Stream: genomics/committers
Topic: search guidance
Patrick Werner (Oct 09 2019 at 11:54):
@Bret H
- pushed the IG to version 0.4 (was 0.3)
Patrick Werner (Oct 09 2019 at 11:55):
- fixed search guidance
Bret H (Oct 09 2019 at 16:55):
great. Anything needed from me at this point?
Kevin Power (Oct 09 2019 at 16:56):
@Bret H - Can you review the changes I made to your validation additions?
http://build.fhir.org/ig/HL7/genomics-reporting/index.html
Bret H (Oct 09 2019 at 17:00):
@Kevin Power looks great on the validator stuff.
Kevin Power (Oct 09 2019 at 17:02):
The page you reference (and pages it references) provides the 'generic terms', so I thought that a more concrete example would be more helpful?
Bret H (Oct 09 2019 at 17:02):
@Patrick Werner are you happy with the search page?
Jamie Jones (Oct 09 2019 at 17:04):
the preformatted text seems to go into the margins forever, can we wrap it?
Bret H (Oct 09 2019 at 17:04):
also we've got blue text.
pasted image
Bret H (Oct 09 2019 at 17:05):
Should I work on it? or leave it for one of you @Kevin Power @James Jones @Patrick Werner don't want to comitt on anyones feeet
Kevin Power (Oct 09 2019 at 17:05):
@Bret H - Feel free to fix the Search page 'blue text' issue.
Kevin Power (Oct 09 2019 at 17:06):
the preformatted text seems to go into the margins forever, can we wrap it?
I will take a look at that
Jamie Jones (Oct 09 2019 at 17:06):
actually, that example probably ought to use {sitepath} or whatever, so it updates to the actual version
Jamie Jones (Oct 09 2019 at 17:06):
rather than telling people just how to validate against build
Kevin Power (Oct 09 2019 at 17:06):
What example?
Kevin Power (Oct 09 2019 at 17:07):
Oh, you mean the 'here is how to use the validator' example?
Bret H (Oct 09 2019 at 17:07):
james means the examples in the validator, I beleive
Jamie Jones (Oct 09 2019 at 17:07):
yeah, would be nice if it would automatically update to the published version
Jamie Jones (Oct 09 2019 at 17:09):
(not that I know how to make that work at this time)
Patrick Werner (Oct 09 2019 at 17:22):
the ig parameter should be: -ig hl7.fhir.uv.genomics-reporting
Bret H (Oct 09 2019 at 17:23):
the ig parameter should be:
-ig hl7.fhir.uv.genomics-reporting
@Kevin Power
Jamie Jones (Oct 09 2019 at 17:24):
I think that defaults to the most recent hosted version, right? Have to use tricks to point to CI build
Patrick Werner (Oct 09 2019 at 17:25):
or is the url also valid. Fails if i try. I'll have a look
Kevin Power (Oct 09 2019 at 17:27):
Those examples all worked for me, but using what Patrick says also worked.
Or did it? Now I tried what I did, and it doesn't work :frown:
Kevin Power (Oct 09 2019 at 17:27):
I am fixing
Patrick Werner (Oct 09 2019 at 17:27):
java -jar org.hl7.fhir.validator.jar http://build.fhir.org/ig/HL7/genomics-reporting/Observation-SNVexample.xml -version 4.0.0 -ig http://build.fhir.org/ig/HL7/genomics-reporting/ImplementationGuide-hl7.fhir.uv.genomics-reporting.xml -profile http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-variant.xml
doesn't work on my end
Bret H (Oct 09 2019 at 17:28):
@James Jones @Kevin Power @Patrick Werner unrealted to validation, but the usecase.xml page seems good now. Jamie's suggestion worked.
Kevin Power (Oct 09 2019 at 17:29):
Thanks @Bret H - feel free to commit.
Bret H (Oct 09 2019 at 17:29):
done
Patrick Werner (Oct 09 2019 at 17:30):
also we've got blue text.
pasted image
can't find the blue text
Bret H (Oct 09 2019 at 17:30):
@Patrick Werner it has been fixed. needed <a name="something> in the usecase.xml page. all good now.
Patrick Werner (Oct 09 2019 at 17:31):
@Kevin Power the -version also should be -version 4.0.0 4.0 fails at my end
Kevin Power (Oct 09 2019 at 17:32):
Hmm, 4.0 works for me? What error do you get?
Jamie Jones (Oct 09 2019 at 17:33):
4.0 finds core 4.0.0 fine on mine
Kevin Power (Oct 09 2019 at 17:33):
> java -jar org.hl7.fhir.validator.jar report-CYP2C19.xml -version 4.0 -ig hl7.fhir.uv.genomics-reporting -profile http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-genomics-report.xml Picked up JAVA_TOOL_OPTIONS: -Djava.awt.headless=true FHIR Validation tool Version 4.0.23-SNAPSHOT - Built 2019-10-02T15:02:10.634+10:00 - Git 17e7333bcab7 Detected Java version: 1.8.0_112 from /Library/Java/JavaVirtualMachines/jdk1.8.0_112.jdk/Contents/Home/jre on x86_64 (64bit). 3641MB available Arguments: report-CYP2C19.xml -version 4.0 -ig hl7.fhir.uv.genomics-reporting -profile http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-genomics-report.xml Directories: Current = /Users/cerkyp/Documents/GitHub/genomics-reporting/src/examples, Package Cache = /Users/cerkyp/.fhir/packages .. connect to tx server @ http://tx.fhir.org .. definitions from hl7.fhir.core#4.0.0 (v4.0.0) + .. load IG from hl7.fhir.uv.genomics-reporting ... Using version 0.4 Fetch Profile from http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-genomics-report.xml .. validate [report-CYP2C19.xml] against [http://build.fhir.org/ig/HL7/genomics-reporting/StructureDefinition-genomics-report.xml] Terminology server: Check for supported code systems for http://loinc.org *FAILURE* validating report-CYP2C19.xml: error:75 warn:149 info:148
Patrick Werner (Oct 09 2019 at 17:36):
oh then something is wrong on my end. sorry.
Kevin Power (Oct 09 2019 at 17:36):
What error do you get?
Jamie Jones (Oct 09 2019 at 17:39):
mine still tries to grab 0.3 :thinking:
Patrick Werner (Oct 09 2019 at 17:39):
java -jar ~/Downloads/org.hl7.fhir.validator.jar http://build.fhir.org/ig/HL7/genomics-reporting/Observation-SNVexample.xml -version 4.0 -ig hl7.fhir.uv.genomics-reporting
works
Jamie Jones (Oct 09 2019 at 17:41):
i probably have to update my package list
Patrick Werner (Oct 09 2019 at 17:41):
as first example i would include
java -jar ~/Downloads/org.hl7.fhir.validator.jar localFile.xml -version 4.0 -ig hl7.fhir.uv.genomics-reporting
Patrick Werner (Oct 09 2019 at 17:42):
most obvious: local file against latest IG (should mention that the Instance has to declare the profile in meta)
Kevin Power (Oct 09 2019 at 17:42):
That is why I included a reference to the -profile, but that note is fine as well?
Patrick Werner (Oct 09 2019 at 17:43):
does -ig hl7.fhir.uv.genomics-reporting#0.4or 0.3 work for anyone?
Kevin Power (Oct 09 2019 at 17:43):
I wasn't going to include complexities that 'what if the validator.jar was in another directory'
Kevin Power (Oct 09 2019 at 17:45):
If I put a version # on our IG, it does NOT work
Patrick Werner (Oct 09 2019 at 17:45):
That is why I included a reference to the -profile, but that note is fine as well?
i would say that best practice is to include it in meta and dont use -profile. Just using -profile doesn't persist the conformance in the instance to be tested. Mentioning -profile could lead implementers to think that -profile is mandatory. But that is just my personal opinion.
Patrick Werner (Oct 09 2019 at 17:45):
ok, IG package versioning seems to be broken?
Patrick Werner (Oct 09 2019 at 17:48):
so just guide to use -ig hl7.fhir.uv.genomics-reporting ?
Would be bad as implementers can't validate against an stable Ig unless they install the package manually.
Kevin Power (Oct 09 2019 at 17:49):
Aren't all the packages on GitHub somewhere?
Patrick Werner (Oct 09 2019 at 17:59):
created a thread: https://chat.fhir.org/#narrow/stream/179177-conformance/topic/java.20validator.20version.20on.20-ig.20argument
Patrick Werner (Oct 09 2019 at 17:59):
without a version it loads 0.4
Patrick Werner (Oct 09 2019 at 18:00):
with #0.4 it fails
Patrick Werner (Oct 09 2019 at 18:02):
from the other thread:
related: https://wiki.hl7.org/Using_the_FHIR_Validator says
In this case, the current published version of the IG is used.
With the genomics IG it just loads the last commit, not the last published version.
Jamie Jones (Oct 09 2019 at 18:53):
aligning our examples with the current guidance should be good enough for publication, can just replace the build version with the package as above and submit
Kevin Power (Oct 09 2019 at 19:25):
Will push up new version shortly
Last updated: Apr 12 2022 at 19:14 UTC
