Collections are inscrutable

[jakebeal]

I would like to combine five devices into one collection, cannot figure out how to browse the contents of collections in SBOLDesigner

[cjmyers]

The procedure should be as follows but will only work completely in 3.0:

1. Create a new SBOL document (far left icon)
2. Build your first device be sure to give it a unique id using pencil icon.
3. Save your current design (fifth icon)
4. Upload your design to a SynBioHub instance selecting to create a new Collection.
5. Create a new part in this document (third icon)
6. Build your second device again with a new id.
7. Save your current design.
8. Upload your design to a SynBioHub instance selecting to add to an existing Collection.
9. Repeat for next 3 devices.
10. You should now be able to browse your new collection on SynBioHub in your private repository.

Would be great to create a video for this potentially very common use case. Also, we should add to SynBioHub a way to upload an entire working document rather than just the design being edited.

[jakebeal]

• The pencil icon is non-intuitive. I kept clicking on the "> Unnamed Part" button to try to name it and edit its information. Editing the selected part by double-clicking is quite intuitive to me --- I never even went looking for an icon. The "> Unnamed Part" button really invites a similar interaction.
• The "create a new part in this document" button implies the ability to create and manage collections in the document. It's even sort-of doing it.
• If I uploaded to SynBioHub and found that only some of the parts in the document had uploaded, I would be confused and frustrated. The common semantics of the button as we are trained from other applications are "save to cloud", not "export a small fragment to the cloud"
• Uploading to SynBioHub is misnamed right now, as "SBOL stack"

[cjmyers]

On Jan 16, 2018, at 4:58 PM, Jacob Beal ***@***.***> wrote: The pencil icon is non-intuitive. I kept clicking on the "> Unnamed Part" button to try to name it and edit its information. Editing the selected part by double-clicking is quite intuitive to me --- I never even went looking for an icon. The "> Unnamed Part" button really invites a similar interaction.

Agreed. Good suggestion.

The "create a new part in this document" button implies the ability to create and manage collections in the document. It's even sort-of doing it.

Indeed, we could create a Collection object in the working document that references all the parts you have built. We have not done this since SynBioHub does this for you, but it actually makes a lot of sense.

If I uploaded to SynBioHub and found that only some of the parts in the document had uploaded, I would be confused and frustrated. The common semantics of the button as we are trained from other applications are "save to cloud", not "export a small fragment to the cloud”

Agreed. We have had a lot of issues with coming to grips with the idea of working document and current design. Essentially the idea is more like say a workspace in eclipse that includes a bunch of projects. When you commit a project to SynBioHub, you are committing just the project you are working on and not your entire workspace. This enables you to commit things individually which has been my workflow, but I see the point of also being able to do a “bulk” upload. We can add another dialog or check box to ask you if you want to commit just the current design or the entire working document. MIchael: please also force a save before upload. I found that I would upload one, then start editing again and upload again for the 2nd device, but then realize that I never saved the first device!

Uploading to SynBioHub is misnamed right now, as "SBOL stack”

Thanks.

[michael13162]

Designs must now be saved before uploading to SynBioHub. I also found and fixed some bugs along the way. Should probably test more as well.

[cjmyers]

It does appear to be working.

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On Jan 25, 2018, at 11:28 AM, Michael Zhang ***@***.***> wrote: Designs must now be saved before uploading to SynBioHub. I also found and fixed some bugs along the way. Should probably test more before as well. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#222 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADWD99LaHQYfnioibqayrQgTCJQNL9dZks5tOMe-gaJpZM4RfsCl>.

[cjmyers]

Still need to do the following:

1. Add ability to edit part by clicking on the name in the left corner.
2. Add an option to the upload that allows the user to select to upload only the current working design. If checked, it is the current behavior, else it should upload the entire working document. The later should be the default.

As for creating a collection for the document, I think we can let SynBioHub handle that when the parts are uploaded.

[michael13162]

The user is now asked whether they want to upload the current design or working document. I've tested it, and it seems to be working. I think this is useful to always bring up since it makes it more clear what's being uploaded (people may assume the wrong thing and be confused/accidentally lose data).

[cjmyers]

I didn’t see this dialog. Is this checked in?

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On Jan 29, 2018, at 8:57 PM, Michael Zhang ***@***.***> wrote: The user is now asked whether they want to upload the current design or working document. I've tested it, and it seems to be working. I think this is useful to always bring up since it makes it more clear what's being uploaded (people may assume the wrong thing and be confused/accidentally lose data). — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#222 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADWD99-pMETFcK0C9u8lgpUMuG8Z-WjEks5tPpMzgaJpZM4RfsCl>.

[michael13162]

It is checked in. It should pop up whenever you go to upload something.

[cjmyers]

Ok, I got confused. I was running this from an earlier Jar. It is there. However, there are now a lot of windows to submit potentially. I still think a checkbox would be preferred, since it would avoid one window at least. Right now, to submit I ran into: 1) It is unnamed, do you want to change the name, said yes and edited the name. 2) It is not saved, do you want to save. Then asked Overwrite or New Version 3) Select repository 4) Was asked to login. 5) Was asked New Collection or Existing 6) Was asked for details about the collection. Now mixing this additional question into the mix. If you are doing this many times and answering the same each time, it will get to be a bit tedious. Perhaps okay for now, but we definitely need to figure out a way to combine several of these steps.

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On Jan 29, 2018, at 9:29 PM, Michael Zhang ***@***.***> wrote: It is checked in. It should pop up whenever you go to upload something. — You are receiving this because you were assigned. Reply to this email directly, view it on GitHub <#222 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/ADWD989FAX8TxbhoLb7ncJ3D-sKkJYZDks5tPpqhgaJpZM4RfsCl>.

[michael13162]

Edit part by clicking on the top left corner name is actually difficult because of 1) updating the internal SBOLDesigner data model and 2) refreshing the UI properly.