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Schema defined for fhir in persistence.json not used correctly when running Docker fhir-persistence-schema #1795

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holger-stenzhorn opened this issue Dec 4, 2020 · 6 comments · Fixed by #1799
Closed

Schema defined for fhir in persistence.json not used correctly when running Docker fhir-persistence-schema #1795

holger-stenzhorn opened this issue Dec 4, 2020 · 6 comments · Fixed by #1799
Assignees
@prb112
Labels
bug Something isn't working cloud portability
Milestone
Sprint 21

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@holger-stenzhorn
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Describe the bug
The schema defined for fhir in persistence.json is not used correctly when running Docker fhir-persistence-schema.

To Reproduce

  1. Define the following persistence.json where schema for fhir is set to the value somefhirschema, i.e. to some value other than fhirdata: 
    {
    "persistence": [
        {
            "db":  {
                "host": "postgres",
                "port": "5432",
                "database": "fhir",
                "user": "fhir",
                "password": "change-password",
                "type": "postgresql"
            },
            "schema": {
                "fhir": "somefhirschema"
            },
            "behavior": "onboard"
        }
    ]
}
  2. Run the Docker image/container fhir-persistence-schema: 
    holger@homer:~$ ENV_TOOL_INPUT=$(cat persistence.json)
holger@homer:~$ docker run --env ENV_TOOL_INPUT=$ENV_TOOL_INPUT ibmcom/ibm-fhir-schematool:4.5.2
  3. See the result: 
       base64: invalid input
The tool behavior being executed is onboard
run.sh - [INFO]: 2020-12-04_20:10:06 - Starting the onboard behavior
run.sh - [INFO]: 2020-12-04_20:10:06 - Activating Network Path Connection...
run.sh - [INFO]: 2020-12-04_20:10:06 - [NETWORK_PATH_CHECK] - SUCCESS - Connected to the database - postgres:5432
run.sh - [INFO]: 2020-12-04_20:10:06 - creating the schema
+ /opt/java/openjdk/bin/java -jar /opt/schematool/fhir-persistence-schema-4.5.2-cli.jar --prop db.host=postgres --prop db.port=5432 --prop db.database=fhir --prop user=fhir --prop password=change-password --db-type postgresql --create-schemas --pool-size 2
+ tee out.log
2020-12-04 20:10:07.483 00000001    INFO   com.ibm.fhir.schema.app.Main Opening connection to: jdbc:postgresql://postgres:5432/fhir
2020-12-04 20:10:07.860 00000001    INFO s.postgresql.PostgreSqlAdapter The schema 'FHIR_ADMIN' is created or already exists
2020-12-04 20:10:07.863 00000001    INFO s.postgresql.PostgreSqlAdapter The schema 'FHIRDATA' is created or already exists
2020-12-04 20:10:07.867 00000001    INFO s.postgresql.PostgreSqlAdapter The schema 'FHIR_OAUTH' is created or already exists
2020-12-04 20:10:07.870 00000001    INFO s.postgresql.PostgreSqlAdapter The schema 'FHIR_JBATCH' is created or already exists
2020-12-04 20:10:07.876 00000001    INFO   com.ibm.fhir.schema.app.Main Processing took:   0.435 s
2020-12-04 20:10:07.878 00000001    INFO   com.ibm.fhir.schema.app.Main SCHEMA CHANGE: OK
+ set +x
run.sh - [INFO]: 2020-12-04_20:10:07 - done creating the schema
+ /opt/java/openjdk/bin/java -jar /opt/schematool/fhir-persistence-schema-4.5.2-cli.jar --prop db.host=postgres --prop db.port=5432 --prop db.database=fhir --prop user=fhir --prop password=change-password --db-type postgresql --schema-name somefhirschema --update-schema --pool-size 1
+ tee out.log
2020-12-04 20:10:09.406 00000001    INFO .common.JdbcConnectionProvider Opening connection to database: jdbc:postgresql://postgres:5432/fhir
2020-12-04 20:10:09.844 00000001    INFO   com.ibm.fhir.schema.app.Main Collecting model update tasks
2020-12-04 20:10:10.090 00000001    INFO   com.ibm.fhir.schema.app.Main Starting model updates
2020-12-04 20:10:10.097 00000017    INFO ase.utils.model.DatabaseObject Applying change [v1]: TABLESPACE:FHIR_TS:1
2020-12-04 20:10:10.099 00000017 WARNING s.postgresql.PostgreSqlAdapter [ONCE] Create tablespace not supported in PostgreSql
2020-12-04 20:10:10.110 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLESPACE:FHIR_TS:1
2020-12-04 20:10:10.115 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: SEQUENCE:FHIR_ADMIN.TENANT_SEQUENCE:1
2020-12-04 20:10:10.117 00000017 WARNING s.postgresql.PostgreSqlAdapter [ONCE] PostgreSql does not support CREATE VARIABLE for: SV_TENANT_ID
2020-12-04 20:10:10.122 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: VARIABLE:FHIR_ADMIN.SV_TENANT_ID:1
2020-12-04 20:10:10.129 00000017  SEVERE atabase.utils.model.BaseObject [FAILED] SEQUENCE:SOMEFHIRSCHEMA.FHIR_SEQUENCE:1
2020-12-04 20:10:10.131 00000017 WARNING ls.pool.PoolConnectionProvider Rolling back transaction
2020-12-04 20:10:10.134 00000017  SEVERE .fhir.task.core.impl.TaskGroup SEQUENCE:SOMEFHIRSCHEMA.FHIR_SEQUENCE:1

org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
com.ibm.fhir.database.utils.api.DataAccessException: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlTranslator.translate(PostgreSqlTranslator.java:104)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:227)
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlAdapter.createSequence(PostgreSqlAdapter.java:204)
	at com.ibm.fhir.database.utils.model.Sequence.apply(Sequence.java:48)
	at com.ibm.fhir.database.utils.model.Sequence.apply(Sequence.java:60)
	at com.ibm.fhir.database.utils.model.BaseObject.applyVersion(BaseObject.java:263)
	at com.ibm.fhir.database.utils.model.BaseObject.applyTx(BaseObject.java:214)
	at com.ibm.fhir.database.utils.model.BaseObject.lambda$collect$0(BaseObject.java:201)
	at com.ibm.fhir.database.utils.model.BaseObject$$Lambda$89/0x00000000cc7ee230.run(Unknown Source)
	at com.ibm.fhir.task.core.impl.TaskGroup.runTask(TaskGroup.java:137)
	at com.ibm.fhir.task.core.impl.TaskGroup.lambda$runTask$0(TaskGroup.java:129)
	at com.ibm.fhir.task.core.impl.TaskGroup$$Lambda$90/0x00000000cc66dd10.run(Unknown Source)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2533)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2268)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:313)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:310)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:296)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:273)
	at org.postgresql.jdbc.PgStatement.executeUpdate(PgStatement.java:247)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:246)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:225)
	... 15 more
2020-12-04 20:10:10.144 00000017    INFO hir.task.core.impl.TaskManager Task failed callback for taskId: SEQUENCE:SOMEFHIRSCHEMA.FHIR_SEQUENCE:1
2020-12-04 20:10:10.146 00000017    INFO .common.JdbcConnectionProvider Opening connection to database: jdbc:postgresql://postgres:5432/fhir
2020-12-04 20:10:10.158 00000017  SEVERE atabase.utils.model.BaseObject [FAILED] SEQUENCE:SOMEFHIRSCHEMA.FHIR_REF_SEQUENCE:1
2020-12-04 20:10:10.159 00000017 WARNING ls.pool.PoolConnectionProvider Rolling back transaction
2020-12-04 20:10:10.162 00000017  SEVERE .fhir.task.core.impl.TaskGroup SEQUENCE:SOMEFHIRSCHEMA.FHIR_REF_SEQUENCE:1

org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
com.ibm.fhir.database.utils.api.DataAccessException: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlTranslator.translate(PostgreSqlTranslator.java:104)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:227)
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlAdapter.createSequence(PostgreSqlAdapter.java:204)
	at com.ibm.fhir.database.utils.model.Sequence.apply(Sequence.java:48)
	at com.ibm.fhir.database.utils.model.Sequence.apply(Sequence.java:60)
	at com.ibm.fhir.database.utils.model.BaseObject.applyVersion(BaseObject.java:263)
	at com.ibm.fhir.database.utils.model.BaseObject.applyTx(BaseObject.java:214)
	at com.ibm.fhir.database.utils.model.BaseObject.lambda$collect$0(BaseObject.java:201)
	at com.ibm.fhir.database.utils.model.BaseObject$$Lambda$89/0x00000000cc7ee230.run(Unknown Source)
	at com.ibm.fhir.task.core.impl.TaskGroup.runTask(TaskGroup.java:137)
	at com.ibm.fhir.task.core.impl.TaskGroup.lambda$runTask$0(TaskGroup.java:129)
	at com.ibm.fhir.task.core.impl.TaskGroup$$Lambda$90/0x00000000cc66dd10.run(Unknown Source)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2533)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2268)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:313)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:310)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:296)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:273)
	at org.postgresql.jdbc.PgStatement.executeUpdate(PgStatement.java:247)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:246)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:225)
	... 15 more
2020-12-04 20:10:10.172 00000017    INFO hir.task.core.impl.TaskManager Task failed callback for taskId: SEQUENCE:SOMEFHIRSCHEMA.FHIR_REF_SEQUENCE:1
2020-12-04 20:10:10.175 00000017    INFO .common.JdbcConnectionProvider Opening connection to database: jdbc:postgresql://postgres:5432/fhir
2020-12-04 20:10:10.191 00000017  SEVERE atabase.utils.model.BaseObject [FAILED] SEQUENCE:SOMEFHIRSCHEMA.REFERENCES_SEQUENCE:1
2020-12-04 20:10:10.194 00000017 WARNING ls.pool.PoolConnectionProvider Rolling back transaction
2020-12-04 20:10:10.197 00000017  SEVERE .fhir.task.core.impl.TaskGroup SEQUENCE:SOMEFHIRSCHEMA.REFERENCES_SEQUENCE:1

org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
com.ibm.fhir.database.utils.api.DataAccessException: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlTranslator.translate(PostgreSqlTranslator.java:104)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:227)
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlAdapter.createSequence(PostgreSqlAdapter.java:204)
	at com.ibm.fhir.database.utils.model.Sequence.apply(Sequence.java:48)
	at com.ibm.fhir.database.utils.model.Sequence.apply(Sequence.java:60)
	at com.ibm.fhir.database.utils.model.BaseObject.applyVersion(BaseObject.java:263)
	at com.ibm.fhir.database.utils.model.BaseObject.applyTx(BaseObject.java:214)
	at com.ibm.fhir.database.utils.model.BaseObject.lambda$collect$0(BaseObject.java:201)
	at com.ibm.fhir.database.utils.model.BaseObject$$Lambda$89/0x00000000cc7ee230.run(Unknown Source)
	at com.ibm.fhir.task.core.impl.TaskGroup.runTask(TaskGroup.java:137)
	at com.ibm.fhir.task.core.impl.TaskGroup.lambda$runTask$0(TaskGroup.java:129)
	at com.ibm.fhir.task.core.impl.TaskGroup$$Lambda$90/0x00000000cc66dd10.run(Unknown Source)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2533)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2268)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:313)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:310)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:296)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:273)
	at org.postgresql.jdbc.PgStatement.executeUpdate(PgStatement.java:247)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:246)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:225)
	... 15 more
2020-12-04 20:10:10.206 00000017    INFO hir.task.core.impl.TaskManager Task failed callback for taskId: SEQUENCE:SOMEFHIRSCHEMA.REFERENCES_SEQUENCE:1
2020-12-04 20:10:10.209 00000017    INFO .common.JdbcConnectionProvider Opening connection to database: jdbc:postgresql://postgres:5432/fhir
2020-12-04 20:10:10.245 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_OAUTH.OAUTH20CACHE:1
2020-12-04 20:10:10.258 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_OAUTH.OAUTH20CLIENTCONFIG:1
2020-12-04 20:10:10.268 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_OAUTH.OAUTH20CONSENTCACHE:1
2020-12-04 20:10:10.283 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_JBATCH.JOBINSTANCE:1
2020-12-04 20:10:10.295 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_ADMIN.TENANTS:1
2020-12-04 20:10:10.298 00000017 WARNING s.postgresql.PostgreSqlAdapter [ONCE] PostgreSql does support not multi-tenancy: CODE_SYSTEMS
2020-12-04 20:10:10.320 00000017  SEVERE atabase.utils.model.BaseObject [FAILED] TABLE:SOMEFHIRSCHEMA.CODE_SYSTEMS:1
2020-12-04 20:10:10.322 00000017 WARNING ls.pool.PoolConnectionProvider Rolling back transaction
2020-12-04 20:10:10.325 00000017  SEVERE .fhir.task.core.impl.TaskGroup TABLE:SOMEFHIRSCHEMA.CODE_SYSTEMS:1

org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
  Position: 14
com.ibm.fhir.database.utils.api.DataAccessException: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
  Position: 14
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlTranslator.translate(PostgreSqlTranslator.java:104)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:227)
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlAdapter.createTable(PostgreSqlAdapter.java:101)
	at com.ibm.fhir.database.utils.model.Table.apply(Table.java:117)
	at com.ibm.fhir.database.utils.model.Table.apply(Table.java:145)
	at com.ibm.fhir.database.utils.model.BaseObject.applyVersion(BaseObject.java:263)
	at com.ibm.fhir.database.utils.model.BaseObject.applyTx(BaseObject.java:214)
	at com.ibm.fhir.database.utils.model.BaseObject.lambda$collect$0(BaseObject.java:201)
	at com.ibm.fhir.database.utils.model.BaseObject$$Lambda$89/0x00000000cc7ee230.run(Unknown Source)
	at com.ibm.fhir.task.core.impl.TaskGroup.runTask(TaskGroup.java:137)
	at com.ibm.fhir.task.core.impl.TaskGroup.lambda$runTask$0(TaskGroup.java:129)
	at com.ibm.fhir.task.core.impl.TaskGroup$$Lambda$90/0x00000000cc66dd10.run(Unknown Source)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
  Position: 14
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2533)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2268)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:313)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:310)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:296)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:273)
	at org.postgresql.jdbc.PgStatement.executeUpdate(PgStatement.java:247)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:246)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:225)
	... 15 more
2020-12-04 20:10:10.334 00000017    INFO hir.task.core.impl.TaskManager Task failed callback for taskId: TABLE:SOMEFHIRSCHEMA.CODE_SYSTEMS:1
2020-12-04 20:10:10.336 00000017    INFO .common.JdbcConnectionProvider Opening connection to database: jdbc:postgresql://postgres:5432/fhir
2020-12-04 20:10:10.355 00000017  SEVERE atabase.utils.model.BaseObject [FAILED] TABLE:SOMEFHIRSCHEMA.PARAMETER_NAMES:1
2020-12-04 20:10:10.358 00000017 WARNING ls.pool.PoolConnectionProvider Rolling back transaction
2020-12-04 20:10:10.363 00000017  SEVERE .fhir.task.core.impl.TaskGroup TABLE:SOMEFHIRSCHEMA.PARAMETER_NAMES:1

org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
  Position: 14
com.ibm.fhir.database.utils.api.DataAccessException: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
  Position: 14
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlTranslator.translate(PostgreSqlTranslator.java:104)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:227)
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlAdapter.createTable(PostgreSqlAdapter.java:101)
	at com.ibm.fhir.database.utils.model.Table.apply(Table.java:117)
	at com.ibm.fhir.database.utils.model.Table.apply(Table.java:145)
	at com.ibm.fhir.database.utils.model.BaseObject.applyVersion(BaseObject.java:263)
	at com.ibm.fhir.database.utils.model.BaseObject.applyTx(BaseObject.java:214)
	at com.ibm.fhir.database.utils.model.BaseObject.lambda$collect$0(BaseObject.java:201)
	at com.ibm.fhir.database.utils.model.BaseObject$$Lambda$89/0x00000000cc7ee230.run(Unknown Source)
	at com.ibm.fhir.task.core.impl.TaskGroup.runTask(TaskGroup.java:137)
	at com.ibm.fhir.task.core.impl.TaskGroup.lambda$runTask$0(TaskGroup.java:129)
	at com.ibm.fhir.task.core.impl.TaskGroup$$Lambda$90/0x00000000cc66dd10.run(Unknown Source)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
  Position: 14
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2533)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2268)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:313)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:310)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:296)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:273)
	at org.postgresql.jdbc.PgStatement.executeUpdate(PgStatement.java:247)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:246)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:225)
	... 15 more
2020-12-04 20:10:10.373 00000017    INFO hir.task.core.impl.TaskManager Task failed callback for taskId: TABLE:SOMEFHIRSCHEMA.PARAMETER_NAMES:1
2020-12-04 20:10:10.376 00000017    INFO .common.JdbcConnectionProvider Opening connection to database: jdbc:postgresql://postgres:5432/fhir
2020-12-04 20:10:10.392 00000017  SEVERE atabase.utils.model.BaseObject [FAILED] TABLE:SOMEFHIRSCHEMA.RESOURCE_TYPES:1
2020-12-04 20:10:10.395 00000017 WARNING ls.pool.PoolConnectionProvider Rolling back transaction
2020-12-04 20:10:10.401 00000017  SEVERE .fhir.task.core.impl.TaskGroup TABLE:SOMEFHIRSCHEMA.RESOURCE_TYPES:1

org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
  Position: 14
com.ibm.fhir.database.utils.api.DataAccessException: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
  Position: 14
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlTranslator.translate(PostgreSqlTranslator.java:104)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:227)
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlAdapter.createTable(PostgreSqlAdapter.java:101)
	at com.ibm.fhir.database.utils.model.Table.apply(Table.java:117)
	at com.ibm.fhir.database.utils.model.Table.apply(Table.java:145)
	at com.ibm.fhir.database.utils.model.BaseObject.applyVersion(BaseObject.java:263)
	at com.ibm.fhir.database.utils.model.BaseObject.applyTx(BaseObject.java:214)
	at com.ibm.fhir.database.utils.model.BaseObject.lambda$collect$0(BaseObject.java:201)
	at com.ibm.fhir.database.utils.model.BaseObject$$Lambda$89/0x00000000cc7ee230.run(Unknown Source)
	at com.ibm.fhir.task.core.impl.TaskGroup.runTask(TaskGroup.java:137)
	at com.ibm.fhir.task.core.impl.TaskGroup.lambda$runTask$0(TaskGroup.java:129)
	at com.ibm.fhir.task.core.impl.TaskGroup$$Lambda$90/0x00000000cc66dd10.run(Unknown Source)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)
	at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
	at java.base/java.lang.Thread.run(Unknown Source)
Caused by: org.postgresql.util.PSQLException: ERROR: schema "somefhirschema" does not exist
  Position: 14
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2533)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2268)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:313)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:310)
	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:296)
	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:273)
	at org.postgresql.jdbc.PgStatement.executeUpdate(PgStatement.java:247)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:246)
	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:225)
	... 15 more
2020-12-04 20:10:10.415 00000017    INFO hir.task.core.impl.TaskManager Task failed callback for taskId: TABLE:SOMEFHIRSCHEMA.RESOURCE_TYPES:1
2020-12-04 20:10:10.418 00000017    INFO .common.JdbcConnectionProvider Opening connection to database: jdbc:postgresql://postgres:5432/fhir
2020-12-04 20:10:10.456 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_JBATCH.JOBEXECUTION:1
2020-12-04 20:10:10.470 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_JBATCH.GROUPASSOCIATION:1
2020-12-04 20:10:10.496 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_ADMIN.TENANT_KEYS:1
2020-12-04 20:10:10.511 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_JBATCH.JOBPARAMETER:1
2020-12-04 20:10:10.538 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_JBATCH.STEPTHREADEXECUTION:1
2020-12-04 20:10:10.541 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: NOP:FHIR_ADMIN.allAdminTablesComplete:0
2020-12-04 20:10:10.576 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_JBATCH.STEPTHREADINSTANCE:1
2020-12-04 20:10:10.601 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: TABLE:FHIR_JBATCH.REMOTABLEPARTITION:1
2020-12-04 20:10:10.610 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: PROCEDURE:FHIR_ADMIN.SET_TENANT:2
2020-12-04 20:10:10.613 00000017    INFO hir.task.core.impl.TaskManager Task complete callback for taskId: NOP:FHIR_ADMIN.adminSchemaComplete:0
2020-12-04 20:10:10.617 00000001  SEVERE   com.ibm.fhir.schema.app.Main List of failed task groups: SEQUENCE:SOMEFHIRSCHEMA.FHIR_SEQUENCE:1,SEQUENCE:SOMEFHIRSCHEMA.FHIR_REF_SEQUENCE:1,SEQUENCE:SOMEFHIRSCHEMA.REFERENCES_SEQUENCE:1,TABLE:SOMEFHIRSCHEMA.CODE_SYSTEMS:1,TABLE:SOMEFHIRSCHEMA.PARAMETER_NAMES:1,TABLE:SOMEFHIRSCHEMA.RESOURCE_TYPES:1
2020-12-04 20:10:10.620 00000001    INFO   com.ibm.fhir.schema.app.Main tenantId [default] is being pre-populated with lookup table data.
2020-12-04 20:10:10.626 00000001 WARNING ls.pool.PoolConnectionProvider Rolling back transaction
2020-12-04 20:10:10.629 00000001  SEVERE   com.ibm.fhir.schema.app.Main schema tool failed

org.postgresql.util.PSQLException: ERROR: relation "somefhirschema.resource_types" does not exist
  Position: 45
com.ibm.fhir.database.utils.api.UndefinedNameException: org.postgresql.util.PSQLException: ERROR: relation "somefhirschema.resource_types" does not exist
  Position: 45
	at com.ibm.fhir.database.utils.postgresql.PostgreSqlTranslator.translate(PostgreSqlTranslator.java:100)
	at com.ibm.fhir.schema.control.PopulateResourceTypes.run(PopulateResourceTypes.java:69)
	at com.ibm.fhir.schema.app.Main.populateResourceTypeAndParameterNameTableEntries(Main.java:387)
	at com.ibm.fhir.schema.app.Main.updateSchema(Main.java:362)
	at com.ibm.fhir.schema.app.Main.process(Main.java:1436)
	at com.ibm.fhir.schema.app.Main.main(Main.java:1513)
Caused by: org.postgresql.util.PSQLException: ERROR: relation "somefhirschema.resource_types" does not exist
  Position: 45
	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2533)
	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2268)
	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:313)
	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
	at org.postgresql.jdbc.PgPreparedStatement.executeWithFlags(PgPreparedStatement.java:159)
	at org.postgresql.jdbc.PgPreparedStatement.execute(PgPreparedStatement.java:148)
	at com.ibm.fhir.schema.control.PopulateResourceTypes.run(PopulateResourceTypes.java:61)
	... 4 more
2020-12-04 20:10:10.635 00000001  SEVERE   com.ibm.fhir.schema.app.Main SCHEMA CHANGE: RUNTIME ERROR

Expected behavior
n/a

Additional context
If one looks at the above log one can see that in the commands like...
+ /opt/java/openjdk/bin/java -jar /opt/schematool/fhir-persistence-schema-4.5.2-cli.jar --prop db.host=postgres --prop db.port=5432 --prop db.database=fhir --prop user=fhir --prop password=change-password --db-type postgresql --create-schemas --pool-size 2
...the property for schema.name.fhir is missing.

So to fix this issue the commands should contain that property and read something like ...
+ /opt/java/openjdk/bin/java -jar /opt/schematool/fhir-persistence-schema-4.5.2-cli.jar --prop db.host=postgres --prop db.port=5432 --prop db.database=fhir --prop schema.name.fhir=somefhirschema --prop user=fhir --prop password=change-password --db-type postgresql --create-schemas --pool-size 2
@holger-stenzhorn holger-stenzhorn added the bug Something isn't working label Dec 4, 2020
@prb112 prb112 self-assigned this Dec 4, 2020
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prb112 commented Dec 4, 2020

Thanks, I'll look at it early Monday

@holger-stenzhorn
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Just for completeness: The same error occurs also if not persistence.json but the command line parameters are used:

docker run --network ibm-fhir-server-postgres-docker-compose_default ibmcom/ibm-fhir-schematool:4.5.2 --tool.behavior=onboard --db.type=postgresql --db.host=postgres --db.port=5432 --db.database=fhir --schema.name.fhir=somefhirschema --user=fhir --password=change-password

@prb112
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prb112 commented Dec 4, 2020

Right - it's in create-schemas - I only specified the defaults, I'll change this on monday

@prb112
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prb112 commented Dec 4, 2020

p.s. thank you

@prb112 prb112 linked a pull request Dec 5, 2020 that will close this issue
Invalid SQL object name --pool-size exception when running Docker fhir-persistence-schema on PostgreSQL #1797 #1799
Merged
@prb112 prb112 added this to the Sprint 21 milestone Dec 5, 2020
prb112 added a commit that referenced this issue Dec 5, 2020
@prb112
Schema defined for fhir in persistence.json not used correctly when
e90807c 
running Docker `fhir-persistence-schema`
#1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>
prb112 added a commit that referenced this issue Dec 7, 2020
@prb112
Add tests case and fixes for #1795
097b88b 
Signed-off-by: Paul Bastide <pbastide@us.ibm.com>
prb112 added a commit that referenced this issue Dec 7, 2020
@prb112
Add tests case and fixes for #1795
8e3bf47 
Signed-off-by: Paul Bastide <pbastide@us.ibm.com>
prb112 added a commit that referenced this issue Dec 7, 2020
@prb112
Add tests case and fixes for #1795
3bc5486 
Signed-off-by: Paul Bastide <pbastide@us.ibm.com>
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prb112 commented Dec 7, 2020

Added a test for this one in #1799
Had to add a couple of spots for schema_name support for oauth and jbatch and fhirdata

@lmsurpre lmsurpre reopened this Dec 8, 2020
JohnTimm added a commit that referenced this issue Dec 15, 2020
@JohnTimm @prb112
@michaelwschroeder @punktilious @lmsurpre
Merge master into fhir-term-graph (#1828)
a796ab6 
* Enable OpenLiberty override the fhiropenapi functionality #1760

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Issue #1780 - add compartment search/search parameter config section

Signed-off-by: Mike Schroeder <mschroed@us.ibm.com>

* issue #1789 refresh-tenants does not handle Db2 multi-tenant/multi-schema scenarios

Signed-off-by: Robin Arnold <robin.arnold23@ibm.com>

* Invalid SQL object name `--pool-size` exception when running Docker
`fhir-persistence-schema` on PostgreSQL #1797

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Misleading error messages when using command line parameters and not
`persistence.json` for Docker `fhir-persistence-schema` #1796

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Schema defined for `fhir` in `persistence.json` not used correctly when
running Docker `fhir-persistence-schema`
#1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: update must gather to include open shift details

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* use the fhiruser password from helm (set by overrides from KeyProtect)

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* Fix the definition for List-identifier search

A workaround for https://jira.hl7.org/browse/FHIR-29937

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* #1802

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* #1802

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Fix up the Must Gather

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* IBM FHIR Server audit does not log bundles correctly. #1803

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update documentation for the mustgather

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: per code review changed the compare, and added an additional ignore
for the metadata endpoints

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Update fhir-server/src/main/java/com/ibm/fhir/server/util/RestAuditLogger.java

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

Co-authored-by: Lee Surprenant <lmsurpre@us.ibm.com>

* doc: compilation errors are now fixed

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: compilation errors are now fixed

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1796

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1797

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests for cp and #1802

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: #1808

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests for plain and base64 encoded environment variables

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix per comments in code review and issue

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Prevent unauthorized reads before they happen

This prevents us from leaking information about what patient resources
exist / don't exist on the system, which was deemed as useful in case an
implementer uses sensitive data for the Resource.id of the Patient
resources (which still isn't advised).

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* Prevent unauthorized vread and history operations against Patient too

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* doc: adding code of conduct md file to root of repository

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: update to clarify the experimental use of the ibm-fhir-schematool

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: update to clarify the experimental use of the ibm-fhir-schematool

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: adding code of conduct md file to root of repository

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* add communication method

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* Audit Refactoring #1542

- Refactor to separate Configuration, Mapping and AuditService
- Configuration to use EventStreams Binding by default
- Add a MapperFactory to split between cadf and auditevent types
	- AuditEventMapper - Wraps the AuditLogEntry into AuditEvent format
	- CADFMapper - Wraps the AuditLogEntry into CADF format
- Audit Service is now KafkaService, NoOpService separating the
Streaming framework from the mapping actions.
- Removed duplicate code for Event/EventStrams processing
- Add Test Coverage for Uncovered Classes

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Clean up spare printStackTrace

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update the documentation for fhir-audit

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* updates per team code review

- Change NoOp to Nop Service
- Remove references to WHC/Disabled
- Changed and clarified package names
- Changed references to specific default places to generic/unknown
places (e.g. dallas to unknown)
- added examples for audit from config and audit from environment

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* issue #1818 reindex resource selection update slows down as reindex progresses

Signed-off-by: Robin Arnold <robin.arnold23@ibm.com>

* updates per team code review

- changed package names to remove logging.api and .model (reconciling it
to a flatter structure)

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update docs

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* change formatting slightly on MapperFactory

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: it tests were not running for drug formulary and c4bb

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix incorrect variable in minor startup log message

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* Convert Strings to Constants for Kafka Key-Value in Properties objects

- Per Code Review with Robin Arnold

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Code Review for FHIR Audit

- CadfEvent doesn't write out target
- Addresses Written Twice in CadfResource

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Added Test for FHIR Audit so it doesn't have multiple address blocks

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update docs

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Removed auditLogService <extension url="http://ibm.com/fhir/extension/auditLogProperties">

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: referenced license was incorrect

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

Co-authored-by: Paul Bastide <pbastide@us.ibm.com>
Co-authored-by: Mike Schroeder <mschroed@us.ibm.com>
Co-authored-by: Robin Arnold <robin.arnold23@ibm.com>
Co-authored-by: Lee Surprenant <lmsurpre@us.ibm.com>
Co-authored-by: Michael W Schroeder <66479070+michaelwschroeder@users.noreply.github.com>
JohnTimm added a commit that referenced this issue Dec 22, 2020
@JohnTimm @prb112
@michaelwschroeder @punktilious @lmsurpre @tbieste
Merge master into fhir-term-graph (#1838)
00c2aa8 
* Enable OpenLiberty override the fhiropenapi functionality #1760

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Issue #1780 - add compartment search/search parameter config section

Signed-off-by: Mike Schroeder <mschroed@us.ibm.com>

* issue #1789 refresh-tenants does not handle Db2 multi-tenant/multi-schema scenarios

Signed-off-by: Robin Arnold <robin.arnold23@ibm.com>

* Invalid SQL object name `--pool-size` exception when running Docker
`fhir-persistence-schema` on PostgreSQL #1797

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Misleading error messages when using command line parameters and not
`persistence.json` for Docker `fhir-persistence-schema` #1796

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Schema defined for `fhir` in `persistence.json` not used correctly when
running Docker `fhir-persistence-schema`
#1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: update must gather to include open shift details

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* use the fhiruser password from helm (set by overrides from KeyProtect)

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* Fix the definition for List-identifier search

A workaround for https://jira.hl7.org/browse/FHIR-29937

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* #1802

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* #1802

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Fix up the Must Gather

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* IBM FHIR Server audit does not log bundles correctly. #1803

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update documentation for the mustgather

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: per code review changed the compare, and added an additional ignore
for the metadata endpoints

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Update fhir-server/src/main/java/com/ibm/fhir/server/util/RestAuditLogger.java

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

Co-authored-by: Lee Surprenant <lmsurpre@us.ibm.com>

* doc: compilation errors are now fixed

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: compilation errors are now fixed

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1795

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1796

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests case and fixes for #1797

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests for cp and #1802

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: #1808

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Add tests for plain and base64 encoded environment variables

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix per comments in code review and issue

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Prevent unauthorized reads before they happen

This prevents us from leaking information about what patient resources
exist / don't exist on the system, which was deemed as useful in case an
implementer uses sensitive data for the Resource.id of the Patient
resources (which still isn't advised).

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* Prevent unauthorized vread and history operations against Patient too

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* doc: adding code of conduct md file to root of repository

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: update to clarify the experimental use of the ibm-fhir-schematool

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: update to clarify the experimental use of the ibm-fhir-schematool

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* doc: adding code of conduct md file to root of repository

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* add communication method

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* Audit Refactoring #1542

- Refactor to separate Configuration, Mapping and AuditService
- Configuration to use EventStreams Binding by default
- Add a MapperFactory to split between cadf and auditevent types
	- AuditEventMapper - Wraps the AuditLogEntry into AuditEvent format
	- CADFMapper - Wraps the AuditLogEntry into CADF format
- Audit Service is now KafkaService, NoOpService separating the
Streaming framework from the mapping actions.
- Removed duplicate code for Event/EventStrams processing
- Add Test Coverage for Uncovered Classes

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Clean up spare printStackTrace

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update the documentation for fhir-audit

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* updates per team code review

- Change NoOp to Nop Service
- Remove references to WHC/Disabled
- Changed and clarified package names
- Changed references to specific default places to generic/unknown
places (e.g. dallas to unknown)
- added examples for audit from config and audit from environment

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* issue #1818 reindex resource selection update slows down as reindex progresses

Signed-off-by: Robin Arnold <robin.arnold23@ibm.com>

* updates per team code review

- changed package names to remove logging.api and .model (reconciling it
to a flatter structure)

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update docs

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* change formatting slightly on MapperFactory

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: it tests were not running for drug formulary and c4bb

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix incorrect variable in minor startup log message

Signed-off-by: Lee Surprenant <lmsurpre@us.ibm.com>

* Convert Strings to Constants for Kafka Key-Value in Properties objects

- Per Code Review with Robin Arnold

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Update to 4.6.0-SNAPSHOT

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Code Review for FHIR Audit

- CadfEvent doesn't write out target
- Addresses Written Twice in CadfResource

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Added Test for FHIR Audit so it doesn't have multiple address blocks

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update docs

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Removed auditLogService <extension url="http://ibm.com/fhir/extension/auditLogProperties">

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* fix: referenced license was incorrect

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* Package name consistency issue after Code Review of FHIR-Audit Config
Examples

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* issue #1831 - fix search parameter filtering issue

Signed-off-by: Mike Schroeder <mschroed@us.ibm.com>

* issue #1739 - Update _include and _revinclude parameter checking

Signed-off-by: Troy Biesterfeld <tbieste@us.ibm.com>

* Update .index.json

Warning about invalid entry when discovering HREX profile. 
An example snuck into the .index.json. 

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

* update changelog.md

Signed-off-by: Paul Bastide <pbastide@us.ibm.com>

Co-authored-by: Paul Bastide <pbastide@us.ibm.com>
Co-authored-by: Mike Schroeder <mschroed@us.ibm.com>
Co-authored-by: Robin Arnold <robin.arnold23@ibm.com>
Co-authored-by: Lee Surprenant <lmsurpre@us.ibm.com>
Co-authored-by: Michael W Schroeder <66479070+michaelwschroeder@users.noreply.github.com>
Co-authored-by: Troy Biesterfeld <tbieste@us.ibm.com>
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d0roppe commented Jan 7, 2021

Verified that specifying a schema name other than fhirdata works fine now. Using the same information as in the recreate steps of this issue.

@d0roppe d0roppe closed this as completed Jan 7, 2021
This was referenced Jan 24, 2021
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