Can't import parts any more

[jakebeal]

3.0 prerelease, trying to import a CDS: when I select the CDS, the part edit dialogue disappears and I'm back to the top-level screen, with nothing having appeared in the part information from the attempted import.

[cjmyers]

Unable to reproduce. Can you perhaps provide the file for the part you tried to import?

[jakebeal]

It wasn't a file, it was importing from the registry.

[cjmyers]

Hmm, strange. I cannot reproduce this. I just built a design and imported parts from synbiohub.org igem collection. Which registry/collection were you trying to import from?

On Feb 6, 2018, at 6:21 PM, Jacob Beal notifications@github.com wrote:

It wasn't a file, it was importing from the registry.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/SBOLDesigner/issues/246#issuecomment-363623281, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD9_S7un-V8_qJgNTj6MUt1ornjT-Eks5tSPqIgaJpZM4R7XUg.

[jakebeal]

I am trying to import BBa_M45215 from the synbiohub iGEM registry into the CDS of the attached SBOL file (renamed to .txt so github will accept it as an attachment)

red.sbol.txt

[cjmyers]

Ok, I can reproduce this now. So, you imported the file rather than directly from the registry. @michael13162 when import, it asks to me to select what to import from the file, then it does not actually import the information.

[jakebeal]

I first imported the file, then tried to fill in the blank part from the registry.

[cjmyers]

Hmm, now I'm not sure I'm understanding. I just looked into your file, and your CDS does indeed not have a sequence, so I think I was wrong when I said it was not imported from the file. It was imported as a part without a sequence, which is actually the correct behavior.

Now, if you then try to import BBa_M45215 from the registry, it will overwrite the previously assigned part that you loaded from the file, at least that is what happens for me. This is intended. There is not currently a way to "merge" information. If what you are trying to do is to obtain the sequence from BBa_M45215 and attach it to your new part id, then the approach would be download the part from the registry, then edit the part and agree when you save to move it into your local namespace.

Perhaps I'm still missing the steps you took.

[jakebeal]

I do want BBA_M45215 to overwrite, and this is not what happens for me. When I run the current pre-release 3, it simply fails and leaves me with the same blank part.

[cjmyers]

Hmm, this one is very strange. I cannot reproduce. I wonder if I’m still missing some step that you are taking. Are you pulling this part from SynBioHub or Built-in Parts? If you don’t first associate from a file, can you associate from the registry?

My guess is it might be related to the namespace issues you have been having, since we don’t typically change them on the fly. There does appear to be an issue that if you change the domain in the preferences, that I’ve had to restart to get it to register properly. Maybe that is related, but I’m not sure.

On Feb 7, 2018, at 1:12 PM, Jacob Beal notifications@github.com wrote:

I do want BBA_M45215 to overwrite, and this is not what happens for me. When I run the current pre-release 3, it simply fails and leaves me with the same blank part.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/SynBioDex/SBOLDesigner/issues/246#issuecomment-363895602, or mute the thread https://github.com/notifications/unsubscribe-auth/ADWD9zmzzSIUPCGnDt5D_fNQREbDJ7NRks5tSgO0gaJpZM4R7XUg.

[michael13162]

If Chris is right about this being related to the namespace issue, it may be fixed now since https://github.com/SynBioDex/SBOLDesigner/issues/244 is potentially fixed.

[jakebeal]

This now imports the part correctly, but then automatically closes not just the import window but also the editing window, which is jarring and a violation of UI principles. Then I have to reopen the part editing window in order to finish my editing.

[cjmyers]

Agreed. @michael13162 is this a small change or a large change? If small, please execute it before the release of 3.0 otherwise you can delay to 3.1.

[michael13162]

Given the semantics of importing a part, it probably makes more sense to use the magnifying glass (search) button after highlighting a part in the canvas. To this end, I can remove the "import registry part" button in the PartEditDialog. Do you want me to do this? The button is there purely for convenience, so maybe it's not worth having if the result is a violation of UI principles. It may also be simpler/more intuitive to just have one correct way of doing things.

[cjmyers]

No, we need to keep the buttons here. Can you just leave the edit window open? What exactly makes this difficult?

[michael13162]

Currently, the only way to have a CD in the PartEditDialog persist in the SBOLDocument is if "save" is clicked. However, since a part imported from SynBioHub is not in the user's namespace, saving is not allowed. Therefore, it might make sense to not initially give the user the ability to edit until it's completely persisted in the SBOLDocument?

[cjmyers]

I actually concur with this. If the edit part dialog does not close, it would be strange, since you are not supposed to edit parts that you do not own (not in your namespace). The import from registry button is mostly on the edit page, since we often end up there by accident. We meant to click import from registry, but accidentally clicked on edit, so rather than making you close and click on import, it is convenient to have this button here to allow you to import from registry.