Mb new token search index (#3386)
* New token search param indexing. * New token query test cases for sql extraction * Retire JPA fk ugly nams
This commit is contained in:
michaelabuckley
GitHub
parent
dfd99c5471
commit
80d1a5a6f8
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@ -285,7 +285,7 @@ public class TestUtil {
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Validate.notNull(fk);
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Validate.isTrue(isNotBlank(fk.name()), "Foreign key on " + theAnnotatedElement + " has no name()");
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List<String> legacySPHibernateFKNames = Arrays.asList(
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"FK7ULX3J1GG3V7MAQREJGC7YBC4", "FKC97MPK37OKWU8QVTCEG2NH9VN", "FKCLTIHNC5TGPRJ9BHPT7XI5OTB", "FKGXSREUTYMMFJUWDSWV3Y887DO");
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"FKC97MPK37OKWU8QVTCEG2NH9VN", "FKCLTIHNC5TGPRJ9BHPT7XI5OTB", "FKGXSREUTYMMFJUWDSWV3Y887DO");
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if (legacySPHibernateFKNames.contains(fk.name())) {
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// wipmb temporarily allow the hibernate legacy sp fk names
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} else {
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@ -87,70 +87,138 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
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private void init600() {
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Builder version = forVersion(VersionEnum.V6_0_0);
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/*
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/**
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* New indexing for the core SPIDX tables.
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* Ensure all queries can be satisfied by the index directly,
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* either as left or right table in a hash or sort join.
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*
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* new date search indexing
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* @see ca.uhn.fhir.jpa.search.builder.predicate.DatePredicateBuilder
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* @see ResourceIndexedSearchParamDate
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*/
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// new date search indexes
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Builder.BuilderWithTableName dateTable = version.onTable("HFJ_SPIDX_DATE");
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{
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Builder.BuilderWithTableName dateTable = version.onTable("HFJ_SPIDX_DATE");
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// replace and drop IDX_SP_DATE_HASH
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dateTable
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.addIndex("20220207.1", "IDX_SP_DATE_HASH_V2" )
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.unique(false)
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.online(true)
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.withColumns("HASH_IDENTITY", "SP_VALUE_LOW", "SP_VALUE_HIGH", "RES_ID", "PARTITION_ID");
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dateTable.dropIndexOnline("20220207.2", "IDX_SP_DATE_HASH");
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// replace and drop IDX_SP_DATE_HASH
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dateTable
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.addIndex("20220207.1", "IDX_SP_DATE_HASH_V2")
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.unique(false)
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.online(true)
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.withColumns("HASH_IDENTITY", "SP_VALUE_LOW", "SP_VALUE_HIGH", "RES_ID", "PARTITION_ID");
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dateTable.dropIndexOnline("20220207.2", "IDX_SP_DATE_HASH");
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// drop redundant
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dateTable.dropIndexOnline("20220207.3", "IDX_SP_DATE_HASH_LOW");
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// drop redundant
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dateTable.dropIndexOnline("20220207.3", "IDX_SP_DATE_HASH_LOW");
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// replace and drop IDX_SP_DATE_HASH_HIGH
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dateTable
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.addIndex("20220207.4", "IDX_SP_DATE_HASH_HIGH_V2" )
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.unique(false)
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.online(true)
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.withColumns("HASH_IDENTITY", "SP_VALUE_HIGH", "RES_ID", "PARTITION_ID");
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dateTable.dropIndexOnline("20220207.5", "IDX_SP_DATE_HASH_HIGH");
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// replace and drop IDX_SP_DATE_HASH_HIGH
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dateTable
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.addIndex("20220207.4", "IDX_SP_DATE_HASH_HIGH_V2")
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.unique(false)
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.online(true)
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.withColumns("HASH_IDENTITY", "SP_VALUE_HIGH", "RES_ID", "PARTITION_ID");
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dateTable.dropIndexOnline("20220207.5", "IDX_SP_DATE_HASH_HIGH");
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// replace and drop IDX_SP_DATE_ORD_HASH
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dateTable
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.addIndex("20220207.6", "IDX_SP_DATE_ORD_HASH_V2" )
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.unique(false)
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.online(true)
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.withColumns("HASH_IDENTITY", "SP_VALUE_LOW_DATE_ORDINAL", "SP_VALUE_HIGH_DATE_ORDINAL", "RES_ID", "PARTITION_ID");
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dateTable.dropIndexOnline("20220207.7", "IDX_SP_DATE_ORD_HASH");
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// replace and drop IDX_SP_DATE_ORD_HASH
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dateTable
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.addIndex("20220207.6", "IDX_SP_DATE_ORD_HASH_V2")
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.unique(false)
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.online(true)
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.withColumns("HASH_IDENTITY", "SP_VALUE_LOW_DATE_ORDINAL", "SP_VALUE_HIGH_DATE_ORDINAL", "RES_ID", "PARTITION_ID");
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dateTable.dropIndexOnline("20220207.7", "IDX_SP_DATE_ORD_HASH");
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// replace and drop IDX_SP_DATE_ORD_HASH_HIGH
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dateTable
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.addIndex("20220207.8", "IDX_SP_DATE_ORD_HASH_HIGH_V2" )
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.unique(false)
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.online(true)
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.withColumns("HASH_IDENTITY", "SP_VALUE_HIGH_DATE_ORDINAL", "RES_ID", "PARTITION_ID");
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dateTable.dropIndexOnline("20220207.9", "IDX_SP_DATE_ORD_HASH_HIGH");
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// replace and drop IDX_SP_DATE_ORD_HASH_HIGH
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dateTable
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.addIndex("20220207.8", "IDX_SP_DATE_ORD_HASH_HIGH_V2")
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.unique(false)
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.online(true)
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.withColumns("HASH_IDENTITY", "SP_VALUE_HIGH_DATE_ORDINAL", "RES_ID", "PARTITION_ID");
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dateTable.dropIndexOnline("20220207.9", "IDX_SP_DATE_ORD_HASH_HIGH");
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// drop redundant
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dateTable.dropIndexOnline("20220207.10", "IDX_SP_DATE_ORD_HASH_LOW");
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// drop redundant
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dateTable.dropIndexOnline("20220207.10", "IDX_SP_DATE_ORD_HASH_LOW");
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// replace and drop IDX_SP_DATE_RESID
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dateTable
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.addIndex("20220207.11", "IDX_SP_DATE_RESID_V2" )
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.unique(false)
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.online(true)
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.withColumns("RES_ID", "HASH_IDENTITY", "SP_VALUE_LOW", "SP_VALUE_HIGH", "SP_VALUE_LOW_DATE_ORDINAL", "SP_VALUE_HIGH_DATE_ORDINAL", "PARTITION_ID");
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// some engines tie the FK constraint to a particular index.
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// So we need to drop and recreate the constraint to drop the old RES_ID index.
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// Rename it while we're at it. FK17s70oa59rm9n61k9thjqrsqm was not a pretty name.
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dateTable.dropForeignKey("20220207.12", "FK17S70OA59RM9N61K9THJQRSQM", "HFJ_RESOURCE");
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dateTable.dropIndexOnline("20220207.13", "IDX_SP_DATE_RESID");
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dateTable.dropIndexOnline("20220207.14", "FK17S70OA59RM9N61K9THJQRSQM");
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// replace and drop IDX_SP_DATE_RESID
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dateTable
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.addIndex("20220207.11", "IDX_SP_DATE_RESID_V2")
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.unique(false)
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.online(true)
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.withColumns("RES_ID", "HASH_IDENTITY", "SP_VALUE_LOW", "SP_VALUE_HIGH", "SP_VALUE_LOW_DATE_ORDINAL", "SP_VALUE_HIGH_DATE_ORDINAL", "PARTITION_ID");
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// some engines tie the FK constraint to a particular index.
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// So we need to drop and recreate the constraint to drop the old RES_ID index.
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// Rename it while we're at it. FK17s70oa59rm9n61k9thjqrsqm was not a pretty name.
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dateTable.dropForeignKey("20220207.12", "FK17S70OA59RM9N61K9THJQRSQM", "HFJ_RESOURCE");
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dateTable.dropIndexOnline("20220207.13", "IDX_SP_DATE_RESID");
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dateTable.dropIndexOnline("20220207.14", "FK17S70OA59RM9N61K9THJQRSQM");
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dateTable.addForeignKey("20220207.15", "FK_SP_DATE_RES")
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.toColumn("RES_ID").references("HFJ_RESOURCE", "RES_ID");
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dateTable.addForeignKey("20220207.15", "FK_SP_DATE_RES")
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.toColumn("RES_ID").references("HFJ_RESOURCE", "RES_ID");
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// drop obsolete
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dateTable.dropIndexOnline("20220207.16", "IDX_SP_DATE_UPDATED");
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// drop obsolete
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dateTable.dropIndexOnline("20220207.16", "IDX_SP_DATE_UPDATED");
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}
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/**
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* new token search indexing
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* @see ca.uhn.fhir.jpa.search.builder.predicate.TokenPredicateBuilder
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* @see ResourceIndexedSearchParamToken
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*/
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{
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Builder.BuilderWithTableName tokenTable = version.onTable("HFJ_SPIDX_TOKEN");
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// replace and drop IDX_SP_DATE_HASH for sorting
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tokenTable
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.addIndex("20220208.1", "IDX_SP_TOKEN_HASH_V2")
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.unique(false).online(true)
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.withColumns("HASH_IDENTITY", "SP_SYSTEM", "SP_VALUE", "RES_ID", "PARTITION_ID");
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tokenTable.dropIndexOnline("20220208.2", "IDX_SP_TOKEN_HASH");
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// for search by system
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tokenTable
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.addIndex("20220208.3", "IDX_SP_TOKEN_HASH_S_V2")
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.unique(false).online(true)
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.withColumns("HASH_SYS", "RES_ID", "PARTITION_ID");
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tokenTable.dropIndexOnline("20220208.4", "IDX_SP_TOKEN_HASH_S");
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// for search by system+value
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tokenTable
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.addIndex("20220208.5", "IDX_SP_TOKEN_HASH_SV_V2")
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.unique(false).online(true)
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.withColumns("HASH_SYS_AND_VALUE", "RES_ID", "PARTITION_ID");
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tokenTable.dropIndexOnline("20220208.6", "IDX_SP_TOKEN_HASH_SV");
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// for search by value
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tokenTable
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.addIndex("20220208.7", "IDX_SP_TOKEN_HASH_V_V2")
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.unique(false).online(true)
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.withColumns("HASH_VALUE", "RES_ID", "PARTITION_ID");
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tokenTable.dropIndexOnline("20220208.8", "IDX_SP_TOKEN_HASH_V");
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// obsolete. We're dropping this column.
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tokenTable.dropIndexOnline("20220208.9", "IDX_SP_TOKEN_UPDATED");
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// for joining as second table:
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{
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// replace and drop IDX_SP_TOKEN_RESID, and the associated fk constraint
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tokenTable
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.addIndex("20220208.10", "IDX_SP_TOKEN_RESID_V2")
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.unique(false).online(true)
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.withColumns("RES_ID", "HASH_SYS_AND_VALUE", "HASH_VALUE", "HASH_SYS", "HASH_IDENTITY", "PARTITION_ID");
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// some engines tie the FK constraint to a particular index.
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// So we need to drop and recreate the constraint to drop the old RES_ID index.
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// Rename it while we're at it. FK7ULX3J1GG3V7MAQREJGC7YBC4 was not a pretty name.
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tokenTable.dropForeignKey("20220208.11", "FK7ULX3J1GG3V7MAQREJGC7YBC4", "HFJ_RESOURCE");
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tokenTable.dropIndexOnline("20220208.12", "IDX_SP_TOKEN_RESID");
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tokenTable.dropIndexOnline("20220208.13", "FK7ULX3J1GG3V7MAQREJGC7YBC4");
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tokenTable.addForeignKey("20220208.14", "FK_SP_TOKEN_RES")
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.toColumn("RES_ID").references("HFJ_RESOURCE", "RES_ID");
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}
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}
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// fix for https://github.com/hapifhir/hapi-fhir/issues/3316
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// index must have same name that indexed FK or SchemaMigrationTest complains because H2 sets this index automatically
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@ -201,6 +269,7 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
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batchChunk.addColumn("ERROR_COUNT").nonNullable().type(ColumnTypeEnum.INT);
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batchChunk.addIndex("20220227.4", "IDX_BT2WC_II_SEQ").unique(false).withColumns("INSTANCE_ID", "SEQ");
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batchChunk.addForeignKey("20220227.5", "FK_BT2WC_INSTANCE").toColumn("INSTANCE_ID").references("BT2_JOB_INSTANCE", "ID");
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}
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/**
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@ -1298,19 +1367,23 @@ public class HapiFhirJpaMigrationTasks extends BaseMigrationTasks<VersionEnum> {
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spidxToken
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.addIndex("20180903.35", "IDX_SP_TOKEN_HASH")
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.unique(false)
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.withColumns("HASH_IDENTITY");
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.withColumns("HASH_IDENTITY")
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.doNothing();
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spidxToken
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.addIndex("20180903.36", "IDX_SP_TOKEN_HASH_S")
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.unique(false)
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.withColumns("HASH_SYS");
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.withColumns("HASH_SYS")
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.doNothing();
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spidxToken
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.addIndex("20180903.37", "IDX_SP_TOKEN_HASH_SV")
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.unique(false)
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.withColumns("HASH_SYS_AND_VALUE");
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.withColumns("HASH_SYS_AND_VALUE")
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.doNothing();
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spidxToken
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.addIndex("20180903.38", "IDX_SP_TOKEN_HASH_V")
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.unique(false)
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.withColumns("HASH_VALUE");
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.withColumns("HASH_VALUE")
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.doNothing();
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spidxToken
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.addTask(new CalculateHashesTask(VersionEnum.V3_5_0, "20180903.39")
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.setColumnName("HASH_IDENTITY")
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@ -5329,7 +5329,7 @@ public class FhirResourceDaoR4LegacySearchBuilderTest extends BaseJpaR4Test {
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}
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@Override
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protected Fixture getFixture() {
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protected Fixture constructFixture() {
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return new TestDataBuilderFixture(FhirResourceDaoR4LegacySearchBuilderTest.this, myObservationDao);
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}
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}
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@ -1,58 +0,0 @@
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package ca.uhn.fhir.jpa.dao.r4;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.config.TestHibernateSearchAddInConfig;
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import ca.uhn.fhir.jpa.config.TestR4Config;
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import ca.uhn.fhir.jpa.dao.BaseDateSearchDaoTests;
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import ca.uhn.fhir.jpa.dao.BaseJpaTest;
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import ca.uhn.fhir.jpa.dao.DaoTestDataBuilder;
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import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
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import org.hl7.fhir.r4.model.Observation;
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import org.junit.jupiter.api.Nested;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.test.annotation.DirtiesContext;
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import org.springframework.test.context.ContextConfiguration;
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import org.springframework.test.context.junit.jupiter.SpringExtension;
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import org.springframework.transaction.PlatformTransactionManager;
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@ExtendWith(SpringExtension.class)
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@ContextConfiguration(classes = {TestR4Config.class, TestHibernateSearchAddInConfig.NoFT.class})
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@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
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public class FhirResourceDaoR4LuceneDisabledStandardQueries extends BaseJpaTest {
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private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4LuceneDisabledStandardQueries.class);
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@Autowired
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PlatformTransactionManager myTxManager;
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@Autowired
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FhirContext myFhirCtx;
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@Autowired
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@Qualifier("myObservationDaoR4")
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IFhirResourceDao<Observation> myObservationDao;
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@Autowired
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protected DaoRegistry myDaoRegistry;
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@Override
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protected PlatformTransactionManager getTxManager() {
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return myTxManager;
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}
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@Override
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protected FhirContext getFhirContext() {
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return myFhirCtx;
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}
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@Nested
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public class DateSearchTests extends BaseDateSearchDaoTests {
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@Override
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protected Fixture getFixture() {
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DaoTestDataBuilder testDataBuilder = new DaoTestDataBuilder(myFhirCtx, myDaoRegistry, new SystemRequestDetails());
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return new TestDataBuilderFixture<>(testDataBuilder, myObservationDao);
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}
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}
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}
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@ -756,11 +756,10 @@ public class FhirResourceDaoR4SearchWithElasticSearchIT extends BaseJpaTest {
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public class DateSearchIT extends BaseDateSearchDaoTests {
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@Override
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protected Fixture getFixture() {
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protected Fixture constructFixture() {
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DaoTestDataBuilder testDataBuilder = new DaoTestDataBuilder(myFhirCtx, myDaoRegistry, new SystemRequestDetails());
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return new TestDataBuilderFixture<>(testDataBuilder, myObservationDao);
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}
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}
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}
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@ -0,0 +1,252 @@
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package ca.uhn.fhir.jpa.dao.r4;
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import ca.uhn.fhir.context.FhirContext;
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import ca.uhn.fhir.jpa.api.dao.DaoRegistry;
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import ca.uhn.fhir.jpa.api.dao.IFhirResourceDao;
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import ca.uhn.fhir.jpa.config.TestHibernateSearchAddInConfig;
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import ca.uhn.fhir.jpa.config.TestR4Config;
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import ca.uhn.fhir.jpa.dao.BaseDateSearchDaoTests;
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import ca.uhn.fhir.jpa.dao.BaseJpaTest;
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import ca.uhn.fhir.jpa.dao.DaoTestDataBuilder;
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import ca.uhn.fhir.jpa.partition.SystemRequestDetails;
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import ca.uhn.fhir.jpa.searchparam.MatchUrlService;
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import ca.uhn.fhir.jpa.searchparam.ResourceSearch;
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import ca.uhn.fhir.jpa.searchparam.SearchParameterMap;
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import ca.uhn.fhir.rest.api.SortSpec;
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import ca.uhn.fhir.rest.api.server.IBundleProvider;
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import ca.uhn.fhir.rest.server.method.SortParameter;
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import ca.uhn.fhir.test.utilities.ITestDataBuilder;
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import org.apache.commons.lang3.tuple.ImmutableTriple;
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import org.hl7.fhir.instance.model.api.IBaseResource;
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import org.hl7.fhir.instance.model.api.IIdType;
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import org.hl7.fhir.r4.model.Observation;
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import org.junit.jupiter.api.AfterEach;
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import org.junit.jupiter.api.Nested;
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import org.junit.jupiter.api.Test;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.springframework.beans.factory.annotation.Autowired;
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import org.springframework.beans.factory.annotation.Qualifier;
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import org.springframework.test.annotation.DirtiesContext;
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import org.springframework.test.context.ContextConfiguration;
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import org.springframework.test.context.junit.jupiter.SpringExtension;
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import org.springframework.transaction.PlatformTransactionManager;
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import org.springframework.web.util.UriComponents;
|
||||
import org.springframework.web.util.UriComponentsBuilder;
|
||||
|
||||
import javax.annotation.Nonnull;
|
||||
import java.util.ArrayList;
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
import java.util.function.Consumer;
|
||||
|
||||
import static org.hamcrest.MatcherAssert.assertThat;
|
||||
import static org.hamcrest.Matchers.equalTo;
|
||||
import static org.hamcrest.Matchers.hasItem;
|
||||
import static org.hamcrest.Matchers.hasItems;
|
||||
import static org.hamcrest.Matchers.not;
|
||||
|
||||
@ExtendWith(SpringExtension.class)
|
||||
@ContextConfiguration(classes = {TestR4Config.class, TestHibernateSearchAddInConfig.NoFT.class})
|
||||
@DirtiesContext(classMode = DirtiesContext.ClassMode.AFTER_CLASS)
|
||||
public class FhirResourceDaoR4StandardQueriesNoFTTest extends BaseJpaTest {
|
||||
private static final Logger ourLog = LoggerFactory.getLogger(FhirResourceDaoR4StandardQueriesNoFTTest.class);
|
||||
@Autowired
|
||||
PlatformTransactionManager myTxManager;
|
||||
@Autowired
|
||||
FhirContext myFhirCtx;
|
||||
@Autowired
|
||||
@Qualifier("myObservationDaoR4")
|
||||
IFhirResourceDao<Observation> myObservationDao;
|
||||
@Autowired
|
||||
protected DaoRegistry myDaoRegistry;
|
||||
@Autowired
|
||||
MatchUrlService myMatchUrlService;
|
||||
|
||||
@Override
|
||||
protected PlatformTransactionManager getTxManager() {
|
||||
return myTxManager;
|
||||
}
|
||||
|
||||
@Override
|
||||
protected FhirContext getFhirContext() {
|
||||
return myFhirCtx;
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class DateSearchTests extends BaseDateSearchDaoTests {
|
||||
@Override
|
||||
protected Fixture constructFixture() {
|
||||
DaoTestDataBuilder testDataBuilder = new DaoTestDataBuilder(myFhirCtx, myDaoRegistry, new SystemRequestDetails());
|
||||
return new TestDataBuilderFixture<>(testDataBuilder, myObservationDao);
|
||||
}
|
||||
}
|
||||
|
||||
public static class TokenTestCase {
|
||||
|
||||
private Consumer<IBaseResource>[] myBuilders;
|
||||
private List<ImmutableTriple<Boolean, String, String>> mySearchCases = new ArrayList<>();
|
||||
|
||||
public static TokenTestCase onObservation(Consumer<IBaseResource>... theBuilders) {
|
||||
TokenTestCase result = new TokenTestCase();
|
||||
result.myBuilders = theBuilders;
|
||||
return result;
|
||||
}
|
||||
|
||||
public TokenTestCase finds(String theMessage, String theQuery) {
|
||||
mySearchCases.add(new ImmutableTriple(true,theMessage, theQuery));
|
||||
return this;
|
||||
}
|
||||
public TokenTestCase doesNotFind(String theMessage, String theQuery) {
|
||||
mySearchCases.add(new ImmutableTriple(false,theMessage, theQuery));
|
||||
return this;
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class TokenSearch {
|
||||
// wipmb make this generic and share with ES, and Mongo.
|
||||
/*
|
||||
String criteria = "_has:Condition:subject:code=http://snomed.info/sct|55822003,http://snomed.info/sct|55822005&" +
|
||||
"_has:Condition:asserter:code=http://snomed.info/sct|55822003,http://snomed.info/sct|55822004";
|
||||
*/
|
||||
|
||||
ITestDataBuilder myDataBuilder = new DaoTestDataBuilder(myFhirCtx, myDaoRegistry, new SystemRequestDetails());
|
||||
Set<IIdType> myCreatedIds = new HashSet<>();
|
||||
|
||||
@AfterEach
|
||||
public void cleanup() {
|
||||
ourLog.info("cleanup {}", myCreatedIds);
|
||||
myCreatedIds.forEach(myObservationDao::delete);
|
||||
}
|
||||
|
||||
|
||||
@Nested
|
||||
public class Queries {
|
||||
IIdType myObservationId;
|
||||
|
||||
@Test
|
||||
public void systemAndCode() {
|
||||
withObservation(myDataBuilder.withObservationCode("http://example.com", "value"));
|
||||
|
||||
assertFind("by system and code", "/Observation?code=http://example.com|value");
|
||||
assertFind("by system, any code", "/Observation?code=http://example.com|");
|
||||
assertFind("by code, any system", "/Observation?code=value");
|
||||
assertNotFind("by same system, different code", "/Observation?code=http://example.com|other");
|
||||
assertNotFind("by same code, different system", "/Observation?code=http://example2.com|value");
|
||||
assertNotFind("by different code, different system", "/Observation?code=http://example2.com|otherValue");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void emptySystem() {
|
||||
withObservation(myDataBuilder.withObservationCode("", "value"));
|
||||
|
||||
assertFind("by system and code", "/Observation?code=|value");
|
||||
assertFind("by system, any code", "/Observation?code=|");
|
||||
assertFind("by code, any system", "/Observation?code=value");
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class NotModifier {
|
||||
@Test
|
||||
public void simple() {
|
||||
withObservation(myDataBuilder.withObservationCode("http://example.com", "value"));
|
||||
|
||||
assertFind("by same system, different code", "/Observation?code:not=http://example.com|other");
|
||||
assertFind("by same code, different system", "/Observation?code:not=http://example2.com|value");
|
||||
assertFind("by different code, different system", "/Observation?code:not=http://example2.com|otherValue");
|
||||
assertNotFind("by system and code", "/Observation?code:not=http://example.com|value");
|
||||
assertNotFind("by system, any code", "/Observation?code:not=http://example.com|");
|
||||
assertNotFind("by code, any system", "/Observation?code:not=value");
|
||||
}
|
||||
|
||||
@Test
|
||||
public void findsEmpty() {
|
||||
withObservation();
|
||||
|
||||
assertFind("by system and code", "/Observation?code:not=http://example.com|value");
|
||||
assertFind("by system, any code", "/Observation?code:not=http://example.com|");
|
||||
assertFind("by code, any system", "/Observation?code:not=value");
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class TextModifier {
|
||||
@Test
|
||||
public void systemAndCode() {
|
||||
withObservation(myDataBuilder.withObservationCode("http://example.com", "value", "the display text"));
|
||||
assertFind("by code display", "/Observation?code:text=the%20display%20text");
|
||||
}
|
||||
}
|
||||
|
||||
@Nested
|
||||
public class Sorting {
|
||||
@Test
|
||||
public void sortBySystemThenValue() {
|
||||
String idAlphaM = withObservation(myDataBuilder.withObservationCode("http://alpha.org", "Mvalue")).getIdPart();
|
||||
String idAlphaA = withObservation(myDataBuilder.withObservationCode("http://alpha.org", "Avalue")).getIdPart();
|
||||
String idAlphaZ = withObservation(myDataBuilder.withObservationCode("http://alpha.org", "Zvalue")).getIdPart();
|
||||
|
||||
String idExD = withObservation(myDataBuilder.withObservationCode("http://example.org", "DValue")).getIdPart();
|
||||
String idExA = withObservation(myDataBuilder.withObservationCode("http://example.org", "AValue")).getIdPart();
|
||||
String idExM = withObservation(myDataBuilder.withObservationCode("http://example.org", "MValue")).getIdPart();
|
||||
|
||||
List<String> allIds = searchForIds("/Observation?_sort=code");
|
||||
assertThat(allIds, hasItems(idAlphaA, idAlphaM, idAlphaZ, idExA, idExD, idExM));
|
||||
|
||||
allIds = searchForIds("/Observation?_sort=code&code=http://example.org|");
|
||||
assertThat(allIds, hasItems(idExA, idExD, idExM));
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
private IIdType withObservation(Consumer<IBaseResource>... theBuilder) {
|
||||
myObservationId = myDataBuilder.createObservation(theBuilder);
|
||||
myCreatedIds.add(myObservationId);
|
||||
return myObservationId;
|
||||
}
|
||||
|
||||
private void assertFind(String theMessage, String theUrl) {
|
||||
List<String> resourceIds = searchForIds(theUrl);
|
||||
assertThat(theMessage, resourceIds, hasItem(equalTo(myObservationId.getIdPart())));
|
||||
}
|
||||
|
||||
private void assertNotFind(String theMessage, String theUrl) {
|
||||
List<String> resourceIds = searchForIds(theUrl);
|
||||
assertThat(theMessage, resourceIds, not(hasItem(equalTo(myObservationId.getIdPart()))));
|
||||
}
|
||||
}
|
||||
|
||||
private List<String> searchForIds(String theQueryUrl) {
|
||||
// fake out the server url parsing
|
||||
ResourceSearch search = myMatchUrlService.getResourceSearch(theQueryUrl);
|
||||
SearchParameterMap map = search.getSearchParameterMap();
|
||||
map.setLoadSynchronous(true);
|
||||
SystemRequestDetails request = fakeRequestDetailsFromUrl(theQueryUrl);
|
||||
SortSpec sort = (SortSpec) new SortParameter(myFhirCtx).translateQueryParametersIntoServerArgument(request, null);
|
||||
if (sort != null) {
|
||||
map.setSort(sort);
|
||||
}
|
||||
|
||||
IBundleProvider result = myObservationDao.search(map);
|
||||
|
||||
List<String> resourceIds = result.getAllResourceIds();
|
||||
return resourceIds;
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
@Nonnull
|
||||
private SystemRequestDetails fakeRequestDetailsFromUrl(String theQueryUrl) {
|
||||
SystemRequestDetails request = new SystemRequestDetails();
|
||||
UriComponents uriComponents = UriComponentsBuilder.fromUriString(theQueryUrl).build();
|
||||
uriComponents.getQueryParams().entrySet().forEach(nextEntry -> {
|
||||
request.addParameter(nextEntry.getKey(), nextEntry.getValue().toArray(new String[0]));
|
||||
});
|
||||
return request;
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -70,6 +70,7 @@ import org.slf4j.LoggerFactory;
|
|||
import java.util.Date;
|
||||
import java.util.List;
|
||||
import java.util.Locale;
|
||||
import java.util.TimeZone;
|
||||
import java.util.concurrent.atomic.AtomicInteger;
|
||||
import java.util.function.Supplier;
|
||||
import java.util.stream.Collectors;
|
||||
|
|
@ -101,6 +102,9 @@ public class PartitioningSqlR4Test extends BasePartitioningR4Test {
|
|||
@BeforeEach
|
||||
public void disableAdvanceIndexing() {
|
||||
myDaoConfig.setAdvancedLuceneIndexing(false);
|
||||
// ugh - somewhere the hibernate round trip is mangling LocalDate to h2 date column unless the tz=GMT
|
||||
TimeZone.setDefault(TimeZone.getTimeZone("GMT"));
|
||||
ourLog.info("Running with Timezone {}", TimeZone.getDefault().getID());
|
||||
}
|
||||
|
||||
@Test
|
||||
|
|
|
|||
|
|
@ -53,89 +53,88 @@ class TokenAutocompleteAggregationTest {
|
|||
@Nested
|
||||
public class ResultExtraction {
|
||||
// Sample result from elastic for Observation.code
|
||||
String resultJson = """
|
||||
{
|
||||
"doc_count": 22770,
|
||||
"search": {
|
||||
"doc_count": 4,
|
||||
"group_by_token": {
|
||||
"doc_count_error_upper_bound": 0,
|
||||
"sum_other_doc_count": 0,
|
||||
"buckets": [
|
||||
{
|
||||
"key": "http://loinc.org|59460-6",
|
||||
"doc_count": 2,
|
||||
"top_tags_hits": {
|
||||
"hits": {
|
||||
"total": {
|
||||
"value": 2,
|
||||
"relation": "eq"
|
||||
},
|
||||
"max_score": 4.9845064e-05,
|
||||
"hits": [
|
||||
{
|
||||
"_index": "resourcetable-000001",
|
||||
"_type": "_doc",
|
||||
"_id": "1405280",
|
||||
"_nested": {
|
||||
"field": "nsp.code",
|
||||
"offset": 0
|
||||
},
|
||||
"_score": 4.9845064e-05,
|
||||
"_source": {
|
||||
"string": {
|
||||
"text": "Fall risk total [Morse Fall Scale]"
|
||||
},
|
||||
"token": {
|
||||
"code": "59460-6",
|
||||
"system": "http://loinc.org",
|
||||
"code-system": "http://loinc.org|59460-6"
|
||||
}
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
},
|
||||
{
|
||||
"key": "http://loinc.org|59461-4",
|
||||
"doc_count": 2,
|
||||
"top_tags_hits": {
|
||||
"hits": {
|
||||
"total": {
|
||||
"value": 2,
|
||||
"relation": "eq"
|
||||
},
|
||||
"max_score": 4.9845064e-05,
|
||||
"hits": [
|
||||
{
|
||||
"_index": "resourcetable-000001",
|
||||
"_type": "_doc",
|
||||
"_id": "1405281",
|
||||
"_nested": {
|
||||
"field": "nsp.code",
|
||||
"offset": 0
|
||||
},
|
||||
"_score": 4.9845064e-05,
|
||||
"_source": {
|
||||
"string": {
|
||||
"text": "Fall risk level [Morse Fall Scale]"
|
||||
},
|
||||
"token": {
|
||||
"code": "59461-4",
|
||||
"system": "http://loinc.org",
|
||||
"code-system": "http://loinc.org|59461-4"
|
||||
}
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
}""";
|
||||
String resultJson = "{ " +
|
||||
" \"doc_count\": 22770, " +
|
||||
" \"search\": { " +
|
||||
" \"doc_count\": 4, " +
|
||||
" \"group_by_token\": { " +
|
||||
" \"doc_count_error_upper_bound\": 0, " +
|
||||
" \"sum_other_doc_count\": 0, " +
|
||||
" \"buckets\": [ " +
|
||||
" { " +
|
||||
" \"key\": \"http://loinc.org|59460-6\", " +
|
||||
" \"doc_count\": 2, " +
|
||||
" \"top_tags_hits\": { " +
|
||||
" \"hits\": { " +
|
||||
" \"total\": { " +
|
||||
" \"value\": 2, " +
|
||||
" \"relation\": \"eq\" " +
|
||||
" }, " +
|
||||
" \"max_score\": 4.9845064e-05, " +
|
||||
" \"hits\": [ " +
|
||||
" { " +
|
||||
" \"_index\": \"resourcetable-000001\", " +
|
||||
" \"_type\": \"_doc\", " +
|
||||
" \"_id\": \"1405280\", " +
|
||||
" \"_nested\": { " +
|
||||
" \"field\": \"nsp.code\", " +
|
||||
" \"offset\": 0 " +
|
||||
" }, " +
|
||||
" \"_score\": 4.9845064e-05, " +
|
||||
" \"_source\": { " +
|
||||
" \"string\": { " +
|
||||
" \"text\": \"Fall risk total [Morse Fall Scale]\" " +
|
||||
" }, " +
|
||||
" \"token\": { " +
|
||||
" \"code\": \"59460-6\", " +
|
||||
" \"system\": \"http://loinc.org\", " +
|
||||
" \"code-system\": \"http://loinc.org|59460-6\" " +
|
||||
" } " +
|
||||
" } " +
|
||||
" } " +
|
||||
" ] " +
|
||||
" } " +
|
||||
" } " +
|
||||
" }, " +
|
||||
" { " +
|
||||
" \"key\": \"http://loinc.org|59461-4\", " +
|
||||
" \"doc_count\": 2, " +
|
||||
" \"top_tags_hits\": { " +
|
||||
" \"hits\": { " +
|
||||
" \"total\": { " +
|
||||
" \"value\": 2, " +
|
||||
" \"relation\": \"eq\" " +
|
||||
" }, " +
|
||||
" \"max_score\": 4.9845064e-05, " +
|
||||
" \"hits\": [ " +
|
||||
" { " +
|
||||
" \"_index\": \"resourcetable-000001\", " +
|
||||
" \"_type\": \"_doc\", " +
|
||||
" \"_id\": \"1405281\", " +
|
||||
" \"_nested\": { " +
|
||||
" \"field\": \"nsp.code\", " +
|
||||
" \"offset\": 0 " +
|
||||
" }, " +
|
||||
" \"_score\": 4.9845064e-05, " +
|
||||
" \"_source\": { " +
|
||||
" \"string\": { " +
|
||||
" \"text\": \"Fall risk level [Morse Fall Scale]\" " +
|
||||
" }, " +
|
||||
" \"token\": { " +
|
||||
" \"code\": \"59461-4\", " +
|
||||
" \"system\": \"http://loinc.org\", " +
|
||||
" \"code-system\": \"http://loinc.org|59461-4\" " +
|
||||
" } " +
|
||||
" } " +
|
||||
" } " +
|
||||
" ] " +
|
||||
" } " +
|
||||
" } " +
|
||||
" } " +
|
||||
" ] " +
|
||||
" } " +
|
||||
" } " +
|
||||
"}";
|
||||
JsonObject parsedResult = new Gson().fromJson(resultJson, JsonObject.class);
|
||||
TokenAutocompleteAggregation myAutocompleteAggregation = new TokenAutocompleteAggregation("code", 22, null, null);
|
||||
|
||||
|
|
|
|||
|
|
@ -97,7 +97,10 @@ public class ResourceIndexedSearchParamDate extends BaseResourceIndexedSearchPar
|
|||
@GeneratedValue(strategy = GenerationType.AUTO, generator = "SEQ_SPIDX_DATE")
|
||||
@Column(name = "SP_ID")
|
||||
private Long myId;
|
||||
|
||||
/**
|
||||
* Composite of resourceType, paramName, and partition info if configured.
|
||||
* Combined with the various date fields for a query.
|
||||
* @since 3.5.0 - At some point this should be made not-null
|
||||
*/
|
||||
@Column(name = "HASH_IDENTITY", nullable = true)
|
||||
|
|
|
|||
|
|
@ -34,7 +34,6 @@ import org.apache.commons.lang3.builder.ToStringStyle;
|
|||
import javax.persistence.Column;
|
||||
import javax.persistence.Embeddable;
|
||||
import javax.persistence.Entity;
|
||||
import javax.persistence.FetchType;
|
||||
import javax.persistence.ForeignKey;
|
||||
import javax.persistence.GeneratedValue;
|
||||
import javax.persistence.GenerationType;
|
||||
|
|
|
|||
|
|
@ -59,16 +59,12 @@ import static org.apache.commons.lang3.StringUtils.trim;
|
|||
* IDX_SP_TOKEN_UNQUAL
|
||||
*/
|
||||
|
||||
// TODO PERF Recommend to drop this index (added by JA - I don't actually think we even need the identity hash for this type, we could potentially drop the column too):
|
||||
@Index(name = "IDX_SP_TOKEN_HASH", columnList = "HASH_IDENTITY"),
|
||||
@Index(name = "IDX_SP_TOKEN_HASH_S", columnList = "HASH_SYS"),
|
||||
@Index(name = "IDX_SP_TOKEN_HASH_SV", columnList = "HASH_SYS_AND_VALUE"),
|
||||
// TODO PERF change this to:
|
||||
// @Index(name = "IDX_SP_TOKEN_HASH_V", columnList = "HASH_VALUE,RES_ID"),
|
||||
@Index(name = "IDX_SP_TOKEN_HASH_V", columnList = "HASH_VALUE"),
|
||||
@Index(name = "IDX_SP_TOKEN_HASH_V2", columnList = "HASH_IDENTITY,SP_SYSTEM,SP_VALUE,RES_ID,PARTITION_ID"),
|
||||
@Index(name = "IDX_SP_TOKEN_HASH_S_V2", columnList = "HASH_SYS,RES_ID,PARTITION_ID"),
|
||||
@Index(name = "IDX_SP_TOKEN_HASH_SV_V2", columnList = "HASH_SYS_AND_VALUE,RES_ID,PARTITION_ID"),
|
||||
@Index(name = "IDX_SP_TOKEN_HASH_V_V2", columnList = "HASH_VALUE,RES_ID,PARTITION_ID"),
|
||||
|
||||
@Index(name = "IDX_SP_TOKEN_UPDATED", columnList = "SP_UPDATED"),
|
||||
@Index(name = "IDX_SP_TOKEN_RESID", columnList = "RES_ID")
|
||||
@Index(name = "IDX_SP_TOKEN_RESID_V2", columnList = "RES_ID,HASH_SYS_AND_VALUE,HASH_VALUE,HASH_SYS,HASH_IDENTITY,PARTITION_ID")
|
||||
})
|
||||
public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchParam {
|
||||
|
||||
|
|
@ -112,11 +108,10 @@ public class ResourceIndexedSearchParamToken extends BaseResourceIndexedSearchPa
|
|||
private Long myHashValue;
|
||||
|
||||
@ManyToOne(optional = false, fetch = FetchType.LAZY, cascade = {})
|
||||
@JoinColumn(foreignKey = @ForeignKey(name = "FK7ULX3J1GG3V7MAQREJGC7YBC4"),
|
||||
@JoinColumn(foreignKey = @ForeignKey(name="FK_SP_TOKEN_RES"),
|
||||
name = "RES_ID", referencedColumnName = "RES_ID", nullable = false)
|
||||
private ResourceTable myResource;
|
||||
|
||||
|
||||
/**
|
||||
* Constructor
|
||||
*/
|
||||
|
|
|
|||
|
|
@ -8,13 +8,18 @@ import ca.uhn.fhir.rest.param.DateParam;
|
|||
import ca.uhn.fhir.test.utilities.ITestDataBuilder;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
import org.hl7.fhir.instance.model.api.IIdType;
|
||||
import org.junit.jupiter.api.AfterEach;
|
||||
import org.junit.jupiter.api.BeforeEach;
|
||||
import org.junit.jupiter.params.ParameterizedTest;
|
||||
import org.junit.jupiter.params.provider.Arguments;
|
||||
import org.junit.jupiter.params.provider.MethodSource;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import java.util.HashSet;
|
||||
import java.util.List;
|
||||
import java.util.Set;
|
||||
import java.util.TimeZone;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
|
@ -30,6 +35,29 @@ public abstract class BaseDateSearchDaoTests {
|
|||
*/
|
||||
IIdType myObservationId;
|
||||
|
||||
Fixture myFixture;
|
||||
|
||||
//time zone set to EST
|
||||
@BeforeEach
|
||||
public void setTimeZoneEST() {
|
||||
TimeZone.setDefault(TimeZone.getTimeZone("EST"));
|
||||
}
|
||||
|
||||
//reset time zone back to match the system
|
||||
@AfterEach
|
||||
public void resetTimeZone() {
|
||||
TimeZone.setDefault(null);
|
||||
}
|
||||
|
||||
@BeforeEach
|
||||
public void setupFixture() {
|
||||
myFixture = constructFixture();
|
||||
}
|
||||
@AfterEach
|
||||
public void cleanup() {
|
||||
myFixture.cleanup();
|
||||
}
|
||||
|
||||
/**
|
||||
* Test for our date search operators.
|
||||
* <p>
|
||||
|
|
@ -50,15 +78,14 @@ public abstract class BaseDateSearchDaoTests {
|
|||
//@CsvSource("2019-12-31T08:00:00,eq2020,false,inline,1")
|
||||
@MethodSource("dateSearchCases")
|
||||
public void testDateSearchMatching(String theResourceDate, String theQuery, boolean theExpectedMatch, String theFileName, int theLineNumber) {
|
||||
Fixture fixture = getFixture();
|
||||
if (isShouldSkip(theResourceDate, theQuery)) {
|
||||
return;
|
||||
}
|
||||
// setup
|
||||
myObservationId = fixture.createObservationWithEffectiveDate(theResourceDate);
|
||||
myObservationId = myFixture.createObservationWithEffectiveDate(theResourceDate);
|
||||
|
||||
// run the query
|
||||
boolean matched = fixture.isObservationSearchMatch(theQuery, myObservationId);
|
||||
boolean matched = myFixture.isObservationSearchMatch(theQuery, myObservationId);
|
||||
|
||||
assertExpectedMatch(theResourceDate, theQuery, theExpectedMatch, matched, theFileName, theLineNumber);
|
||||
}
|
||||
|
|
@ -91,7 +118,7 @@ public abstract class BaseDateSearchDaoTests {
|
|||
*
|
||||
* Use an abstract method instead of a constructor because JUnit has a such a funky lifecycle.
|
||||
*/
|
||||
protected abstract Fixture getFixture();
|
||||
protected abstract Fixture constructFixture();
|
||||
|
||||
public interface Fixture {
|
||||
/**
|
||||
|
|
@ -104,11 +131,13 @@ public abstract class BaseDateSearchDaoTests {
|
|||
*/
|
||||
boolean isObservationSearchMatch(String theQuery, IIdType theObservationId);
|
||||
|
||||
void cleanup();
|
||||
}
|
||||
|
||||
public static class TestDataBuilderFixture<O extends IBaseResource> implements Fixture {
|
||||
final ITestDataBuilder myTestDataBuilder;
|
||||
final IFhirResourceDao<O> myObservationDao;
|
||||
final Set<IIdType> myCreatedIds = new HashSet<>();
|
||||
|
||||
public TestDataBuilderFixture(ITestDataBuilder theTestDataBuilder, IFhirResourceDao<O> theObservationDao) {
|
||||
myTestDataBuilder = theTestDataBuilder;
|
||||
|
|
@ -117,7 +146,9 @@ public abstract class BaseDateSearchDaoTests {
|
|||
|
||||
@Override
|
||||
public IIdType createObservationWithEffectiveDate(String theResourceDate) {
|
||||
return myTestDataBuilder.createObservation(myTestDataBuilder.withEffectiveDate(theResourceDate));
|
||||
IIdType id = myTestDataBuilder.createObservation(myTestDataBuilder.withEffectiveDate(theResourceDate));
|
||||
myCreatedIds.add(id);
|
||||
return id;
|
||||
}
|
||||
|
||||
@Override
|
||||
|
|
@ -131,5 +162,11 @@ public abstract class BaseDateSearchDaoTests {
|
|||
boolean matched = results.getAllResourceIds().contains(theObservationId.getIdPart());
|
||||
return matched;
|
||||
}
|
||||
|
||||
@Override
|
||||
public void cleanup() {
|
||||
myCreatedIds.forEach(myObservationDao::delete);
|
||||
myCreatedIds.clear();
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -25,6 +25,7 @@ import ca.uhn.fhir.context.BaseRuntimeElementCompositeDefinition;
|
|||
import ca.uhn.fhir.context.FhirContext;
|
||||
import ca.uhn.fhir.context.RuntimeResourceDefinition;
|
||||
import ca.uhn.fhir.util.FhirTerser;
|
||||
import org.apache.commons.lang3.StringUtils;
|
||||
import org.hl7.fhir.instance.model.api.IBase;
|
||||
import org.hl7.fhir.instance.model.api.IBaseReference;
|
||||
import org.hl7.fhir.instance.model.api.IBaseResource;
|
||||
|
|
@ -185,11 +186,18 @@ public interface ITestDataBuilder {
|
|||
}
|
||||
|
||||
default Consumer<IBaseResource> withObservationCode(@Nullable String theSystem, @Nullable String theCode) {
|
||||
return withObservationCode(theSystem, theCode, null);
|
||||
}
|
||||
|
||||
default Consumer<IBaseResource> withObservationCode(@Nullable String theSystem, @Nullable String theCode, String theDisplay) {
|
||||
return t -> {
|
||||
FhirTerser terser = getFhirContext().newTerser();
|
||||
IBase coding = terser.addElement(t, "code.coding");
|
||||
terser.addElement(coding, "system", theSystem);
|
||||
terser.addElement(coding, "code", theCode);
|
||||
if (StringUtils.isNotEmpty(theDisplay)) {
|
||||
terser.addElement(coding, "display", theDisplay);
|
||||
}
|
||||
};
|
||||
}
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue