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Fix Reference Resolution on Extended Primitive References #758

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astruebi opened this issue Jul 4, 2022 · 0 comments
Closed

Fix Reference Resolution on Extended Primitive References #758

astruebi opened this issue Jul 4, 2022 · 0 comments
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bug Something isn't working module:fhir-structure
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@astruebi
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astruebi commented Jul 4, 2022

Happens in the latest build, which runs on WSL Ubuntu for me. When uploading the newly generated Polar test data, nothing is uploaded and the following error occurs:

`C:\Users\Ich>blazectl --server http://localhost:8082/fhir upload "G:\Projekte\smith\TestDataGenerator\outputGlobal" -c 2
Starting Upload to http://localhost:8082/fhir ...
Inspecting files eligible for upload from G:\Projekte\smith\TestDataGenerator\outputGlobal... DONE
Found 1 bundles in total (from 1 JSON files and from 0 NDJSON files)
Uploads          [total, concurrency]     1, 2
Success          [ratio]                  0.00 %
Duration         [total]                  85ms
Requ. Latencies  [mean, 50, 95, 99, max]  77ms, 77ms, 77ms, 77ms 77ms
Bytes In         [total, mean]            10.25 KiB, 10.25 KiB
Bytes Out        [total, mean]            634.31 KiB, 634.31 KiB
Status Codes     [code:count]             200:0, 500:1

Non-OK Responses:

File: G:\Projekte\smith\TestDataGenerator\outputGlobal\POLAR_Testdaten_Original_UKB-UKB-0001.json [Bundle: 1]
    StatusCode  : 500
    Severity    : Error
    Code        : An unexpected internal error has occurred.
    Diagnostics :                                                                      java.lang.Thread.run                  Thread.java:  833
                                    org.eclipse.jetty.util.thread.QueuedThreadPool$Runner.run        QueuedThreadPool.java: 1034
                                        org.eclipse.jetty.util.thread.QueuedThreadPool.runJob        QueuedThreadPool.java:  883
                      org.eclipse.jetty.util.thread.ReservedThreadExecutor$ReservedThread.run  ReservedThreadExecutor.java:  409
                                    org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.run          EatWhatYouKill.java:  131
                             org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.tryProduce          EatWhatYouKill.java:  173
                              org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.doProduce          EatWhatYouKill.java:  315
                                org.eclipse.jetty.util.thread.strategy.EatWhatYouKill.runTask          EatWhatYouKill.java:  338
                                                   org.eclipse.jetty.io.ChannelEndPoint$1.run         ChannelEndPoint.java:  104
                                                   org.eclipse.jetty.io.FillInterest.fillable            FillInterest.java:  105
                               org.eclipse.jetty.io.AbstractConnection$ReadCallback.succeeded      AbstractConnection.java:  311
                                           org.eclipse.jetty.server.HttpConnection.onFillable          HttpConnection.java:  277
                                                  org.eclipse.jetty.server.HttpChannel.handle             HttpChannel.java:  479
                                                org.eclipse.jetty.server.HttpChannel.dispatch             HttpChannel.java:  732
                                         org.eclipse.jetty.server.HttpChannel.lambda$handle$1             HttpChannel.java:  487
                                                       org.eclipse.jetty.server.Server.handle                  Server.java:  516
                                       org.eclipse.jetty.server.handler.HandlerWrapper.handle          HandlerWrapper.java:  127
    ring.adapter.jetty.proxy$org.eclipse.jetty.server.handler.AbstractHandler$ff19274a.handle
                                                    ring.adapter.jetty/async-proxy-handler/fn                    jetty.clj:   59
                                                                  blaze.server/wrap-server/fn                   server.clj:   22
                                                                                          ...
                                                                  reitit.ring/ring-handler/fn                    ring.cljc:  339
                                                    blaze.rest-api.middleware.log/wrap-log/fn                      log.clj:   18
                                                                                          ...
                                                  blaze.rest-api.middleware.cors/wrap-cors/fn                     cors.clj:   12
                                                                  reitit.ring/ring-handler/fn                    ring.cljc:  338
                                                                        reitit.ring/routes/fn                    ring.cljc:  122
                                                                      reitit.ring/routes/fn/f                    ring.cljc:  120
                                                        ring.middleware.params/wrap-params/fn                   params.clj:   77
                                              blaze.rest-api.middleware.output/wrap-output/fn                   output.clj:  102
                                                    blaze.middleware.fhir.error/wrap-error/fn                    error.clj:    9
                                        blaze.rest-api.middleware.forwarded/wrap-forwarded/fn                forwarded.clj:   37
                                                                  blaze.rest-api.routes/fn/fn                   routes.clj:   61
                                          blaze.rest-api.middleware.resource/wrap-resource/fn                 resource.clj:  106
                                blaze.rest-api.middleware.batch-handler/wrap-batch-handler/fn            batch_handler.clj:    6
                               blaze.middleware.fhir.metrics/wrap-observe-request-duration/fn                  metrics.clj:   52
                                       blaze.interaction.transaction/wrap-interaction-name/fn              transaction.clj:  522
                                                     blaze.interaction.transaction/handler/fn              transaction.clj:  513
                                                                blaze.async.comp/then-compose                     comp.clj:  200
                                           java.util.concurrent.CompletableFuture.thenCompose       CompletableFuture.java:  144
                                           java.util.concurrent.CompletableFuture.thenCompose       CompletableFuture.java: 2309
                                       java.util.concurrent.CompletableFuture.uniComposeStage       CompletableFuture.java: 1187
                                                                blaze.async.comp//reify/apply                     comp.clj:  161
                                                  blaze.interaction.transaction/handler/fn/fn              transaction.clj:  516
                                                                                          ...
                                                   blaze.interaction.transaction/eval41959/fn              transaction.clj:  483
                                                                        blaze.db.api/transact                      api.clj:   62
                                                                blaze.db.node.Node/-submit-tx                     node.clj:  254
                                                        blaze.db.node.transaction/prepare-ops              transaction.clj:   80
                                                                            clojure.core/mapv                     core.clj: 6970
                                                                          clojure.core/reduce                     core.clj: 6885
                                                                                          ...
                                                                         clojure.core/mapv/fn                     core.clj: 6979
                                                                      clojure.core/partial/fn                     core.clj: 2641
                                                                                          ...
                                                       blaze.db.node.transaction/eval23580/fn              transaction.clj:   36
                                                              blaze.fhir.spec.type/references                     type.clj:   66
                                                blaze.fhir.spec.type.protocols/eval11095/fn/G                protocols.clj:    4
                                                            blaze.fhir.spec.type/eval16903/fn                     type.clj: 1106
                                                                       clojure.core/transduce                     core.clj: 6947
                                                                  clojure.core.protocols/fn/G                protocols.clj:   13
                                                                    clojure.core.protocols/fn                protocols.clj:   75
                                                           clojure.core.protocols/iter-reduce                protocols.clj:   49
                                                                       clojure.core/map/fn/fn                     core.clj: 2759
                                                blaze.fhir.spec.type.protocols/eval11095/fn/G                protocols.clj:    4
                                                            blaze.fhir.spec.type/eval16859/fn                     type.clj: 1073
                                                                          clojure.core/reduce                     core.clj: 6885
                                                                                          ...
                                                         blaze.fhir.spec.type/eval16859/fn/fn                     type.clj: 1073
                                                blaze.fhir.spec.type.protocols/eval11095/fn/G                protocols.clj:    4
                                                            blaze.fhir.spec.type/eval16903/fn                     type.clj: 1106
                                                                       clojure.core/transduce                     core.clj: 6947
                                                                  clojure.core.protocols/fn/G                protocols.clj:   13
                                                                    clojure.core.protocols/fn                protocols.clj:   75
                                                           clojure.core.protocols/iter-reduce                protocols.clj:   49
                                                                       clojure.core/map/fn/fn                     core.clj: 2759
                                                blaze.fhir.spec.type.protocols/eval11095/fn/G                protocols.clj:    4 (repeats 2 times)
                                                   blaze.fhir.spec.type.Reference/-references                     type.clj: 1212
                                                     blaze.fhir.spec.type/reference-reference                     type.clj: 1199
                                                                         clojure.string/split                   string.clj:  219
    java.lang.ClassCastException: class blaze.fhir.spec.type.ExtendedString cannot be cast to class java.lang.CharSequence (blaze.fhir.spec.type.ExtendedString is in unnamed module of loader clojure.lang.DynamicClassLoader @62b92df8; java.lang.CharSequence is in module java.base of loader 'bootstrap')`

POLAR_Testdaten_Original_UKB-UKB-0001.zip

@alexanderkiel alexanderkiel added the bug Something isn't working label Jul 4, 2022
@alexanderkiel alexanderkiel changed the title Class Cast Exception on data upload Reference Resolution Fails on Extended Primitive References Jul 4, 2022
@alexanderkiel alexanderkiel changed the title Reference Resolution Fails on Extended Primitive References Fix Reference Resolution on Extended Primitive References Jul 4, 2022
@alexanderkiel alexanderkiel added this to the v0.17.10 milestone Jul 4, 2022
@alexanderkiel alexanderkiel self-assigned this Jul 5, 2022
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