_refresh produces errors

[cmoesel]

Taking a fresh clone, I ran _updateCQLTooling and then _refresh. The _refresh script failed with a few errors. It seems the big ones are:

• Could not find input/resources/Library-FHIRHelpers.json
• Could not resolve library url Library/phq-9-logic (probably related to above?)

I noticed that FHIRHelpers is not provided in the cql source or the libraries. Should it be?

Full log:

❯ ./_refresh.sh
Checking internet connection...
Online
-fs https://cds-sandbox.alphora.com/cqf-ruler-r4/fhir/
fhir-version was not specified in the ini file. Trying FHIR version 4.0.1
Core Package hl7.fhir.r4.core#4.0.1
Dependency 'example.fhir.uv.myig' has no id, so can't be referred to in markdown in the IG
Load u32113965f5e045b6842fd95fc812c9f6 (http://somewhere.org/fhir/uv/myig) from example.fhir.uv.myig#dev
Load cpg (http://hl7.org/fhir/uv/cpg) from hl7.fhir.uv.cpg#1.0.0
Load cqf (http://fhir.org/guides/cqf/common) from fhir.cqf.common#dev
[main] INFO ca.uhn.fhir.util.VersionUtil - HAPI FHIR version 5.6.3 - Rev b54b29145c
[main] INFO ca.uhn.fhir.context.FhirContext - Creating new FHIR context for FHIR version [R4]
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - IGProcessor.publishIG - refreshIG
fhir-version was not specified in the ini file. Trying FHIR version 4.0.1
Core Package hl7.fhir.r4.core#4.0.1
Dependency 'example.fhir.uv.myig' has no id, so can't be referred to in markdown in the IG
Load ub86c691957d44443965ba432e952c668 (http://somewhere.org/fhir/uv/myig) from example.fhir.uv.myig#dev
Load cpg (http://hl7.org/fhir/uv/cpg) from hl7.fhir.uv.cpg#1.0.0
Load cqf (http://fhir.org/guides/cqf/common) from fhir.cqf.common#dev
No directory found by convention for: cql
No directory found by convention for: library
No directory found by convention for: measure
No directory found by convention for: plandefinition
Refreshing libraries...
[main] INFO org.opencds.cqf.tooling.library.LibraryProcessor - No output directory found for libraries.  Any existing libraries will be overwritten.
[main] INFO ca.uhn.fhir.util.XmlUtil - Unable to determine StAX implementation: java.xml/META-INF/MANIFEST.MF not found
[main] WARN ca.uhn.fhir.parser.LenientErrorHandler - Found incorrect type for element subject - Expected OBJECT and found SCALAR (STRING)
Translating CQL source
Translating CQL source in folder /Users/cmoesel/git/cqframework/sample-content-ig/input/cql
cql-options loaded from: /Users/cmoesel/git/cqframework/sample-content-ig/input/cql/cql-options.json
Translating CQL source in file /Users/cmoesel/git/cqframework/sample-content-ig/input/cql/RetrieveExample.cql
CQL translation completed successfully.
Translating CQL source in file /Users/cmoesel/git/cqframework/sample-content-ig/input/cql/DependencyExample.cql
CQL translation completed successfully.
Translating CQL source in file /Users/cmoesel/git/cqframework/sample-content-ig/input/cql/ExtensionAndSlicingExample.cql
CQL translation completed successfully.
Translating CQL source in file /Users/cmoesel/git/cqframework/sample-content-ig/input/cql/PHQ9Logic.cql
CQL translation completed successfully.
Translating CQL source in file /Users/cmoesel/git/cqframework/sample-content-ig/input/cql/FirstExample.cql
CQL translation completed successfully.
Translating CQL source in file /Users/cmoesel/git/cqframework/sample-content-ig/input/cql/QuestionnaireMeasure.cql
CQL translation completed successfully.
Refreshing measures...
Refreshing tests
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - IGProcessor.publishIG - bundleIg
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - libraryUrlMap Size: 6
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - libraryUrlMap Entry: http://somewhere.org/fhir/uv/mycontentig/Library/FirstExample
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - libraryUrlMap Entry: http://somewhere.org/fhir/uv/mycontentig/Library/RetrieveExample
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - libraryUrlMap Entry: http://somewhere.org/fhir/uv/mycontentig/Library/PHQ9Logic
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - libraryUrlMap Entry: http://somewhere.org/fhir/uv/mycontentig/Library/DependencyExample
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - libraryUrlMap Entry: http://somewhere.org/fhir/uv/mycontentig/Library/ExtensionAndSlicingExample
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - libraryUrlMap Entry: http://somewhere.org/fhir/uv/mycontentig/Library/QuestionnaireMeasure
cql-options loaded from: /Users/cmoesel/git/cqframework/sample-content-ig/input/cql/cql-options.json
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - Measure will not be bundled because ValueSet bundling failed.
java.lang.RuntimeException: Error reading resource from path /Users/cmoesel/git/cqframework/sample-content-ig/input/resources/Library-FHIRHelpers.json: /Users/cmoesel/git/cqframework/sample-content-ig/input/resources/Library-FHIRHelpers.json (No such file or directory)
	at org.opencds.cqf.tooling.utilities.IOUtils.readResource(IOUtils.java:259)
	at org.opencds.cqf.tooling.utilities.IOUtils.readResource(IOUtils.java:216)
	at org.opencds.cqf.tooling.utilities.ResourceUtils.getR4DepLibraryResources(ResourceUtils.java:226)
	at org.opencds.cqf.tooling.utilities.ResourceUtils.getDepLibraryResources(ResourceUtils.java:139)
	at org.opencds.cqf.tooling.library.LibraryProcessor.bundleLibraryDependencies(LibraryProcessor.java:96)
	at org.opencds.cqf.tooling.measure.MeasureProcessor.bundleMeasures(MeasureProcessor.java:124)
	at org.opencds.cqf.tooling.processor.IGBundleProcessor.bundleIg(IGBundleProcessor.java:28)
	at org.opencds.cqf.tooling.processor.IGProcessor.publishIG(IGProcessor.java:100)
	at org.opencds.cqf.tooling.operation.RefreshIGOperation.execute(RefreshIGOperation.java:41)
	at org.opencds.cqf.tooling.Main.main(Main.java:220)
Caused by: java.io.FileNotFoundException: /Users/cmoesel/git/cqframework/sample-content-ig/input/resources/Library-FHIRHelpers.json (No such file or directory)
	at java.base/java.io.FileInputStream.open0(Native Method)
	at java.base/java.io.FileInputStream.open(FileInputStream.java:219)
	at java.base/java.io.FileInputStream.<init>(FileInputStream.java:157)
	at java.base/java.io.FileReader.<init>(FileReader.java:75)
	at org.opencds.cqf.tooling.utilities.IOUtils.readResource(IOUtils.java:252)
	... 9 more
No paths found for the Directory /Users/cmoesel/git/cqframework/sample-content-ig/input/tests/measure/QuestionnaireMeasure:
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - Measure-QuestionnaireMeasure could not be processed:
          Resource could not be processed: QuestionnaireMeasure
                    1 included cql Libraries not found:
FHIRHelpers MISSING
          Resource could not be processed: Library-QuestionnaireMeasure
                    Error reading resource from path /Users/cmoesel/git/cqframework/sample-content-ig/input/resources/Library-FHIRHelpers.json: /Users/cmoesel/git/cqframework/sample-content-ig/input/resources/Library-FHIRHelpers.json (No such file or directory)
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils -
0 Measures successfully bundled:
0 Measures refreshed, but not bundled (due to issues):
1 Measures failed refresh:
     /Users/cmoesel/git/cqframework/sample-content-ig/input/resources/Measure-QuestionnaireMeasure.json FAILED
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils -
0 PlanDefinitions successfully bundled:
0 PlanDefinitions refreshed, but not bundled (due to issues):
0 PlanDefinitions failed refresh:
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - primaryLibraryUrl: Library/phq-9-logic
java.lang.IllegalArgumentException: Could not resolve library url Library/phq-9-logic
	at org.opencds.cqf.tooling.questionnaire.QuestionnaireProcessor.bundleQuestionnaires(QuestionnaireProcessor.java:64)
	at org.opencds.cqf.tooling.processor.IGBundleProcessor.bundleIg(IGBundleProcessor.java:34)
	at org.opencds.cqf.tooling.processor.IGProcessor.publishIG(IGProcessor.java:100)
	at org.opencds.cqf.tooling.operation.RefreshIGOperation.execute(RefreshIGOperation.java:41)
	at org.opencds.cqf.tooling.Main.main(Main.java:220)
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils - Questionnaire-phq-9-questionnaire could not be processed:
          Resource could not be processed: Questionnaire-phq-9-questionnaire
                    Could not resolve library url Library/phq-9-logic
[main] WARN org.opencds.cqf.tooling.utilities.LogUtils -
0 Questionnaires successfully bundled:
0 Questionnaires refreshed, but not bundled (due to issues):
1 Questionnaires failed refresh:
     /Users/cmoesel/git/cqframework/sample-content-ig/input/resources/Questionnaire-phq-9-questionnaire.json FAILED

[cmoesel]

I've played with this a bit and made some progress getting it working (with various tweaks). There are still a bunch of errors in the QA due to issues w/ the resources, but it's a lot closer than it was before. Here's my branch if you want to take a look: https://github.com/cqframework/sample-content-ig/tree/cmm-fixes

I'm not sure when I'll get back to it again.