anonymous git clone of iDROP fails

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F Lengyel

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Apr 6, 2012, 12:52:27 AM4/6/12

to irod...@googlegroups.com

Hi,

After upgrading the site from 3.0 to 3,1, we found that the

webstart iDrop no longer functioned. The old phpwebapp

still works (somewhat--I understand this is superseded).

The command

git clone ssh://anon...@code.renci.org/gitroot/irodsidrop

is documented here: https://code.renci.org/gf/project/irodsidrop/scmgit/?action=AccessInfo

But so far, my attempts to git clone according to the instructions

(use a blank password for username anonymous) have failed:

flengyel@netbook:~/Dropbox/Programming$ git clone ssh://anon...@code.renci.org/gitroot/irodsidrop

Cloning into irodsidrop...

Warning: Permanently added 'code.renci.org,152.54.4.114' (RSA) to the list of known hosts.

anon...@code.renci.org's password:

Permission denied, please try again.

anon...@code.renci.org's password:

Permission denied, please try again.

anon...@code.renci.org's password:

Permission denied (publickey,gssapi-with-mic,password).

fatal: The remote end hung up unexpectedly

flengyel@netbook:~/Dropbox/Programming$

My understanding is that the iDrop webstart client is behind toe git

version...

Conway, Mike

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Apr 6, 2012, 8:23:58 AM4/6/12

to irod...@googlegroups.com

use the user id of irodsguest and a password of irodsguest

This is a substitute for anonymous we set up due to a bug in Gforge/GIT.

Let me know what's going on with iDrop, I do test this against 3.1.

---------------------

Mike Conway

Interface and Java API/Integration Developer – DICE

www.irods.org

skype:michael.c.conway

LinkedIn: http://www.linkedin.com/pub/mike-conway/5/78a/231

--
"iRODS: the Integrated Rule-Oriented Data-management System; A community driven, open source, data grid software solution" https://www.irods.org

iROD-Chat: http://groups.google.com/group/iROD-Chat

F Lengyel

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Apr 6, 2012, 1:19:16 PM4/6/12

to irod...@googlegroups.com

Fortunately I have Maven on my netbook (I like Clojure and have used Leiningen).

Mvn clean install yields a a build failure:

Tests run: 29, Failures: 0, Errors: 5, Skipped: 0

[INFO] ------------------------------------------------------------------------

[ERROR] BUILD FAILURE

[INFO] ------------------------------------------------------------------------

[INFO] There are test failures.

Please refer to /home/flengyel/Dropbox/Programming/irodsidrop/idrop-swing/target/surefire-reports for the individual test results.

[INFO] ------------------------------------------------------------------------

[INFO] For more information, run Maven with the -e switch

[INFO] ------------------------------------------------------------------------

[INFO] Total time: 5 minutes

[INFO] Finished at: Fri Apr 06 13:11:11 EDT 2012

[INFO] Final Memory: 20M/49M

[INFO] ------------------------------------------------------------------------

flengyel@netbook:~/Dropbox/Programming/irodsidrop/idrop-swing$

flengyel@netbook:~/Dropbox/Programming/irodsidrop/idrop-swing/target/surefire-reports$ more org.irods.jargon.idrop.desktop.unittest.AllTests.txt

-------------------------------------------------------------

------------------

Test set: org.irods.jargon.idrop.desktop.unittest.AllTests

-------------------------------------------------------------

------------------

Tests run: 29, Failures: 0, Errors: 5, Skipped: 0, Time elaps

ed: 60.487 sec <<< FAILURE!

org.irods.jargon.idrop.desktop.systraygui.viscomponents.FileS

ystemModelTest Time elapsed: 1.232 sec <<< ERROR!

org.irods.jargon.testutils.TestingUtilsException: error clear

ing irods scratch dir

at org.irods.jargon.testutils.IRODSTestSetupUtilities

.clearIrodsScratchDirectory(IRODSTestSetupUtilities.java:52)

at org.irods.jargon.testutils.IRODSTestSetupUtilities

.initializeIrodsScratchDirectory(IRODSTestSetupUtilities.java

:66)

at org.irods.jargon.idrop.desktop.systraygui.viscompo

nents.FileSystemModelTest.setUpBeforeClass(FileSystemModelTes

t.java:41)

at sun.reflect.NativeMethod...

Conway, Mike

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Apr 6, 2012, 1:33:19 PM4/6/12

to irod...@googlegroups.com

ahh, use the mvn package –Dmaven.test.skip=true

You are trying to run the Junit tests without having an iRODS sandbox set up. The iPlant folks are building web interfaces right now with Jargon + Clojure…it's neat stuff. See if that helps…

F Lengyel

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Apr 6, 2012, 1:45:06 PM4/6/12

to irod...@googlegroups.com

On Friday, April 6, 2012 1:33:19 PM UTC-4, Conway, Mike wrote:

ahh, use the mvn package –Dmaven.test.skip=true

You are trying to run the Junit tests without having an iRODS sandbox set up.

A new piece of information -- would need to know how to set that up.

The iPlant folks are building web interfaces right now with Jargon + Clojure…it's neat stuff. See if that helps…

MC

Thanks -- did that (meaning the mvn without junit) shortly after I posted.

Now I get a read timeout. I'm bracing myself for firewall politics and the

collision of an irresistible force with an immovable object: (This use of

iRODS is for an NSF grant):

2012-04-06 13:32:02,323 242782 [Thread-6] INFO org.irods.jargon.core.transfer.ParallelGetFileTransferStrategy - initiating transfer for: ParallelGetFileTransferStrategy

host:134.74.46.208

port:20182

numberOfThreads:4

localFile:/home/flengyel/Niger_Network_HydroSTNv100_15sec_Static.gdbn

transferLength:879673268

2012-04-06 13:32:02,323 242782 [Thread-6] INFO org.irods.jargon.core.connection.IRODSSession - getting the ParallelTransferThreadPool

2012-04-06 13:32:02,332 242791 [Thread-6] INFO org.irods.jargon.core.connection.IRODSSession - I am not using the parallel transfer threads pool, return null

2012-04-06 13:32:02,333 242792 [Thread-6] INFO org.irods.jargon.core.transfer.ParallelGetFileTransferStrategy - no pool available, transfer using single executor

2012-04-06 13:32:02,390 242849 [Thread-6] INFO org.irods.jargon.core.transfer.ParallelGetFileTransferStrategy - invoking executor threads for get

2012-04-06 13:35:11,848 432307 [pool-1-thread-1] ERROR org.irods.jargon.core.transfer.ParallelGetTransferThread - IOExeption in parallel transfer

2012-04-06 13:35:11,850 432309 [pool-1-thread-2] ERROR org.irods.jargon.core.transfer.ParallelGetTransferThread - IOExeption in parallel transfer

2012-04-06 13:35:11,850 432309 [pool-1-thread-4] ERROR org.irods.jargon.core.transfer.ParallelGetTransferThread - IOExeption in parallel transfer

2012-04-06 13:35:11,850 432309 [pool-1-thread-3] ERROR org.irods.jargon.core.transfer.ParallelGetTransferThread - IOExeption in parallel transfer

2012-04-06 13:35:11,860 432319 [Thread-6] INFO org.irods.jargon.core.transfer.ParallelGetFileTransferStrategy - executor completed

2012-04-06 13:35:11,860 432319 [Thread-6] INFO org.irods.jargon.core.transfer.ParallelGetFileTransferStrategy - transfer process has returned

2012-04-06 13:35:11,861 432320 [Thread-6] INFO org.irods.jargon.core.pub.DataObjectAOImpl - looking for executable to set flag on local file

2012-04-06 13:35:11,861 432320 [Thread-6] INFO org.irods.jargon.core.pub.IRODSFileSystemAOImpl - isFileExecutable()

2012-04-06 13:35:11,861 432320 [Thread-6] INFO org.irods.jargon.core.pub.IRODSFileSystemAOImpl - checking existence of: /CCNYZone/home/irods/Niger_Network_HydroSTNv100_15sec_Static.gdbn

2012-04-06 13:35:11,862 432321 [Thread-6] INFO org.irods.jargon.core.pub.io.IRODSFileImpl - isDirectory() for path:/CCNYZone/home/irods/Niger_Network_HydroSTNv100_15sec_Static.gdbn

2012-04-06 13:35:11,862 432321 [Thread-6] INFO org.irods.jargon.core.pub.IRODSGenQueryExecutorImpl - executeIRODSQueryAndCloseResultInZone()

2012-04-06 13:35:11,863 432322 [Thread-6] INFO org.irods.jargon.core.pub.IRODSGenQueryExecutorImpl - query: SELECT DATA_MODE WHERE COLL_NAME = '/CCNYZone/home/irods' AND DATA_NAME = 'Niger_Network_HydroSTNv100_15sec_Static.gdbn'

2012-04-06 13:35:11,864 432323 [Thread-6] INFO org.irods.jargon.core.connection.IRODSCommands - calling irods function with byte array

2012-04-06 13:35:11,865 432324 [Thread-6] INFO org.irods.jargon.core.connection.IRODSCommands - reading message from irods

2012-04-06 13:37:11,989 552448 [Thread-6] ERROR org.irods.jargon.core.connection.IRODSConnection - exception reading from socket

java.net.SocketTimeoutException: Read timed out

at java.net.SocketInputStream.socketRead0(Native Method)

at java.net.SocketInputStream.read(SocketInputStream.java:146)

at java.io.BufferedInputStream.fill(BufferedInputStream.java:235)

at java.io.BufferedInputStream.read1(BufferedInputStream.java:275)

at java.io.BufferedInputStream.read(BufferedInputStream.java:334)

at org.irods.jargon.core.connection.IRODSConnection.read(IRODSConnection.java:732)

at org.irods.jargon.core.connection.IRODSCommands.readHeaderLength(IRODSCommands.java:992)

at org.irods.jargon.core.connection.IRODSCommands.readHeader(IRODSCommands.java:872)

at org.irods.jargon.core.connection.IRODSCommands.readMessage(IRODSCommands.java:684)

at org.irods.jargon.core.connection.IRODSCommands.readMessage(IRODSCommands.java:667)

at org.irods.jargon.core.connection.IRODSCommands.irodsFunction(IRODSCommands.java:269)

at org.irods.jargon.core.connection.IRODSCommands.irodsFunction(IRODSCommands.java:192)

at org.irods.jargon.core.pub.IRODSGenQueryExecutorImpl.sendGenQueryAndReturnResponse(IRODSGenQueryExecutorImpl.java:310)

at org.irods.jargon.core.pub.IRODSGenQueryExecutorImpl.executeTranslatedIRODSQuery(IRODSGenQueryExecutorImpl.java:257)

at org.irods.jargon.core.pub.IRODSGenQueryExecutorImpl.executeIRODSQueryAndCloseResultInZone(IRODSGenQueryExecutorImpl.java:163)

at org.irods.jargon.core.pub.IRODSFileSystemAOImpl.checkIfDataObjectExecutable(IRODSFileSystemAOImpl.java:185)

at org.irods.jargon.core.pub.IRODSFileSystemAOImpl.isFileExecutable(IRODSFileSystemAOImpl.java:139)

at org.irods.jargon.core.pub.io.IRODSFileImpl.canExecute(IRODSFileImpl.java:1403)

at org.irods.jargon.core.pub.DataObjectAOImpl.processGetAfterResourceDetermined(DataObjectAOImpl.java:1120)

at org.irods.jargon.core.pub.DataObjectAOImpl.getDataObjectFromIrods(DataObjectAOImpl.java:854)

at org.irods.jargon.core.pub.TransferOperationsHelper.processGetOfSingleFile(TransferOperationsHelper.java:255)

at org.irods.jargon.core.pub.DataTransferOperationsImpl.processGetOfSingleFile(DataTransferOperationsImpl.java:749)

at org.irods.jargon.core.pub.DataTransferOperationsImpl.processGetAfterAnyConnectionRerouting(DataTransferOperationsImpl.java:539)

at org.irods.jargon.core.pub.DataTransferOperationsImpl.getOperation(DataTransferOperationsImpl.java:364)

at org.irods.jargon.transfer.engine.IRODSLocalTransferEngine.transferTypeGet(IRODSLocalTransferEngine.java:425)

at org.irods.jargon.transfer.engine.IRODSLocalTransferEngine.processOperation(IRODSLocalTransferEngine.java:171)

at org.irods.jargon.transfer.engine.TransferRunner.run(TransferRunner.java:103)

at java.lang.Thread.run(Thread.java:679)

2012-04-06 13:37:12,005 552464 [Thread-6] INFO org.irods.jargon.core.connection.IRODSConnection - disconnecting...

2012-04-06 13:37:12,006 552465 [Thread-6] WARN org.irods.jargon.core.connection.IRODSSimpleProtocolManager - connection returned with IOException, will forcefully close and remove from session cache

2012-04-06 13:37:12,006 552465 [Thread-6] INFO org.irods.jargon.core.connection.IRODSConnection - closing underlying iRODS socket connections, errors will be discarded

2012-04-06 13:37:12,006 552465 [Thread-6] WARN org.irods.jargon.core.connection.IRODSSession - discarding irods session for: irods://ir...@irods.ccny.cuny.edu:1247

2012-04-06 13:37:12,007 552466 [Thread-6] ERROR org.irods.jargon.core.connection.IRODSCommands - interrupted io