Improve preparation tab in GUI

[antgonza]

After discussing with @mestaki, we thought it would be a good idea to reformat the prep information tab to make it more helpful.

As background we currently display:

A. If the prep info has been submitted to EBI-ENA (the logo) and how many samples were submitted; nothing if it hasn't
B. The preparation name - ID - visibility status
C. The raw artifact type and ID
D. The last children name and artifact type

What about having:
A. If the prep info has been submitted to EBI-ENA (the logo) and how many samples were submitted; and if it hasn't, the total number of samples in the prep
B. The preparation name (ID) - visibility - (total artifacts in the preparation)
C. Initial creation time
D. Last time it was updated

@justinshaffer, @adswafford, any suggestions?

[justinshaffer]

Hello! Great idea! Here are my suggestions:

What about having: A. If the prep info has been submitted to EBI-ENA (the logo) and how many samples were submitted; and if it hasn't, the total number of samples in the prep B. The preparation name (ID) - visibility - (total artifacts in the preparation) C. Initial creation time D. Last time it was updated

For A, it would be good to know the total samples in the prep regardless of if the data were submitted to EBI-ENA, so I suggest to include this value in both cases, perhaps like this: ENA (382) Total (382) Also for A, it would be great to have a column added to the prep info file that indicates which samples were submitted to EBI-ENA, and perhaps also the EBI-ENA accession number as the value for each sample in that column. This would only happen if/once the data are submitted to EBI-ENA. For C and D, I like the original and the updated - can we include both? Justin

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-- Justin Shaffer, PhD IRACDA Postdoctoral Fellow Rob Knight Group Department of Pediatrics, School of Medicine University of California, San Diego justinshafferbio.wordpress.com

[antgonza]

Thank you for the suggestions. We can add both original/new C/D but IMOO the original C/D are not actually useful as this information was planned when we only had one kind of processing and a single final biom artifact but now that we have multiple final artifacts, I actually find it confusing; thus, wondering what's your use case? Note that is pretty easy to keep both.

[wasade]

Both C/D are useful for examining AG preps. It would be really helpful to be able to sort them as well, either by name, prep ID or chronologically

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On Nov 24, 2020, at 1:46 PM, Antonio Gonzalez ***@***.***> wrote: Thank you for the suggestions. We can add both original/new C/D but IMOO the original C/D are not actually useful as this information was planned when we only had one kind of processing and a single final biom artifact but now that we have multiple final artifacts, I actually find it confusing; thus, wondering what's your use case? Note that is pretty easy to keep both. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/biocore/qiita/issues/3054*issuecomment-733251630__;Iw!!Mih3wA!ScUKyYs-VwK43QWD13Dd5Q4sCKZMSVHimSWW4tAUi3rYWFd_qbtgFtKD3cQV-Nme_ipK$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AADTZMQX4E4FNK7KW34I2OTSRQSUDANCNFSM4UBMH5AA__;!!Mih3wA!ScUKyYs-VwK43QWD13Dd5Q4sCKZMSVHimSWW4tAUi3rYWFd_qbtgFtKD3cQV-Kf7pzOA$>.

[justinshaffer]

Hi Antonio, I agree with you as well as Daniel - they are mostly useful for projects like the AGP / EMP where we create preps for special use cases - however I can see how recording the prep ID could also be used for this - I've just gotten used to using C / D. Justin On Tue, Nov 24, 2020 at 1:58 PM Daniel McDonald <notifications@github.com> wrote:

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Both C/D are useful for examining AG preps. It would be really helpful to be able to sort them as well, either by name, prep ID or chronologically > On Nov 24, 2020, at 1:46 PM, Antonio Gonzalez ***@***.***> wrote: > > > Thank you for the suggestions. We can add both original/new C/D but IMOO the original C/D are not actually useful as this information was planned when we only had one kind of processing and a single final biom artifact but now that we have multiple final artifacts, I actually find it confusing; thus, wondering what's your use case? Note that is pretty easy to keep both. > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub < https://urldefense.com/v3/__https://github.com/biocore/qiita/issues/3054*issuecomment-733251630__;Iw!!Mih3wA!ScUKyYs-VwK43QWD13Dd5Q4sCKZMSVHimSWW4tAUi3rYWFd_qbtgFtKD3cQV-Nme_ipK$>, or unsubscribe < https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AADTZMQX4E4FNK7KW34I2OTSRQSUDANCNFSM4UBMH5AA__;!!Mih3wA!ScUKyYs-VwK43QWD13Dd5Q4sCKZMSVHimSWW4tAUi3rYWFd_qbtgFtKD3cQV-Kf7pzOA$ >. > — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3054 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADSDCGCM6ILSCWVOEFDRW73SRQUADANCNFSM4UBMH5AA> .

-- Justin Shaffer, PhD IRACDA Postdoctoral Fellow Rob Knight Group Department of Pediatrics, School of Medicine University of California, San Diego justinshafferbio.wordpress.com

[adswafford]

I like the sorting option; for something as massive as 10317 would it make sense to have them grouped in some way as well based on sandbox, private, public and submitted?

For original D, I agree that it's a useful shorthand to know whether the prep has been processed. I have an idea in my head that maybe instead of the latest artifact name (in addition to the new D info), could we have some sort of color-code or progress bar based on prep type?
Raw files: 1 tick
Processed non-biom files: 2 ticks
Biom tables: 3 ticks

And could there be some sort of color indicator as to which have running processes?

[antgonza]

I think I understand how old C/D are being used and I think having the "total number artifacts in the
preparation" should work the same - without having all those names there, no? Basically, 0 it hasn't been processed, 1 only has raw data, 2-3 it has been demuxed or done some QC, 4+ it has been deblured or bowtie2-woltka ... @justinshaffer, @wasade @adswafford ?

[adswafford]

Yes, but then we have to teach a code => information system that is less intuitive. Can you do the same, but instead of the number have the progress bar with ticks representing numbers?

[antgonza]

Got it! Makes sense; this can also help in the EBI-ENA submission by saying in the documentation that we can only submit things with at least 3 ticks.

Proposed tab (up to now):
A. # samples [if submitted to EBI: logo (samples)]
B. The preparation name (ID) - visibility
C. Ticks with (raw files: 1 tick, processed non-biom files: 2 ticks, biom tables: 3 ticks - if direct biom upload no ticks)
D. Initial creation timestamp
E. Last update timestamp

The list should be sorted by name, prep ID or chronologically

[adswafford]

This looks good to me. @wasade @justinshaffer any last suggestions/edits?

[wasade]

👍, thank you!!

[justinshaffer]

Looks good to me. Thanks!

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On Wed, Nov 25, 2020 at 10:09 AM Daniel McDonald ***@***.***> wrote: 👍, thank you!! — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3054 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADSDCGH73S4CE3IECNYLFPDSRVB7NANCNFSM4UBMH5AA> .

-- Justin Shaffer, PhD IRACDA Postdoctoral Fellow Rob Knight Group Department of Pediatrics, School of Medicine University of California, San Diego justinshafferbio.wordpress.com

[mestaki]

I'm really liking all the ideas proposed here! Being able to sort through these by date created, last updated, or file-name would be super useful. I propose the default view be sorted with date-created.
Here is how I think the current proposal would look like? Two variations with an added [ok to submit] box in the second one. If this gets too noisy, there's a lot of empty real estate on the main page for when you actually click on the Preps file. So if needed we can expand on some details there, for example, if a prep is not ok to submit, then it can be explained why in the main space instead.

Var1

Var2

[justinshaffer]

Var2 looks good to me!

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On Wed, Nov 25, 2020 at 12:51 PM Bod ***@***.***> wrote: I'm really liking all the ideas proposed here! Being able to sort through these by date created, last updated, or file-name would be super useful. I propose the default view be sorted with date-created. Here is how I *think* the current proposal would look like? Two variations with an added [ok to submit] box in the second one. If this gets too noisy, there's a lot of empty real estate on the main page for when you actually click on the Preps file. So if needed we can expand on some details there, for example, if a prep is not ok to submit, then it can be explained why in the main space instead. Var1 [image: image] <https://user-images.githubusercontent.com/17439092/100280300-d12e6300-2f1c-11eb-9e30-a155921a97e8.png> Var2 [image: image] <https://user-images.githubusercontent.com/17439092/100280310-d8ee0780-2f1c-11eb-96c9-e0c299d44d9a.png> — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#3054 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ADSDCGCA2ZN3KCIMWBODGF3SRVU6RANCNFSM4UBMH5AA> .

-- Justin Shaffer, PhD IRACDA Postdoctoral Fellow Rob Knight Group Department of Pediatrics, School of Medicine University of California, San Diego justinshafferbio.wordpress.com

[ackermag]

Do you need any input from me? Gail On Wed, Nov 25, 2020 at 12:56 PM Justin Shaffer <notifications@github.com> wrote:

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Var2 looks good to me! On Wed, Nov 25, 2020 at 12:51 PM Bod ***@***.***> wrote: > I'm really liking all the ideas proposed here! Being able to sort through > these by date created, last updated, or file-name would be super useful. I > propose the default view be sorted with date-created. > Here is how I *think* the current proposal would look like? Two > variations with an added [ok to submit] box in the second one. If this gets > too noisy, there's a lot of empty real estate on the main page for when you > actually click on the Preps file. So if needed we can expand on some > details there, for example, if a prep is not ok to submit, then it can be > explained why in the main space instead. > > Var1 > [image: image] > < https://user-images.githubusercontent.com/17439092/100280300-d12e6300-2f1c-11eb-9e30-a155921a97e8.png > > > Var2 > [image: image] > < https://user-images.githubusercontent.com/17439092/100280310-d8ee0780-2f1c-11eb-96c9-e0c299d44d9a.png > > > — > You are receiving this because you were mentioned. > Reply to this email directly, view it on GitHub > <#3054 (comment)>, or > unsubscribe > < https://github.com/notifications/unsubscribe-auth/ADSDCGCA2ZN3KCIMWBODGF3SRVU6RANCNFSM4UBMH5AA > > . > -- Justin Shaffer, PhD IRACDA Postdoctoral Fellow Rob Knight Group Department of Pediatrics, School of Medicine University of California, San Diego justinshafferbio.wordpress.com — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#3054 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAPL3ADM5V53GLFMWLGAB5TSRVVO3ANCNFSM4UBMH5AA> .

-- Gail Ackermann Knight Lab UCSD glackermann@ucsd.edu <ackermag@ucsd.edu>