Order of development Sequencing Workflow before bulk import?

[rintoult]

Hi All,

I had a thought after the demo of the sequencing workflow last week, I would have shared it in a meeting but since it is two weeks before our next meeting I would like to bring it up here.

I couldn't find Dieter to add him to this conversation - so if he needs to be included could someone please add him.

What I am wondering about is if the bulk import of new material samples is currently being developed? It was nice to see that the sequencing workflow is being addressed but in the priority of us being able to get data in and handle it I think that sequencing should come after us being able to bulk import original material samples. This has been an ongoing issue - for us to be able to test the system and also to prove that it will be able to support our day to day work. We can't sequence things until they are in DINA and right now we have no reasonable way to add things to the database.

Please let us know where we are at in developing a bulk import system, and when we might expect to be able to test that out.

I invite the other collection managers to agree or disagree with me on this one, but I think this feature/function should be of highest priority. We need this in order to support any testing of future functions and for us to be supportive of the system when people outside the development process ask us how it is going.

Tara

[ron-reade]

Thanks Tara, I have just forwarded this to Dieter for now, we are in a seminar/workshop for the next two days. Cheers Ron

From: Tara Rintoul @.> Sent: Wednesday, October 26, 2022 8:41 AM To: AAFC-BICoE/dina-planning @.> Cc: ron-reade @.>; Assign @.> Subject: [AAFC-BICoE/dina-planning] Order of development Sequencing Workflow before bulk import? (Issue #344)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. ATTENTION: Ce courriel provient de l’extérieur de l’organisation. Ne cliquez pas sur les liens et n’ouvrez pas les pièces jointes à moins que vous ne reconnaissiez l’expéditeur et que vous sachiez que le contenu est sûr.

Hi All,

I had a thought after the demo of the sequencing workflow last week, I would have shared it in a meeting but since it is two weeks before our next meeting I would like to bring it up here.

I couldn't find Dieter to add him to this conversation - so if he needs to be included could someone please add him.

What I am wondering about is if the bulk import of new material samples is currently being developed? It was nice to see that the sequencing workflow is being addressed but in the priority of us being able to get data in and handle it I think that sequencing should come after us being able to bulk import original material samples. This has been an ongoing issue - for us to be able to test the system and also to prove that it will be able to support our day to day work. We can't sequence things until they are in DINA and right now we have no reasonable way to add things to the database.

Please let us know where we are at in developing a bulk import system, and when we might expect to be able to test that out.

I invite the other collection managers to agree or disagree with me on this one, but I think this feature/function should be of highest priority. We need this in order to support any testing of future functions and for us to be supportive of the system when people outside the development process ask us how it is going.

Tara

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[cgendreau]

Bulk importing in what sense? What would be the source? If the source is SeqDB yes, this is part of data migration.

[rintoult]

In the sense that I receive 15 new parent material samples from a client to be added to the collection. How do I upload the data I receive from them. Not data migration, data creation.

And not 1 by 1 in the GUI.

[cgendreau]

It depends on the format and where the records are coming from. If the client is AAFC and the records are in DINA there is nothing special to do, you will simply use them as a source to do your work.

For things that are from outside, I would need to see the format of the data.

[rintoult]

Data from outside, not in DINA format will be unknown unless we have a format that we provide. For example here is how I have received data the last time material was being added. This is based on SeqDB templates since that is what we do now. D2022-012_LobnaDataProvided.xlsx

[rintoult]

To use an analogy - Where is the loading dock for DINA and how does it work?

Right now in the GUI we have a 1 person at a time elevator.

Tara

[banchinic]

We also need to bulk import data in DINA. We use SeqDB's bulk import spreadsheet right now (which we modify in Excel). We've mentioned this from the beginning of the DINA meetings. I thought it was in scope to develop a similar way to bulk import into DINA soon? It is the reason why I haven't added our data into DINA yet because it would take too long to manually add it but we will also need that function in the future when everything is already into DINA. We are taking 300 soil samples every summer right now for the Soil Biodiversity Project. I don't want to manually add 300 material samples and all the related metadata into DINA.

[rintoult]

Another example of how I receive data for deposit to the collection and addition to the database. D2022-015_locationcorrectionRedhead isolates 1987 (002).docx

[ssbilkhu]

We can plan to discuss these items at the next meeting on Nov 3. We will show what is possible with the new form template and "bulk add" via the GUI. Additionally there is allocated time to work on spreadsheet support which we can prioritized to happen sooner then we planned in the roadmap for the rebaseline work.

[ron-reade]

Thanks Satpal, Excited to see what you guys have been working on. Cheers Ron

From: Satpal Bilkhu @.> Sent: Friday, October 28, 2022 9:25 AM To: AAFC-BICoE/dina-planning @.> Cc: ron-reade @.>; Assign @.> Subject: Re: [AAFC-BICoE/dina-planning] Order of development Sequencing Workflow before bulk import? (Issue #344)

CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. ATTENTION: Ce courriel provient de l’extérieur de l’organisation. Ne cliquez pas sur les liens et n’ouvrez pas les pièces jointes à moins que vous ne reconnaissiez l’expéditeur et que vous sachiez que le contenu est sûr.

We can plan to discuss these items at the next meeting on Nov 3. We will show what is possible with the new form template and "bulk add" via the GUI. Additionally there is allocated time to work on spreadsheet support which we can prioritized to happen sooner then we planned in the roadmap for the rebaseline work.

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