Prevent result files to be included in a 'partial' submission

[Tobias-Ternent]

Currently it is possible to include 'result' files in a 'partial' submission. This is not allowed and should be prevented.

[edeutsch]

I am startled by this. Why would we want to disallow result files ever? Surely result files should be required for a partial submission. It is sad that they cannot be fully read by the repository, but one may presume that some interested party might be able to read and use them. And perhaps someday the repository might be able to go back and read them. And surely they should be archived in any case. Am I misunderstanding?

From: Tobias Ternent [mailto:notifications@github.com] Sent: Thursday, October 29, 2015 7:23 AM To: proteomexchange/px-submission-tool < px-submission-tool@noreply.github.com> Subject: [px-submission-tool] Prevent result files to be included in 'partial' a submission (#22)

Currently it is possible to include 'result' files in a 'partial' submission. This is not allowed and should be prevented.

— Reply to this email directly or view it on GitHub https://github.com/proteomexchange/px-submission-tool/issues/22.[image: Image removed by sender.]

[Tobias-Ternent]

Hi Eric,

I think may have misunderstood what I had meant. We classify PRIDE XML or mzIdentML as 'result' files with the px submission tool. These are supposed to be for 'complete' submissions only. So the tool should prevent a user from adding 'result' files to a 'partial' submission.

'Partial' submissions still have to have identification files included as 'search' data along with the 'raw' data. Sorry for any confusion about this.

In the future, if 'result' files can be generated for a particular 'partial' project, then it can be updated to be 'complete' through a 'resubmission' as long as the project is still private. If such a project was public, then perhaps a new submission for reanalysis data would be best.

[edeutsch]

Ah, I think I see. If there is a ‘result’ file present, then it should be classified as complete by definition, not partial. I conflated ‘result’ files and ‘search’ files.

Thanks,

Eric

From: Tobias Ternent [mailto:notifications@github.com] Sent: Thursday, October 29, 2015 7:51 AM To: proteomexchange/px-submission-tool Cc: Eric Deutsch Subject: Re: [px-submission-tool] Prevent result files to be included in a 'partial' submission (#22)

Hi Eric,

I think may have misunderstood what I had meant. We classify PRIDE XML or mzIdentML as 'result' files with the px submission tool. These are supposed to be for 'complete' submissions only. So the tool should prevent a user from adding 'result' files to a 'partial' submission.

'Partial' submissions still have to have identification files included as 'search' data along with the 'raw' data. Sorry for any confusion about this.

In the future, if 'result' files can be generated for a particular 'partial' project, then it can be updated to be 'complete' through a 'resubmission' as long as the project is still private. If such a project was public, then perhaps a new submission for reanalysis data would be best.

— Reply to this email directly or view it on GitHub https://github.com/proteomexchange/px-submission-tool/issues/22#issuecomment-152203658 .

[mbdebian]

This is already implemented according to what I've seen in the code here, please, see screen capture as well.