[Bioc-devel] Best Practices for Renaming S4 Slots

Message received. I will leave that branch for later. Is this information available on the Bioconductor website at all? It would have been useful to find out sooner.

Best,
Chris

-----Original Message-----
From: Bioc-devel <bioc-devel-bounces at r-project.org> On Behalf Of Chris Eeles
Sent: October 15, 2021 1:10 PM
To: Herv? Pag?s <hpages.on.github at gmail.com>; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Best Practices for Renaming S4 Slots

Thanks Herve,

I actually got the updateObject method working after sending this email, but thanks for the information. Maybe it is worth adding a section on this topic to the Bioconductor developer section?

Unfortunately, I was unaware that the start of development cycle was the best time to implement this change. I am currently planning to have this done for the 3.14 release.

I am introducing new accessors as well but keeping the old ones for backwards compatibility using aliases.

How discouraged are slot name changes in a release? A lot of the changes on our road map require the slots to be renamed so it would significantly delay required features if I were to wait.

I plan to put in the work so that those using accessors shouldn't notice a difference.

Best,
Chris

-----Original Message-----
From: Herv? Pag?s <hpages.on.github at gmail.com>
Sent: October 15, 2021 12:39 PM
To: Chris Eeles <christopher.eeles at outlook.com>; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Best Practices for Renaming S4 Slots

Hi Chris,

There was some formatting issues with my previous answer so I'm sending it again. Hopefully this time the formatting is better. See below.

On 14/10/2021 13:08, Chris Eeles wrote:

Hello BioC community,

I am the lead developer for the CoreGx, PharmacoGx, RadioGx and ToxicoGx packages. We have recently been working on major updates to the structure of a CoreSet, which is inherited by the main class in all three of the other packages listed.

While making these changes, we would like to rename some CoreSet slots to increase the amount of code that can be refactored into CoreGx, simplifying maintenance and development of inheriting packages in the future.

The slot names and their accessors will be made more generic, for example the 'cell' slot will become 'sample' to allow a CoreSet derived class to store Biological model systems other than cancer cell lines. Similarly, 'drug' or 'radiation' slots in inheriting packages will be replaced with a 'treatment' slot in the CoreSet. This will allow us to simplify inheritance, removing much redundant code from the inheriting packages and setting us up to integrate other lab packages, such as Xeva for PDX models, into the general CoreSet infrastructure.

I took a brief look through the Bioconductor developer documentation but didn't see anything talking about best practices for renaming slots.

It is easy enough to make the code changes, but my major concern is being able to update existing objects from these packages to use the new slot names.

I am aware of the updateObject function in BiocGenerics, but tried using it to update some example data in CoreGx without success.

Is this the proper function to use when you wish to update an S4 object whose class definition has been modified? If not, is there existing infrastructure for accomplishing this task?

Yes updateObject() is the proper function to use but the function has no way to guess how to fix your objects. The way you tell it what to do is by implementing methods for your objects.

For example if you renamed the 'cell' slot -> 'sample', your
updateObject() method will be something like this:


setMethod("updateObject", "CoreSet",
      function(object, ..., verbose=FALSE)
      {
          ## The "cell" slot was renamed -> "sample" in CoreGx_1.7.1.
          if (.hasSlot(object, "cell")) {
              object <- new("CoreSet",
                            sensitivity=object at sensitivity,
                            annotation=object at annotation,
                            molecularProfiles=object at molecularProfiles,
                            sample=object at cell,
                            datasetType=object at datasetType,
                            perturbation=object at perturbation,
                            curation=object at curation)
              return(object)
          }
          object
      }
)

The best time to do this internal renaming is at the beginning of the BioC 3.15 development cycle (i.e. right after the 3.14 release).

If in the future, other slots get renamed or added, you'll need to modify the updateObject() method above like this:

setMethod("updateObject", "CoreSet",
      function(object, ..., verbose=FALSE)
      {
          ## The "cell" slot was renamed -> "sample" in CoreGx_1.7.1.
          if (.hasSlot(object, "cell")) {
              object <- new("CoreSet",
                            sensitivity=object at sensitivity,
                            annotation=object at annotation,
                            molecularProfiles=object at molecularProfiles,
                            sample=object at cell,
                            datasetType=object at datasetType,
                            perturbation=object at perturbation,
                            titi=object at curation)  # use "titi" here too!
              return(object)
          }
          ## The "curation" slot was renamed -> "titi" in CoreGx_1.9.1.
          if (.hasSlot(object, "curation")) {
              object <- new("CoreSet",
                            sensitivity=object at sensitivity,
                            annotation=object at annotation,
                            molecularProfiles=object at molecularProfiles,
                            sample=object at sample,  # use "sample" here!
                            datasetType=object at datasetType,
                            perturbation=object at perturbation,
                            titi=object at curation)
              return(object)
          }
          object
      }
)

And so on...

Hope this helps,
H.

Any tips for implementing slot renaming, as well as links to existing documentation or articles on the topic would be appreciated.

Best,
---
Christopher Eeles
Software Developer
BHK
Laboratory<https://na01.safelinks.protection.outlook.com/?url=http%3A%
2F%2Fwww.bhklab.ca%2F&amp;data=04%7C01%7C%7C170e009bdbda4e7f182308d990
000468%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637699152031882488
%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6I
k1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=eu7jm6LiWISZ01etllrdipTAkVtI4a7
rZumELnt0siI%3D&amp;reserved=0> Princess Margaret Cancer
Centre<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%
2Fwww.pmgenomics.ca%2Fpmgenomics%2F&amp;data=04%7C01%7C%7C170e009bdbda
4e7f182308d990000468%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C6376
99152031882488%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2l
uMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&amp;sdata=g8gXrDgyJ5YRHdiBv
q77WiDkCgWcYhWWW9R7OWKMxqw%3D&amp;reserved=0>
University Health
Network<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%
2Fwww.uhn.ca%2F&amp;data=04%7C01%7C%7C170e009bdbda4e7f182308d990000468
%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C637699152031882488%7CUnk
nown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWw
iLCJXVCI6Mn0%3D%7C1000&amp;sdata=IJKtucTmctj0z227jGpqnBeZ0D9ruvODNLkmT
QBdX%2Bs%3D&amp;reserved=0>


	[[alternative HTML version deleted]]

--
Herv? Pag?s

Bioconductor Core Team
hpages.on.github at gmail.com