Unable To Import Dataset From History Into Data Library

Question: Unable To Import Dataset From History Into Data Library

8.1 years ago by

gerrit • 50

gerrit • 50 wrote:

Dear Galaxy Users, Since I've updated my Galaxy version I'm unable to import any dataset from my history into my data library. It returns a message of e.g. "Invalid item id (1464) specified". I then did a complete new test installation to make sure that this problem wasn't because of the update. But the error still remains. I've included a screen shot in which the error is reported. When I queried the database the dataset id does exist in the history_dataset_association table. I went through the paster.log file and found the following warning message: Unknown library item type: <class 'galaxy.model.="" historydatasetassociation'="">. Can it be that this class is not loaded or found? Is anyone experiencing the same problem? Thanks,

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modified 8.1 years ago by Greg Von Kuster ♦ 810 • written 8.1 years ago by gerrit • 50

8.1 years ago by

Greg Von Kuster ♦ 810

Penn State University

Greg Von Kuster ♦ 810 wrote:

Hello, I am not able to reproduce this problem, and in fact, the message being displayed looks like it comes from very old code ( this particular message "Invalid item id..." is no longer in the most recent version of the code. From where are you getting your updates? You should be getting them from here: hg clone https://<your account="">@bitbucket.org/galaxy/galaxy-dist To make sure you are running the latest distribution, go to your Galaxy root directory and type: hg heads and you should see 4354 d681ef7538ed Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

ADD COMMENT • link written 8.1 years ago by Greg Von Kuster ♦ 810

Hi Greg, It is a long time since I've read the documentation on your site, but since I've started with galaxy I checked it out like this: hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist The strange thing is then when I run "hg heads" it shows the exact version which you have. changeset: 4354:d681ef7538ed tag: tip user: Greg Von Kuster <greg@bx.psu.edu> date: Wed Sep 29 12:39:39 2010 -0400 summary: Fix for rendering hidden widget field values associated with library templates whose fields are displayed on the upload form when importing a dataset from the current history. Added new functional test to cover behavior. I will test a checkout with the other update site. Thanks, Gerrit

ADD REPLY • link written 8.1 years ago by gerrit • 50

8.1 years ago by

Greg Von Kuster ♦ 810

Penn State University

Greg Von Kuster ♦ 810 wrote:

Gerrit, Renaud and others, We apologize for the inconvenience - it seems that you have uncovered a bug that has been corrected in our development repo, but has not yet made it to our distribution repo. This fix should reach the distribution repo some time next week. Thanks very much for reporting this! Greg Von Kuster Galaxy Development Team greg@bx.psu.edu

ADD COMMENT • link written 8.1 years ago by Greg Von Kuster ♦ 810

Hi Greg, Thanks for taking Renaud's and my issue seriously. Just strange that no other users complained, since the distribution is more than a month old. I find the functionality extremely useful for keeping processed data sorted and categorised. Looking forward for the new distro! Regards, Gerrit

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8.1 years ago by

Renaud Gaujoux • 10

Renaud Gaujoux • 10 wrote:

Hi, I also get the same error. To reproduce: 1. install a fresh Galaxy from the repository (via: hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist). 2. run the setup.sh script 3. create a user 'test' 4. stop galaxy, make user 'test' admin in universe_wsgi.ini, restart galaxy 5. create a new data library 'Lib' 6. give the user all permission on this data library 7. upload some fasta file 'seq.fas' via: Get Data > Upload File 8. go to Shared Data > Data Libraries > 'Lib' - Add datasets 9. use upload option: import datasets from current history 10. select file 'seq.fas', and hit 'import to library' => Invalid item id (2) specified. The direct import 'Upload files' in 'Upload files to a data library' view works fine. Any help or bug fix is welcome. Thank you. Bests, Renaud ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

ADD COMMENT • link written 8.1 years ago by Renaud Gaujoux • 10

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