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Schema defined for fhir
in persistence.json
not used correctly when running Docker fhir-persistence-schema
#1795
Comments
Thanks, I'll look at it early Monday |
Just for completeness: The same error occurs also if not 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 |
Right - it's in create-schemas - I only specified the defaults, I'll change this on monday |
p.s. thank you |
running Docker `fhir-persistence-schema` #1795 Signed-off-by: Paul Bastide <pbastide@us.ibm.com>
Signed-off-by: Paul Bastide <pbastide@us.ibm.com>
Signed-off-by: Paul Bastide <pbastide@us.ibm.com>
Signed-off-by: Paul Bastide <pbastide@us.ibm.com>
Added a test for this one in #1799 |
* 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>
* 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>
Verified that specifying a schema name other than fhirdata works fine now. Using the same information as in the recreate steps of this issue. |
Describe the bug
The schema defined for
fhir
inpersistence.json
is not used correctly when running Dockerfhir-persistence-schema
.To Reproduce
persistence.json
whereschema
forfhir
is set to the valuesomefhirschema
, i.e. to some value other thanfhirdata
:fhir-persistence-schema
: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
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