alphaville / q-edit Goto Github PK

Hi,
I followed the example of Creating a new QPRF report and enter compound data from opentox
in the end of the tutorial, the pdf file that I exported was corrupted
I had two failed output:

Download Expl Value:

GRAVE: qedit.task.ExperimentalValueRetriever@167e003 failed: java.lang.NullPointerException
java.lang.NullPointerException
at qedit.task.ExperimentalValueRetriever.doInBackground(ExperimentalValueRetriever.java:34)
at org.jdesktop.swingworker.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at org.jdesktop.swingworker.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)

export to pdf:

GRAVE: qedit.task.PDFExportTask@18adce0 failed: java.lang.NullPointerException
java.lang.NullPointerException
at qedit.export.PDFReporter.createPdf(PDFReporter.java:235)
at qedit.task.PDFExportTask.doInBackground(PDFExportTask.java:45)
at org.jdesktop.swingworker.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at org.jdesktop.swingworker.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)

all commands:
mezhoud@kirus:~/Opentox$ java -jar Q-edit.jar
Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading configurations from ~/.fonts.conf is deprecated.
Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading configurations from ~/.fonts.conf is deprecated.
Fontconfig warning: "/etc/fonts/conf.d/50-user.conf", line 9: reading configurations from ~/.fonts.conf is deprecated.
17 mai 2013 16:15:04 java.util.prefs.FileSystemPreferences$7 run
ATTENTION: Prefs file removed in background /home/mezhoud/.java/.userPrefs/prefs.xml
Compound found with URI : http://apps.ideaconsult.net:8080/ambit2/compound/17/conformer/143852
URI : http://apps.ideaconsult.net:8080/ambit2/compound/17/conformer/143852
Smiles : C[C@]12CC@H[C@H]3C@@H[C@@h]1CC[C@@h]2C(=O)CO
CAS-RN : 50-22-6
EINECS : 200-019-6
Regist : 30.11.2010
InChi : InChI=1S/C21H30O4/c1-20-8-7-13(23)9-12(20)3-4-14-15-5-6-16(18(25)11-22)21(15,2)10-17(24)19(14)20/h9,14-17,19,22,24H,3-8,10-11H2,1-2H3/t14-,15-,16+,17-,19+,20-,21-/m0/s1
InChI=1S/C21H30O4/c1-20-8-7-13(23)9-12(20)3-4-14-15-5-6-16(18(25)11-22)21(15,2)10-17(24)19(14)20/h9,14-17,19,22,24H,3-8,10-11H2,1-2H3
InChI=1S/C21H30O4/c1-20-8-7-13(23)9-12(20)3-4-14-15-5-6-16(18(25)11-22)21(15,2)10-17(24)19(14)20/h9,14-17,19,22,24H,3-8,10-11H2,1-2H3/t14-,15+,16-,17+,19-,20-,21-/m0/s1
InChI=1S/C21H29O4/c1-20-8-7-13(23)9-12(20)3-4-14-15-5-6-16(18(25)11-22)21(15,2)10-17(24)19(14)20/h9,14-17,19,22,24H,1,3-8,10-11H2,2H3/t14-,15+,16+,17-,19-,21-/m0/s1
InChiKey : OMFXVFTZEKFJBZ-HJTSIMOOSA-N
OMFXVFTZEKFJBZ-UHFFFAOYSA-N
OMFXVFTZEKFJBZ-IQDVQEQVSA-N
SRIZMYYZMDCJOA-QYNIMHRHSA-N
IUPAC : (11beta)-11,21-dihydroxypregn-4-ene-3,20-dione
Depict : Present
Model Algorithm found is : org.opentox.toxotis.core.component.Algorithm@59ebdee6
Value found in DB : 0.06158357858657837^^double
Prediction result : 0.06158357858657837^^double
17 mai 2013 16:17:32 org.jdesktop.application.Task failed
GRAVE: qedit.task.ExperimentalValueRetriever@167e003 failed: java.lang.NullPointerException
java.lang.NullPointerException
at qedit.task.ExperimentalValueRetriever.doInBackground(ExperimentalValueRetriever.java:34)
at org.jdesktop.swingworker.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at org.jdesktop.swingworker.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
Similarity Search engine started
L similar compounds found (listing uris)
L o --> http://apps.ideaconsult.net:8080/ambit2/compound/15104/conformer/155103
L o --> http://apps.ideaconsult.net:8080/ambit2/compound/15771/conformer/155610
L o --> http://apps.ideaconsult.net:8080/ambit2/compound/232883/conformer/699516
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L o --> http://apps.ideaconsult.net:8080/ambit2/compound/107945/conformer/203268
L o --> http://apps.ideaconsult.net:8080/ambit2/compound/228244/conformer/642030
Similar compounds downloaded!
17 mai 2013 16:18:59 org.jdesktop.application.Task failed
GRAVE: qedit.task.PDFExportTask@18adce0 failed: java.lang.NullPointerException
java.lang.NullPointerException
at qedit.export.PDFReporter.createPdf(PDFReporter.java:235)
at qedit.task.PDFExportTask.doInBackground(PDFExportTask.java:45)
at org.jdesktop.swingworker.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at org.jdesktop.swingworker.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
http://apps.ideaconsult.net:8080/ambit2/model/130825

Hi,
I tried with login as guest:
GRAVE: qedit.task.ImportModel@1b814a5 failed: java.lang.Exception: org.opentox.toxotis.exceptions.impl.ForbiddenRequest: Access denied to : 'http://opentox.ntua.gr:8080/model/5fad773b-836b-45c0-af7b-e7b649d143ee' (status 403)
java.lang.Exception: org.opentox.toxotis.exceptions.impl.ForbiddenRequest: Access denied to : 'http://opentox.ntua.gr:8080/model/5fad773b-836b-45c0-af7b-e7b649d143ee' (status 403)
at qedit.task.ImportModel.doInBackground(ImportModel.java:89)
at org.jdesktop.swingworker.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at org.jdesktop.swingworker.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
Caused by: org.opentox.toxotis.exceptions.impl.ForbiddenRequest: Access denied to : 'http://opentox.ntua.gr:8080/model/5fad773b-836b-45c0-af7b-e7b649d143ee' (status 403)
at org.opentox.toxotis.util.spiders.Tarantula.assessHttpStatus(Tarantula.java:303)
at org.opentox.toxotis.util.spiders.ModelSpider.(ModelSpider.java:85)
at org.opentox.toxotis.core.component.Model.loadFromRemote(Model.java:350)
at org.opentox.toxotis.core.component.Model.loadFromRemote(Model.java:89)
at org.opentox.toxotis.core.OTOnlineResource.loadFromRemote(OTOnlineResource.java:151)
at qedit.task.ImportModel.doInBackground(ImportModel.java:85)
... 7 more

and with my username of opentox.
GRAVE: qedit.task.ImportModel@3f97d7 failed: java.lang.Exception: org.opentox.toxotis.exceptions.impl.ForbiddenRequest: Access denied to : 'http://opentox.ntua.gr:8080/model/5fad773b-836b-45c0-af7b-e7b649d143ee' (status 403)
java.lang.Exception: org.opentox.toxotis.exceptions.impl.ForbiddenRequest: Access denied to : 'http://opentox.ntua.gr:8080/model/5fad773b-836b-45c0-af7b-e7b649d143ee' (status 403)
at qedit.task.ImportModel.doInBackground(ImportModel.java:89)
at org.jdesktop.swingworker.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at org.jdesktop.swingworker.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:662)
Caused by: org.opentox.toxotis.exceptions.impl.ForbiddenRequest: Access denied to : 'http://opentox.ntua.gr:8080/model/5fad773b-836b-45c0-af7b-e7b649d143ee' (status 403)
at org.opentox.toxotis.util.spiders.Tarantula.assessHttpStatus(Tarantula.java:303)
at org.opentox.toxotis.util.spiders.ModelSpider.(ModelSpider.java:85)
at org.opentox.toxotis.core.component.Model.loadFromRemote(Model.java:350)
at org.opentox.toxotis.core.component.Model.loadFromRemote(Model.java:89)
at org.opentox.toxotis.core.OTOnlineResource.loadFromRemote(OTOnlineResource.java:151)
at qedit.task.ImportModel.doInBackground(ImportModel.java:85)
... 7 more