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issue 2050 fix1 merged with main
Signed-off-by: Robin Arnold <robin.arnold@ibm.com>
2 parents 83614cc + 44b0d80 commit 44943ec

106 files changed

Lines changed: 3741 additions & 1530 deletions

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‎build/audit/kafka/docker-compose.yml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -68,15 +68,15 @@ services:
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command: bash -c "
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java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
7070
--db-type derby --prop db.database=/output/derby/profile --prop db.create=Y
71-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
71+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
7272
--update-schema &&
7373
java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
7474
--db-type derby --prop db.database=/output/derby/reference --prop db.create=Y
75-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
75+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
7676
--update-schema &&
7777
java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
7878
--db-type derby --prop db.database=/output/derby/study1 --prop db.create=Y
79-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
79+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
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--update-schema &&
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/opt/ol/wlp/bin/server run"
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healthcheck:

‎build/derby-bootstrap.sh‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -26,13 +26,13 @@ java -jar ${WORKSPACE}/fhir-persistence-schema/target/fhir-persistence-schema-*-
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--update-schema
2727
java -jar ${WORKSPACE}/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
2828
--db-type derby --prop db.database=${DB_LOC}/profile --prop db.create=Y \
29-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
29+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
3030
--update-schema
3131
java -jar ${WORKSPACE}/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
3232
--db-type derby --prop db.database=${DB_LOC}/reference --prop db.create=Y \
33-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
33+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
3434
--update-schema
3535
java -jar ${WORKSPACE}/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
3636
--db-type derby --prop db.database=${DB_LOC}/study1 --prop db.create=Y \
37-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
37+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
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--update-schema

‎build/docker/docker-compose.yml‎

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Original file line numberDiff line numberDiff line change
@@ -31,15 +31,15 @@ services:
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command: bash -c "
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java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
3333
--db-type derby --prop db.database=/output/derby/profile --prop db.create=Y
34-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
34+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
3535
--update-schema &&
3636
java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
3737
--db-type derby --prop db.database=/output/derby/reference --prop db.create=Y
38-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
38+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
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--update-schema &&
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java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
4141
--db-type derby --prop db.database=/output/derby/study1 --prop db.create=Y
42-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
42+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
4343
--update-schema &&
4444
/opt/ol/wlp/bin/server run"
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healthcheck:

‎build/migration/db2/4_current-migrate.sh‎

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Original file line numberDiff line numberDiff line change
@@ -56,19 +56,19 @@ java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-sche
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--update-schema
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java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
5858
--db-type derby --prop db.database=${DB_LOC}/profile --prop db.create=Y \
59-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
59+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
6060
--update-schema
6161
java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
6262
--db-type derby --prop db.database=${DB_LOC}/reference --prop db.create=Y \
63-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
63+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
6464
--update-schema
6565
java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
6666
--db-type derby --prop db.database=${DB_LOC}/study1 --prop db.create=Y \
67-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
67+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
6868
--update-schema
6969

7070
# Reset to Original Directory
7171
popd > /dev/null
7272

7373
# EOF
74-
###############################################################################
74+
###############################################################################

‎build/migration/postgres/4_current-migrate.sh‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -70,19 +70,19 @@ java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-sche
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--update-schema
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java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
7272
--db-type derby --prop db.database=${DB_LOC}/profile --prop db.create=Y \
73-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
73+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
7474
--update-schema
7575
java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
7676
--db-type derby --prop db.database=${DB_LOC}/reference --prop db.create=Y \
77-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
77+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
7878
--update-schema
7979
java -jar ${WORKSPACE}/fhir/fhir-persistence-schema/target/fhir-persistence-schema-*-cli.jar \
8080
--db-type derby --prop db.database=${DB_LOC}/study1 --prop db.create=Y \
81-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
81+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
8282
--update-schema
8383

8484
# Reset to Original Directory
8585
popd > /dev/null
8686

8787
# EOF
88-
###############################################################################
88+
###############################################################################

‎build/notifications/kafka/docker-compose.yml‎

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Original file line numberDiff line numberDiff line change
@@ -68,15 +68,15 @@ services:
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command: bash -c "
6969
java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
7070
--db-type derby --prop db.database=/output/derby/profile --prop db.create=Y
71-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
71+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
7272
--update-schema &&
7373
java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
7474
--db-type derby --prop db.database=/output/derby/reference --prop db.create=Y
75-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
75+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
7676
--update-schema &&
7777
java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
7878
--db-type derby --prop db.database=/output/derby/study1 --prop db.create=Y
79-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
79+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
8080
--update-schema &&
8181
/opt/ol/wlp/bin/server run"
8282
healthcheck:

‎build/persistence/postgres/docker-compose.yml‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -47,15 +47,15 @@ services:
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command: bash -c "
4848
java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
4949
--db-type derby --prop db.database=/output/derby/profile --prop db.create=Y
50-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
50+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
5151
--update-schema &&
5252
java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
5353
--db-type derby --prop db.database=/output/derby/reference --prop db.create=Y
54-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
54+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
5555
--update-schema &&
5656
java -jar /opt/ibm-fhir-server/tools/fhir-persistence-schema-*-cli.jar
5757
--db-type derby --prop db.database=/output/derby/study1 --prop db.create=Y
58-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource
58+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet
5959
--update-schema &&
6060
/opt/ol/wlp/bin/server run"
6161
healthcheck:

‎build/pre-integration-test.ps1‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -58,15 +58,15 @@ java -jar $SCHEMATOOL `
5858
--update-schema
5959
java -jar $SCHEMATOOL `
6060
--db-type derby --prop db.database=${DB_LOC}\profile --prop db.create=Y `
61-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource `
61+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet `
6262
--update-schema
6363
java -jar $SCHEMATOOL `
6464
--db-type derby --prop db.database=${DB_LOC}\reference --prop db.create=Y `
65-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource `
65+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet `
6666
--update-schema
6767
java -jar $SCHEMATOOL `
6868
--db-type derby --prop db.database=${DB_LOC}\study1 --prop db.create=Y `
69-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource `
69+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet `
7070
--update-schema
7171

7272
# If the Config Exists, let's wipe it outfind

‎build/pre-integration-test.sh‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -50,15 +50,15 @@ java -jar ${SIT}/fhir-server-dist/tools/fhir-persistence-schema-*-cli.jar \
5050
--update-schema
5151
java -jar ${SIT}/fhir-server-dist/tools/fhir-persistence-schema-*-cli.jar \
5252
--db-type derby --prop db.database=${DB_LOC}/profile --prop db.create=Y \
53-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
53+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Person,RelatedPerson,Organization,Location,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
5454
--update-schema
5555
java -jar ${SIT}/fhir-server-dist/tools/fhir-persistence-schema-*-cli.jar \
5656
--db-type derby --prop db.database=${DB_LOC}/reference --prop db.create=Y \
57-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
57+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Medication,Observation,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
5858
--update-schema
5959
java -jar ${SIT}/fhir-server-dist/tools/fhir-persistence-schema-*-cli.jar \
6060
--db-type derby --prop db.database=${DB_LOC}/study1 --prop db.create=Y \
61-
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet,Resource \
61+
--prop resourceTypes=Patient,Group,Practitioner,PractitionerRole,Device,Organization,Location,Encounter,AllergyIntolerance,Observation,Condition,CarePlan,Provenance,Medication,MedicationAdministration,StructureDefinition,ElementDefinition,CodeSystem,ValueSet \
6262
--update-schema
6363

6464
echo "Copying configuration to install location..."

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