NIHVIVO-3005 NIHVIVO-3007 Merged r3374 from maint-rel-1.3 branch.
This commit is contained in:
cappadona
parent
48b4ded3af
commit
eb567572bd
4 changed files with 337 additions and 217 deletions
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@ -52,6 +52,8 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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private static final Log log = LogFactory.getLog(FileHarvestController.class);
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private static final String TEMPLATE_DEFAULT = "fileharvest.ftl";
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private static final String NORMAL_TERMINATION_LAST_OUTPUT = "File Harvest completed successfully";
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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_MODE = "mode";
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@ -140,6 +142,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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FileHarvestJob jobObject = getJob(vreq, job);
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Map<String, Object> body = new HashMap<String, Object>();
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String harvesterPath = getHarvesterPath(vreq);
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//body.put("uploadPostback", "false");
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body.put("paramFirstUpload", PARAMETER_FIRST_UPLOAD);
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body.put("paramUploadedFile", PARAMETER_UPLOADED_FILE);
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@ -150,6 +153,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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body.put("modeDownloadTemplate", MODE_DOWNLOAD_TEMPLATE);
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body.put("job", job);
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body.put("jobKnown", jobKnown);
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body.put("harvesterLocation", harvesterPath);
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body.put("postTo", POST_TO + "?" + PARAMETER_JOB + "=" + job);
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body.put("jobSpecificHeader", (jobObject != null) ? jobObject.getPageHeader() : "");
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body.put("jobSpecificLinkHeader", (jobObject != null) ? jobObject.getLinkHeader() : "");
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@ -284,7 +288,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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private void doFileUploadPost(HttpServletRequest request, HttpServletResponse response)
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throws IOException, ServletException {
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JSONObject json = new JSONObject();
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JSONObject json = generateJson(false);
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try {
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VitroRequest vreq = new VitroRequest(request);
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@ -392,7 +396,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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}
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} catch(Exception e) {
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log.error(e, e);
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return;
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json = generateJson(true);
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}
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//write the prepared response
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@ -407,6 +411,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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*/
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private void doHarvestPost(HttpServletRequest request, HttpServletResponse response) {
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JSONObject json;
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try {
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VitroRequest vreq = new VitroRequest(request);
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FileHarvestJob job = getJob(vreq, vreq.getParameter(PARAMETER_JOB));
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@ -416,18 +421,23 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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String script = job.getScript();
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String additionsFilePath = job.getAdditionsFilePath();
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String scriptFileLocation = getScriptFileLocation(vreq);
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runScript(getSessionId(request), script, additionsFilePath, scriptFileLocation);
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runScript(getSessionId(request), script, additionsFilePath, scriptFileLocation, job);
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JSONObject json = new JSONObject();
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json = generateJson(false);
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json.put("progressSinceLastCheck", "");
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json.put("scriptText", script);
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json.put("finished", false);
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response.getWriter().write(json.toString());
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} catch(Exception e) {
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json = generateJson(true);
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log.error(e, e);
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}
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try {
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response.getWriter().write(json.toString());
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} catch(IOException e) {
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log.error(e, e);
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}
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}
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/**
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@ -439,6 +449,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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*/
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private void doCheckHarvestStatusPost(HttpServletRequest request, HttpServletResponse response) {
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JSONObject json;
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try {
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String newline = "\n";
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@ -463,6 +474,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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}
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boolean finished = sessionInfo.isFinished();
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boolean abnormalTermination = false;
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VitroRequest vreq = new VitroRequest(request);
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ArrayList<String> newlyAddedUrls = new ArrayList<String>();
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@ -478,21 +490,35 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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//remove all entries in "sessionIdTo..." mappings for this session ID
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clearSessionInfo(sessionId);
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if(sessionInfo.getAbnormalTermination())
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abnormalTermination = true;
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}
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JSONObject json = new JSONObject();
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json.put("progressSinceLastCheck", progressSinceLastCheck);
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json.put("finished", finished);
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json.put("newlyAddedUris", newlyAddedUris);
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json.put("newlyAddedUrls", newlyAddedUrls);
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response.getWriter().write(json.toString());
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if(!abnormalTermination) {
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json = generateJson(false);
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json.put("progressSinceLastCheck", progressSinceLastCheck);
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json.put("finished", finished);
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json.put("newlyAddedUris", newlyAddedUris);
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json.put("newlyAddedUrls", newlyAddedUrls);
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} else {
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json = generateJson(true);
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log.error("File harvest terminated abnormally.");
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}
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} else { //if we have not started a harvest thread, the browser should not have made this request to begin with. Bad browser, very bad browser.
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json = generateJson(true);
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log.error("Attempt to check status of a harvest that was never started! (Session ID " + sessionId + ")");
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}
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} catch(Exception e) {
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json = generateJson(true);
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log.error(e, e);
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}
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try {
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response.getWriter().write(json.toString());
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} catch(IOException e) {
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log.error(e, e);
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}
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}
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private void doDownloadTemplatePost(HttpServletRequest request, HttpServletResponse response) {
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@ -549,10 +575,10 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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}
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private void runScript(String sessionId, String script, String additionsFilePath, String scriptFileLocation) {
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private void runScript(String sessionId, String script, String additionsFilePath, String scriptFileLocation, FileHarvestJob job) {
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clearSessionInfo(sessionId);
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ScriptRunner runner = new ScriptRunner(sessionId, script, additionsFilePath, scriptFileLocation);
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ScriptRunner runner = new ScriptRunner(sessionId, script, additionsFilePath, scriptFileLocation, job);
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SessionInfo info = new SessionInfo(sessionId, runner);
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sessionIdToSessionInfo.put(sessionId, info);
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runner.start();
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@ -604,7 +630,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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* @param additionsFile the file containing the newly-added RDF/XML
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* @param newlyAddedUris a list in which to place the newly added URIs
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*/
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private void extractNewlyAddedUris(File additionsFile, List<String> newlyAddedUris) {
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private void extractNewlyAddedUris(File additionsFile, List<String> newlyAddedUris, FileHarvestJob job) {
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try {
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DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
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@ -618,7 +644,16 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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Node node = descriptionNodes.item(i);
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ArrayList<String> types = getRdfTypes(node);
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if(types.contains("http://vivoweb.org/ontology/core#Grant")) { //todo: generalize
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boolean match = false;
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String[] validRdfTypesForJob = job.getRdfTypesForLinks();
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for(String rdfType : validRdfTypesForJob) {
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if(types.contains(rdfType))
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match = true;
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break;
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}
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if(match) {
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NamedNodeMap attributes = node.getAttributes();
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Node aboutAttribute = attributes.getNamedItemNS("http://www.w3.org/1999/02/22-rdf-syntax-ns#", "about");
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@ -705,6 +740,21 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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}
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/**
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* Create a new JSON object
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* @param fatalError whether the fatal error flag should be set on this object
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* @return the new JSON object
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*/
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private JSONObject generateJson(boolean fatalError) {
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JSONObject json = null;
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try {
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json = new JSONObject();
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json.put("fatalError", fatalError);
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} catch(JSONException e) {
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log.error(e.getMessage(), e);
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}
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return json;
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}
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@ -743,6 +793,11 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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*/
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private boolean finished = false;
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/**
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* Flag indicating that the thread finished abnormally.
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*/
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private boolean abnormalTermination = false;
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/**
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* Newly added entries to VIVO, for this user session.
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@ -757,6 +812,13 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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this.harvestThread = harvestThread;
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}
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public void setAbnormalTermination() {
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abnormalTermination = true;
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}
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public boolean getAbnormalTermination() {
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return abnormalTermination;
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}
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public void finish() {
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finished = true;
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}
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@ -786,14 +848,16 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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private final String script;
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private final String additionsFilePath;
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private final String scriptFileLocation;
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private final FileHarvestJob job;
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private volatile boolean abort = false;
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public ScriptRunner(String sessionId, String script, String additionsFilePath, String scriptFileLocation) {
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public ScriptRunner(String sessionId, String script, String additionsFilePath, String scriptFileLocation, FileHarvestJob job) {
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this.sessionId = sessionId;
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this.script = script;
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this.additionsFilePath = additionsFilePath;
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this.scriptFileLocation = scriptFileLocation;
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this.job = job;
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}
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public void abortRun() {
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@ -804,6 +868,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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@Override
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public void run() {
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SessionInfo sessionInfo = sessionIdToSessionInfo.get(sessionId);
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boolean normalTerminationLineFound = false;
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if(sessionInfo != null) {
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try {
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ArrayList<String> unsentLogLines = sessionInfo.unsentLogLines;
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@ -820,6 +885,8 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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BufferedReader processOutputReader = new BufferedReader(new InputStreamReader(pr.getInputStream()));
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for(String line = processOutputReader.readLine(); line != null; line = processOutputReader.readLine()) {
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normalTerminationLineFound = line.endsWith(NORMAL_TERMINATION_LAST_OUTPUT); //set every read to ensure it's the last line
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//don't add stuff to this list if the main thread is running a "transaction" of copying out the data to send to client and then clearing the list
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synchronized(unsentLogLines) {
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unsentLogLines.add(line);
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@ -857,7 +924,7 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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File additionsFile = new File(this.additionsFilePath);
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if(additionsFile.exists())
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extractNewlyAddedUris(additionsFile, sessionInfo.newlyAddedUris);
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extractNewlyAddedUris(additionsFile, sessionInfo.newlyAddedUris, this.job);
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else
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log.error("Additions file not found: " + this.additionsFilePath);
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}
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@ -867,10 +934,10 @@ public class FileHarvestController extends FreemarkerHttpServlet {
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log.error(e, e);
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} finally {
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sessionInfo.finish();
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if(!normalTerminationLineFound)
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sessionInfo.setAbnormalTermination();
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}
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}
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}
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}
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}
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}
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