POC of nested reverseResolve. #3809
piotrszultest.yml
on: push
Encoders
6m 15s
FHIR server (tranche 1)
8m 26s
FHIR server (tranche 2)
7m 33s
FHIR server (tranche 3)
6s
Docker image
5m 18s
Python API
5m 26s
JavaScript client
47s
Import lambda
52s
R API
0s
Site
4m 39s
Pre-release deployment
0s
Upload coverage
0s
Annotations
65 errors and 16 warnings
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R API
This request has been automatically failed because it uses a deprecated version of `actions/upload-artifact: v2`. Learn more: https://github.blog/changelog/2024-02-13-deprecation-notice-v1-and-v2-of-the-artifact-actions/
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FHIR server (tranche 3)
Credentials could not be loaded, please check your action inputs: Could not load credentials from any providers
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Site
Process completed with exit code 1.
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Docker image
Process completed with exit code 1.
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Python API
Process completed with exit code 1.
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ManifestConverterTest.convertsManifest:
fhir-server/src/test/java/au/csiro/pathling/security/ga4gh/ManifestConverterTest.java#L126
[DATATYPE_MISMATCH.BINARY_OP_DIFF_TYPES] Cannot resolve "(Procedure.performer.actor.reference = Procedure__REF@Patient__ckey)" due to data type mismatch: the left and right operands of the binary operator have incompatible types ("ARRAY<STRING>" and "STRING").;
'Join LeftOuter, (Procedure#21738.performer.actor.reference = Procedure__REF@Patient__ckey#22635)
:- Project [id#21657, id_versioned#21658 AS key#21737, struct(id, id#21657, id_versioned, id_versioned#21658, meta, meta#21659, implicitRules, implicitRules#21660, language, language#21661, text, text#21662, identifier, identifier#21663, instantiatesCanonical, instantiatesCanonical#21664, instantiatesUri, instantiatesUri#21665, basedOn, basedOn#21666, partOf, partOf#21667, status, status#21668, statusReason, statusReason#21669, category, category#21670, code, code#21671, subject, subject#21672, encounter, encounter#21673, performedAge, performedAge#21674, performedDateTime, performedDateTime#21675, performedPeriod, performedPeriod#21676, performedRange, performedRange#21677, performedString, performedString#21678, recorder, recorder#21679, asserter, asserter#21680, performer, performer#21681, location, location#21682, reasonCode, reasonCode#21683, reasonReference, reasonReference#21684, bodySite, bodySite#21685, outcome, outcome#21686, report, report#21687, complication, complication#21688, complicationDetail, complicationDetail#21689, followUp, followUp#21690, note, note#21691, focalDevice, focalDevice#21692, usedReference, usedReference#21693, usedCode, usedCode#21694) AS Procedure#21738, _fid#21695, _extension#21696]
: +- Relation [id#21657,id_versioned#21658,meta#21659,implicitRules#21660,language#21661,text#21662,identifier#21663,instantiatesCanonical#21664,instantiatesUri#21665,basedOn#21666,partOf#21667,status#21668,statusReason#21669,category#21670,code#21671,subject#21672,encounter#21673,performedAge#21674,performedDateTime#21675,performedPeriod#21676,performedRange#21677,performedString#21678,recorder#21679,asserter#21680,performer#21681,location#21682,reasonCode#21683,reasonReference#21684,bodySite#21685,outcome#21686,report#21687,complication#21688,complicationDetail#21689,followUp#21690,note#21691,focalDevice#21692,usedReference#21693,usedCode#21694,_fid#21695,_extension#21696] parquet
+- Project [key#22618 AS Procedure__REF@Patient__ckey#22635, Procedure__REF@Patient__value#22626]
+- Project [id#22566, key#22618, Patient#22619, _fid#22590, _extension#22591, CASE WHEN isnotnull(CASE WHEN isnotnull(filter(filter(Patient#22619.identifier, lambdafunction((lambda x_6#22627.system = https://github.com/synthetichealth/synthea), lambda x_6#22627, false)), lambdafunction(coalesce(array_contains(concat(concat(concat(CASE WHEN isnotnull(0dc85075-4f59-4e4f-b75d-a2f601d0cf24) THEN array(0dc85075-4f59-4e4f-b75d-a2f601d0cf24) END, CASE WHEN isnotnull(1f276fc3-7e91-4fc9-a287-be19228e8807) THEN array(1f276fc3-7e91-4fc9-a287-be19228e8807) END), CASE WHEN isnotnull(f34e77c9-df31-49c4-92e2-e871fa76026e) THEN array(f34e77c9-df31-49c4-92e2-e871fa76026e) END), CASE WHEN isnotnull(2cc8ffdd-6233-4dd4-ba71-36eccb8204e2) THEN array(2cc8ffdd-6233-4dd4-ba71-36eccb8204e2) END), lambda x_7#22628.value), false), lambda x_7#22628, false))) THEN (size(filter(filter(Patient#22619.identifier, lambdafunction((lambda x_6#22627.system = https://github.com/synthetichealth/synthea), lambda x_6#22627, false)), lambdafunction(coalesce(array_contains(concat(concat(concat(CASE WHEN isnotnull(0dc85075-4f59-4e4f-b75d-a2f601d0cf24) THEN array(0dc85075-4f59-4e4f-b75d-a2f601d0cf24) END, CASE WHEN isnotnull(1f276fc3-7e91-4fc9-a287-be19228e8807) THEN array(1f276fc3-7e91-4fc9-a287-be19228e8807) END), CASE WHEN isnotnull(f34e77c9-df31-49c4-92e2-e871fa76026e) THEN array(f34e77c9-df31-49c4-92e2-e871fa76026e) END), CASE WHEN isnotnull(2cc8ffdd-6233-4dd4-ba71-36eccb8204e2) THEN array(2cc8ffdd-6233-4dd4-ba71-36eccb8204e2) END), lambda x_7#22628.value), false), lambda x_7#22628, false)), true) = 0) ELSE true END) THEN NOT CASE WHEN isnotnull(filter(filter(Patient#22619.identifier, lambdafunction((lambda x_6#22627.system = https://github.com/synthetichealth/synthea), lambda x_6#22627, false)), lambdafunction(coalesce(array_contains(concat(concat(concat(CASE WHEN isnotnull(0dc85075-4f59-4e4f-b75d-a2f601d0cf24) THEN array(0dc85075-4f59-4e4f-b75d-a2f601d0cf24) END, CASE WHEN isnotnull(1f276fc3-7e91-4fc9-a287-be19228e8807) THEN array(1f276fc3-7e91-4fc9-a287-be19228e8807) END), CASE WHEN isnotnull(f34e77c9-df31-49c4-92e2-e871fa76026e) THEN array(f34e77c9-df31-49c4-92e2-e871fa76026e) END), CASE WHEN isnotnull(2cc8ffdd-6233-4dd4-ba71-36eccb8204e2) THEN array(2cc8ffdd-6233-4dd4-ba71-36eccb8204e2) END), lambda x_7#22628.value), false), lambda x_7#22628, false))) THEN (size(filter(filter(Patient#22619.identifier, lambdafunction((lambda x_6#22627.system = https://github.com/synthetichealth/synthea), lambda x_6#22627, false)), lambdafunction(coalesce(array_contains(concat(concat(concat(CASE WHEN isnotnull(0dc85075-4f59-4e4f-b75d-a2f601d0cf24) THEN array(0dc85075-4f59-4e4f-b75d-a2f601d0cf24) END, CASE WHEN isnotnull(1f276fc3-7e91-4fc9-a287-be19228e8807) THEN array(1f276fc3-7e91-4fc9-a287-be19228e8807) END), CASE WHEN isnotnull(f34e77c9-df31-49c4-92e2-e871fa76026e) THEN array(f34e77c9-df31-49c4-92e2-e871fa76026e) END), CASE WHEN isnotnull(2cc8ffdd-6233-4dd4-ba71-36eccb8204e2) THEN array(2cc8ffdd-6233-4dd4-ba71-36eccb8204e2) END), lambda x_7#22628.value), false), lambda x_7#22628, false)), true) = 0) ELSE true END END AS Procedure__REF@Patient__value#22626]
+- Project [id#22566, id_versioned#22567 AS key#22618, struct(id, id#22566, id_versioned, id_versioned#22567, meta, meta#22568, implicitRules, implicitRules#22569, language, language#22570, text, text#22571, identifier, identifier#22572, active, active#22573, name, name#22574, telecom, telecom#22575, gender, gender#22576, birthDate, birthDate#22577, deceasedBoolean, deceasedBoolean#22578, deceasedDateTime, deceasedDateTime#22579, address, address#22580, maritalStatus, maritalStatus#22581, multipleBirthBoolean, multipleBirthBoolean#22582, multipleBirthInteger, multipleBirthInteger#22583, photo, photo#22584, contact, contact#22585, communication, communication#22586, generalPractitioner, generalPractitioner#22587, managingOrganization, managingOrganization#22588, link, link#22589) AS Patient#22619, _fid#22590, _extension#22591]
+- Relation [id#22566,id_versioned#22567,meta#22568,implicitRules#22569,language#22570,text#22571,identifier#22572,active#22573,name#22574,telecom#22575,gender#22576,birthDate#22577,deceasedBoolean#22578,deceasedDateTime#22579,address#22580,maritalStatus#22581,multipleBirthBoolean#22582,multipleBirthInteger#22583,photo#22584,contact#22585,communication#22586,generalPractitioner#22587,managingOrganization#22588,link#22589,_fid#22590,_extension#22591] parquet
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AsyncTest.asyncExtract:
fhir-server/src/test/java/au/csiro/pathling/test/integration/AsyncTest.java#L84
expected: <202 ACCEPTED> but was: <500 INTERNAL_SERVER_ERROR>
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CachedSearchTest.searchWithNoFilter:
fhir-server/src/test/java/au/csiro/pathling/test/integration/CachedSearchTest.java#L57
expected: <true> but was: <false>
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CapabilityStatementTest.capabilityStatement:
fhir-server/src/test/java/au/csiro/pathling/test/integration/CapabilityStatementTest.java#L61
rest[mode=server].resource[]: Expected 141 values but got 142
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ExtractTest.extract:
fhir-server/src/test/java/au/csiro/pathling/test/integration/ExtractTest.java#L77
expected: <true> but was: <false>
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SearchTest.searchWithNoFilter:
fhir-server/src/test/java/au/csiro/pathling/test/integration/SearchTest.java#L62
expected: <true> but was: <false>
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FHIR server (tranche 2)
There were 8 failed tests
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AggregateQueryExecutorTest.simpleQueryWithLabels:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryExecutorTest.java#L99
array lengths differ, expected: <2> but was: <0>
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AggregateQueryTest.queryMultipleGroupingCounts:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L229
Expected: parameter
but none found
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AggregateQueryTest.queryWithLargeScaleDecimalResult:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L574
Expected: parameter
but none found
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AggregateQueryTest.queryWithWhereInAggregation:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L383
Expected: parameter
but none found
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AggregateQueryTest.queryWithNestedAggregation:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L398
Expected: parameter
but none found
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AggregateQueryTest.queryWithCombineResultInSecondFilter:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L604
Expected: parameter
but none found
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AggregateQueryTest.simpleQuery:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L58
Expected: parameter
but none found
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AggregateQueryTest.queryWithReverseResolveAndCounts:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L212
Expected: parameter
but none found
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AggregateQueryTest.queryWithIntegerGroupings:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L108
Expected: parameter
but none found
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AggregateQueryTest.queryWithWhereAsComparisonOperand:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L318
Expected: parameter
but none found
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AggregateQueryTest.queryWithAmbiguousSelfJoin:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L335
Expected: parameter
but none found
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AggregateQueryTest.queryMultipleCountAggregations:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L245
Expected: parameter
but none found
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AggregateQueryTest.queryWithUriValueInGrouping:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L427
Expected: parameter
but none found
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AggregateQueryTest.queryWithWhereAndMembership:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L351
Expected: parameter
but none found
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AggregateQueryTest.queryWithLiteralAggregation:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L463
Expected: parameter
but none found
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AggregateQueryTest.queryWithComparisonInAggregation:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L445
Expected: parameter
but none found
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AggregateQueryTest.queryWithReverseResolve:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L197
Expected: parameter
but none found
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AggregateQueryTest.queryWithNonSingularBooleanGrouping:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L532
Expected: parameter
but none found
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AggregateQueryTest.queryWithMemberOf:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L286
Expected: parameter
but none found
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AggregateQueryTest.queryWithDateComparison:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L153
Expected: parameter
but none found
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AggregateQueryTest.queryWithPolymorphicResolve:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L182
Expected: parameter
but none found
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AggregateQueryTest.queryWithChoiceElement:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L138
Expected: parameter
but none found
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AggregateQueryTest.queryWithMultipleTrivialAggregations:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L619
Expected: parameter
but none found
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AggregateQueryTest.queryWithWhere:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L261
Expected: parameter
but none found
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AggregateQueryTest.queryWithCanonicalGrouping:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L561
Expected: parameter
but none found
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AggregateQueryTest.queryWithDateTimeGrouping:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L300
Expected: parameter
but none found
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AggregateQueryTest.queryWithWhereAndBoolean:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L367
Expected: parameter
but none found
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AggregateQueryTest.queryWithWhereAndGroupedData:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L478
Expected: parameter
but none found
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AggregateQueryTest.queryWithResolve:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L168
Expected: parameter
but none found
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AggregateQueryTest.multipleAggregations:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L92
Expected: parameter
but none found
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AggregateQueryTest.multipleGroupingsAndAggregations:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L76
Expected: parameter
but none found
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AggregateQueryTest.queryWithBracketing:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L547
Expected: parameter
but none found
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AggregateQueryTest.queryWithMathExpression:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L123
Expected: parameter
but none found
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AggregateQueryTest.queryWithWhereAggregationAndCount:
fhir-server/src/test/java/au/csiro/pathling/aggregate/AggregateQueryTest.java#L588
Expected: parameter
but none found
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ExtractQueryTest.whereInMultipleColumns:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L315
[INTERNAL_ERROR] The Spark SQL phase analysis failed with an internal error. You hit a bug in Spark or the Spark plugins you use. Please, report this bug to the corresponding communities or vendors, and provide the full stack trace.
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ExtractQueryTest.multipleIndependentUnnestings:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L367
[INTERNAL_ERROR] The Spark SQL phase analysis failed with an internal error. You hit a bug in Spark or the Spark plugins you use. Please, report this bug to the corresponding communities or vendors, and provide the full stack trace.
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ExtractQueryTest.simpleQueryWithAliases:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L113
Error invoking method-defined function
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ExtractQueryTest.linkedUnnesting:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L349
[INTERNAL_ERROR] The Spark SQL phase analysis failed with an internal error. You hit a bug in Spark or the Spark plugins you use. Please, report this bug to the corresponding communities or vendors, and provide the full stack trace.
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ExtractQueryTest.literalColumn:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L185
[INTERNAL_ERROR] The Spark SQL phase analysis failed with an internal error. You hit a bug in Spark or the Spark plugins you use. Please, report this bug to the corresponding communities or vendors, and provide the full stack trace.
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ExtractQueryTest.combineWithUnequalCardinalities:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L502
[INTERNAL_ERROR] The Spark SQL phase analysis failed with an internal error. You hit a bug in Spark or the Spark plugins you use. Please, report this bug to the corresponding communities or vendors, and provide the full stack trace.
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ExtractQueryTest.multipleNonSingularColumnsWithDifferentTypes:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L331
[INTERNAL_ERROR] The Spark SQL phase analysis failed with an internal error. You hit a bug in Spark or the Spark plugins you use. Please, report this bug to the corresponding communities or vendors, and provide the full stack trace.
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ExtractQueryTest.combineResultInSecondFilter:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L299
[INTERNAL_ERROR] The Spark SQL phase analysis failed with an internal error. You hit a bug in Spark or the Spark plugins you use. Please, report this bug to the corresponding communities or vendors, and provide the full stack trace.
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ExtractQueryTest.limit:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L270
expected: <[[9360820c-8602-4335-8b50-c88d627a0c20,female]:1, [7001ad9c-34d2-4eb5-8165-5fdc2147f469,female]:1, [121503c8-9564-4b48-9086-a22df717948e,female]:1]> but was: <[[9360820c-8602-4335-8b50-c88d627a0c20,female]:1, [7001ad9c-34d2-4eb5-8165-5fdc2147f469,female]:1, [e62e52ae-2d75-4070-a0ae-3cc78d35ed08,female]:1, [121503c8-9564-4b48-9086-a22df717948e,female]:1]>
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ExtractQueryTest.multipleReverseResolves:
fhir-server/src/test/java/au/csiro/pathling/extract/ExtractQueryTest.java#L151
Error invoking method-defined function
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FHIR server (tranche 1)
There were 61 failed tests
|
|
R API
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v2. Please update your workflow to use the latest version of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-09-16-notice-of-upcoming-deprecations-and-changes-in-github-actions-services/
|
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Site
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v2. Please update your workflow to use the latest version of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-09-16-notice-of-upcoming-deprecations-and-changes-in-github-actions-services/
|
|
R API
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
FHIR server (tranche 3)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
JavaScript client
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Import lambda
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Site
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
Python API
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Encoders
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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Encoders
No files were found with the provided path: **/*.dump
**/*.dumpstream. No artifacts will be uploaded.
|
|
FHIR server (tranche 2)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
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FHIR server (tranche 2)
No files were found with the provided path: fhir-server/target/timing.log. No artifacts will be uploaded.
|
|
FHIR server (tranche 2)
No files were found with the provided path: **/*.dump
**/*.dumpstream. No artifacts will be uploaded.
|
|
FHIR server (tranche 1)
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
|
|
FHIR server (tranche 1)
No files were found with the provided path: fhir-server/target/timing.log. No artifacts will be uploaded.
|
|
FHIR server (tranche 1)
No files were found with the provided path: **/*.dump
**/*.dumpstream. No artifacts will be uploaded.
|
Artifacts
Produced during runtime
| Name | Size | |
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encoders-coverage
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32 KB |
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encoders-surefire-reports
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57.4 KB |
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fhir-server-1-coverage
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97.5 KB |
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fhir-server-1-surefire-reports
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112 KB |
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fhir-server-2-coverage
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98.8 KB |
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fhir-server-2-surefire-reports
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231 KB |
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import-lambda
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19.6 MB |
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