Delete Dataset

[eaquigley]

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Author Name: Elda Sotiri (@esotiri)
Original Redmine Issue: 3544, https://redmine.hmdc.harvard.edu/issues/3544
Original Date: 2014-02-11
Original Assignee: Gustavo Durand

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Add option to Delete Dataset.

[eaquigley]

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Original Redmine Comment
Author Name: Michael Bar-Sinai (@michbarsinai)
Original Date: 2014-03-27T18:18:14Z

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Supported by API call

DELETE http://{{SERVER}}/api/datasets/{{id}}?key={{apikey}}

Api's readme updated.

[eaquigley]

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Original Redmine Comment
Author Name: Kevin Condon (@kcondon)
Original Date: 2014-04-07T19:48:08Z

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Tested on 4/7

Deleting a dataset works fine, respects ownership but throws a 500 error if dataset contains a file.

1. Does dataset need to be empty like dv?
2. Deleting a dv that is not empty catches error and informs user it needs to be empty.

Passing back to Michael for comment.

[eaquigley]

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Original Redmine Comment
Author Name: Michael Bar-Sinai (@michbarsinai)
Original Date: 2014-04-09T15:09:21Z

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Passing to Gustavo - this is really a requirement question.

[eaquigley]

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Original Redmine Comment
Author Name: Gustavo Durand (@scolapasta)
Original Date: 2014-04-09T16:09:19Z

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Deleting a dataset should delete the files - this is different that deleting a dataverse (in that scenario, you can move the datasets; files are an inherent part of the dataset).

[eaquigley]

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Original Redmine Comment
Author Name: Michael Bar-Sinai (@michbarsinai)
Original Date: 2014-04-14T16:15:56Z

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Updated the command to issue DeleteDataFileCommnads.
These commands throw a foreign key constraint violation exception, though:

Call: DELETE FROM DVOBJECT WHERE (ID = ?)
    bind => [1 parameter bound]
Query: DeleteObjectQuery([Dataset id:11 ])
    at org.eclipse.persistence.internal.jpa.EntityManagerSetupImpl$1.handleException(EntityManagerSetupImpl.java:692)
    at org.eclipse.persistence.transaction.AbstractSynchronizationListener.handleException(AbstractSynchronizationListener.java:275)
    at org.eclipse.persistence.transaction.AbstractSynchronizationListener.beforeCompletion(AbstractSynchronizationListener.java:170)
    at org.eclipse.persistence.transaction.JTASynchronizationListener.beforeCompletion(JTASynchronizationListener.java:68)
    at com.sun.enterprise.transaction.JavaEETransactionImpl.commit(JavaEETransactionImpl.java:452)
    ... 67 more
Caused by: Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.5.0.v20130507-3faac2b): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: org.postgresql.util.PSQLException: ERROR: update or delete on table "dvobject" violates foreign key constraint "fk_dvobject_owner_id" on table "dvobject"
  Detail: Key (id)=(11) is still referenced from table "dvobject".

[eaquigley]

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Original Redmine Comment
Author Name: Leonid Andreev (@landreev)
Original Date: 2014-04-16T18:11:52Z

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Michael, could you please take another look at this ticket.
I haven't been able to reproduce the condition; I've deleted a bunch of datasets, with files, and it seemed to have worked like a charm.

From looking at your exception:

Detail: Key (id)=(11) is still referenced from table "dvobject".

"11" was the id of the dataset in your example; so it appears that the exception was thrown by the DeleteDataset command, not one of the DeleteDatafile commands; which, I'm assuming means that some files didn't get deleted, and were still referencing the id of the parent...

Not sure how this would happen though... if a physical file failed to delete on the filesystem, the DeleteDatafile command would throw an exception, and then the DatasetDelete command would not get to the point where it tries to delete the dataset from the databse. Confused.

Could you take a look and see if you can find a way to reproduce this error?

(thinking about it, is DataSet.getDatafiles() guaranteed to return all the files that belong to the dataset?)

I committed my curl command that I used for testing under scripts/issues/3544; it was simply

curl -X DELETE http://localhost:8080/api/datasets/?key=pete

[eaquigley]

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Original Redmine Comment
Author Name: Michael Bar-Sinai (@michbarsinai)
Original Date: 2014-04-21T20:12:11Z

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Seems to have been an issue with my files dir setup: /tmp/files does not exist. So - setup issue, not that important.

[eaquigley]

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Original Redmine Comment
Author Name: Kevin Condon (@kcondon)
Original Date: 2014-04-30T19:28:54Z

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Retested, now getting foreign key constraint on deleting an unpublished dataet without files:

Kevin-Condons-MacBook-Pro:~ kevincondon$ curl -X DELETE http://dvn-build.hmdc.harvard.edu/api/datasets/187?key=pete

<title>GlassFish Server Open Source Edition 4.0 - Error report</title><style type="text/css"></style>

HTTP Status 500 - Internal Server Error

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type Exception report

messageInternal Server Error

descriptionThe server encountered an internal error that prevented it from fulfilling this request.

exception `javax.servlet.ServletException: javax.ejb.EJBException: Transaction aborted

</p><p><b>root cause</b> javax.ejb.EJBException: Transaction aborted
</p><p><b>root cause</b> javax.transaction.RollbackException: Transaction marked for rollback.
</p><p><b>root cause</b> javax.persistence.PersistenceException: Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.5.0.v20130507-3faac2b): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: org.postgresql.util.PSQLException: ERROR: update or delete on table "dvobject" violates foreign key constraint "fk_roleassignment_definitionpoint_id" on table "roleassignment"
Detail: Key (id)=(187) is still referenced from table "roleassignment".
Error Code: 0
Call: DELETE FROM DVOBJECT WHERE (ID = ?)
bind => [1 parameter bound]
Query: DeleteObjectQuery([Dataset id:187 ])
</p><p><b>root cause</b> Exception [EclipseLink-4002] (Eclipse Persistence Services - 2.5.0.v20130507-3faac2b): org.eclipse.persistence.exceptions.DatabaseException
Internal Exception: org.postgresql.util.PSQLException: ERROR: update or delete on table "dvobject" violates foreign key constraint "fk_roleassignment_definitionpoint_id" on table "roleassignment"
Detail: Key (id)=(187) is still referenced from table "roleassignment".
Error Code: 0
Call: DELETE FROM DVOBJECT WHERE (ID = ?)
bind => [1 parameter bound]
Query: DeleteObjectQuery([Dataset id:187 ])
</p><p><b>root cause</b> org.postgresql.util.PSQLException: ERROR: update or delete on table "dvobject" violates foreign key constraint "fk_roleassignment_definitionpoint_id" on table "roleassignment"
Detail: Key (id)=(187) is still referenced from table "roleassignment".
`

note The full stack traces of the exception and its root causes are available in the GlassFish Server Open Source Edition 4.0 logs.

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GlassFish Server Open Source Edition 4.0

Kevin-Condons-MacBook-Pro:~ kevincondon$

[eaquigley]

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Original Redmine Comment
Author Name: Michael Bar-Sinai (@michbarsinai)
Original Date: 2014-05-05T18:08:48Z

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Updates DeleteDatasetCommand to delete assignments and roles defined at it.

[eaquigley]

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Original Redmine Comment
Author Name: Kevin Condon (@kcondon)
Original Date: 2014-05-06T17:17:23Z

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Tested on 5/6

Basic delete works: a user can delete a dataset they created if it is an unpublished draft, with or without files.

There are several issues relating to permissions and deacession/destroy that will be addressed later when that workflow is defined.

The main areas I tested were:

authorization: only authorized users (dv and dataset creator) can delete a dataset,
version: only an unpublished draft can be deleted. once there is a published version, even a draft cannot be deleted.
files: datasets with files are now deleted.
index: deleting a dataset does not run index to remove it from the index.

All of the above are deemed acceptable until further refinement of permissions with the exception of not indexing after delete.

I've checked with Michael and he asked that I send this ticket to Phil to make sure the api delete dataset call invokes the appropriate index command.

[eaquigley]

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Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-05-27T14:54:51Z

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Kevin Condon wrote:

version: only an unpublished draft can be deleted. once there is a published version, even a draft cannot be deleted.

I'm running into this limitation right now. For now I'm having the Data Deposit API throw this error:

"This dataset has been published and subsequently a draft has been created. You are trying to delete that draft but this is not yet supported."

I'm assigning this ticket to Gustavo for review. We have DeleteDatasetCommand (that nicely reports "Cannot delete a released dataset) but we probably need DeleteDatasetEditVersionCommand (or whatever we want to call it). In DVN 3.x we had studyService.destroyWorkingCopyVersion().

[eaquigley]

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Original Redmine Comment
Author Name: Philip Durbin (@pdurbin)
Original Date: 2014-05-27T15:52:45Z

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Philip Durbin wrote:

I'm assigning this ticket to Gustavo for review. We have DeleteDatasetCommand (that nicely reports "Cannot delete a released dataset) but we probably need DeleteDatasetEditVersionCommand (or whatever we want to call it). In DVN 3.x we had studyService.destroyWorkingCopyVersion().

I made a separate ticket for this: https://redmine.hmdc.harvard.edu/issues/4032