scriptDirectory.mkdirs();
|
||||
}
|
||||
|
||||
File tempFile = File.createTempFile("harv", ".sh", scriptDirectory);
|
||||
|
||||
FileWriter writer = new FileWriter(tempFile);
|
||||
writer.write(script);
|
||||
writer.close();
|
||||
|
||||
return tempFile;
|
||||
}
|
||||
|
||||
|
||||
private void runScript(String sessionId, String script) {
|
||||
|
||||
if(!sessionIdToHarvestThread.containsKey(sessionId)) {
|
||||
|
||||
ScriptRunner runner = new ScriptRunner(sessionId, script);
|
||||
sessionIdToHarvestThread.put(sessionId, runner);
|
||||
runner.start();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* Handles a name conflict in a directory by providing a new name that does not conflict with the
|
||||
|
|
@ -228,7 +355,7 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
* @param request the request coming in from the browser
|
||||
* @return the session ID
|
||||
*/
|
||||
private String getSessionId(HttpServletRequest request) {
|
||||
private static String getSessionId(HttpServletRequest request) {
|
||||
return request.getSession().getId();
|
||||
}
|
||||
|
||||
|
|
@ -237,25 +364,10 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
|
||||
|
||||
|
||||
@SuppressWarnings("unused")
|
||||
private void doHarvest() {
|
||||
/*
|
||||
Harvest will entail:
|
||||
|
||||
D2RMapFetch
|
||||
Transfer to local temp model
|
||||
Diffs
|
||||
Transfers
|
||||
|
||||
If this is being done with a script, then we should probably use a templating system.
|
||||
run-csv.sh
|
||||
|
||||
*/
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
|
@ -265,7 +377,7 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
|
||||
|
||||
/**
|
||||
* Provides a way of throwing an exception whose message it is OK to display unedited to the user.
|
||||
* Provides a way of throwing an exception whose message it is OK to display unedited to the user.
|
||||
*/
|
||||
private class ExceptionVisibleToUser extends Exception {
|
||||
private static final long serialVersionUID = 1L;
|
||||
|
|
@ -273,11 +385,83 @@ public class TestFileController extends FreemarkerHttpServlet {
|
|||
super(cause);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private Map<String, ScriptRunner> sessionIdToHarvestThread = new Hashtable<String, ScriptRunner>(); //Hashtable is threadsafe, HashMap is not
|
||||
private Map<String, ArrayList<String>> sessionIdToUnsentLogLines = new Hashtable<String, ArrayList<String>>(); //Hashtable is threadsafe, HashMap is not
|
||||
private class ScriptRunner extends Thread {
|
||||
|
||||
private final String sessionId;
|
||||
private final String script;
|
||||
|
||||
public ScriptRunner(String sessionId, String script) {
|
||||
this.sessionId = sessionId;
|
||||
this.script = script;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void run() {
|
||||
try {
|
||||
ArrayList<String> unsentLogLines = sessionIdToUnsentLogLines.get(sessionId);
|
||||
if(unsentLogLines == null) {
|
||||
unsentLogLines = new ArrayList<String>();
|
||||
sessionIdToUnsentLogLines.put(sessionId, unsentLogLines);
|
||||
}
|
||||
|
||||
File scriptFile = createScriptFile(script);
|
||||
|
||||
String command = "/bin/bash " + getHarvesterPath() + "scripts/temp/" + scriptFile.getName();
|
||||
|
||||
log.info("Running command: " + command);
|
||||
Process pr = Runtime.getRuntime().exec(command);
|
||||
|
||||
//try { Thread.sleep(15000); } catch(InterruptedException e) {log.error(e, e);}
|
||||
|
||||
BufferedReader processOutputReader = new BufferedReader(new InputStreamReader(pr.getInputStream()));
|
||||
for(String line = processOutputReader.readLine(); line != null; line = processOutputReader.readLine()) {
|
||||
synchronized(unsentLogLines) {
|
||||
unsentLogLines.add(line);
|
||||
}
|
||||
log.info("Harvester output: " + line);
|
||||
}
|
||||
|
||||
BufferedReader processErrorReader = new BufferedReader(new InputStreamReader(pr.getErrorStream()));
|
||||
for(String line = processErrorReader.readLine(); line != null; line = processErrorReader.readLine()) {
|
||||
log.info("Harvester error: " + line);
|
||||
}
|
||||
|
||||
int exitVal;
|
||||
|
||||
try {
|
||||
exitVal = pr.waitFor();
|
||||
}
|
||||
catch(InterruptedException e) {
|
||||
throw new IOException(e.getMessage(), e);
|
||||
}
|
||||
log.debug("Harvester script exited with error code " + exitVal);
|
||||
log.info("Harvester script execution complete");
|
||||
} catch (IOException e) {
|
||||
log.error(e, e);
|
||||
} finally {
|
||||
if(sessionIdToHarvestThread.containsKey(sessionId)) {
|
||||
sessionIdToHarvestThread.remove(sessionId);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
|
||||
/**
|
||||
* An implementation of FileHarvestJob that can be used for any CSV file harvest.
|
||||
* An implementation of FileHarvestJob that can be used for any CSV file harvest.
|
||||
*/
|
||||
class CsvHarvestJob implements FileHarvestJob {
|
||||
|
||||
|
|
@ -285,18 +469,30 @@ class CsvHarvestJob implements FileHarvestJob {
|
|||
* Logger.
|
||||
*/
|
||||
private static final Log log = LogFactory.getLog(CsvHarvestJob.class);
|
||||
|
||||
|
||||
/**
|
||||
* The HTTP request.
|
||||
*/
|
||||
private VitroRequest vreq;
|
||||
|
||||
/**
|
||||
* The template file against which uploaded CSV files will be validated.
|
||||
*/
|
||||
private File templateFile;
|
||||
|
||||
|
||||
/**
|
||||
* The namespace to be used for the harvest.
|
||||
*/
|
||||
private final String namespace;
|
||||
|
||||
/**
|
||||
* Constructor.
|
||||
* @param templateFileName just the name of the template file. The directory is assumed to be standard.
|
||||
*/
|
||||
public CsvHarvestJob(String templateFileName) {
|
||||
templateFile = new File(getTemplateFileDirectory() + templateFileName);
|
||||
public CsvHarvestJob(VitroRequest vreq, String templateFileName, String namespace) {
|
||||
this.vreq = vreq;
|
||||
this.templateFile = new File(getTemplateFileDirectory() + templateFileName);
|
||||
this.namespace = namespace;
|
||||
}
|
||||
|
||||
/**
|
||||
|
|
@ -315,17 +511,17 @@ class CsvHarvestJob implements FileHarvestJob {
|
|||
public String validateUpload(File file) {
|
||||
try {
|
||||
SimpleReader reader = new SimpleReader();
|
||||
|
||||
|
||||
List templateCsv = reader.parse(this.templateFile);
|
||||
String[] templateFirstLine = (String[])templateCsv.get(0);
|
||||
|
||||
List csv = reader.parse(file);
|
||||
|
||||
|
||||
int length = csv.size();
|
||||
|
||||
if(length == 0)
|
||||
return "No data in file";
|
||||
|
||||
|
||||
for(int i = 0; i < length; i++) {
|
||||
String[] line = (String[])csv.get(i);
|
||||
if(i == 0) {
|
||||
|
|
@ -334,8 +530,14 @@ class CsvHarvestJob implements FileHarvestJob {
|
|||
return errorMessage;
|
||||
}
|
||||
else if(line.length != 0) {
|
||||
if(line.length != templateFirstLine.length)
|
||||
return "Mismatch in number of entries in row " + i;
|
||||
if(line.length != templateFirstLine.length) {
|
||||
String retval = "Mismatch in number of entries in row " + i + ": expected , " + templateFirstLine.length + ", found " + line.length + " ";
|
||||
for(int j = 0; j < line.length; j++) {
|
||||
retval += "\"" + line[j] + "\", ";
|
||||
}
|
||||
//return retval;
|
||||
return "Mismatch in number of entries in row " + i + ": expected , " + templateFirstLine.length + ", found " + line.length;
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
|
@ -369,9 +571,9 @@ class CsvHarvestJob implements FileHarvestJob {
|
|||
@Override
|
||||
public String getScript()
|
||||
{
|
||||
String path = ""; //todo: complete
|
||||
String path = TestFileController.getHarvesterPath() + "scripts/" + "testCSVtoRDFgrant.sh"; //todo: complete
|
||||
File scriptTemplate = new File(path);
|
||||
|
||||
|
||||
String scriptTemplateContents = readScriptTemplate(scriptTemplate);
|
||||
String replacements = performScriptTemplateReplacements(scriptTemplateContents);
|
||||
return replacements;
|
||||
|
|
@ -380,9 +582,14 @@ class CsvHarvestJob implements FileHarvestJob {
|
|||
|
||||
private String performScriptTemplateReplacements(String scriptTemplateContents) {
|
||||
String replacements = scriptTemplateContents;
|
||||
|
||||
String fileDirectory = TestFileController.getUploadPath(vreq);
|
||||
|
||||
replacements = replacements.replace("${UPLOADS_FOLDER}", fileDirectory);
|
||||
|
||||
/*
|
||||
* What needs to be replaced?
|
||||
*
|
||||
*
|
||||
* task directory name
|
||||
*/
|
||||
//todo: complete
|
||||
|
|
@ -409,147 +616,17 @@ class CsvHarvestJob implements FileHarvestJob {
|
|||
log.error(e, e);
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
return scriptTemplateContents;
|
||||
}
|
||||
|
||||
|
||||
|
||||
@Override
|
||||
public void performHarvest(File directory) {
|
||||
|
||||
/* //COMMENTED OUT UNTIL HARVESTER INTEGRATION IS WORKING
|
||||
String vivoconfig = "config/models/vivo.xml";
|
||||
String scorebatchsize = "100";
|
||||
String checkempty = "true";
|
||||
String namespace = ""; //todo: get namespace
|
||||
String h2model = "config/models/h2-sdb.xml";
|
||||
String prevharvdburlbase = "jdbc:h2:harvested-data/prevHarvs/";
|
||||
String tfrh = "config/recordhandlers/h2-jdbc.xml";
|
||||
|
||||
String harvesterTask = "csv";
|
||||
|
||||
String basedir = "harvested-data/" + harvesterTask;
|
||||
|
||||
String rawrhdir = basedir + "/rh-raw";
|
||||
String rdfrhdir = basedir + "/rh-rdf";
|
||||
String modeldir = basedir + "/model";
|
||||
String scoredatadir = basedir + "/score-data";
|
||||
|
||||
String modeldburl = "jdbc:h2:" + modeldir + "/store";
|
||||
String scoredatadburl = "jdbc:h2:" + scoredatadir + "/store";
|
||||
|
||||
String modelname = "csvTempTransfer";
|
||||
String scoredataname = "csvScoreData";
|
||||
|
||||
String tempcopydir = basedir + "/temp-copy";
|
||||
|
||||
String[] scoreinput = Harvester.stringsToArray("-i", h2model, "-ImodelName=" + modelname, "-IdbUrl=" + modeldburl, "-IcheckEmpty=" + checkempty);
|
||||
String[] scoredata = Harvester.stringsToArray("-s", h2model, "-SmodelName=" + scoredataname, "-SdbUrl=" + scoredatadburl, "-ScheckEmpty=" + checkempty);
|
||||
String[] scoremodels = Harvester.stringsToArray(scoreinput, "-v", vivoconfig, "-VcheckEmpty=" + checkempty, scoredata, "-t", tempcopydir, "-b", scorebatchsize);
|
||||
|
||||
String[] cnflags = Harvester.stringsToArray(scoreinput, "-v", vivoconfig, "-n", namespace);
|
||||
|
||||
String eqtest = "org.vivoweb.harvester.score.algorithm.EqualityTest";
|
||||
|
||||
String grantidnum = "http://vivoweb.org/ontology/score#grantID";
|
||||
String rdfslabel = "http://www.w3.org/2000/01/rdf-schema#label";
|
||||
String personidnum = "http://vivoweb.org/ontology/score#personID";
|
||||
String deptidnum = "http://vivoweb.org/ontology/score#deptID";
|
||||
String rolein = "http://vivoweb.org/ontology/core#roleIn";
|
||||
String piroleof = "http://vivoweb.org/ontology/core#principalInvestigatorRoleOf";
|
||||
String copiroleof = "http://vivoweb.org/ontology/core#co-PrincipalInvestigatorRoleOf";
|
||||
String datetime = "http://vivoweb.org/ontology/core#dateTime";
|
||||
String baseuri = "http://vivoweb.org/harvest/csvfile/";
|
||||
|
||||
|
||||
|
||||
//execute fetch
|
||||
Harvester.runCSVtoRDF("-o", tfrh, "-O", "fileDir=" + rawrhdir, "-i", "filepath");
|
||||
|
||||
//execute translate
|
||||
Harvester.runXSLTranslator("-i", tfrh, "-IfileDir=" + rawrhdir, "-o", tfrh, "-OfileDir=" + rdfrhdir, "-x", "config/datamaps/csv-grant-to-vivo.xsl");
|
||||
|
||||
//execute transfer to import from record handler into local temp model
|
||||
Harvester.runTransfer("-o", h2model, "-OmodelName=" + modelname, "-OdbUrl=" + modeldburl, "-h", tfrh, "-HfileDir=" + rdfrhdir, "-n", namespace);
|
||||
|
||||
//smushes in-place(-r) on the Grant id THEN on the person ID then deptID
|
||||
Harvester.runSmush(scoreinput, "-P", grantidnum, "-P", personidnum, "-P", deptidnum, "-P", datetime, "-n", baseuri, "-r");
|
||||
|
||||
//scoring of Grants on GrantNumber
|
||||
Harvester.runScore(scoremodels, "-AGrantNumber=" + eqtest, "-WGrantNumber=1.0", "-FGrantNumber=" + grantidnum, "-PGrantNumber=" + grantidnum, "-n", baseuri + "grant/");
|
||||
|
||||
//scoring of people on PERSONIDNUM
|
||||
Harvester.runScore(scoremodels, "-Aufid=" + eqtest, "-Wufid=1.0", "-Fufid=" + personidnum, "-Pufid=" + personidnum, "-n", baseuri + "person/");
|
||||
|
||||
Harvester.runSmush(scoreinput, "-P", deptidnum, "-n", baseuri + "org/", "-r");
|
||||
|
||||
//scoring of orgs on DeptID
|
||||
Harvester.runScore(scoremodels, "-AdeptID=" + eqtest, "-WdeptID=1.0", "-FdeptID=" + deptidnum, "-PdeptID=" + deptidnum, "-n", baseuri + "org/");
|
||||
|
||||
|
||||
Harvester.runSmush(scoreinput, "-P", rdfslabel, "-n", baseuri + "sponsor/", "-r");
|
||||
|
||||
//scoring sponsors by labels
|
||||
Harvester.runScore(scoremodels, "-Alabel=" + eqtest, "-Wlabel=1.0", "-Flabel=" + rdfslabel, "-Plabel=" + rdfslabel, "-n", baseuri + "sponsor/");
|
||||
|
||||
//scoring of PI Roles
|
||||
String[] piuri = Harvester.stringsToArray("-Aperson=" + eqtest, "-Wperson=0.5", "-Fperson=" + piroleof, "-Pperson=" + piroleof);
|
||||
String[] granturi = Harvester.stringsToArray("-Agrant=" + eqtest, "-Wgrant=0.5", "-Fgrant=" + rolein, "-Pgrant=" + rolein);
|
||||
Harvester.runScore(scoremodels, piuri, granturi, "-n", baseuri + "piRole/");
|
||||
|
||||
//scoring of coPI Roles
|
||||
String[] copiuri = Harvester.stringsToArray("-Aperson=" + eqtest, "-Wperson=0.5", "-Fperson=" + copiroleof, "-Pperson=" + copiroleof);
|
||||
Harvester.runScore(scoremodels, copiuri, granturi, "-n", baseuri + "coPiRole/");
|
||||
|
||||
//find matches using scores and rename nodes to matching uri
|
||||
Harvester.runMatch(scoreinput, scoredata, "-b", scorebatchsize, "-t", "1.0", "-r");
|
||||
|
||||
//execute ChangeNamespace to get grants into current namespace
|
||||
Harvester.runChangeNamespace(cnflags, "-u", baseuri + "grant/");
|
||||
|
||||
//execute ChangeNamespace to get orgs into current namespace
|
||||
Harvester.runChangeNamespace(cnflags, "-u", baseuri + "org/");
|
||||
|
||||
//execute ChangeNamespace to get sponsors into current namespace
|
||||
Harvester.runChangeNamespace(cnflags, "-u", baseuri + "sponsor/");
|
||||
|
||||
//execute ChangeNamespace to get people into current namespace
|
||||
Harvester.runChangeNamespace(cnflags, "-u", baseuri + "person/");
|
||||
|
||||
//execute ChangeNamespace to get PI roles into current namespace
|
||||
Harvester.runChangeNamespace(cnflags, "-u", baseuri + "piRole/");
|
||||
|
||||
//execute ChangeNamespace to get co-PI roles into current namespace
|
||||
Harvester.runChangeNamespace(cnflags, "-u", baseuri + "coPiRole/");
|
||||
|
||||
//execute ChangeNamespace to get co-PI roles into current namespace
|
||||
Harvester.runChangeNamespace(cnflags, "-u", baseuri + "timeInterval");
|
||||
|
||||
|
||||
//todo: we probably don't want to do prev harvest stuff for this
|
||||
String prevharvestmodel = "http://vivoweb.org/ingest/dsr";
|
||||
String addfile = basedir + "/additions.rdf.xml";
|
||||
String subfile = basedir + "/subtractions.rdf.xml";
|
||||
|
||||
//find Subtractions
|
||||
Harvester.runDiff("-m", h2model, "-MdbUrl=" + prevharvdburlbase + harvesterTask + "/store", "-McheckEmpty=" + checkempty, "-MmodelName=" + prevharvestmodel, "-s", h2model, "-ScheckEmpty=" + checkempty, "-SdbUrl=" + modeldburl, "-SmodelName=" + modelname, "-d", subfile);
|
||||
|
||||
//find Additions
|
||||
Harvester.runDiff("-m", h2model, "-McheckEmpty=" + checkempty, "-MdbUrl=" + modeldburl, "-MmodelName=" + modelname, "-s", h2model, "-ScheckEmpty=" + checkempty, "-SdbUrl=" + prevharvdburlbase + harvesterTask + "/store", "-SmodelName=" + prevharvestmodel, "-d", addfile);
|
||||
|
||||
//apply Subtractions to Previous model
|
||||
Harvester.runTransfer("-o", h2model, "-OdbUrl=" + prevharvdburlbase + harvesterTask + "/store", "-OcheckEmpty=" + checkempty, "-OmodelName=" + prevharvestmodel, "-r", subfile, "-m");
|
||||
|
||||
//apply Additions to Previous model
|
||||
Harvester.runTransfer("-o", h2model, "-OdbUrl=" + prevharvdburlbase + harvesterTask + "/store", "-OcheckEmpty=" + checkempty, "-OmodelName=" + prevharvestmodel, "-r", addfile);
|
||||
|
||||
//apply Subtractions to VIVO
|
||||
Harvester.runTransfer("-o", vivoconfig, "-OcheckEmpty=" + checkempty, "-r", subfile, "-m");
|
||||
|
||||
//apply Additions to VIVO
|
||||
Harvester.runTransfer("-o", vivoconfig, "-OcheckEmpty=" + checkempty, "-r", addfile);
|
||||
*/
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Add table
Reference in a new issue