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bmrb-io / BMRB-API

BMRB API server and client implementations.
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Software descriptions saveframe should not have default value for sf_framecode #46

Open jonwedell opened 5 years ago

jonwedell commented 5 years ago

Otherwise the enumerations are not suggested.

elulrich commented 5 years ago

I guess I am confused as usual. The Sf_framecode is different from the software name tag. In entries, 'software_1', 'software_2', etc. are often used as Sf_framecodes. However, for the software name, there has been an enumerated list. Now for a deposition, it would be nice if they could use an actual software name for the Sf_framecode, but the Sf_framecode is not meant for querying so consistency is not required. The software name tag does need to be remediated for consistency and this has been worked on, but I am not sure if the work was ever implemented.

Eldon

On 11/1/18 10:58 AM, Jon Wedell wrote:

Otherwise the enumerations are not suggested.

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dmaziuk commented 5 years ago

Also keep in mind that summary page scripts look for "sample_1", "sample_conditions_1" and who knows what else (those two are the ones I know of, in metabolomics summary pages), so there may be side effects to dropping those defaults.

jonwedell commented 5 years ago

Also keep in mind that summary page scripts look for "sample_1", "sample_conditions_1"

I wouldn't change the default for all saveframe categories, just this specific one (and only in the context of creating a "new template deposition").

@elulrich - The current state of the dictionary is that the tag _Software.Sf_framecode is a mandatory field, with the ADIT description Software name. Furthermore, the tag is enumerated with a list of software package names. (At least one of them have a space in the name, so that enumeration isn't valid.)

I know we discussed before that ADIT was taking the Software.Name tag and converting it into an acceptable value for the "Software.Sf_framecode" tag. But apparently in the dictionary Software.Name is specified as hidden in the deposition interface. I don't believe we had yet decided on how to handle these sorts of auto-generated Sf_framecode tags.

Do we:

  1. Pre-fill all Sf_framecode tags with just category_name_1 and category_name_2 and so on and capture the real information from the user in a different tag (for example, Software.Name)?
  2. Do it as ADIT did. (Requires updating the dictionary and creating a list of which saveframe categories have this "auto sf_framecode generation" code such that it can be implemented on the new server)?
  3. Other ideas?

My preference is option 1.

jonwedell commented 5 years ago

Also this is related to issues 3 and 16 on the InstantDep Github repo.

dmaziuk commented 5 years ago

There must be an override somewhere as Software name comes up in the interface, with enumeration drop-down, and it's one of 3 required fields in the entire software section.

Also note that there are no saveframes in ADIT, there's only various ID tags.