diff --git a/src/main/java/org/nrg/xnat/restlet/actions/AutomationBasedImporter.java b/src/main/java/org/nrg/xnat/restlet/actions/AutomationBasedImporter.java
index 3d02fb72f854c1b4e99de643fefb8fd953ca5b6f..74de506e3c1e4f7ddd3c3e2c54f5d708472f867a 100644
--- a/src/main/java/org/nrg/xnat/restlet/actions/AutomationBasedImporter.java
+++ b/src/main/java/org/nrg/xnat/restlet/actions/AutomationBasedImporter.java
@@ -18,6 +18,7 @@ import com.google.gson.Gson;
import com.google.gson.JsonParseException;
import com.google.gson.reflect.TypeToken;
import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
import org.json.JSONArray;
import org.json.JSONException;
@@ -187,8 +188,10 @@ public class AutomationBasedImporter extends ImporterHandlerA implements Callabl
final Object configuredResourceParam = params.get("configuredResource");
final Object buildPathParam = params.get("buildPath");
final Object eventHandlerParam = params.get("eventHandler");
+ final Object escapeHtmlParam = params.get("escapeHtml");
// final Object sendemailParam = params.get("sendemail");
final boolean doProcess = processParam != null && processParam.toString().equalsIgnoreCase("true");
+ final boolean escapeHtml = escapeHtmlParam != null && escapeHtmlParam.toString().equalsIgnoreCase("true");
configuredResource = (configuredResourceParam != null) ? configuredResourceParam.toString() : CACHE_CONSTANT;
// Uploads to configured resources are handled on the client side. Only
@@ -198,7 +201,7 @@ public class AutomationBasedImporter extends ImporterHandlerA implements Callabl
return;
}
if (doProcess && !configuredResource.equalsIgnoreCase(CACHE_CONSTANT)) {
- doAutomation();
+ doAutomation(escapeHtml);
return;
}
@@ -239,7 +242,7 @@ public class AutomationBasedImporter extends ImporterHandlerA implements Callabl
// Conditionally process cache location files, otherwise return cache
// location
if (doProcess) {
- doAutomation();
+ doAutomation(escapeHtml);
/*
* if (sendemailParam!=null &&
* sendemailParam.toString().equalsIgnoreCase("true")) {
@@ -465,7 +468,7 @@ public class AutomationBasedImporter extends ImporterHandlerA implements Callabl
* the server exception
*/
@SuppressWarnings({ "rawtypes", "static-access" })
- private void doAutomation() throws ClientException, ServerException {
+ private void doAutomation(boolean escapeHtml) throws ClientException, ServerException {
returnList.add("<b>BEGIN PROCESSING UPLOADED FILES</b>");
@@ -663,47 +666,77 @@ public class AutomationBasedImporter extends ImporterHandlerA implements Callabl
for (ScriptOutput scriptOut : scriptOutputs) {
returnList.add("<br><b>SCRIPT EXECUTION RESULT</b>");
returnList.add("<br><b>FINAL STATUS: " + scriptOut.getStatus() + "</b>");
- StringWriter writer = new StringWriter();
if (scriptOut.getStatus().equals(Status.ERROR) && scriptOut.getResults() != null
&& scriptOut.getResults().toString().length() > 0) {
returnList.add("<br><b>SCRIPT RESULTS</b><br>");
try {
- StringEscapeUtils.escapeHtml(writer, scriptOut.getResults().toString());
- returnList.add(writer.toString().replace("\n", "<br>"));
- writer.close();
+ if (escapeHtml) {
+ final StringWriter writer = new StringWriter();
+ StringEscapeUtils.escapeHtml(writer, scriptOut.getResults().toString());
+ returnList.add(writer.toString().replace("\n", "<br>"));
+ writer.close();
+ } else {
+ returnList.add(conditionallyAddHtmlBreaks(scriptOut.getResults().toString()));
+ }
} catch (IOException e) {
- returnList.add(scriptOut.getResults().toString().replace("\n", "<br>"));
+ returnList.add(conditionallyAddHtmlBreaks(scriptOut.getResults().toString()));
}
}
if (scriptOut.getOutput() != null && scriptOut.getOutput().length() > 0) {
returnList.add("<br><b>SCRIPT STDOUT</b><br>");
try {
- StringEscapeUtils.escapeHtml(writer, scriptOut.getOutput());
- returnList.add(writer.toString().replace("\n", "<br>"));
- writer.close();
+ if (escapeHtml) {
+ final StringWriter writer = new StringWriter();
+ StringEscapeUtils.escapeHtml(writer, scriptOut.getOutput());
+ returnList.add(writer.toString().replace("\n", "<br>"));
+ writer.close();
+ } else {
+ returnList.add(conditionallyAddHtmlBreaks(scriptOut.getOutput().toString()));
+ }
} catch (IOException e) {
- returnList.add(scriptOut.getOutput().replace("\n", "<br>"));
+ returnList.add(conditionallyAddHtmlBreaks(scriptOut.getOutput().toString()));
}
}
if (scriptOut.getErrorOutput() != null && scriptOut.getErrorOutput().length() > 0) {
returnList.add("<br><b>SCRIPT STDERR/EXCEPTION</b><br>");
try {
- StringEscapeUtils.escapeHtml(writer, scriptOut.getErrorOutput());
- returnList.add(writer.toString().replace("\n", "<br>"));
- writer.close();
+ if (escapeHtml) {
+ final StringWriter writer = new StringWriter();
+ StringEscapeUtils.escapeHtml(writer, scriptOut.getErrorOutput());
+ returnList.add(writer.toString().replace("\n", "<br>"));
+ writer.close();
+ } else {
+ returnList.add(conditionallyAddHtmlBreaks(scriptOut.getErrorOutput().toString()));
+ }
} catch (IOException e) {
- returnList.add(scriptOut.getErrorOutput().replace("\n", "<br>"));
+ returnList.add(conditionallyAddHtmlBreaks(scriptOut.getErrorOutput().toString()));
}
}
}
} else {
returnList.add("<br><b>No output was returned from the script</b>");
}
- returnList.add("<br><b>FINISHED PROCESSING");
+ returnList.add("<br><b>PROCESSING COMPLETE");
+
}
+ private String conditionallyAddHtmlBreaks(String output) {
+ // An (overly) simplistic check just trying to see if the output is doing its own line breaking. Otherwise we'll add them.
+ // I'm not sure we want to do this, but some currently in used scripts plan on the importer doing the breaks and
+ // this could be useful for text output that doesn't request the html to be escaped.
+ return output.replace("\n", ((double)((StringUtils.countMatches(output,"<br>")+
+ StringUtils.countMatches(output,"<br/>")+
+ StringUtils.countMatches(output,"<p>")+
+ StringUtils.countMatches(output,"<tr>")+
+ StringUtils.countMatches(output,"<ul>")+
+ StringUtils.countMatches(output,"<ul>")+
+ StringUtils.countMatches(output,"<ol>")+
+ StringUtils.countMatches(output,"<li>")+
+ StringUtils.countMatches(output,"<dl>")
+ ))/((double)(StringUtils.countMatches(output,"\n")+1))>0.95) ? "" : "<br>") + "<br>";
+ }
- /**
+ /**
* Builds the workflow.
*
* @param proj the proj
diff --git a/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequestListener.java b/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequestListener.java
index ea7ebaded96f2c37432267578e85a47e97bc1625..a3a3efbbb86149296ef8db19666e3259810ad0d8 100644
--- a/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequestListener.java
+++ b/src/main/java/org/nrg/xnat/services/messaging/automation/AutomatedScriptRequestListener.java
@@ -101,7 +101,7 @@ public class AutomatedScriptRequestListener {
(automationCompletionEvent.getScriptOutputs() != null && automationCompletionEvent.getScriptOutputs().size() > 0) ?
scriptOutputToHtmlString(automationCompletionEvent.getScriptOutputs()) :
"<h3>No output was returned from the script run</h3>";
- final String EMAIL_SUBJECT = "Automation Results";
+ final String EMAIL_SUBJECT = "Automation Results (" + request.getScriptId() + ")";
AdminUtils.sendUserHTMLEmail(EMAIL_SUBJECT, scriptOutStr, false, notifyList.toArray(new String[0]));
}
}
diff --git a/src/main/webapp/scripts/uploaders/AutomationBasedUploader.js b/src/main/webapp/scripts/uploaders/AutomationBasedUploader.js
index 880f428cc195971c0241d7cf620e9de677cbe4ce..7997da012a0193d6a2930fb9e179ed9ecd9a8960 100644
--- a/src/main/webapp/scripts/uploaders/AutomationBasedUploader.js
+++ b/src/main/webapp/scripts/uploaders/AutomationBasedUploader.js
@@ -923,17 +923,20 @@ XNAT.app.abu.processFiles=function() {
var eventHandlerScope = eventHandlerElement.className;
}
+ this.currentUploaderConfig = undefined;
this.paramsToPass = undefined;
for (var i=0;i<this.uploaderConfig.length;i++) {
- if (this.uploaderConfig[i].eventTriggerId==eventHandler && this.uploaderConfig[i].eventScope==eventHandlerScope &&
- (this.uploaderConfig[i].parameters!=undefined && this.uploaderConfig[i].parameters!=null && this.uploaderConfig[i].parameters.length>0)) {
- this.paramsToPass = this.uploaderConfig[i].parameters;
+ if (this.uploaderConfig[i].eventTriggerId==eventHandler && this.uploaderConfig[i].eventScope==eventHandlerScope) {
+ this.currentUploaderConfig = this.uploaderConfig[i];
break;
}
}
+ this.paramsToPass = undefined;
+ if (this.currentUploaderConfig.parameters!=undefined && this.currentUploaderConfig.parameters!=null && this.currentUploaderConfig.parameters.length>0) {
+ this.paramsToPass = this.currentUploaderConfig.parameters;
+ }
if (typeof(this.paramsToPass) !== 'undefined' && this.paramsToPass != null && this.paramsToPass.length>0) {
-
var pModalOpts = {
width: 740,
height: 480,
@@ -1003,6 +1006,10 @@ XNAT.app.abu.continueProcessing=function() {
if (eventHandler != undefined && eventHandler != null && eventHandler.length>0) {
params['eventHandler'] = eventHandler;
}
+ var escapeHtml = (typeof this.currentUploaderConfig !== 'undefined') ? this.currentUploaderConfig.escapeHtml : undefined;
+ if (escapeHtml != undefined && escapeHtml != null) {
+ params['escapeHtml'] = escapeHtml;
+ }
params['xsiType'] = XNAT.data.context.xsiType;
var queryParams = "?import-handler=" + XNAT.app.abu.importHandler + "&" + $.param(params);
@@ -1102,6 +1109,7 @@ XNAT.app.abu.saveUploaderConfiguration=function(configTriggerId, configEvent, sc
newConfigObj.launchFromResourceUploads = $('#ULC_RB_launchFromResourceUploads').is(':checked');
newConfigObj.launchWithoutUploads = $('#ULC_RB_launchWithoutUploads').is(':checked');
newConfigObj.doNotUseUploader = $('#ULC_RB_doNotUseUploader').is(':checked');
+ newConfigObj.escapeHtml = $('#ULC_RB_outputText').is(':checked');
newConfigObj.parameters = undefined;
$(".ULC_parametersDiv").each(function() {
var parameterField = $(this).find(".ULC_parametersField").val();
@@ -1244,6 +1252,7 @@ XNAT.app.abu.configureUploaderForEventHandler=function(configTriggerId, configEv
configObj.launchFromResourceUploads = false;
configObj.launchWithoutUploads = false;
configObj.doNotUseUploader = true;
+ configObj.escapeHtml = false;
// best to leave these undefined, I think
//configObj.parameters = [ ];
//configObj.contexts = [ 'xnat:projectData','xnat:subjectAssessorData','xnat:imageAssessorData','xnat:imageSessionData','xnat:imageScanData','xnat:subjectData' ];
@@ -1278,19 +1287,28 @@ XNAT.app.abu.configureUploaderForEventHandler=function(configTriggerId, configEv
/** NOTE: These radio buttons were originally coded as checkboxes, assuming the same scripts might be triggered from different upload/launch contexts. **
** It was later decided that each event handler should only be triggered from a single upload/launch context. The code that uses these still **
** treats them as check boxes in case we change our desired usage. **/
+
+
configHtml+='<div style="margin-left:20px;width:100%"><p><b>Usage:</b>';
- configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_launchFromCacheUploads" name="ULC_RB" value="launchFromCacheUploads"' +
+ configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_launchFromCacheUploads" name="ULC_RB_USAGE" value="launchFromCacheUploads"' +
((configObj.launchFromCacheUploads) ? ' checked' : '') + '> <b> Use for cache space uploads</b> </div>';
if (scope!='site') {
- configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_launchFromResourceUploads" name="ULC_RB" value="launchFromResourceUploads"' +
+ configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_launchFromResourceUploads" name="ULC_RB_USAGE" value="launchFromResourceUploads"' +
((configObj.launchFromResourceUploads) ? ' checked' : '') + '> <b> Use for configured resource uploads </b> </div>';
}
- configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_launchWithoutUploads" name="ULC_RB" value="launchWithoutUploads"' +
+ configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_launchWithoutUploads" name="ULC_RB_USAGE" value="launchWithoutUploads"' +
((configObj.launchWithoutUploads) ? ' checked' : '') + '> <b> Trigger without uploads </b> </div>';
- configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_doNotUseUploader" name="ULC_RB" value="doNotUseUploader"' +
+ configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_doNotUseUploader" name="ULC_RB_USAGE" value="doNotUseUploader"' +
((configObj.doNotUseUploader) ? ' checked' : '') + '> <b> Do not use uploader </b> </div>';
configHtml+='</div></p>';
configHtml+='<p>';
+ configHtml+='<div style="margin-left:20px;width:100%"><p><b>Output Type:</b>';
+ configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_outputHtml" name="ULC_RB_OUTPUT" value="outputHtml"' +
+ ((configObj.escapeHtml) ? '' : 'checked') + '> <b> HTML </b> </div>';
+ configHtml+='<div style="margin-left:20px;width:100%"><input type="radio" id="ULC_RB_outputText" name="ULC_RB_OUTPUT" value="outputText"' +
+ ((configObj.escapeHtml) ? ' checked' : '') + '> <b> Text (escape HTML characters) </b> </div>';
+ configHtml+='</div></p>';
+ configHtml+='<p>';
configHtml+='<div style="margin-left:20px;width:100%"><p><b>User Supplied Parameters:</b><p><div id="ULC_parameters">';
for (var i=0;i<((typeof(configObj.parameters)!=='undefined' && configObj.parameters.length>0) ? configObj.parameters.length : 0);i++) {
var hasValue = (typeof(configObj.parameters)!=='undefined' && configObj.parameters.length>=(i+1));
diff --git a/src/main/webapp/style/uploaders/fileuploader.css b/src/main/webapp/style/uploaders/fileuploader.css
index fe323e24d1c0f126c3b975e2cfaea3ff59b3d952..ac753346bcdf7116040874c536e3604a97af6dce 100644
--- a/src/main/webapp/style/uploaders/fileuploader.css
+++ b/src/main/webapp/style/uploaders/fileuploader.css
@@ -125,3 +125,6 @@ div.abu-xnat-interactivity-area-sub {
.passParamText { margin-left: 30px; margin-right: 10px; }
.interactivityAreaSpan { margin-left: 15px; margin-right: 10px; }
+
+#configUploadDiv { overflow-x: hidden; }
+