Stream: research
Topic: CDISC LAB IG
Hugh Glover (Nov 26 2018 at 12:09):
@Lloyd McKenzie We need to create a new IG repository in GItHub to start authoring this IG. I've read the wiki stuff and watched the video, but I can't figure out where I get a template IG to start from - the link in the wiki just gives a 404. Guidance please.
Lloyd McKenzie (Nov 26 2018 at 18:06):
You can use SDC or genomics-reporting as a starting point
Douglas Denney (Mar 31 2019 at 03:26):
@Hugh Glover and @Lloyd McKenzie , I'm new to the FHIR framework and setting up items to be used in this context. I've been working with Hugh to help with the IG repository. I have tried following the instructions found here: http://wiki.hl7.org/index.php?title=IG_Publisher_Documentation
I've downloaded the SDC IG source from the github repository and looked through that. I've tried modifying items in the /src folder to use the cdisc_lab designation. Things don't seem to be working as I was hoping and the process still has me a bit confused at this point. I have a few questions:
1. For the /src folder, do we just add the content, excel spreadsheets, text files, xml files, etc., into this folder structure?
2. The "jekyll build" commands will create a /_site folder in the /src tree, which has a copy of the /src tree. Does jekyll do conversion on the excel files, and other formatting options?
3. In the downloaded SDC IG, I see that there is a /src and a /src-generated folder. What generated that folder?
4. What tools/process get you from "provided content" to a set of HTML files for viewing in a browser?
I had thought that the igpublisher jar file would do some of this, but it seems to need a JSON file to execute. When I've tried getting the /src folder to generate anything, it doesn't produce a JSON file. So, how does the JSON file get there?
Any help you can provide would be appreciated.
Thanks.
Lloyd McKenzie (Mar 31 2019 at 05:59):
You shouldn't invoke jekyll build directly. The IGPublisher will do that for you. The whole thing off is run using the _genonce.bat file. That does a bunch of pre-processing (including generating the needed ig.json file) and puts the results in src-generated (including grabbing the current igpublisher jar), then invoking it. The continuous integration build doesn't do the pre-processing, so src-generated needs to be checked in, even though the content is 'generated'.
Putting things in the proper folders in the src folder is one step. The other is referencing them from the [ig].xml file that's at the root of the src folder.
There's a bit of documentation here: http://wiki.hl7.org/index.php?title=FHIR_IG_Framework, though it's somewhat out-of-date. I'm holding off fixing it because all of this is getting refactored over the next couple of months as we move to a template-based publication scheme.
Lloyd McKenzie (Mar 31 2019 at 05:59):
See if you can get SDC to publish locally "unchanged" and then start tweaking after that.
Douglas Denney (Apr 01 2019 at 03:28):
@Lloyd McKenzie Thanks for the link. With that info I was able to get the sdc IG to "build" on my local machine (MacOS). Once I did that I changed "sdc" to "cdl". Had a question...started getting errors when trying to use the name "cdisc_lab", so all the prefixes and such were "cdisc_lab-master", etc. The build kept failing with invalid resource type/id for things like "StructuredQuestionaire/cdisc_lab-form-designer". When I changed it to be "StructuredQuestionaire/cdl-form-designer", it got past that point.
Anyway, are there any other places for tips on this? How does one get a spreadsheet to display correctly?
I'll keep playing around with it. Thanks again for the help.
Lloyd McKenzie (Apr 01 2019 at 03:35):
The 'id' element in resources is quite strict. It can't contain dashes. Your resource id for the implementation guide should just be cdisc_lab, or possibly cdisclab. (The latter would be more typical of existing convention). No reason to indicate 'master'. No need to prefix your profiles with cdisc_lab unless you really want to (as they're already in the namespace). SDC started prefixing before we'd figured that out and has continued to do that to minimize transition, but you're starting fresh, so may as well keep the names simple. E.g. formDesigner or form_designer.
Lloyd McKenzie (Apr 01 2019 at 03:36):
That said, there's no such thing as StructuredQuestionnaire - should be Questionnaire or StructureDefinition, depending what you're doing...
Douglas Denney (Apr 01 2019 at 03:42):
Thanks, I couldn't remember the exact text of the message as it had scrolled off the screen. I'll bring up your other points with the rest of the group and get some guidance from them on how they'd like to handle it.
Douglas Denney (Apr 01 2019 at 13:36):
@Lloyd McKenzie thanks for your help so far. Is there any guidance on getting content from a wiki (where we have cdisc_lab currently staged) I to this source tree? Or is it a manual process to format and save each CML file? Also how do you save spreadsheets?
Lloyd McKenzie (Apr 01 2019 at 14:12):
The framework will take .md files (cramdown markdown) or .xml files (XHTML compliant with HL7's XHTML rules with a root of <div/>). How you get source into one of those two formats is up to you.
Lloyd McKenzie (Apr 01 2019 at 14:12):
Spreadsheets should be saved as XML (one of the options within Excel)
Christine D (Apr 02 2019 at 18:21):
@Lloyd McKenzie I am looking at the CRN and CDMH guides because SDC had so much content that we will not need. It was difficult to strip out the extraneous parts. Both CRN and CDMH use .md files. It seems more straightforward to use those as templates. The issue is that those github repositories do not have the executables that were in SDC's framework directory. e.g., https://github.com/HL7/coordinated-registry-network
Any thoughts on the missing pieces?
Lloyd McKenzie (Apr 02 2019 at 19:04):
The template supports both .md and .xml files - just identify which you're dealing with when you reference them in the implementation guide. I personally find .md much more annoying to work with than XHTML, but recognize that there are others where the reverse is true.
Lloyd McKenzie (Apr 02 2019 at 19:04):
CRDN and CDMH weren't created with my framework, so I can't help much there. You can look at CRD that does use markdown if you wish.
Christine D (Apr 03 2019 at 12:05):
@Lloyd McKenzie Thank you for your help!
Douglas Denney (Apr 27 2019 at 03:29):
@Lloyd McKenzie, @Nagesh Bashyam, @Hugh Glover, @Christine D : Everyone, we have an IG that's building and I'm trying to find the next steps. I followed the steps to create my own GitHub repository, uploaded my files and even added the webhook for CI build. When I add files to the repo, my webhook says it delivered the payload but I don't see anything show up on the HL7 site (https://chat.fhir.org/#narrow/stream/committers/topic/ig-build) or in the possible location where it should appear (http://build.fhir.org/ig/HL7/cdl/). So, I guess the simplest question for all of you is: What am I doing wrong here?
Lloyd McKenzie (Apr 27 2019 at 05:20):
Is there an ig.json in the root folder?
Douglas Denney (Apr 27 2019 at 11:48):
Yes. There is a ig.json in the root folder.
Lloyd McKenzie (Apr 27 2019 at 14:03):
Unfortunately I've only got my phone for the next couple of days so I can't debug right now. @Grahame Grieve @Josh Mandel?
Josh Mandel (Apr 27 2019 at 14:42):
I'm not seeing source at https://github.com/HL7/cdl/ -- can you clarify where the repo is located?
Josh Mandel (Apr 27 2019 at 14:43):
(If you want it published at http://build.fhir.org/ig/HL7/cdl/ it'd need to originate there.)
Douglas Denney (Apr 27 2019 at 17:17):
@Josh Mandel I guess that's where I have a disconnect. I followed these instructions: https://github.com/hl7-fhir/auto-ig-builder/blob/master/README.md. So, I created the GitHub archive "in my own organization". My username on GitHub is "DDenney". Should the GitHub archive be created in an HL7 repository? I guess, how do I get from my GitHub repository to yours and have it auto build?
Douglas Denney (Apr 27 2019 at 17:20):
@Josh Mandel Or, does "my own organization" mean someplace in the HL7 hierarchy? And if so, how to do get one of those?
Douglas Denney (Apr 27 2019 at 17:22):
@Josh Mandel @Lloyd McKenzie @Hugh Glover @Christine D
I found my repository. It's in the org "DDenney" on the build site here: http://build.fhir.org/ig/DDenney/cdl/. So, how do I get it on the HL7 org?
Josh Mandel (Apr 27 2019 at 17:25):
This starts with a policy question, I think -- but technically, you just need support from an admin on the HL7 org. @Lloyd McKenzie might be able to point you in the right direction for that step.
Lloyd McKenzie (Apr 27 2019 at 18:52):
Are you developing content for hl7 ballot/publication?
Douglas Denney (Apr 28 2019 at 00:29):
@Lloyd McKenzie @Hugh Glover @Christine D Yes. For September ballot. I’m working with Hugh and Christine on this.
Lloyd McKenzie (Apr 28 2019 at 03:44):
OK. Please send me an email as a reminder and I'll try to set you up with an HL7 git repository tomorrow night once I'm in front of a computer again. Do you have an fmg- approved IG proposal? If not, what is your proposed IG code?
Christine D (Apr 29 2019 at 11:44):
Hi @Lloyd McKenzie
Yes, this has been approved and is planned for the September ballot as an STU. This is the "CDISC Lab Semantics in FHIR" project that is co-sponsored by BR&R and O+O. The Project Insight Number is 1425. FMG approval date was Feb 6, 2019. We were using the acronym CLD (CDISC lab Mapping).
@Douglas Denney @Hugh Glover @Christine D
Christine D (Apr 29 2019 at 13:10):
@Lloyd McKenzie @Hugh Glover @Douglas Denney slight typo above - it's CDL (not CLD)
Lloyd McKenzie (Apr 29 2019 at 14:53):
Ok, I've created the repository. I don't have a Github id for Hugh Glover. For Douglas and whoever else needs committer access will need to send me an email confirming that they have read and agree to abide by Chapter 16 of the GOM and to actively monitor #committers/announce for so long as they maintain committer privileges.
Christine D (Apr 29 2019 at 15:39):
Tagging Doug -
Ok, I've created the repository. I don't have a Github id for Hugh Glover. For Douglas and whoever else needs committer access will need to send me an email confirming that they have read and agree to abide by Chapter 16 of the GOM and to actively monitor #committers/announce for so long as they maintain committer privileges.
@Douglas Denney
Christine D (Apr 29 2019 at 15:39):
Thank you @Lloyd McKenzie !
Douglas Denney (Apr 29 2019 at 23:07):
@Lloyd McKenzie I found the GOM at this link: http://www.hl7.org/documentcenter/public_temp_316B800E-1C23-BA17-0C99536C70D6CB24/membership/HL7_Governance_and_Operations_Manual.pdf.
I have read and agree to abide by Chapter 16 of the GOM and to actively monitor #committers/announce for so long as I maintain committer privileges.
Thanks!
@Christine D @Hugh Glover
Last updated: Apr 12 2022 at 19:14 UTC
