incf / ids-tools Goto Github PK

INCF Dataspace utilities

License: Other

Python 98.95% Rebol 1.05%

ids-tools's Introduction

INCF Dataspace tools

Introduction

ids-tools is a set of scripts and python packages for managing and interacting with the INCF Dataspace. See the main INCF Dataspace on the INCF website.

The main source code repository for ids-tools is hosted on github.com.

Quickstart

After registering an account at INCF Dataspace you might want to install ids-tools package:

pip install incf.ids-tools

If you are familiar with iRODS, that would be enough to get you started. Otherwise, please refer to our in-depth tutorial in the github wiki.

ids-tools's People

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ids-tools's Issues

ids-init behaviour and irodsEnv management

Issue reported by "Neil Edward" from the Australian node:

When one runs ids-init it assumes the server is ids.incf.net (and there is no command line argument to change it).

If one’s data is not hosted there (my test data is available only on ids-eu.incf.net), how does
one change the host.

Is the only methodology to edit the .irods/.irodsEnv file ?

Public link sharing (idrop-web) not working: 404

First, the ids-eu.incf.net EIP was de-attached from AWS, causing problems on ids-eu:

root@ids-eu-1:~# icd ..
No such directory (collection): /incf/resources/se.kth.pdc

After fixing that, I tried to generate a public link and share it as exposed in iRODS-Chat:

https://groups.google.com/forum/#!topic/iROD-Chat/Nb4nvW40GUg

Fails with 404:

https://ids-eu.incf.net/idrop-web/home/file/download/incf/resources/org.incf/public/INCF%20Dataspace%20Architecture%20v1.3.pdf

Tomcat errors from idrop-web are not very informative, catalina.out:

2014-06-27 12:34:59,022 [ajp-bio-8009-exec-180] INFO  pub.CollectionAndDataObjectListAndSearchAOImpl  - queryForPathAndReturnResultSet for: /incf/resources/org.incf/public
2014-06-27 12:34:59,022 [ajp-bio-8009-exec-180] INFO  pub.IRODSGenQueryExecutorImpl  - executeIRODSQueryWithPagingInZone()
2014-06-27 12:34:59,022 [ajp-bio-8009-exec-180] INFO  pub.IRODSGenQueryExecutorImpl  - query: IRODSQuery:
   queryString:SELECT DISTINCT COLL_NAME,DATA_NAME,DATA_CREATE_TIME,DATA_MODIFY_TIME,DATA_ID,DATA_SIZE,DATA_REPL_NUM,DATA_OWNER_NAME WHERE COLL_NAME = '/incf/resources/org.incf/public'
    numberOfResultsDesired:5000
2014-06-27 12:34:59,022 [ajp-bio-8009-exec-180] INFO  connection.IRODSCommands  - calling irods function with byte array
2014-06-27 12:34:59,022 [ajp-bio-8009-exec-180] INFO  connection.IRODSCommands  - reading message from irods
2014-06-27 12:34:59,093 [ajp-bio-8009-exec-180] INFO  pub.IRODSGenQueryExecutorImpl  - continuation value: 0
2014-06-27 12:34:59,093 [ajp-bio-8009-exec-180] INFO  query.QueryResultProcessingUtils  - rows returned from iRODS query: 2
2014-06-27 12:34:59,093 [ajp-bio-8009-exec-180] INFO  pub.IRODSGenQueryExecutorImpl  - auto closing result set
2014-06-27 12:34:59,093 [ajp-bio-8009-exec-180] INFO  pub.IRODSGenQueryExecutorImpl  - getting more results for query
2014-06-27 12:34:59,093 [ajp-bio-8009-exec-180] INFO  pub.IRODSGenQueryExecutorImpl  - no results to close, ignore
2014-06-27 12:34:59,094 [ajp-bio-8009-exec-180] INFO  connection.IRODSSession  - closing all irods sessions
2014-06-27 12:34:59,094 [ajp-bio-8009-exec-180] INFO  connection.IRODSCommands  - closing connection
2014-06-27 12:34:59,094 [ajp-bio-8009-exec-180] INFO  connection.IRODSCommands  - shutdown()...check if executor service is running for reconnect
2014-06-27 12:34:59,094 [ajp-bio-8009-exec-180] INFO  connection.IRODSCommands  - shutting down, need to send disconnect to irods
2014-06-27 12:34:59,094 [ajp-bio-8009-exec-180] INFO  connection.IRODSCommands  - sending disconnect message
2014-06-27 12:34:59,094 [ajp-bio-8009-exec-180] INFO  connection.IRODSConnection  - shutting down connection: true
2014-06-27 12:34:59,094 [ajp-bio-8009-exec-180] INFO  connection.IRODSConnection  - closing underlying iRODS socket connections, errors will be discarded
2014-06-27 12:34:59,164 [ajp-bio-8009-exec-184] INFO  controller.TagsController  - getting tag cloud for user: irods://[email protected]:1247
2014-06-27 12:34:59,165 [ajp-bio-8009-exec-184] INFO  usertagging.UserTagCloudServiceImpl  - buildTagCloudEntryListForDataObjects, user=anonymous
2014-06-27 12:34:59,165 [ajp-bio-8009-exec-184] INFO  connection.AuthenticationFactoryImpl  - instanceAuthMechanism()
2014-06-27 12:34:59,165 [ajp-bio-8009-exec-184] INFO  connection.AuthenticationFactoryImpl  - account is anonymous, use default auth scheme
2014-06-27 12:34:59,165 [ajp-bio-8009-exec-184] INFO  connection.AuthenticationFactoryImpl  - authScheme:STANDARD
2014-06-27 12:34:59,166 [ajp-bio-8009-exec-184] INFO  connection.AuthenticationFactoryImpl  - using standard auth
2014-06-27 12:34:59,166 [ajp-bio-8009-exec-184] INFO  connection.IRODSConnection  - pipeline configuration:PipelineConfiguration
   irodsSocketTimeout:0
   irodsParallelSocketTimeout:120
   internalInputStreamBufferSize:0
   internalOutputStreamBufferSize:-1
   internalCacheBufferSize:65535
  localFileOutputStreamBufferSize:16384
  localFileInputStreamBufferSize:16384
   defaultEncoding:utf-8
   inputToOutputCopyBufferByteSize:65536
  instrument:false
   reconnect:false
   reconnect time in millis:600000
(...)

And localhost_access_log.2014-06-27:

127.0.0.1 - - [27/Jun/2014:12:34:58 +0000] "GET /idrop-web/browse/ajaxDirectoryListingUnderParent?dir=%2Fincf%2Fresources%2Forg.incf%2Fpublic&type=path&_=1403872498457 HTTP/1.1" 200 200
127.0.0.1 - - [27/Jun/2014:12:34:58 +0000] "GET /idrop-web/browse/ajaxDirectoryListingUnderParent?type=list&dir=%2Fincf%2Fresources%2Forg.incf%2Fpublic&_=1403872498768 HTTP/1.1" 200 1008
127.0.0.1 - - [27/Jun/2014:12:34:59 +0000] "GET /idrop-web/browse/displayBrowseGridDetails?absPath=%2Fincf%2Fresources%2Forg.incf%2Fpublic&_=1403872498730 HTTP/1.1" 200 5376
127.0.0.1 - - [27/Jun/2014:12:34:59 +0000] "GET /idrop-web/tags/tagCloudFormatted?_=1403872498467 HTTP/1.1" 200 2
127.0.0.1 - - [27/Jun/2014:12:35:01 +0000] "GET /idrop-web/home/file/download/incf/resources/org.incf/public/INCF%20Dataspace%20Architecture%20v1.3.pdf HTTP/1.1" 404 1261

@ganqqwerty

Please target upload to the official Debian proper

There is an open (but inactive) "ITP" report
http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=668596

I haven't done any review -- do you foresee major problems (licensing issues etc)?

iDrop Web - bulk upload prints error

When I go to Bulk Upload I get ClassNotFound exception. Clicking at Details button doesn't show any details.

I use Oracle Java 7, Firefox browser, Ubuntu 14.04. The same is happening with Mac/Firefox.

Create a ids-federate-zone script

Create a script that automates setting up a federation between two iRODS hosts:

https://www.irods.org/index.php/Federation_Administration

The script should be launched either as client (default) or server (by passing a --listen flag).

The idea would be to bundle a Flask daemon (or even just a SimpleHTTPServer instance) that runs on the DataSpace nodes and exposes a REST interface which allows both ends to federate with minimum human interaction.

Given iRODS servers A and B, A is a new institution willing to join the DataSpace federation. B is an existing node within DataSpace. A new federation would proceed as follows:

`A` sends a `POST` request to `B`, requesting a federation for a given user#fqdn.
`B` checks whether the user is registered within the system.

If it is not there, 404 is returned with an accompanying JSON document describing the error.
If it is there, `B` would check common iRODS ports on `A` (1247 and the RBUDP/TCP ranges).

If some port is not open, 404 is returned with instructions on how to fix it.
If the necessary ports are reachable and replying to iRODS, setup the federation with restrictive ACLs.

Notify the adminstrator. A single authenticated command via REST should suffice to give full default ACL privileges on the new zone.

I might have omitted security and operational details, but I hope the idea is clear.

iDrop desktop - Java exception when moving file

Steps to reproduce:

log in with your INCF account
select the file and push the button Copy/Move
Click Browse
In the file tree click on the arrow ch.epfl.bbp

The stacktrace is the following:

2014-06-27 21:24:17,134 93406 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSCommands  - starting up reconnect service...
2014-06-27 21:24:17,134 93406 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.ReconnectionManager  - current time:1403897057134
2014-06-27 21:24:17,135 93407 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.ReconnectionManager  - reconnect millis:1403897657134
2014-06-27 21:24:17,135 93407 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSCommands  - calling irods function with byte array
2014-06-27 21:24:17,135 93407 [pool-7-thread-1] INFO  org.irods.jargon.core.connection.ReconnectionManager  - reconn namanger run() 
2014-06-27 21:24:17,136 93408 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSCommands  - reading message from irods
2014-06-27 21:24:18,890 95162 [AWT-EventQueue-1] INFO  org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl  - didnt find an objStat for the path, account for cases where there are strict acls and give Jargon a chance to drill down to a place where the user has permissions
2014-06-27 21:24:18,891 95163 [AWT-EventQueue-1] INFO  org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl  - handleNoListingUnderRootOrHomeByLookingForPublicAndHome()
2014-06-27 21:24:18,891 95163 [AWT-EventQueue-1] INFO  org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl  - I am not unde /, /zone/, or /zohe/home/ so I cannot do anything but throw the original exception
2014-06-27 21:24:18,892 95164 [AWT-EventQueue-1] INFO  org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl  - not configured in jargon.properties to look for public and user home, throw the FileNotFoundException
июн 27, 2014 9:24:18 PM org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSNode lazyLoadOfChildrenOfThisNode
SEVERE: null
org.irods.jargon.core.exception.FileNotFoundException: the collection cannot be found
    at org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl.handleNoListingUnderRootOrHomeByLookingForPublicAndHome(CollectionAndDataObjectListAndSearchAOImpl.java:618)
    at org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl.listDataObjectsAndCollectionsUnderPath(CollectionAndDataObjectListAndSearchAOImpl.java:256)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSNode.lazyLoadOfChildrenOfThisNode(IRODSNode.java:97)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSNode.lazyLoadOfChildrenOfThisNode(IRODSNode.java:66)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSFileSystemModel.triggerLazyLoading(IRODSFileSystemModel.java:68)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSFileSystemModel.getChildCount(IRODSFileSystemModel.java:59)
    at org.netbeans.swing.outline.EventBroadcaster.translateEvent(EventBroadcaster.java:687)
    at org.netbeans.swing.outline.EventBroadcaster.treeWillExpand(EventBroadcaster.java:459)
    at org.netbeans.swing.outline.TreePathSupport.fireTreeWillExpand(TreePathSupport.java:173)
    at org.netbeans.swing.outline.TreePathSupport.expandPath(TreePathSupport.java:111)
    at org.netbeans.swing.outline.Outline.editCellAt(Outline.java:734)
    at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleasedDND(BasicTableUI.java:1180)
    at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1150)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
    at java.awt.Component.processMouseEvent(Component.java:6505)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
    at org.netbeans.swing.outline.Outline.processMouseEvent(Outline.java:961)
    at java.awt.Component.processEvent(Component.java:6270)
    at java.awt.Container.processEvent(Container.java:2229)
    at java.awt.Component.dispatchEventImpl(Component.java:4861)
    at java.awt.Container.dispatchEventImpl(Container.java:2287)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.java:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:708)
    at java.awt.EventQueue$4.run(EventQueue.java:706)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:154)
    at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:182)
    at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:221)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:219)
    at java.awt.Dialog.show(Dialog.java:1082)
    at java.awt.Component.show(Component.java:1651)
    at java.awt.Component.setVisible(Component.java:1603)
    at java.awt.Window.setVisible(Window.java:1014)
    at java.awt.Dialog.setVisible(Dialog.java:1005)
    at org.irods.jargon.idrop.desktop.systraygui.CopyMoveDialog.btnBrowseActionPerformed(CopyMoveDialog.java:485)
    at org.irods.jargon.idrop.desktop.systraygui.CopyMoveDialog.access$300(CopyMoveDialog.java:33)
    at org.irods.jargon.idrop.desktop.systraygui.CopyMoveDialog$2.actionPerformed(CopyMoveDialog.java:384)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
    at java.awt.Component.processMouseEvent(Component.java:6505)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
    at java.awt.Component.processEvent(Component.java:6270)
    at java.awt.Container.processEvent(Container.java:2229)
    at java.awt.Component.dispatchEventImpl(Component.java:4861)
    at java.awt.Container.dispatchEventImpl(Container.java:2287)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.java:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:708)
    at java.awt.EventQueue$4.run(EventQueue.java:706)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:154)
    at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:182)
    at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:221)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:219)
    at java.awt.Dialog.show(Dialog.java:1082)
    at java.awt.Component.show(Component.java:1651)
    at java.awt.Component.setVisible(Component.java:1603)
    at java.awt.Window.setVisible(Window.java:1014)
    at java.awt.Dialog.setVisible(Dialog.java:1005)
    at org.irods.jargon.idrop.desktop.systraygui.iDrop.btnMainToolbarCopyActionPerformed(iDrop.java:2103)
    at org.irods.jargon.idrop.desktop.systraygui.iDrop.access$3000(iDrop.java:83)
    at org.irods.jargon.idrop.desktop.systraygui.iDrop$18.actionPerformed(iDrop.java:1695)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
    at java.awt.Component.processMouseEvent(Component.java:6505)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
    at java.awt.Component.processEvent(Component.java:6270)
    at java.awt.Container.processEvent(Container.java:2229)
    at java.awt.Component.dispatchEventImpl(Component.java:4861)
    at java.awt.Container.dispatchEventImpl(Container.java:2287)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.java:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:708)
    at java.awt.EventQueue$4.run(EventQueue.java:706)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

2014-06-27 21:24:18,918 95190 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSCommands  - closing connection
2014-06-27 21:24:18,918 95190 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSCommands  - shutdown()...check if executor service is running for reconnect
2014-06-27 21:24:18,918 95190 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSCommands  - shutting down executor for reconnect...
2014-06-27 21:24:18,918 95190 [pool-7-thread-1] INFO  org.irods.jargon.core.connection.ReconnectionManager  - interrupted...will shut down
2014-06-27 21:24:23,919 100191 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSCommands  - shutting down, need to send disconnect to irods
2014-06-27 21:24:23,920 100192 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSCommands  - sending disconnect message
2014-06-27 21:24:23,920 100192 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSConnection  - shutting down connection: true
2014-06-27 21:24:23,921 100193 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSConnection  - is connected for : irodsSimpleConnection/AWT-EventQueue-1/1403897056834
2014-06-27 21:24:23,921 100193 [AWT-EventQueue-1] INFO  org.irods.jargon.core.connection.IRODSConnection  - now disconnected
июн 27, 2014 9:24:23 PM org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSFileSystemModel triggerLazyLoading
SEVERE: null
org.irods.jargon.idrop.exceptions.IdropException: error occurred accessing collection data
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSNode.lazyLoadOfChildrenOfThisNode(IRODSNode.java:113)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSNode.lazyLoadOfChildrenOfThisNode(IRODSNode.java:66)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSFileSystemModel.triggerLazyLoading(IRODSFileSystemModel.java:68)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSFileSystemModel.getChildCount(IRODSFileSystemModel.java:59)
    at org.netbeans.swing.outline.EventBroadcaster.translateEvent(EventBroadcaster.java:687)
    at org.netbeans.swing.outline.EventBroadcaster.treeWillExpand(EventBroadcaster.java:459)
    at org.netbeans.swing.outline.TreePathSupport.fireTreeWillExpand(TreePathSupport.java:173)
    at org.netbeans.swing.outline.TreePathSupport.expandPath(TreePathSupport.java:111)
    at org.netbeans.swing.outline.Outline.editCellAt(Outline.java:734)
    at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleasedDND(BasicTableUI.java:1180)
    at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1150)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
    at java.awt.Component.processMouseEvent(Component.java:6505)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
    at org.netbeans.swing.outline.Outline.processMouseEvent(Outline.java:961)
    at java.awt.Component.processEvent(Component.java:6270)
    at java.awt.Container.processEvent(Container.java:2229)
    at java.awt.Component.dispatchEventImpl(Component.java:4861)
    at java.awt.Container.dispatchEventImpl(Container.java:2287)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.java:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:708)
    at java.awt.EventQueue$4.run(EventQueue.java:706)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:154)
    at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:182)
    at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:221)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:219)
    at java.awt.Dialog.show(Dialog.java:1082)
    at java.awt.Component.show(Component.java:1651)
    at java.awt.Component.setVisible(Component.java:1603)
    at java.awt.Window.setVisible(Window.java:1014)
    at java.awt.Dialog.setVisible(Dialog.java:1005)
    at org.irods.jargon.idrop.desktop.systraygui.CopyMoveDialog.btnBrowseActionPerformed(CopyMoveDialog.java:485)
    at org.irods.jargon.idrop.desktop.systraygui.CopyMoveDialog.access$300(CopyMoveDialog.java:33)
    at org.irods.jargon.idrop.desktop.systraygui.CopyMoveDialog$2.actionPerformed(CopyMoveDialog.java:384)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
    at java.awt.Component.processMouseEvent(Component.java:6505)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
    at java.awt.Component.processEvent(Component.java:6270)
    at java.awt.Container.processEvent(Container.java:2229)
    at java.awt.Component.dispatchEventImpl(Component.java:4861)
    at java.awt.Container.dispatchEventImpl(Container.java:2287)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.java:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:708)
    at java.awt.EventQueue$4.run(EventQueue.java:706)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:154)
    at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:182)
    at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:221)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:219)
    at java.awt.Dialog.show(Dialog.java:1082)
    at java.awt.Component.show(Component.java:1651)
    at java.awt.Component.setVisible(Component.java:1603)
    at java.awt.Window.setVisible(Window.java:1014)
    at java.awt.Dialog.setVisible(Dialog.java:1005)
    at org.irods.jargon.idrop.desktop.systraygui.iDrop.btnMainToolbarCopyActionPerformed(iDrop.java:2103)
    at org.irods.jargon.idrop.desktop.systraygui.iDrop.access$3000(iDrop.java:83)
    at org.irods.jargon.idrop.desktop.systraygui.iDrop$18.actionPerformed(iDrop.java:1695)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
    at java.awt.Component.processMouseEvent(Component.java:6505)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
    at java.awt.Component.processEvent(Component.java:6270)
    at java.awt.Container.processEvent(Container.java:2229)
    at java.awt.Component.dispatchEventImpl(Component.java:4861)
    at java.awt.Container.dispatchEventImpl(Container.java:2287)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.java:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:708)
    at java.awt.EventQueue$4.run(EventQueue.java:706)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
Caused by: org.irods.jargon.core.exception.FileNotFoundException: the collection cannot be found
    at org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl.handleNoListingUnderRootOrHomeByLookingForPublicAndHome(CollectionAndDataObjectListAndSearchAOImpl.java:618)
    at org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl.listDataObjectsAndCollectionsUnderPath(CollectionAndDataObjectListAndSearchAOImpl.java:256)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSNode.lazyLoadOfChildrenOfThisNode(IRODSNode.java:97)
    ... 134 more

Exception in thread "AWT-EventQueue-1" org.irods.jargon.idrop.exceptions.IdropRuntimeException: org.irods.jargon.idrop.exceptions.IdropException: error occurred accessing collection data
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSFileSystemModel.triggerLazyLoading(IRODSFileSystemModel.java:72)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSFileSystemModel.getChildCount(IRODSFileSystemModel.java:59)
    at org.netbeans.swing.outline.EventBroadcaster.translateEvent(EventBroadcaster.java:687)
    at org.netbeans.swing.outline.EventBroadcaster.treeWillExpand(EventBroadcaster.java:459)
    at org.netbeans.swing.outline.TreePathSupport.fireTreeWillExpand(TreePathSupport.java:173)
    at org.netbeans.swing.outline.TreePathSupport.expandPath(TreePathSupport.java:111)
    at org.netbeans.swing.outline.Outline.editCellAt(Outline.java:734)
    at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleasedDND(BasicTableUI.java:1180)
    at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1150)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:290)
    at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:289)
    at java.awt.Component.processMouseEvent(Component.java:6505)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
    at org.netbeans.swing.outline.Outline.processMouseEvent(Outline.java:961)
    at java.awt.Component.processEvent(Component.java:6270)
    at java.awt.Container.processEvent(Container.java:2229)
    at java.awt.Component.dispatchEventImpl(Component.java:4861)
    at java.awt.Container.dispatchEventImpl(Container.java:2287)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.java:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:708)
    at java.awt.EventQueue$4.run(EventQueue.java:706)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:154)
    at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:182)
    at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:221)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:219)
    at java.awt.Dialog.show(Dialog.java:1082)
    at java.awt.Component.show(Component.java:1651)
    at java.awt.Component.setVisible(Component.java:1603)
    at java.awt.Window.setVisible(Window.java:1014)
    at java.awt.Dialog.setVisible(Dialog.java:1005)
    at org.irods.jargon.idrop.desktop.systraygui.CopyMoveDialog.btnBrowseActionPerformed(CopyMoveDialog.java:485)
    at org.irods.jargon.idrop.desktop.systraygui.CopyMoveDialog.access$300(CopyMoveDialog.java:33)
    at org.irods.jargon.idrop.desktop.systraygui.CopyMoveDialog$2.actionPerformed(CopyMoveDialog.java:384)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
    at java.awt.Component.processMouseEvent(Component.java:6505)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
    at java.awt.Component.processEvent(Component.java:6270)
    at java.awt.Container.processEvent(Container.java:2229)
    at java.awt.Component.dispatchEventImpl(Component.java:4861)
    at java.awt.Container.dispatchEventImpl(Container.java:2287)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.java:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:708)
    at java.awt.EventQueue$4.run(EventQueue.java:706)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:154)
    at java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:182)
    at java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:221)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:219)
    at java.awt.Dialog.show(Dialog.java:1082)
    at java.awt.Component.show(Component.java:1651)
    at java.awt.Component.setVisible(Component.java:1603)
    at java.awt.Window.setVisible(Window.java:1014)
    at java.awt.Dialog.setVisible(Dialog.java:1005)
    at org.irods.jargon.idrop.desktop.systraygui.iDrop.btnMainToolbarCopyActionPerformed(iDrop.java:2103)
    at org.irods.jargon.idrop.desktop.systraygui.iDrop.access$3000(iDrop.java:83)
    at org.irods.jargon.idrop.desktop.systraygui.iDrop$18.actionPerformed(iDrop.java:1695)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
    at java.awt.Component.processMouseEvent(Component.java:6505)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3311)
    at java.awt.Component.processEvent(Component.java:6270)
    at java.awt.Container.processEvent(Container.java:2229)
    at java.awt.Component.dispatchEventImpl(Component.java:4861)
    at java.awt.Container.dispatchEventImpl(Container.java:2287)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
    at java.awt.Container.dispatchEventImpl(Container.java:2273)
    at java.awt.Window.dispatchEventImpl(Window.java:2719)
    at java.awt.Component.dispatchEvent(Component.java:4687)
    at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:735)
    at java.awt.EventQueue.access$200(EventQueue.java:103)
    at java.awt.EventQueue$3.run(EventQueue.java:694)
    at java.awt.EventQueue$3.run(EventQueue.java:692)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
    at java.awt.EventQueue$4.run(EventQueue.java:708)
    at java.awt.EventQueue$4.run(EventQueue.java:706)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:705)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
Caused by: org.irods.jargon.idrop.exceptions.IdropException: error occurred accessing collection data
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSNode.lazyLoadOfChildrenOfThisNode(IRODSNode.java:113)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSNode.lazyLoadOfChildrenOfThisNode(IRODSNode.java:66)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSFileSystemModel.triggerLazyLoading(IRODSFileSystemModel.java:68)
    ... 132 more
Caused by: org.irods.jargon.core.exception.FileNotFoundException: the collection cannot be found
    at org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl.handleNoListingUnderRootOrHomeByLookingForPublicAndHome(CollectionAndDataObjectListAndSearchAOImpl.java:618)
    at org.irods.jargon.core.pub.CollectionAndDataObjectListAndSearchAOImpl.listDataObjectsAndCollectionsUnderPath(CollectionAndDataObjectListAndSearchAOImpl.java:256)
    at org.irods.jargon.idrop.desktop.systraygui.viscomponents.IRODSNode.lazyLoadOfChildrenOfThisNode(IRODSNode.java:97)
    ... 134 more

incf website - the flyer and the poser are is the same thing

In the Documentation section there is a flyer and a poster of Dataspace. They are the same, probably one of them has to be deleted.

jnlp file of iDrop Desktop doesn't run on Mac OS

I identified the following problem with this file: http://iren-web.renci.org/idrop-release/idrop.jnlp on Mac OS X. After tuning the permissions and security this file is not running, displaying the following error:

java.lang.SecurityException: Missing required Permissions manifest attribute in main jar: http://iren-web.renci.org/idrop-release/lib/idrop-swing-2.0.0.jar
    at com.sun.deploy.security.DeployManifestChecker.verifyMainJar(Unknown Source)
    at com.sun.deploy.security.DeployManifestChecker.verifyMainJar(Unknown Source)
    at com.sun.javaws.Launcher.doLaunchApp(Unknown Source)
    at com.sun.javaws.Launcher.run(Unknown Source)
    at java.lang.Thread.run(Thread.java:745)

typo on https://github.com/INCF/ids-tools/wiki/Using-the-INCF-Dataspace

small typo near the end of the above page:

You would see AND error like

should be AN

Stephen

Add rules referred in documentation and auditing .re's under incf.ids-tools/rules

As indicated in the documentation:

(...) Lastly, they will set up some iRODS rules that map your namespace 
to your data resource and an iRODS group (e.g. ids-dbio) that you can 
use for ACLs

These rules, including the audit ones, should be available in the package as well, for future reference, modifications, versioning, etc...

idrop-lite backtrace when trying bulk upload

As reported by a user of DataSpace while trying to upload a bunch of files via idrop-lite:

... we might need to upgrade the jar.

cedTea-Web Plugin version: 1.5 (1.5-1ubuntu1)
Thu Jun 26 16:47:35 CEST 2014
net.sourceforge.jnlp.LaunchException: Fatal: Initialization Error: Could not initialize applet. For more information click "more information button".
    at net.sourceforge.jnlp.Launcher.createApplet(Launcher.java:746)
    at net.sourceforge.jnlp.Launcher.getApplet(Launcher.java:675)
    at net.sourceforge.jnlp.Launcher$TgThread.run(Launcher.java:908)
Caused by: net.sourceforge.jnlp.LaunchException: Fatal: Initialization Error: Unknown Main-Class. Could not determine the main class for this application.
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.initializeResources(JNLPClassLoader.java:681)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.<init>(JNLPClassLoader.java:277)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.createInstance(JNLPClassLoader.java:351)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.getInstance(JNLPClassLoader.java:418)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.getInstance(JNLPClassLoader.java:394)
    at net.sourceforge.jnlp.Launcher.createApplet(Launcher.java:711)
    ... 2 more
Caused by: java.lang.ClassNotFoundException: Could not find class org.irods.jargon.idrop.lite.iDropLiteApplet
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.findClassNonRecursive(JNLPClassLoader.java:2483)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.findClass(JNLPClassLoader.java:1653)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.findClass(JNLPClassLoader.java:2496)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.initializeResources(JNLPClassLoader.java:678)
    ... 7 more
Caused by: java.security.PrivilegedActionException: java.lang.ClassNotFoundException: org.irods.jargon.idrop.lite.iDropLiteApplet
    at java.security.AccessController.doPrivileged(Native Method)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.findClassNonRecursive(JNLPClassLoader.java:2473)
    ... 10 more
Caused by: java.lang.ClassNotFoundException: org.irods.jargon.idrop.lite.iDropLiteApplet
    at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.access$2001(JNLPClassLoader.java:2445)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader$1.run(JNLPClassLoader.java:2476)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader$1.run(JNLPClassLoader.java:2474)
    ... 12 more

Chain:
1) at Thu Jun 26 16:47:25 CEST 2014
net.sourceforge.jnlp.LaunchException: Fatal: Initialization Error: Unknown Main-Class. Could not determine the main class for this application.
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.initializeResources(JNLPClassLoader.java:681)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.<init>(JNLPClassLoader.java:277)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.createInstance(JNLPClassLoader.java:351)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.getInstance(JNLPClassLoader.java:418)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.getInstance(JNLPClassLoader.java:394)
    at net.sourceforge.jnlp.Launcher.createApplet(Launcher.java:711)
    at net.sourceforge.jnlp.Launcher.getApplet(Launcher.java:675)
    at net.sourceforge.jnlp.Launcher$TgThread.run(Launcher.java:908)
Caused by: java.lang.ClassNotFoundException: Could not find class org.irods.jargon.idrop.lite.iDropLiteApplet
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.findClassNonRecursive(JNLPClassLoader.java:2483)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.findClass(JNLPClassLoader.java:1653)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.findClass(JNLPClassLoader.java:2496)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.initializeResources(JNLPClassLoader.java:678)
    ... 7 more
Caused by: java.security.PrivilegedActionException: java.lang.ClassNotFoundException: org.irods.jargon.idrop.lite.iDropLiteApplet
    at java.security.AccessController.doPrivileged(Native Method)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.findClassNonRecursive(JNLPClassLoader.java:2473)
    ... 10 more
Caused by: java.lang.ClassNotFoundException: org.irods.jargon.idrop.lite.iDropLiteApplet
    at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.access$2001(JNLPClassLoader.java:2445)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader$1.run(JNLPClassLoader.java:2476)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader$1.run(JNLPClassLoader.java:2474)
    ... 12 more
2) at Thu Jun 26 16:47:25 CEST 2014
net.sourceforge.jnlp.LaunchException: Fatal: Initialization Error: Could not initialize applet. For more information click "more information button".
    at net.sourceforge.jnlp.Launcher.createApplet(Launcher.java:746)
    at net.sourceforge.jnlp.Launcher.getApplet(Launcher.java:675)
    at net.sourceforge.jnlp.Launcher$TgThread.run(Launcher.java:908)
Caused by: net.sourceforge.jnlp.LaunchException: Fatal: Initialization Error: Unknown Main-Class. Could not determine the main class for this application.
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.initializeResources(JNLPClassLoader.java:681)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.<init>(JNLPClassLoader.java:277)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.createInstance(JNLPClassLoader.java:351)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.getInstance(JNLPClassLoader.java:418)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.getInstance(JNLPClassLoader.java:394)
    at net.sourceforge.jnlp.Launcher.createApplet(Launcher.java:711)
    ... 2 more
Caused by: java.lang.ClassNotFoundException: Could not find class org.irods.jargon.idrop.lite.iDropLiteApplet
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.findClassNonRecursive(JNLPClassLoader.java:2483)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.findClass(JNLPClassLoader.java:1653)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.findClass(JNLPClassLoader.java:2496)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader.initializeResources(JNLPClassLoader.java:678)
    ... 7 more
Caused by: java.security.PrivilegedActionException: java.lang.ClassNotFoundException: org.irods.jargon.idrop.lite.iDropLiteApplet
    at java.security.AccessController.doPrivileged(Native Method)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.findClassNonRecursive(JNLPClassLoader.java:2473)
    ... 10 more
Caused by: java.lang.ClassNotFoundException: org.irods.jargon.idrop.lite.iDropLiteApplet
    at java.net.URLClassLoader$1.run(URLClassLoader.java:366)
    at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader.access$2001(JNLPClassLoader.java:2445)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader$1.run(JNLPClassLoader.java:2476)
    at net.sourceforge.jnlp.runtime.JNLPClassLoader$CodeBaseClassLoader$1.run(JNLPClassLoader.java:2474)
    ... 12 more

broken link in the incf.org documentation

On this page:
File Navigator: Learn more about iRODS FUSE (File system in user space) - goes to a 404 error.

when I try to click on a link Launch iDrop Desktop in my sidebar, I got 404 error

The link is here: http://dl.dropbox.com/u/935446/Selection_008.png

Wrong indentation user ldap sync script

There is a wrong indentation on this and this line.

The else blocks should be moved one level to the left.

Warn about {mis || non}-configured SSH settings

Removing the following requisite from the documentation:

* Before running the ids-setup-data-server script, run 'touch ~/.ssh/config'.

Automate data node creation (mkresc)

Get rid of the last chunk of manual steps on the documentation for a data node:

https://github.com/INCF/ids-tools/wiki/IDS-Data-Server-Setup

The IDS admins will do a couple of things. First, they will create your 
resource definition in iRODS so that some name can be used to 
reference your server and vault path (e.g. a name like 'ids_dbio_1'). 
Second, they will set up part of the IDS namespace for your organization.
(...)

Create helper to reload ids users on INCF portal new user addition

The dataspace REST user API endpoint has been implemented as follows:

$ curl --user braincode:mypassword -XGET http://incf.org/dataspace/v1/users/all
{
    "total_users": 100,
    "username1": { on_ids_group: 1, email: "[email protected]", fullname: "John Doe", terms_accepted: 1},
    "username2": { on_ids_group: 0, email: "[email protected]", fullname: "John Connor", terms_accepted: 0},
    ...
}


$ curl --user braincode:mypassword -XGET http://incf.org/dataspace/v1/users/username1
{
    "username1": "username1": { on_ids_group: 1, email: "[email protected]", fullname: "John Doe", terms_accepted: 1}
}

$ curl --user braincode:mypassword -XPUT http://incf.org/dataspace/v1/users/john
{
   message: "User 'john' has been added into the 'ids' group'"
}

Provide a basic endpoint in incf.ids-tools to ease user manipulation via API and cmdline.

Hardcoded IPs on pg_hba.conf

Find a mechanism to setup PostgresSQL replication that does not involve hardcoded IPs as it is now:

host    replication     postgres        IP1/32       trust
host    replication     postgres        IP2/32       trust
host    replication     postgres        IP3/32         trust

http://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html

Or just migrate to AWS RDS: https://aws.amazon.com/about-aws/whats-new/2013/11/26/announcing-point-and-click-database-replication-across-aws-regions-for-amazon-rds-for-mysql/

iDrop descktop - in Metadata Unit field mustn't be mandatory

When I adding the new Metadata field in iDrop desktop, the Create button doesn't activate when the Unit field is not filled.

As a user, moving/copying files between zones erases metadata

I use iDrop Desktop.

Steps to reproduce the bug:

I uploaded the file to my personal folder (incf/home/katkov)
I added the metadata to this file: 10 fieleds of various datatypes
I click the button Copy/Move and move it to another zone. Particularly I moved it to the folder bbp/home/public .
I see that all the metadata have gone from the file.

Ticket based sharing exposes dataset contents for anonymous users

Giving a specific (authenticated) user READ rights exposes data to anonymous users.

Even if (URL) tickets are supposed to ease data sharing, third parties (including anonymous users) shouldn't be able to guess them and then access its contents.

Thanks @ganqqwerty for reporting this.

Launch ids-sync-ldap-users asyncronously

Currently, syncronization across the federation is performed every 30 min via cronjobs:

30 * * * * ids-sync-ldap-users >> /var/log/irods/ids-sync-ldap-users.out 2>&1

When a user signs up, she receives an email stating that this process could take a while.

A good solution would be to have it evented, so that Plone tells ids-* machines via events that a new user is on board, then letting them access instantly, like any other online service we’re used to.

The next step would be to extend the very freshly implemented federation API (thanks Chris!) to allow for this evented interaction.

@ganqqwerty

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