Stream: genomics/committers
Topic: Planning - Week of Oct 29-Nov 2
Kevin Power (Oct 29 2018 at 20:29):
Hi all - Just checking in on plans for this week. We have a couple of pending FHIR Core changes (vote Oct 30), but other IG changes as well. I might have some time this week, others? @Patrick Werner @James Jones ?
Jamie Jones (Oct 29 2018 at 20:32):
My Wednesday is looking pretty good, and might be able to squeeze some in tomorrow afternoon...
Kevin Power (Oct 30 2018 at 17:38):
OK, we approved the name change - anyone willing to take it on in the next couple of days?
Jamie Jones (Oct 30 2018 at 17:54):
We've got quite a few name changes that will also need to be reflected on diagrams.... since core is priority, if I can update the core diagrams/images and forward the files to one of you guys can you push them to the git?
Kevin Power (Oct 30 2018 at 18:13):
Thanks @James Jones - If you are worried about things being out of sync for a bit (between your diagram changes and other documentation), I don't know if that is much of a concern or not? I would say if you are willing to take those on, you can and push them to git anytime? Or did you have another concern?
Jamie Jones (Oct 30 2018 at 18:16):
I just don't have git rights on core but should be an easy commit just swapping out the files
Kevin Power (Oct 30 2018 at 18:25):
If you want to be a committer, I think @Lloyd McKenzie can hook you up? :slight_smile:
Lloyd McKenzie (Oct 30 2018 at 18:53):
I need your Git id, an email from you saying that you've read and agree to abide by Chapter 16 of the GOM and a commitment to subscribe to and monitor the #committers/announce stream
Kevin Power (Oct 30 2018 at 19:17):
@Lloyd McKenzie - would you be able to help me think through a plan of attack for the renaming? How to approach it, thoughts on steps to take?
Lloyd McKenzie (Oct 30 2018 at 19:25):
You'll need to change the name in all the places listed here http://wiki.hl7.org/index.php?title=FHIR_Guide_to_Authoring_Resources (for creating a resource). As well, you'll have to find any places in the spec the resource is referenced from (e.g. Observation, DiagnosticReport) and fix those. (Doing a cross-file case-sensitive search for Sequence is a good start.) Finally, you'll need to identify the resource as a renamed resource in the fhir.ini file.
Kevin Power (Oct 30 2018 at 19:26):
OK, good start. Any issues with us touching the normative content?
Lloyd McKenzie (Oct 30 2018 at 19:27):
Not to change the name, no. That bit isn't (and can't be) normative.
Kevin Power (Oct 30 2018 at 19:28):
OK - what folder(s) need to be searched? All of them?
Lloyd McKenzie (Oct 30 2018 at 19:32):
source
Lloyd McKenzie (Oct 30 2018 at 19:32):
(and sub-folders)
Kevin Power (Oct 30 2018 at 19:50):
Thanks Lloyd. Should we (gulp) inform the committers channel that we will be doing this so others are aware its coming?
Kevin Power (Oct 30 2018 at 20:52):
BTW - I am working through the details of this now. At least a heads up to this group in case anyone is working on something related.
Kevin Power (Oct 30 2018 at 20:52):
I will push up to a branch later today, and likely let anyone in this group who is interested take a look
Lloyd McKenzie (Oct 30 2018 at 21:35):
Main thing to do is coordinate w/ Rob Hausam and Eric Haas - they're most likely to commit OO stuff - which is what's most likely to conflict.
Kevin Power (Oct 30 2018 at 21:36):
@Lloyd McKenzie - Assume it is OK to skip the 'source\release2' and 'source\release3' folders?
Lloyd McKenzie (Oct 30 2018 at 21:45):
y
Kevin Power (Oct 30 2018 at 22:08):
What about source/history.html?
Kevin Power (Oct 30 2018 at 22:10):
and library/library-fhir-model-definition-content.xml ?
Lloyd McKenzie (Oct 30 2018 at 22:25):
You'll have to update the link in history. Reach out to Bryn Rhodes on what to do with library
Kevin Power (Oct 31 2018 at 01:50):
Hey all - Just FYI. May not get that pull request up tonight. Had a weird issue happen, and it seems I have to redo a lot of the work. :(
Kevin Power (Oct 31 2018 at 16:39):
OK all - if you saw the lights dim, I have pushed up the branch, and made sure to merge master into it. If you compare it to master, you should see the differences: https://github.com/HL7/fhir/compare/CG_RenameSequence
Jamie Jones (Oct 31 2018 at 16:45):
Awesome! Are there more changes you have to do on the IG files right now? I was about to dig into some more updates
Kevin Power (Oct 31 2018 at 16:52):
I haven't touched the IG in a while. Probably need to wait until the name change merges, then can update some references and the like. Of course, we have plenty of other pending trackers that still need to be addressed.
Patrick Werner (Oct 31 2018 at 17:12):
i reviewed @Kevin Power renaming branch, found just one missing camelcase in the spanish translation. Commited the correction, created a PR, waiting for the CI Test to pass, i then will merge it.
Kevin Power (Oct 31 2018 at 17:23):
@Patrick Werner - did you see the build failure?
Patrick Werner (Oct 31 2018 at 17:26):
yes, i'm currently digging into it
Kevin Power (Oct 31 2018 at 17:57):
Obvious enough I suppose, but I did not get an error on validating capabilitystatement examples when I built locally.
Patrick Werner (Oct 31 2018 at 18:09):
it is building without problems locally, i assume the failure is coming from the master branch. I merged the master again and pushed it just now
Kevin Power (Oct 31 2018 at 19:24):
Josh fixed the VM/agent error :electric_plug: we got on your last build, and I just saw the console get by the capabilitystatement error we saw before.
Patrick Werner (Oct 31 2018 at 21:36):
It worked now, i‘ve merged your branch into master.
Kevin Power (Oct 31 2018 at 22:09):
Looks like it is published! http://build.fhir.org/molecularsequence.html
Kevin Power (Oct 31 2018 at 22:10):
Welcome anyone who wants to review and do some QA
Patrick Werner (Oct 31 2018 at 22:30):
i've just applied GF#19000 and pushed it, waiting for CI to build
Patrick Werner (Oct 31 2018 at 22:31):
after that we only have 1 GF on core open
Patrick Werner (Nov 01 2018 at 00:27):
applied GF#19440 as well, waiting for CI to pass and merge to master.
Kevin Power (Nov 01 2018 at 00:28):
Ha - I was just working on it as well - you beat my commit by about 10 minutes :)
Patrick Werner (Nov 01 2018 at 00:28):
sorry, should have announced that i started working on it.
Kevin Power (Nov 01 2018 at 00:29):
I should have as well - just assumed that someone on vacation in Spain wouldn't be working on it :)
Patrick Werner (Nov 01 2018 at 00:33):
:-)
Kevin Power (Nov 01 2018 at 00:34):
Looks like there are two other files with the older comment still. I am not sure they are used any longer, but I will update them and push up the changes.
Patrick Werner (Nov 01 2018 at 00:36):
i've updated anything with the link to the ig, more than in the GF Tracker item
Patrick Werner (Nov 01 2018 at 00:36):
https://github.com/HL7/fhir/pull/199/files
Patrick Werner (Nov 01 2018 at 00:37):
Updated it in 6 files, deleted a zombie HLA Introduction file which was redundant and incomplete
Kevin Power (Nov 01 2018 at 00:37):
I found the older text in these two files:
/Users/cerkyp/Documents/GitHub/fhir/source/observation/observation-consensus-seq-block-introduction.xml:
/Users/cerkyp/Documents/GitHub/fhir/source/observation/observation-genetics-introduction-2.xml:
Patrick Werner (Nov 01 2018 at 00:39):
ah perfect, missed these
Kevin Power (Nov 01 2018 at 00:39):
no worries, I will take care of them. I will wait until until your build finishes - It seems two builds at at a time causes problems.
Kevin Power (Nov 01 2018 at 00:41):
Now - please GET BACK TO YOUR VACATION!
Kevin Power (Nov 01 2018 at 00:42):
Or go to bed
Patrick Werner (Nov 01 2018 at 00:46):
will do.
Kevin Power (Nov 02 2018 at 13:50):
Update - the build of the IG is failing right now. The examples that still use Sequence cause a failure (as they should since we did the rename), but I tried updating everything to MolecularSequence and I am still getting a build failure:
[java] Caused by: org.hl7.fhir.exceptions.FHIRFormatError: Unknown.Unrecognised resource type 'MolecularSequence' (in property 'resourceType')
It is a different error than I got while it said Sequence (which this error makes sense):
[java] Caused by: org.hl7.fhir.exceptions.FHIRFormatError: Contained resource does not appear to be a FHIR resource (unknown name 'Sequence')
Kevin Power (Nov 02 2018 at 14:09):
OK - so looking through the code, which I assume is generated, I see it still has Sequence in the code, not MolecularSequence. @Lloyd McKenzie - When will that code be regenerated?
Kevin Power (Nov 02 2018 at 14:09):
Do I need to do that in some way?
Lloyd McKenzie (Nov 02 2018 at 14:52):
That's something Graham will do - possibly today now that substantive changes are done. Ping him with a PM and let him know where you're hitting the code issue and he'll be able to give you an ETA
Kevin Power (Nov 02 2018 at 20:08):
Hi all - Just an FYI. I took on several trackers to try and harmonize names between profiles, text, and diagrams. It means I have fairly broad changes. I never heard back from GG as to when he will regenerate the code and resolve our build error.
In case others are making changes, I don't want to get to far apart, so I am removing the 'Sequence/MolecularSequence' part of our examples, because when I do the IG builds fine. We can restore them at a later date once the publisher handles our name change. So I will be doing a push shortly.
Thanks.
Kevin Power (Nov 02 2018 at 21:23):
OK, I pushed all of my changes. Also, Grahame said he would regenerate code within the next 48 hours.
Last updated: Apr 12 2022 at 19:14 UTC
