FYI to Kepler-users. -------- Original Message -------- Message-ID: <4A36A447.8070206 at eecs.berkeley.edu> Date: Mon, 15 Jun 2009 12:43:03 -0700 From: Christopher Brooks <[email protected]> User-Agent: Thunderbird 2.0.0.21 (Macintosh/20090302) MIME-Version: 1.0 To: Trina Myers <t.myers at bigpond.net.au> Subject: Re: [kepler-users] problem with the URL To Local File actor and a symbol References: <000001c9ec85$51847310$f48d5930$%myers at bigpond.net.au> <4A353096.4010100 at eecs.berkeley.edu> <002601c9ed4b$33187220$99495660$%myers at bigpond.net.au> In-Reply-To: <002601c9ed4b$33187220$99495660$%myers at bigpond.net.au> Content-Type: multipart/mixed; boundary="------------040105060009070608070504"
[Apologies about the corrupted message, I'm not sure what happened] Hi Trina, Yep, the model I sent fails for me in Kepler-1.0.0. Yesterday, URLToLocalFile2.xml worked for me in the devel version of Kepler, today it does not. I'll look into this. The devel version can be built with Eclipse, see https://kepler-project.org/developers/reference/kepler-and-eclipse Another idea would be to use the StringReplace actor to replace the | with &7C There is a description of what encodings are used in URLs at http://www.blooberry.com/indexdot/html/topics/urlencoding.htm The attached model uses StringReplace to replace \| with &7C. _Christopher Trina Myers wrote: > Hi Chris, > > Thankyou for you fast reply. > I am using version 1.0.0 on Windows with java.runtime.version = 1.5.0_12-b04 > > I tried the example you sent and there were multiple errors in opening the > file (below), when it did open I used the URL with | and received the same > error message as I did with my workflow: > Error encountered in:<property name="derivedFrom" > class="org.kepler.moml.NamedObjIdReferralList"> > org.kepler.moml.NamedObjReferralList > Error encountered in:<property name="timeResolution" > class="ptolemy.actor.parameters.SharedParameter" value ="1E-10"> > Error encountered in:<property name="" > class="org.kepler.moml.NamedObjReferralList" > value="urn:lsid:kepler-project.org:director:1:1"> > Error encountered in:<property name="derivedFrom" > class="org.kepler.moml.NamedObjIdReferralList" > value="urn:lsid:kepler-project.org:director:1:1"> > Error encountered in:<property name="" > class="org.kepler.moml.NamedObjReferralList" > value="urn:lsid:kepler-project.org:actor:252:1"> > Error encountered in:<property name="derivedFrom" > class="org.kepler.moml.NamedObjReferralList" > value="urn:lsid:kepler-project.org:actor:252:1"> > Error encountered in:<property name="title" > class="ptolemy.data.expr.StringParameter" value=""> Attempt to insert object > named "title" into a container that already contains an object with that > name > > java.lang.ClassNotFoundException: org.kepler.moml.NamedObjIdReferralList > at java.net.URLClassLoader$1.run(Unknown Source) > at java.security.AccessController.doPrivileged(Native Method) > at java.net.URLClassLoader.findClass(Unknown Source) > at java.lang.ClassLoader.loadClass(Unknown Source) > at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source) > at java.lang.ClassLoader.loadClass(Unknown Source) > at java.lang.ClassLoader.loadClassInternal(Unknown Source) > at java.lang.Class.forName0(Native Method) > at java.lang.Class.forName(Unknown Source) > at > ptolemy.moml.MoMLParser._handlePropertyElement(MoMLParser.java:4976) > at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2784) > at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921) > at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104) > at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924) > at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481) > at com.microstar.xml.XmlParser.doParse(XmlParser.java:159) > at com.microstar.xml.XmlParser.parse(XmlParser.java:132) > at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1334) > at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1292) > at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1265) > at > ptolemy.actor.gui.PtolemyEffigy$Factory.createEffigy(PtolemyEffigy.java:412) > at > ptolemy.actor.gui.EffigyFactory.createEffigy(EffigyFactory.java:209) > at ptolemy.actor.gui.Configuration.openModel(Configuration.java:595) > at ptolemy.actor.gui.Configuration.openModel(Configuration.java:555) > at ptolemy.actor.gui.TableauFrame._read(TableauFrame.java:893) > at ptolemy.gui.Top._open(Top.java:704) > at ptolemy.gui.Top$FileMenuListener.actionPerformed(Top.java:1045) > at > ptolemy.vergil.basic.MenuMapper$1.actionPerformed(MenuMapper.java:326) > at javax.swing.AbstractButton.fireActionPerformed(Unknown Source) > at javax.swing.AbstractButton$Handler.actionPerformed(Unknown > Source) > at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown > Source) > at javax.swing.DefaultButtonModel.setPressed(Unknown Source) > at javax.swing.AbstractButton.doClick(Unknown Source) > at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source) > at > javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source) > at java.awt.Component.processMouseEvent(Unknown Source) > at javax.swing.JComponent.processMouseEvent(Unknown Source) > at java.awt.Component.processEvent(Unknown Source) > at java.awt.Container.processEvent(Unknown Source) > at java.awt.Component.dispatchEventImpl(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) > at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) > at java.awt.Container.dispatchEventImpl(Unknown Source) > at java.awt.Window.dispatchEventImpl(Unknown Source) > at java.awt.Component.dispatchEvent(Unknown Source) > at java.awt.EventQueue.dispatchEvent(Unknown Source) > at java.awt.EventDispatchThread.pumpOneEventForHierarchy(Unknown > Source) > at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown > Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.pumpEvents(Unknown Source) > at java.awt.EventDispatchThread.run(Unknown Source) > > I am not a programmer although I understand what you say (I am in a > different area of expertise). I need to use Kepler for my research but would > prefer to stay away from the developers version as it would be quite a large > learning hurdle at this time. > > I am familiar with the URI, it appears the "|" symbol is "unsafe" in both > the URL and URI RFC's, is there some way to work around this within the > URL-to-LocalFile actor (AIMS is not the only organisation that seems to use > it in their url's)? > Sincerely > Trina > > > -----Original Message----- > From: Christopher Brooks [mailto:cxh at eecs.berkeley.edu] > Sent: Monday, 15 June 2009 3:17 AM > To: Trina Myers > Cc: Kepler-users at ecoinformatics.org > Subject: Re: [kepler-users] problem with the URL To Local File actor and a > symbol > > Hi Trina, > > I can't get this to fail for me, what version of Kepler are you using > (Kepler 1.0.0? Kepler 1.x from the svn tree?) and what version of Java? > To get the version of Java: start Kepler and go to Tools -> Check System > Settings and find the the java.runtime.version property. > For example, I have: > java.runtime.version = 1.5.0_16-b06-284 > > I've attached a model that works for me in the development version of > Kepler. I did not test it in Kepler-1.0.0. > > Does the attached model fail for you? If not, can you send a test case that > does fail? The URI issue is fairly tricky, I have no doubt that there are > bugs to be found. > > I think the reason the error would occur is because | is probably not > permitted in URIs. The relationship between URIs and URLs is tricky. > http://java.sun.com/j2se/1.5.0/docs/api/java/net/URI.html says: > "A URI is a uniform resource identifier while a URL is a uniform resource > locator. Hence every URL is a URI, abstractly speaking, but not > every URI is a URL. This is because there is another subcategory of > URIs, uniform resource names (URNs), which name resources but do not > specify how to locate them. The mailto, news, and isbn URIs shown above > are examples of URNs." > > In Java, java.net.URI was introduced after java.net.URL. The URI class > gives us certain methods not present in the URL class. > > The reason you would see the error is because | is not permitted in Java's > URI class. To replicate this, note that creating a URI fails: > > bash-3.2$ java -classpath $PTII:${PTII}/lib/ptjacl.jar tcl.lang.Shell % > java::new java.net.URI > http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00&; > thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4h > &dataLevel=level0&bleach=0&vers=2 > java.net.URISyntaxException: Illegal character in query at index 140: > http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00&; > thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4h > &dataLevel=level0&bleach=0&vers=2 > % > > > However, for me, running nameToURL works: > % set a [java::call ptolemy.util.FileUtilities nameToURL > "http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00 > &thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4 > h&dataLevel=level0&bleach=0&vers=2" > [java::null] [java::null]] > java0x3 > % $a toString > http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00&; > thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4h > &dataLevel=level0&bleach=0&vers=2 > % > > I tried the above command under Ptolemy II 7.0.1, which is the version > of Ptolemy used by Kepler 1.0.0. I also tried it under Java 1.5.0_16 > and Java 1.6.0_07. > > _Christopher > > Trina Myers wrote: >> Hi All, >> >> I have a workflow that extracts xml files from a servlet and transforms > the >> data within using the XPATH actor. It has been working very well until I >> have tried to import 2 elements from the site. The only difference between >> the URL in question and the working URL is the use of "|" (separating >> max|avg). >> If I download the xml file with both elements and use the absolute address >> to the file on the local machine the workflow works fine (extracting both >> the avg and max data as required), so I am sure the problem is at the URL > to >> local file actor. >> >> I would appreciate any guidance >> Cheers >> Trina >> >> The error message: >> >> ptolemy.kernel.util.IllegalActionException: Cannot read file >> > 'http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00 > &thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4 >> h&dataLevel=level0&bleach=0&vers=2' >> in .test_url.URL To Local File.fileOrURL >> Because: >> Problem with URI format in >> > 'http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00 > &thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4 >> h&dataLevel=level0&bleach=0&vers=2'. and >> > 'http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00 > &thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4 >> h&dataLevel=level0&bleach=0&vers=2' This can happen if the file name is > not >> absoluteand is not present relative to the directory in which the > specified >> model was read (which was >> > 'file:/C:/Documents%20and%20Settings/Trina/Desktop/THESIS_wORKFLOWS/Hypothes >> isTest_Reef/AIMS_REALTIME/test_url.xml') >> at ptolemy.data.expr.FileParameter.asURL(FileParameter.java:216) >> at util.URLToLocalFile._openAndReadBytes(URLToLocalFile.java:226) >> at util.URLToLocalFile.fire(URLToLocalFile.java:166) >> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:398) >> at >> > ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.j >> ava:170) >> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:400) >> at ptolemy.actor.Manager.iterate(Manager.java:688) >> at ptolemy.actor.Manager.execute(Manager.java:332) >> at ptolemy.actor.Manager.run(Manager.java:1071) >> at ptolemy.actor.Manager$3.run(Manager.java:1112) >> Caused by: java.io.IOException: Problem with URI format in >> > 'http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00 > &thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4 >> h&dataLevel=level0&bleach=0&vers=2'. and >> > 'http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00 > &thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4 >> h&dataLevel=level0&bleach=0&vers=2' This can happen if the file name is > not >> absoluteand is not present relative to the directory in which the > specified >> model was read (which was >> > 'file:/C:/Documents%20and%20Settings/Trina/Desktop/THESIS_wORKFLOWS/Hypothes >> isTest_Reef/AIMS_REALTIME/test_url.xml') >> at ptolemy.util.FileUtilities.nameToURL(FileUtilities.java:356) >> at ptolemy.data.expr.FileParameter.asURL(FileParameter.java:213) >> ... 9 more >> Caused by: java.lang.IllegalArgumentException >> at java.net.URI.create(Unknown Source) >> at java.net.URI.resolve(Unknown Source) >> at ptolemy.util.FileUtilities.nameToURL(FileUtilities.java:353) >> ... 10 more >> Caused by: java.net.URISyntaxException: Illegal character in query at > index >> 140: >> > http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00&; > thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4h >> &dataLevel=level0&bleach=0&vers=2 >> at java.net.URI$Parser.fail(Unknown Source) >> at java.net.URI$Parser.checkChars(Unknown Source) >> at java.net.URI$Parser.parseHierarchical(Unknown Source) >> at java.net.URI$Parser.parse(Unknown Source) >> at java.net.URI.<init>(Unknown Source) >> ... 13 more >> Caused by: java.io.IOException: Problem with URI format in >> > 'http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00 > &thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4 >> h&dataLevel=level0&bleach=0&vers=2'. and >> > 'http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00 > &thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4 >> h&dataLevel=level0&bleach=0&vers=2' This can happen if the file name is > not >> absoluteand is not present relative to the directory in which the > specified >> model was read (which was >> > 'file:/C:/Documents%20and%20Settings/Trina/Desktop/THESIS_wORKFLOWS/Hypothes >> isTest_Reef/AIMS_REALTIME/test_url.xml') >> at ptolemy.util.FileUtilities.nameToURL(FileUtilities.java:356) >> at ptolemy.data.expr.FileParameter.asURL(FileParameter.java:213) >> at util.URLToLocalFile._openAndReadBytes(URLToLocalFile.java:226) >> at util.URLToLocalFile.fire(URLToLocalFile.java:166) >> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:398) >> at >> > ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.j >> ava:170) >> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:400) >> at ptolemy.actor.Manager.iterate(Manager.java:688) >> at ptolemy.actor.Manager.execute(Manager.java:332) >> at ptolemy.actor.Manager.run(Manager.java:1071) >> at ptolemy.actor.Manager$3.run(Manager.java:1112) >> Caused by: java.lang.IllegalArgumentException >> at java.net.URI.create(Unknown Source) >> at java.net.URI.resolve(Unknown Source) >> at ptolemy.util.FileUtilities.nameToURL(FileUtilities.java:353) >> ... 10 more >> Caused by: java.net.URISyntaxException: Illegal character in query at > index >> 140: >> > http://data.aims.gov.au/awsqaqc/XmlDataServlet?fromDate=2008-02-01T00:00:00&; > thruDate=2008-02-10T00:00:00&stations=4&agperiod=day&agFunct=max|avg&vars=4h >> &dataLevel=level0&bleach=0&vers=2 >> at java.net.URI$Parser.fail(Unknown Source) >> at java.net.URI$Parser.checkChars(Unknown Source) >> at java.net.URI$Parser.parseHierarchical(Unknown Source) >> at java.net.URI$Parser.parse(Unknown Source) >> at java.net.URI.<init>(Unknown Source) >> ... 13 more >> >> _______________________________________________ >> Kepler-users mailing list >> Kepler-users at kepler-project.org >> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users > -- Christopher Brooks (cxh at eecs berkeley edu) University of California CHESS Executive Director US Mail: 337 Cory Hall Programmer/Analyst CHESS/Ptolemy/Trust Berkeley, CA 94720-1774 ph: 510.643.9841 fax:510.642.2718 (Office: 545Q Cory) home: (F-Tu) 707.665.0131 (W-F) 510.655.5480 -- Christopher Brooks (cxh at eecs berkeley edu) University of California CHESS Executive Director US Mail: 337 Cory Hall Programmer/Analyst CHESS/Ptolemy/Trust Berkeley, CA 94720-1774 ph: 510.643.9841 fax:510.642.2718 (Office: 545Q Cory) home: (F-Tu) 707.665.0131 (W-F) 510.655.5480 -------------- next part -------------- A non-text attachment was scrubbed... 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