Fiji update fails with [Fatal Error] :1:50: White spaces are required between publicId and systemId

fiji
imagej
updater

#1

Can’t update Fiji:

[Fatal Error] :1:50: White spaces are required between publicId and systemId.
[ERROR] Error processing available update sites from ImageJ wiki
java.io.IOException: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
	at net.imagej.util.MediaWikiClient.request(MediaWikiClient.java:238)
	at net.imagej.util.MediaWikiClient.query(MediaWikiClient.java:243)
	at net.imagej.util.MediaWikiClient.getPageSource(MediaWikiClient.java:109)
	at net.imagej.updater.util.AvailableSites.getAvailableSites(AvailableSites.java:66)
	at net.imagej.updater.util.AvailableSites.initializeSites(AvailableSites.java:148)
	at net.imagej.updater.util.AvailableSites.initializeAndAddSites(AvailableSites.java:206)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:112)
	at fiji.updater.IJ2Updater.run(IJ2Updater.java:78)
	at fiji.updater.Updater.run(Updater.java:30)
	at ij.IJ.runUserPlugIn(IJ.java:228)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:748)
Caused by: org.xml.sax.SAXParseException; lineNumber: 1; columnNumber: 50; White spaces are required between publicId and systemId.
	at org.apache.xerces.parsers.DOMParser.parse(Unknown Source)
	at org.apache.xerces.jaxp.DocumentBuilderImpl.parse(Unknown Source)
	at javax.xml.parsers.DocumentBuilder.parse(DocumentBuilder.java:121)
	at org.scijava.util.XML.loadXML(XML.java:286)
	at org.scijava.util.XML.<init>(XML.java:103)
	at net.imagej.util.MediaWikiClient.request(MediaWikiClient.java:234)
	... 13 more

#2

Hello Albert -

My attempt to update Fiji fails differently. See below.

I launch Fiji (Image 2.0.0-rc-68/1.52h, up to date as of yesterday).
Its status bar displays “Running command: Up-to-date check”.
After about two minutes, the status bar changes to “Command
finished: Up-to-date check”. (Nothing else happens – no errors
reported.)

I then run Help > Update... The status bar first displays
“Running command: Update…”. Then after about two minutes,
the status bar changes to “Command finished: Update…”, and
the Console window opens with the error:

[ERROR] Cannot connect to the Internet.
Do you have a network connection?
Are your proxy settings correct?
[ERROR] null
java.net.ConnectException: Connection timed out
	at java.net.PlainSocketImpl.socketConnect(Native Method)
	at java.net.AbstractPlainSocketImpl.doConnect(AbstractPlainSocketImpl.java:350)
	at java.net.AbstractPlainSocketImpl.connectToAddress(AbstractPlainSocketImpl.java:206)
	at java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:188)
	at java.net.SocksSocketImpl.connect(SocksSocketImpl.java:392)
	at java.net.Socket.connect(Socket.java:589)
	at java.net.Socket.connect(Socket.java:538)
	at sun.net.NetworkClient.doConnect(NetworkClient.java:180)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:432)
	at sun.net.www.http.HttpClient.openServer(HttpClient.java:527)
	at sun.net.www.http.HttpClient.<init>(HttpClient.java:211)
	at sun.net.www.http.HttpClient.New(HttpClient.java:308)
	at sun.net.www.http.HttpClient.New(HttpClient.java:326)
	at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1169)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1105)
	at sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:999)
	at sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:933)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1513)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441)
	at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480)
	at net.imagej.ui.swing.updater.ImageJUpdater.testNetworkConnection(ImageJUpdater.java:355)
	at net.imagej.ui.swing.updater.ImageJUpdater.errorIfNetworkInaccessible(ImageJUpdater.java:308)
	at net.imagej.ui.swing.updater.ImageJUpdater.run(ImageJUpdater.java:106)
	at org.scijava.command.CommandModule.run(CommandModule.java:199)
	at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127)
	at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66)
	at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238)
	at java.util.concurrent.FutureTask.run(FutureTask.java:266)
	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
	at java.lang.Thread.run(Thread.java:745)

(I do have an internet connection before, during, and after this process,
and I am not using a proxy. This is on ubuntu 16.04 LTS.)

Thanks, mm


#3

Hey @mountain_man and @albertcardona

I just updated Fiji on Windows and Fedora Linux. Everything worked fine. Does the issue still persist on your side?

Cheers,
Robert


#4

Hello Robert -

Fiji update is back to working normally for me. (Just to note, there is
nothing for me to update at the moment.)

Thanks, mm


#5

@mountain_man Your error was likely caused by the server downtime earlier today, announced here:

I am not sure what caused the error seen by @albertcardona, since that happened before the downtime occurred.