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Issue/268 port 1 7 0 to 2 0 0 #269

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Jan 24, 2025
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6bb34b8
Merge remote-tracking branch 'origin/main' into develop
hhund Oct 16, 2024
98e89c2
version to 1.6.1-SNAPSHOT
hhund Oct 16, 2024
7f658c9
fix: different organization roles need to be different codes not codings
hhund Nov 19, 2024
4c9c1b2
added check to make sure StructureDefinition defines a base definition
hhund Nov 19, 2024
7e23ea6
transaction bundle error message fix
hhund Nov 19, 2024
c7aa50c
added "throws WebApplicationException" to improve method signatures
hhund Nov 19, 2024
b8923ea
code cleanup
hhund Nov 19, 2024
0cbf256
database constraint trigger to ensure resource unique criteria
hhund Nov 19, 2024
84170d5
added missing connection parameter
hhund Nov 20, 2024
283e725
code cleanup, removed empty line
hhund Nov 20, 2024
598838f
test fix
hhund Nov 20, 2024
5a0fe23
fixed db lock value and exception message typo
hhund Dec 10, 2024
01e6518
delete queries to remove duplicate resources
hhund Dec 10, 2024
f45177b
debug/audit log typo fixes
hhund Dec 16, 2024
5dd67ea
improved audit log message
hhund Dec 16, 2024
2d2ab80
improved unique constraints
hhund Dec 16, 2024
b434470
fixed typos, added missing tests, improved test constants
hhund Dec 16, 2024
56d6943
unique draft Task rules, db constraint, duplicate delete query and tests
hhund Dec 16, 2024
7c8ce81
typo fix
hhund Dec 16, 2024
09819af
dependency and maven plugin version upgrades
hhund Dec 17, 2024
ca15fd2
Merge remote-tracking branch 'origin/issue/247_Duplicate_Resources' into
hhund Dec 17, 2024
fa94813
Merge remote-tracking branch 'origin/develop' into
hhund Dec 17, 2024
1d2114b
removed highmed.org, added bzkf.de and nct.dkfz.de
hhund Dec 18, 2024
722fca9
version to 1.7.0-SNAPSHOT
hhund Dec 18, 2024
6915a19
Merge remote-tracking branch
hhund Dec 18, 2024
66ad05e
Merge remote-tracking branch 'origin/issue/253_Upgrade_Dependencies'
hhund Dec 18, 2024
0d41f44
updated entries from IANA list and added application/x-ndjson
hhund Jan 7, 2025
13da222
Merge branch 'develop' into issue/253_Upgrade_Dependencies
hhund Jan 7, 2025
ab7c242
dependency version upgrades
hhund Jan 7, 2025
a6c02e0
Merge remote-tracking branch 'origin/issue/253_Upgrade_Dependencies'
hhund Jan 7, 2025
22cafe5
Merge remote-tracking branch 'origin/issue/256_update_urn_ietf_bcp_13'
hhund Jan 7, 2025
e07af97
empty folder README.md file content harmonization
hhund Jan 20, 2025
b366967
maven-clean-plugin config cleanup
hhund Jan 20, 2025
e810168
moved default trusted server & client ca certificates into docker images
hhund Jan 20, 2025
422b10e
removed period characters
hhund Jan 20, 2025
61833f7
removed empty line at end
hhund Jan 20, 2025
c3abb4b
changed pem file name format: CamelCase to lower_case_with_underscores
hhund Jan 20, 2025
500d991
typo fix
hhund Jan 20, 2025
f267551
Merge remote-tracking branch 'origin/issue/259_Default_Root_CAs' into
hhund Jan 21, 2025
d6764ea
extends the docker secrets reader to work for _SECRET_FILE variables
hhund Jan 21, 2025
2c68e47
subject/issuer checks optional if auth not via client cert (oidc)
hhund Jan 21, 2025
e8ad0e8
Merge remote-tracking branch 'origin/issue/261_Secrets_Reader' into
hhund Jan 22, 2025
a6ecf92
Merge remote-tracking branch 'origin/issue/259_Default_Root_CAs' into
hhund Jan 22, 2025
fa50359
update to latest published release by IANA
hhund Jan 22, 2025
e45a868
dependency version upgrades
hhund Jan 22, 2025
a523fd9
1.7.0 release
hhund Jan 22, 2025
a470e4e
Merge remote-tracking branch 'origin/release/1.7.0' into main
hhund Jan 22, 2025
fb8362b
Merge remote-tracking branch 'origin/main' into
hhund Jan 22, 2025
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26 changes: 18 additions & 8 deletions .gitignore
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ dsf-bpe/dsf-bpe-server-jetty/api/v2/*.jar
dsf-bpe/dsf-bpe-server-jetty/conf/config.properties
dsf-bpe/dsf-bpe-server-jetty/docker/api/v1/*.jar
dsf-bpe/dsf-bpe-server-jetty/docker/api/v2/*.jar
dsf-bpe/dsf-bpe-server-jetty/docker/ca/*.pem
dsf-bpe/dsf-bpe-server-jetty/docker/dsf_bpe.jar
dsf-bpe/dsf-bpe-server-jetty/docker/dsf_status_client.jar
dsf-bpe/dsf-bpe-server-jetty/docker/lib/*.jar
Expand All @@ -25,15 +26,10 @@ dsf-bpe/dsf-bpe-server-jetty/process/*.jar
dsf-bpe/dsf-bpe-server-jetty/ui

###
# dsf-fhir ignores
# dsf-docker ignore
###
dsf-fhir/dsf-fhir-server-jetty/conf/bundle.xml
dsf-fhir/dsf-fhir-server-jetty/conf/config.properties
dsf-fhir/dsf-fhir-server-jetty/docker/dsf_fhir.jar
dsf-fhir/dsf-fhir-server-jetty/docker/dsf_status_client.jar
dsf-fhir/dsf-fhir-server-jetty/docker/lib/*.jar
dsf-fhir/dsf-fhir-server-jetty/ui
dsf-fhir/dsf-fhir-validation/src/main/resources/fhir/bundle.xml
dsf-docker/bpe_proxy/ca/*.pem
dsf-docker/fhir_proxy/ca/*.pem

###
# dsf-docker-test-setup ignores
Expand Down Expand Up @@ -66,9 +62,23 @@ dsf-docker-test-setup-3dic-ttp/secrets/*.jks
dsf-docker-test-setup-3dic-ttp/.env
dsf-docker-test-setup-3dic-ttp/docker-compose.override.yml

###
# dsf-fhir ignores
###
dsf-fhir/dsf-fhir-server-jetty/conf/bundle.xml
dsf-fhir/dsf-fhir-server-jetty/conf/config.properties
dsf-fhir/dsf-fhir-server-jetty/docker/ca/*.pem
dsf-fhir/dsf-fhir-server-jetty/docker/dsf_fhir.jar
dsf-fhir/dsf-fhir-server-jetty/docker/dsf_status_client.jar
dsf-fhir/dsf-fhir-server-jetty/docker/lib/*.jar
dsf-fhir/dsf-fhir-server-jetty/ui
dsf-fhir/dsf-fhir-validation/src/main/resources/fhir/bundle.xml

###
# dsf-tools ignores
###
dsf-tools/dsf-tools-default-ca-files-generator/cert/*.pem

dsf-tools/dsf-tools-test-data-generator/bundle/*.xml

dsf-tools/dsf-tools-test-data-generator/cert/**/*.pem
Expand Down
4 changes: 2 additions & 2 deletions CITATION.cff
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ preferred-citation:
type: proceedings
title: "Data Sharing Framework (DSF)"
version: 2.0.0
date-released: 2024-10-15
date-released: 2025-01-22
url: https://dsf.dev
repository-code: https://github.com/datasharingframework/dsf
repository-artifact: https://github.com/datasharingframework/dsf/releases
Expand Down Expand Up @@ -252,7 +252,7 @@ references:
- family-names: Zilske
given-names: Christoph
- family-names: Böhringer
given-names: Jan P.
given-names: Jan Philipp
- family-names: Fegeler
given-names: Christian
title: "Handling Complexity in Decentralized Research Networks: The Data Sharing Framework Allowlist Management Application"
Expand Down
7 changes: 4 additions & 3 deletions dsf-bpe/dsf-bpe-server-jetty/docker/.dockerignore
Original file line number Diff line number Diff line change
@@ -1,9 +1,10 @@
.dockerignore
Dockerfile
api/v1/README.md
api/v2/README.md
ca/README.md
lib/README.md
lib_external/README.md
log/README.md
process/README.md
ui/README.md
ui/README.md
.dockerignore
Dockerfile
4 changes: 2 additions & 2 deletions dsf-bpe/dsf-bpe-server-jetty/docker/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ RUN adduser --system --no-create-home --group --uid 2202 java
WORKDIR /opt/bpe
COPY --chown=root:java ./ ./
RUN chown root:java ./ && \
chmod 750 ./ ./api ./api/v1 ./api/v2 ./conf ./lib ./lib_external ./process ./ui ./dsf_bpe_start.sh ./healthcheck.sh && \
chmod 440 ./conf/log4j2.xml ./dsf_bpe.jar ./lib/*.jar && \
chmod 750 ./ ./api ./api/v1 ./api/v2 ./ca ./conf ./lib ./lib_external ./process ./ui ./dsf_bpe_start.sh ./healthcheck.sh && \
chmod 440 ./ca/client_cert_ca_chains.pem ./ca/server_cert_root_cas.pem ./conf/log4j2.xml ./dsf_bpe.jar ./lib/*.jar && \
chmod 1775 ./log


Expand Down
1 change: 1 addition & 0 deletions dsf-bpe/dsf-bpe-server-jetty/docker/ca/README.md
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
Empty `ca` directory for maven/docker build, will contain default certificate authority pem files after maven build
2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server-jetty/docker/dsf_bpe_start.sh
Original file line number Diff line number Diff line change
Expand Up @@ -17,4 +17,4 @@ if [ $JAVA_EXIT -eq 143 ]; then
else
echo java exited with code $JAVA_EXIT
exit $JAVA_EXIT
fi
fi
2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server-jetty/docker/lib/README.md
Original file line number Diff line number Diff line change
@@ -1 +1 @@
Empty lib directory for jar-files used in docker container
Empty `lib` directory for maven/docker build, will contain dependency jar files after maven build
2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server-jetty/docker/lib_external/README.md
Original file line number Diff line number Diff line change
@@ -1 +1 @@
empty lib_external directory for docker build
Empty `lib_external` directory for docker build, can be used at runtime to add custom dependency jar files
2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server-jetty/docker/log/README.md
Original file line number Diff line number Diff line change
@@ -1 +1 @@
empty log directory for docker build
Empty `log` directory for docker build, will contain log files at runtime
2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server-jetty/docker/process/README.md
Original file line number Diff line number Diff line change
@@ -1 +1 @@
empty process directory for docker build
Empty `process` directory for docker build, used at runtime to place process plugin jar files
2 changes: 1 addition & 1 deletion dsf-bpe/dsf-bpe-server-jetty/docker/ui/README.md
Original file line number Diff line number Diff line change
@@ -1 +1 @@
empty ui directory for static override resources
Empty `ui` directory for docker build, can be used at runtime to place static override resources
Original file line number Diff line number Diff line change
Expand Up @@ -26,27 +26,27 @@ public class BpeDbMigratorConfig implements DbMigratorConfig
private static final String DB_CAMUNDA_USER = "db.camunda_user";
private static final String DB_CAMUNDA_USER_PASSWORD = "db.camunda_user_password";

// Documentation in dsf-bpe-server/src/main/java/dev/dsf/bpe/spring/config/PropertiesConfig.java
@Documentation(required = true, description = "Address of the database used for the DSF BPE server", recommendation = "Change only if you don't use the provided docker-compose from the installation guide or made changes to the database settings/networking in the docker-compose", example = "jdbc:postgresql://db/bpe")
@Value("${dev.dsf.bpe.db.url}")
private String dbUrl;

@Documentation(description = "The user name to access the database from the DSF BPE server to execute database migrations")
@Documentation(description = "Username to access the database from the DSF BPE server to execute database migrations")
@Value("${dev.dsf.bpe.db.liquibase.username:liquibase_user}")
private String dbLiquibaseUsername;

@Documentation(required = true, description = "The password to access the database from the DSF BPE server to execute database migrations", recommendation = "Use docker secret file to configure by using *${env_variable}_FILE*", example = "/run/secrets/db_liquibase.password")
@Documentation(required = true, description = "Password to access the database from the DSF BPE server to execute database migrations", recommendation = "Use docker secret file to configure by using *${env_variable}_FILE*", example = "/run/secrets/db_liquibase.password")
@Value("${dev.dsf.bpe.db.liquibase.password}")
private char[] dbLiquibasePassword;

@Documentation(description = "The name of the user group to access the database from the DSF BPE server")
@Documentation(description = "Name of the user group to access the database from the DSF BPE server")
@Value("${dev.dsf.bpe.db.user.group:bpe_users}")
private String dbUsersGroup;

// Documentation in dsf-bpe-server/src/main/java/dev/dsf/bpe/spring/config/PropertiesConfig.java
@Documentation(description = "Username to access the database from the DSF BPE server")
@Value("${dev.dsf.bpe.db.user.username:bpe_server_user}")
private String dbUsername;

// Documentation in dsf-bpe-server/src/main/java/dev/dsf/bpe/spring/config/PropertiesConfig.java
@Documentation(required = true, description = "Password to access the database from the DSF BPE server", recommendation = "Use docker secret file to configure using *${env_variable}_FILE*", example = "/run/secrets/db_user.password")
@Value("${dev.dsf.bpe.db.user.password}")
private char[] dbPassword;

Expand All @@ -58,15 +58,15 @@ public class BpeDbMigratorConfig implements DbMigratorConfig
@Value("${dev.dsf.bpe.db.liquibase.lockWaitTime:2}")
private long dbLiquibaseLockWaitTime;

@Documentation(description = "The name of the user group to access the database from the DSF BPE server for camunda processes")
@Documentation(description = "Name of the user group to access the database from the DSF BPE server for camunda processes")
@Value("${dev.dsf.bpe.db.user.camunda.group:camunda_users}")
private String dbCamundaUsersGroup;

// Documentation in dsf-bpe-server/src/main/java/dev/dsf/bpe/spring/config/PropertiesConfig.java
@Documentation(description = "Username to access the database from the DSF BPE server for camunda processes", recommendation = "Use a different user then in *DEV_DSF_BPE_DB_USER_USERNAME*")
@Value("${dev.dsf.bpe.db.user.camunda.username:camunda_server_user}")
private String dbCamundaUsername;

// Documentation in dsf-bpe-server/src/main/java/dev/dsf/bpe/spring/config/PropertiesConfig.java
@Documentation(required = true, description = "Password to access the database from the DSF BPE server for camunda processes", recommendation = "Use docker secret file to configure using *${env_variable}_FILE*", example = "/run/secrets/db_user_camunda.password")
@Value("${dev.dsf.bpe.db.user.camunda.password}")
private char[] dbCamundaPassword;

Expand Down
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