Revision - 5eda18f - Mergeback of rel_6_8 (#5146)

Revision 5eda18f5008154909e101a5ba98b2c6e97115b23 authored by Tadgh on 30 July 2023, 22:28:26 UTC, committed by GitHub on 30 July 2023, 22:28:26 UTC

Mergeback of rel_6_8 (#5146)

* version bump

* Bump to core release 6.0.22 (#5028)

* Bump to core release 6.0.16

* Bump to core version 6.0.20

* Fix errors thrown as a result of VersionSpecificWorkerContextWrapper

* Bump to core 6.0.22

* Resolve 5126 hfj res ver prov might cause migration error on db that automatically indexes the primary key (#5127)

* dropped old index FK_RESVERPROV_RES_PID on RES_PID column before adding IDX_RESVERPROV_RES_PID

* added changelog

* changed to valid version number

* changed to valid version number, need to be ordered by version number...

* 5123 - Use DEFAULT partition for server-based requests if none specified (#5124)

5123 - Use DEFAULT partition for server-based requests if none specified

* consent remove all suppresses next link in bundle (#5119)

* added FIXME with source of issue

* added FIXME with root cause

* added FIXME with root cause

* Providing solution to the issue and removing fixmes.

* Providing changelog

* auto-formatting.

* Adding new test.

* Adding a new test for standard paging

* let's try this and see if it works...?

* fix tests

* cleanup to trigger a new run

* fixing tests

---------

Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>

* 5117 MDM Score for No Match Fields Should Not Be Included in Total Score  (#5118)

* fix, test, changelog

* fix, test, changelog

---------

Co-authored-by: justindar <justin.dar@smilecdr.com>

* Rename file to force IT mode

---------

Co-authored-by: dotasek <david.otasek@smilecdr.com>
Co-authored-by: TynerGjs <132295567+TynerGjs@users.noreply.github.com>
Co-authored-by: Steve Corbett <137920358+steve-corbett-smilecdr@users.noreply.github.com>
Co-authored-by: Ken Stevens <khstevens@gmail.com>
Co-authored-by: Ken Stevens <ken@smilecdr.com>
Co-authored-by: peartree <etienne.poirier@smilecdr.com>
Co-authored-by: jdar8 <69840459+jdar8@users.noreply.github.com>
Co-authored-by: justindar <justin.dar@smilecdr.com>

1 parent 2b91f0a

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sync_ri21.sh

#!/bin/sh

set -e

FHIRTRUNK=~/workspace/fhir/trunk
DIRVERSION=dstu21
PROJVERSION=dstu2.1
PACKAGEVERSION=dstu21

# Resource Definitions
rm hapi-tinder-plugin/src/main/resources/res/$DIRVERSION/*
for i in $(find $FHIRTRUNK/build/source -name *-spreadsheet.xml | egrep "/[a-z0-9]+-spreadsheet"); do cp -v $i hapi-tinder-plugin/src/main/resources/res/$DIRVERSION/; done

# Datatype Definitions
rm hapi-tinder-plugin/src/main/resources/dt/$DIRVERSION/*
for i in $(find $FHIRTRUNK/build/source/datatypes | grep xml | grep -v spreadsheet | grep -v -); do cp -v $i hapi-tinder-plugin/src/main/resources/dt/$DIRVERSION/; done

# Compartments
cp ~/workspace/fhir/trunk/build/source/compartments.xml  hapi-tinder-plugin/src/main/resources/compartment/

# ValueSets
cp $FHIRTRUNK/build/publish/valuesets.xml hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/valueset/
cp $FHIRTRUNK/build/publish/v3-codesystems.xml hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/valueset/
cp $FHIRTRUNK/build/publish/v2-tables.xml hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/valueset/

# Profiles
touch ./hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/profile/_.xml
rm ./hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/profile/*.xml
for i in $(find $FHIRTRUNK/build/publish | grep -E "publish\/[a-z]+\.profile.xml$"); do echo $i; cp $i hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/profile/; done

# Schematron
touch hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/schema/a.sch
rm hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/schema/*.sch
for i in $(ls $FHIRTRUNK/build/publish/*.sch | grep -v -); do cp -v $i ./hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/schema/; done

# Schema
cp $FHIRTRUNK/build/publish/fhir-single.xsd ./hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/schema/
cp $FHIRTRUNK/build/publish/fhir-xhtml.xsd ./hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/schema/
cp $FHIRTRUNK/build/publish/xml.xsd ./hapi-fhir-validation-resources-$PROJVERSION/src/main/resources/org/hl7/fhir/instance/model/$PACKAGEVERSION/schema/

# Copy Model
#TODO reenable
cp -fvR $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/model/*.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/model/
#find hapi-fhir-structures-$PROJVERSION/src -name "*.class" | xargs rm -v

# Exception class
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/exceptions/FHIRException.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/exceptions/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/exceptions/FHIRFormatError.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/exceptions/

cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/Utilities.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/CSFile.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/MyURIResolver.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/ZipURIResolver.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/Inflector.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/FileNotifier.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities
#cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/xhtml/XhtmlNode.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities/xhtml/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/xhtml/XhtmlDocument.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities/xhtml/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/xhtml/NodeType.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities/xhtml/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/xhtml/XhtmlParser.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities/xhtml/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/xhtml/XhtmlComposer.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities/xhtml/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/Table.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/CommaSeparatedStringBuilder.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/xml/XMLUtil.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities/xml/

# Formats
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/formats/IParser.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/formats/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/formats/ParserType.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/formats/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/formats/FormatUtilities.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/formats/

# Terminologies
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/terminologies/ValueSetExpander.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/terminologies/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/terminologies/ValueSetChecker.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/terminologies/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/terminologies/ValueSetExpanderSimple.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/terminologies/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/terminologies/ValueSetExpanderFactory.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/terminologies/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/terminologies/ValueSetCheckerSimple.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/terminologies/

# Utils
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/utils/ToolingExtensions.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/utils/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/utils/IWorkerContext.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/utils/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/utils/INarrativeGenerator.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/utils/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/utils/EOperationOutcome.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/utils/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/utils/FHIRPathEngine.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/utils/

# Validation
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/validation/* hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/validation/
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.$PACKAGEVERSION/src/org/hl7/fhir/$PACKAGEVERSION/exceptions/* hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/exceptions/
rm hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/validation/Validator.java
rm hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/validation/ValidationEngine.java
rm hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/validation/ProfileValidator.java
rm hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/$PACKAGEVERSION/validation/ProfileValidatorTests.java

# XML
cp $FHIRTRUNK/build/implementations/java/org.hl7.fhir.utilities/src/org/hl7/fhir/utilities/xml/IXMLWriter.java hapi-fhir-structures-$PROJVERSION/src/main/java/org/hl7/fhir/utilities/xml/

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