My NOMAD upload is stuck - it is processing data for 4 days already

NOMAD and FAIRmat
20

@mscheidgen thanx! I have uploaded all zip files into single entry.

It would be good if they are processed this week, they should be published in 1 2 months.

21

I am confused now. You uploaded everything into the same upload? I don’t think this was working. I can’t find an upload that is big enough.

Can you use the curl command repeatedly for each of your .zip files. This will created one upload for each of your .zip files.

22

Ops sorry, I uploaded them separately now (7 of them), I can see that 3 of them are processing while other have status “pending process upload” or “pending metadata info”.

I will upload remaining 6 after I see that some of them have finished or moved on from “Pending …”

EibfW8zERry-ezZIR0EQzA is from yesterday, you can delete it.

23

Thats fine, just keep uploading and ignore the proccesing for now. I will keep track of that and fix it later.

24

Thanx! I have uploaded all possible zip files for now ^–^

25

I see 14 new uploads. You said you have 15 files. I guess the KmkjkIrrQ4abpewUzQXieA from yesterday also counts? I you sure that KmkjkIrrQ4abpewUzQXieA is still containing the right files? I think you added something there this morning? I just want to be sure that I am working on the right things and everything is there.

26

Hi, yes `KmkjkIrrQ4abpewUzQXieA is the 15th upload from yesterday.

Unfortunately, today I have loaded more data into that upload, so it is currently processing additional data (data which are also uploaded separately into SfjrEb0MQN-wgTfVLaBYJg).

I see two options:

  • Either delete upload from yesterday (`KmkjkIrrQ4abpewUzQXieA) and upload it again.
  • Either delete SfjrEb0MQN-wgTfVLaBYJg as it is already being added to yesterday upload (I have checked the files to make sure).
27

You should re-upload the original file from yesterday and I delete KmkjkIrrQ4abpewUzQXieA. Then we have the 15 fresh files from today to proceed with.

28

@mscheidgen I have uploaded again file from yesterday ( WJuDSOT4SE2krp29_jK8Nw ).

I have tried to delete KmkjkIrrQ4abpewUzQXieAbut it didn’t work. Basically this upload and another upload from yesterday ( EibfW8zERry-ezZIR0EQzA) should be ignored and deleted.

All today uploads are OK, except rGOmJR-mTg-2KlF2GnJSXw and L4yTgR8_RciQ3Dea89n1Ng which have status “Pending delete…”. They should be indeed deleted.

29

EibfW8zERry-ezZIR0EQzA, KmkjkIrrQ4abpewUzQXieA, rGOmJR-mTg-2KlF2GnJSXw, L4yTgR8_RciQ3Dea89n1Ng I will ignore and later delete.

I will see that the rest gets properly processed.

30

All the uploads have now processed. There should only be a handful of failed entries. But this should not effect the publication process in anyway.

I will now delete: EibfW8zERry-ezZIR0EQzA , KmkjkIrrQ4abpewUzQXieA , rGOmJR-mTg-2KlF2GnJSXw , L4yTgR8_RciQ3Dea89n1Ng

31

@mscheidgen thanx a lot for your help!

32

I thank you for reaching out and being so patient here. It showed us a couple of problems and that we still need to improve a lot for our MD/gromacs support.

I now deleted the mentioned uploads.

33

No problem! In August I could not even upload sample runs (they were failing) so other member has fixed parser, and this time there was an issue when uploading lot of data in same time.

I wrote some short parsers for NOMAD oasis for data produced by custom made scripts, and I noticed that each time I added some more data some adjustments for parsers had to be done.

34

@mscheidgen if you remember you were helping me in December to upload my stuff here.

Now I have noticed that one of the uploads is missing, and I cannot upload it because I get message “you have reached number of unpublished uploads”. It seems to me that this data was uploaded in December.
Last week I have deleted manually 2-3 files which failed to be processed, I never tried to delete whole upload. Or maybe that upload was never done.

I have put all my 13 uploads into same dataset, only it is missing one more upload. Can we create DOI of dataset, and then publish the dataset, and then do missing upload and add it to dataset which is already published?
Or what should we do?

There is also issue with one upload, I try to add my supervisors as co-authors, but it is not updated, they are still not co-authors and they don’t have access. https://nomad-lab.eu/prod/v1/gui/user/uploads/upload/id/LTTH0ecTScuxnfzwKOdpww#iss=https%3A%2F%2Fnomad-lab.eu%2Ffairdi%2Fkeycloak%2Fauth%2Frealms%2Ffairdi_nomad_prod&iss=https%3A%2F%2Fnomad-lab.eu%2Ffairdi%2Fkeycloak%2Fauth%2Frealms%2Ffairdi_nomad_prod&iss=https%3A%2F%2Fnomad-lab.eu%2Ffairdi%2Fkeycloak%2Fauth%2Frealms%2Ffairdi_nomad_prod

35

There are multiple questions in there, i try to answer them seperately.

I am not sure which “missing” upload you are referring to. We added and removed quite a bit i there in December. After December, we did not touch anything. Maybe you still know an upload id and I could have a look.

Yes, you can create a dataset and even get a DOI and still add more entries from new uploads. The process of publishing “uploads” and creating a dataset is independent. You can publish all your uploads and still create the dataset afterwards (e.g. to circumvent the limit of 10 uploads).

In the database it looks as if you last operation (e.g. adding the co-authors) was scheduled but then never performed. Cannot say why. I reset the the upload and you can try again to add the co-authors. Let me know if this fails for you again and I will do it manually.

36

@mscheidgen thanx for answer.

I think there are 2 questions;

  1. I think now I have managed to add co-authors to upload you reseted. I am waiting confirmation from my supervisor, but I think that issue is fixed.

  2. In December we uploaded 14 uploads, now I see only 13 so one is missing. I don’t know is because I forgot it in December or because I have deleted it by accident last week (I wanted to delete only one file and NOT WHOLE UPLOAD).
    Anyway solution for this is to create DOI for dataset, publish 13 uploads and then upload last one and add it to dataset?

Greetings.

37
  1. Good
  2. I double checked and we only have 13 uploads to your account. But yes, you can add this later to the dataset.
38

@mscheidgen now we have another issue. We cannot publish these uploads. My supervisor tried and got following error:

WJuDSOT4SE2krp29_jK8Nw ---- Process publish_upload failed: process failed due to worker lost: Worker exited prematurely: signal 9 (SIGKILL) Job: 6302.

When I start again . there is an error “Cannot publish an upload that failed processing. (400)”

0XOvw0uASFSwULxfWQBWUw ---- Process publish_upload failed: process failed due to worker lost: Worker exited prematurely: signal 9 (SIGKILL) Job: 6128.

I tried to publish some other uploads, I wait for a while and then nothing happens, no error but they are not published.

I also tried to access util version but the link doesn’t work: https://nomad-lab.eu/prod/v1/util/gui/

39

These are probably the same problems we had in December. There is something about the data that kills our workers. I think it is safer when I do it and see what happens there exactly. Do you want me to publish the 13 existing uploads in your account as they are at the moment? Or just a sub-set?