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WIP: Fixing resolve() type resolution for combine and iif. #3819

WIP: Fixing resolve() type resolution for combine and iif.

WIP: Fixing resolve() type resolution for combine and iif. #3819

Triggered via push December 23, 2024 07:03
Status Failure
Total duration 7m 56s
Artifacts 7

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65 errors and 16 warnings
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/
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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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.
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.
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.
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.
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.
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.
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.
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]>
FHIR server (tranche 1)
There were 61 failed tests
ManifestConverterTest.convertsManifest: fhir-server/src/test/java/au/csiro/pathling/security/ga4gh/ManifestConverterTest.java#L126
[DATATYPE_MISMATCH.BINARY_OP_DIFF_TYPES] Cannot resolve "(CASE WHEN (size(filter(CASE WHEN (size(filter(CASE WHEN (size(filter(Procedure.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)), true) = 0) THEN NULL ELSE filter(Procedure.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)) END.actor, lambdafunction(isnotnull(lambda x_21#30539), lambda x_21#30539, false)), true) = 0) THEN NULL ELSE filter(CASE WHEN (size(filter(Procedure.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)), true) = 0) THEN NULL ELSE filter(Procedure.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)) END.actor, lambdafunction(isnotnull(lambda x_21#30539), lambda x_21#30539, false)) END.reference, lambdafunction((namedlambdavariable() IS NOT NULL), namedlambdavariable()))) = 0) THEN NULL ELSE filter(CASE WHEN (size(filter(CASE WHEN (size(filter(Procedure.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)), true) = 0) THEN NULL ELSE filter(Procedure.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)) END.actor, lambdafunction(isnotnull(lambda x_21#30539), lambda x_21#30539, false)), true) = 0) THEN NULL ELSE filter(CASE WHEN (size(filter(Procedure.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)), true) = 0) THEN NULL ELSE filter(Procedure.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)) END.actor, lambdafunction(isnotnull(lambda x_21#30539), lambda x_21#30539, false)) END.reference, lambdafunction((namedlambdavariable() IS NOT NULL), namedlambdavariable())) END = id@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, (CASE WHEN (size(filter(CASE WHEN (size(filter(CASE WHEN (size(filter(Procedure#30383.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)), true) = 0) THEN cast(null as array<struct<id:string,function:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,actor:struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>,onBehalfOf:struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>,_fid:int>>) ELSE filter(Procedure#30383.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)) END.actor, lambdafunction(isnotnull(lambda x_21#30539), lambda x_21#30539, false)), true) = 0) THEN cast(null as array<struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>>) ELSE filter(CASE WHEN (size(filter(Procedure#30383.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)), true) = 0) THEN cast(null as array<struct<id:string,function:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,actor:struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>,onBehalfOf:struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>,_fid:int>>) ELSE filter(Procedure#30383.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)) END.actor, lambdafunction(isnotnull(lambda x_21#30539), lambda x_21#30539, false)) END.reference, lambdafunction(isnotnull(lambda x_22#30540), lambda x_22#30540, false)), true) = 0) THEN cast(null as array<string>) ELSE filter(CASE WHEN (size(filter(CASE WHEN (size(filter(Procedure#30383.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)), true) = 0) THEN cast(null as array<struct<id:string,function:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,actor:struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>,onBehalfOf:struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>,_fid:int>>) ELSE filter(Procedure#30383.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)) END.actor, lambdafunction(isnotnull(lambda x_21#30539), lambda x_21#30539, false)), true) = 0) THEN cast(null as array<struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>>) ELSE filter(CASE WHEN (size(filter(Procedure#30383.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)), true) = 0) THEN cast(null as array<struct<id:string,function:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,actor:struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>,onBehalfOf:struct<id:string,reference:string,type:string,identifier:struct<id:string,use:string,type:struct<id:string,coding:array<struct<id:string,system:string,version:string,code:string,display:string,userSelected:boolean,_fid:int>>,text:string,_fid:int>,system:string,value:string,period:struct<id:string,start:string,end:string,_fid:int>,_fid:int>,display:string,_fid:int>,_fid:int>>) ELSE filter(Procedure#30383.performer, lambdafunction(isnotnull(lambda x_20#30538), lambda x_20#30538, false)) END.actor, lambdafunction(isnotnull(lambda x_21#30539), lambda x_21#30539, false)) END.reference, lambdafunction(isnotnull(lambda x_22#30540), lambda x_22#30540, false)) END = id@Patient__ckey#30534) :- Project [id#30302, id_versioned#30303 AS key#30382, struct(id, id#30302, id_versioned, id_versioned#30303, meta, meta#30304, implicitRules, implicitRules#30305, language, language#30306, text, text#30307, identifier, identifier#30308, instantiatesCanonical, instantiatesCanonical#30309, instantiatesUri, instantiatesUri#30310, basedOn, basedOn#30311, partOf, partOf#30312, status, status#30313, statusReason, statusReason#30314, category, category#30315, code, code#30316, subject, subject#30317, encounter, encounter#30318, performedAge, performedAge#30319, performedDateTime, performedDateTime#30320, performedPeriod, performedPeriod#30321, performedRange, performedRange#30322, performedString, performedString#30323, recorder, recorder#30324, asserter, asserter#30325, performer, performer#30326, location, location#30327, reasonCode, reasonCode#30328, reasonReference, reasonReference#30329, bodySite, bodySite#30330, outcome, outcome#30331, report, report#30332, complication, complication#30333, complicationDetail, complicationDetail#30334, followUp, followUp#30335, note, note#30336, focalDevice, focalDevice#30337, usedReference, usedReference#30338, usedCode, usedCode#30339, _fid, _fid#30340, _extension, _extension#30341) AS Procedure#30383] : +- Relation [id#30302,id_versioned#30303,meta#30304,implicitRules#30305,language#30306,text#30307,identifier#30308,instantiatesCanonical#30309,instantiatesUri#30310,basedOn#30311,partOf#30312,status#30313,statusReason#30314,category#30315,code#30316,subject#30317,encounter#30318,performedAge#30319,performedDateTime#30320,performedPeriod#30321,performedRange#30322,performedString#30323,recorder#30324,asserter#30325,performer#30326,location#30327,reasonCode#30328,reasonReference#30329,bodySite#30330,outcome#30331,report#30332,complication#30333,complicationDetail#30334,followUp#30335,note#30336,focalDevice#30337,usedReference#30338,usedCode#30339,_fid#30340,_extension#30341] parquet +- Project [key#30440 AS id@Patient__ckey#30534, map_from_arrays(array(key#30440), array(Patient#30441)) AS id@Patient_unique#30535] +- Project [id#30388, id_versioned#30389 AS key#30440, struct(id, id#30388, id_versioned, id_versioned#30389, meta, meta#30390, implicitRules, implicitRules#30391, language, language#30392, text, text#30393, identifier, identifier#30394, active, active#30395, name, name#30396, telecom, telecom#30397, gender, gender#30398, birthDate, birthDate#30399, deceasedBoolean, deceasedBoolean#30400, deceasedDateTime, deceasedDateTime#30401, address, address#30402, maritalStatus, maritalStatus#30403, multipleBirthBoolean, multipleBirthBoolean#30404, multipleBirthInteger, multipleBirthInteger#30405, photo, photo#30406, contact, contact#30407, communication, communication#30408, generalPractitioner, generalPractitioner#30409, managingOrganization, managingOrganization#30410, link, link#30411, _fid, _fid#30412, _extension, _extension#30413) AS Patient#30441] +- Relation [id#30388,id_versioned#30389,meta#30390,implicitRules#30391,language#30392,text#30393,identifier#30394,active#30395,name#30396,telecom#30397,gender#30398,birthDate#30399,deceasedBoolean#30400,deceasedDateTime#30401,address#30402,maritalStatus#30403,multipleBirthBoolean#30404,multipleBirthInteger#30405,photo#30406,contact#30407,communication#30408,generalPractitioner#30409,managingOrganization#30410,link#30411,_fid#30412,_extension#30413] parquet
AsyncTest.asyncExtract: fhir-server/src/test/java/au/csiro/pathling/test/integration/AsyncTest.java#L84
expected: <202 ACCEPTED> but was: <500 INTERNAL_SERVER_ERROR>
FHIR server (tranche 2)
There were 8 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 either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
Site
Your workflow is using a version of actions/cache that is scheduled for deprecation, actions/cache@v2. Please update your workflow to use either v3 or v4 of actions/cache to avoid interruptions. Learn more: https://github.blog/changelog/2024-12-05-notice-of-upcoming-releases-and-breaking-changes-for-github-actions/#actions-cache-v1-v2-and-actions-toolkit-cache-package-closing-down
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
Import lambda
ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636
Encoders
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Encoders
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Python API
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
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)
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FHIR server (tranche 1)
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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
FHIR server (tranche 2)
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FHIR server (tranche 2)
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Artifacts

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Name Size
encoders-coverage
32 KB
encoders-surefire-reports
57.6 KB
fhir-server-1-coverage
95.5 KB
fhir-server-1-surefire-reports
112 KB
fhir-server-2-coverage
97 KB
fhir-server-2-surefire-reports
235 KB
import-lambda
19.6 MB