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NPE when element schema is not defined in persistence.json instead of using default schema names #1808

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holger-stenzhorn opened this issue Dec 8, 2020 · 0 comments · Fixed by #1799
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bug Something isn't working cloud portability

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@holger-stenzhorn
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Describe the bug
If no element schema defined is defined in persistence.json then one receives a NPE when running Docker `fhir-persistence-schema.

To Reproduce

  1. Create a file persistence.json with the following content, i.e. no element schema defined:
    {
        "persistence": [
            {
                "db":  {
                    "host": "db",
                    "port": "5432",
                    "database": "fhirdb",
                    "user": "postgres",
                    "password": "change-password",
                    "type": "postgresql",
                    "ssl": "false",
                    "certificate_base64": "empty"
                },
                "behavior": "onboard"
            }
        ]
    }
  2. Run docker run --env ENV_TOOL_INPUT=$(cat persistence.json | base64) ibmcom/ibm-fhir-schematool:latest
  3. See error:
    ibm-fhir-schematool_1  | + /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-schema-oauth null --create-schema-batch null --create-schema-fhir null --pool-size 2
    ibm-fhir-schematool_1  | + tee out.log
    ibm-fhir-schematool_1  | 2020-12-08 12:37:53.830 00000001    INFO   com.ibm.fhir.schema.app.Main Opening connection to: jdbc:postgresql://postgres:5432/fhir
    ibm-fhir-schematool_1  | 2020-12-08 12:37:54.115 00000001    INFO s.postgresql.PostgreSqlAdapter The schema 'FHIR_ADMIN' is created or already exists
    postgres_1             | 2020-12-08 12:37:54.117 UTC [75] ERROR:  syntax error at or near "NULL" at character 29
    postgres_1             | 2020-12-08 12:37:54.117 UTC [75] STATEMENT:  CREATE SCHEMA IF NOT EXISTS NULL
    ibm-fhir-schematool_1  | 2020-12-08 12:37:54.129 00000001  SEVERE   com.ibm.fhir.schema.app.Main schema tool failed
    ibm-fhir-schematool_1  | 
    ibm-fhir-schematool_1  | org.postgresql.util.PSQLException: ERROR: syntax error at or near "NULL"
    ibm-fhir-schematool_1  |   Position: 29
    ibm-fhir-schematool_1  | com.ibm.fhir.database.utils.api.DataAccessException: org.postgresql.util.PSQLException: ERROR: syntax error at or near "NULL"
    ibm-fhir-schematool_1  |   Position: 29
    ibm-fhir-schematool_1  | 	at com.ibm.fhir.database.utils.postgresql.PostgreSqlTranslator.translate(PostgreSqlTranslator.java:104)
    ibm-fhir-schematool_1  | 	at com.ibm.fhir.database.utils.common.JdbcTarget.runStatement(JdbcTarget.java:48)
    ibm-fhir-schematool_1  | 	at com.ibm.fhir.database.utils.common.CommonDatabaseAdapter.runStatement(CommonDatabaseAdapter.java:230)
    ibm-fhir-schematool_1  | 	at com.ibm.fhir.database.utils.postgresql.PostgreSqlAdapter.createSchema(PostgreSqlAdapter.java:304)
    ibm-fhir-schematool_1  | 	at com.ibm.fhir.schema.app.Main.createSchemas(Main.java:300)
    ibm-fhir-schematool_1  | 	at com.ibm.fhir.schema.app.Main.process(Main.java:1438)
    ibm-fhir-schematool_1  | 	at com.ibm.fhir.schema.app.Main.main(Main.java:1513)
    ibm-fhir-schematool_1  | Caused by: org.postgresql.util.PSQLException: ERROR: syntax error at or near "NULL"
    ibm-fhir-schematool_1  |   Position: 29
    ibm-fhir-schematool_1  | 	at org.postgresql.core.v3.QueryExecutorImpl.receiveErrorResponse(QueryExecutorImpl.java:2533)
    ibm-fhir-schematool_1  | 	at org.postgresql.core.v3.QueryExecutorImpl.processResults(QueryExecutorImpl.java:2268)
    ibm-fhir-schematool_1  | 	at org.postgresql.core.v3.QueryExecutorImpl.execute(QueryExecutorImpl.java:313)
    ibm-fhir-schematool_1  | 	at org.postgresql.jdbc.PgStatement.executeInternal(PgStatement.java:448)
    ibm-fhir-schematool_1  | 	at org.postgresql.jdbc.PgStatement.execute(PgStatement.java:369)
    ibm-fhir-schematool_1  | 	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:310)
    ibm-fhir-schematool_1  | 	at org.postgresql.jdbc.PgStatement.executeCachedSql(PgStatement.java:296)
    ibm-fhir-schematool_1  | 	at org.postgresql.jdbc.PgStatement.executeWithFlags(PgStatement.java:273)
    ibm-fhir-schematool_1  | 	at org.postgresql.jdbc.PgStatement.executeUpdate(PgStatement.java:247)
    ibm-fhir-schematool_1  | 	at com.ibm.fhir.database.utils.common.JdbcTarget.runStatement(JdbcTarget.java:45)
    ibm-fhir-schematool_1  | 	... 5 more
    ibm-fhir-schematool_1  | 2020-12-08 12:37:54.137 00000001  SEVERE   com.ibm.fhir.schema.app.Main SCHEMA CHANGE: RUNTIME ERROR
    

Expected behavior
The default schema names, i.e. FHIRDATA, FHIR_OAUTHand FHIR_JBATCH should be used.

Additional context
n/a

@holger-stenzhorn holger-stenzhorn added the bug Something isn't working label Dec 8, 2020
prb112 added a commit that referenced this issue Dec 8, 2020
Signed-off-by: Paul Bastide <pbastide@us.ibm.com>
@prb112 prb112 self-assigned this Dec 8, 2020
JohnTimm added a commit that referenced this issue Dec 15, 2020
* 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
* 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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