From 89fd453c540a80982081b6ed5346bedd0c9e3a7c Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Sun, 12 Jun 2022 21:47:56 +0200 Subject: [PATCH 01/14] DSF version to 0.7.0-SNAPSHOT, some maven dependency upgrades --- CITATION.cff | 4 ++-- dsf-bpe/dsf-bpe-process-base/pom.xml | 2 +- dsf-bpe/dsf-bpe-server-jetty/pom.xml | 2 +- dsf-bpe/dsf-bpe-server/pom.xml | 2 +- dsf-bpe/dsf-bpe-webservice-client/pom.xml | 2 +- dsf-bpe/pom.xml | 2 +- dsf-consent/dsf-consent-client-stub/pom.xml | 2 +- dsf-consent/dsf-consent-client/pom.xml | 2 +- dsf-consent/pom.xml | 2 +- dsf-fhir/dsf-fhir-auth/pom.xml | 2 +- dsf-fhir/dsf-fhir-rest-adapter/pom.xml | 2 +- dsf-fhir/dsf-fhir-server-jetty/pom.xml | 2 +- dsf-fhir/dsf-fhir-server/pom.xml | 2 +- dsf-fhir/dsf-fhir-validation/pom.xml | 4 ++-- dsf-fhir/dsf-fhir-webservice-client/pom.xml | 2 +- dsf-fhir/dsf-fhir-websocket-client/pom.xml | 2 +- dsf-fhir/pom.xml | 2 +- dsf-mpi/dsf-mpi-client-pdq/pom.xml | 2 +- dsf-mpi/dsf-mpi-client-stub/pom.xml | 2 +- dsf-mpi/dsf-mpi-client/pom.xml | 2 +- dsf-mpi/pom.xml | 2 +- dsf-openehr/dsf-openehr-client-impl/pom.xml | 2 +- dsf-openehr/dsf-openehr-client-stub/pom.xml | 2 +- dsf-openehr/dsf-openehr-client/pom.xml | 2 +- dsf-openehr/dsf-openehr-model/pom.xml | 2 +- dsf-openehr/pom.xml | 2 +- dsf-pseudonymization/dsf-pseudonymization-base/pom.xml | 2 +- .../dsf-pseudonymization-client-stub/pom.xml | 2 +- .../dsf-pseudonymization-client/pom.xml | 2 +- .../dsf-pseudonymization-medic/pom.xml | 2 +- dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml | 2 +- dsf-pseudonymization/pom.xml | 2 +- dsf-tools/dsf-tools-build-info-reader/pom.xml | 2 +- dsf-tools/dsf-tools-bundle-generator/pom.xml | 2 +- dsf-tools/dsf-tools-db-migration/pom.xml | 2 +- dsf-tools/dsf-tools-docker-secrets-reader/pom.xml | 2 +- dsf-tools/dsf-tools-documentation-generator/pom.xml | 2 +- dsf-tools/dsf-tools-proxy-test/pom.xml | 2 +- dsf-tools/dsf-tools-test-data-generator/pom.xml | 2 +- dsf-tools/pom.xml | 2 +- pom.xml | 10 +++++----- 41 files changed, 47 insertions(+), 47 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 1cdfc3d3a..eb1d288ce 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -24,8 +24,8 @@ preferred-citation: doi: 10.3233/SHTI210060 type: proceedings title: "HiGHmed Data Sharing Framework (HiGHmed DSF)" -version: 0.6.0 -date-released: 2022-03-10 +version: 0.7.0 +date-released: 2022-06-12 url: https://github.com/highmed/highmed-dsf/wiki repository-code: https://github.com/highmed/highmed-dsf repository-artifact: https://github.com/highmed/highmed-dsf/releases diff --git a/dsf-bpe/dsf-bpe-process-base/pom.xml b/dsf-bpe/dsf-bpe-process-base/pom.xml index e238650dc..5742d8a3f 100755 --- a/dsf-bpe/dsf-bpe-process-base/pom.xml +++ b/dsf-bpe/dsf-bpe-process-base/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-bpe-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-bpe/dsf-bpe-server-jetty/pom.xml b/dsf-bpe/dsf-bpe-server-jetty/pom.xml index d22336383..06464732e 100755 --- a/dsf-bpe/dsf-bpe-server-jetty/pom.xml +++ b/dsf-bpe/dsf-bpe-server-jetty/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-bpe-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-bpe/dsf-bpe-server/pom.xml b/dsf-bpe/dsf-bpe-server/pom.xml index c31a3ac68..d9cdbb2f8 100755 --- a/dsf-bpe/dsf-bpe-server/pom.xml +++ b/dsf-bpe/dsf-bpe-server/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-bpe-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-bpe/dsf-bpe-webservice-client/pom.xml b/dsf-bpe/dsf-bpe-webservice-client/pom.xml index 051bab8be..7bb961c9e 100755 --- a/dsf-bpe/dsf-bpe-webservice-client/pom.xml +++ b/dsf-bpe/dsf-bpe-webservice-client/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-bpe-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-bpe/pom.xml b/dsf-bpe/pom.xml index 80a293478..b81e1db76 100755 --- a/dsf-bpe/pom.xml +++ b/dsf-bpe/pom.xml @@ -8,7 +8,7 @@ org.highmed.dsf dsf-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-consent/dsf-consent-client-stub/pom.xml b/dsf-consent/dsf-consent-client-stub/pom.xml index 1399b7156..67b09bd04 100644 --- a/dsf-consent/dsf-consent-client-stub/pom.xml +++ b/dsf-consent/dsf-consent-client-stub/pom.xml @@ -9,7 +9,7 @@ dsf-consent-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-consent/dsf-consent-client/pom.xml b/dsf-consent/dsf-consent-client/pom.xml index 607f61137..daca69c3f 100644 --- a/dsf-consent/dsf-consent-client/pom.xml +++ b/dsf-consent/dsf-consent-client/pom.xml @@ -9,7 +9,7 @@ dsf-consent-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-consent/pom.xml b/dsf-consent/pom.xml index 389043270..81cb8ff4c 100644 --- a/dsf-consent/pom.xml +++ b/dsf-consent/pom.xml @@ -10,7 +10,7 @@ dsf-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-fhir/dsf-fhir-auth/pom.xml b/dsf-fhir/dsf-fhir-auth/pom.xml index 130ddad04..0295db58a 100644 --- a/dsf-fhir/dsf-fhir-auth/pom.xml +++ b/dsf-fhir/dsf-fhir-auth/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-fhir/dsf-fhir-rest-adapter/pom.xml b/dsf-fhir/dsf-fhir-rest-adapter/pom.xml index f1758d073..42f92179e 100755 --- a/dsf-fhir/dsf-fhir-rest-adapter/pom.xml +++ b/dsf-fhir/dsf-fhir-rest-adapter/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-fhir/dsf-fhir-server-jetty/pom.xml b/dsf-fhir/dsf-fhir-server-jetty/pom.xml index 324a426c8..2aa7c5b0c 100755 --- a/dsf-fhir/dsf-fhir-server-jetty/pom.xml +++ b/dsf-fhir/dsf-fhir-server-jetty/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-fhir/dsf-fhir-server/pom.xml b/dsf-fhir/dsf-fhir-server/pom.xml index d6c203bd4..2b4a8e966 100755 --- a/dsf-fhir/dsf-fhir-server/pom.xml +++ b/dsf-fhir/dsf-fhir-server/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-fhir/dsf-fhir-validation/pom.xml b/dsf-fhir/dsf-fhir-validation/pom.xml index 1f7420a05..609bfdb1f 100644 --- a/dsf-fhir/dsf-fhir-validation/pom.xml +++ b/dsf-fhir/dsf-fhir-validation/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.6.0 + 0.7.0-SNAPSHOT @@ -93,7 +93,7 @@ - diff --git a/dsf-fhir/dsf-fhir-webservice-client/pom.xml b/dsf-fhir/dsf-fhir-webservice-client/pom.xml index 33e184523..398cc7b5c 100755 --- a/dsf-fhir/dsf-fhir-webservice-client/pom.xml +++ b/dsf-fhir/dsf-fhir-webservice-client/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-fhir/dsf-fhir-websocket-client/pom.xml b/dsf-fhir/dsf-fhir-websocket-client/pom.xml index b485da765..f0294dfc3 100755 --- a/dsf-fhir/dsf-fhir-websocket-client/pom.xml +++ b/dsf-fhir/dsf-fhir-websocket-client/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-fhir/pom.xml b/dsf-fhir/pom.xml index 567afc015..00f2a5019 100755 --- a/dsf-fhir/pom.xml +++ b/dsf-fhir/pom.xml @@ -8,7 +8,7 @@ org.highmed.dsf dsf-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-mpi/dsf-mpi-client-pdq/pom.xml b/dsf-mpi/dsf-mpi-client-pdq/pom.xml index 2046d6edc..b3a7a43a9 100644 --- a/dsf-mpi/dsf-mpi-client-pdq/pom.xml +++ b/dsf-mpi/dsf-mpi-client-pdq/pom.xml @@ -9,7 +9,7 @@ dsf-mpi-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-mpi/dsf-mpi-client-stub/pom.xml b/dsf-mpi/dsf-mpi-client-stub/pom.xml index f05ecbaa6..90505a9b4 100644 --- a/dsf-mpi/dsf-mpi-client-stub/pom.xml +++ b/dsf-mpi/dsf-mpi-client-stub/pom.xml @@ -9,7 +9,7 @@ dsf-mpi-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-mpi/dsf-mpi-client/pom.xml b/dsf-mpi/dsf-mpi-client/pom.xml index 9f044b103..e37c298e7 100644 --- a/dsf-mpi/dsf-mpi-client/pom.xml +++ b/dsf-mpi/dsf-mpi-client/pom.xml @@ -9,7 +9,7 @@ dsf-mpi-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-mpi/pom.xml b/dsf-mpi/pom.xml index ac80ddb85..55652ab8d 100644 --- a/dsf-mpi/pom.xml +++ b/dsf-mpi/pom.xml @@ -10,7 +10,7 @@ dsf-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-openehr/dsf-openehr-client-impl/pom.xml b/dsf-openehr/dsf-openehr-client-impl/pom.xml index db821ca68..c9df348c3 100644 --- a/dsf-openehr/dsf-openehr-client-impl/pom.xml +++ b/dsf-openehr/dsf-openehr-client-impl/pom.xml @@ -9,7 +9,7 @@ dsf-openehr-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-openehr/dsf-openehr-client-stub/pom.xml b/dsf-openehr/dsf-openehr-client-stub/pom.xml index 1552c57d3..eb42fa82d 100644 --- a/dsf-openehr/dsf-openehr-client-stub/pom.xml +++ b/dsf-openehr/dsf-openehr-client-stub/pom.xml @@ -8,7 +8,7 @@ dsf-openehr-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-openehr/dsf-openehr-client/pom.xml b/dsf-openehr/dsf-openehr-client/pom.xml index e5022a417..5d6973fcb 100644 --- a/dsf-openehr/dsf-openehr-client/pom.xml +++ b/dsf-openehr/dsf-openehr-client/pom.xml @@ -8,7 +8,7 @@ dsf-openehr-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-openehr/dsf-openehr-model/pom.xml b/dsf-openehr/dsf-openehr-model/pom.xml index 9892557a0..284c3be4d 100644 --- a/dsf-openehr/dsf-openehr-model/pom.xml +++ b/dsf-openehr/dsf-openehr-model/pom.xml @@ -8,7 +8,7 @@ dsf-openehr-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-openehr/pom.xml b/dsf-openehr/pom.xml index cf93fe4ee..ed6907b0f 100755 --- a/dsf-openehr/pom.xml +++ b/dsf-openehr/pom.xml @@ -10,7 +10,7 @@ dsf-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml index f68fe54df..95819d0ee 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-pseudonymization-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-pseudonymization/dsf-pseudonymization-client-stub/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-client-stub/pom.xml index f00ae7876..b55bcfda7 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-client-stub/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-client-stub/pom.xml @@ -9,7 +9,7 @@ dsf-pseudonymization-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-pseudonymization/dsf-pseudonymization-client/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-client/pom.xml index 797a80d45..d3f2bbe35 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-client/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-client/pom.xml @@ -9,7 +9,7 @@ dsf-pseudonymization-pom org.highmed.dsf - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml index 60defdb5c..8713cc96d 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-pseudonymization-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml index c17ded770..f1fe03fcd 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-pseudonymization-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-pseudonymization/pom.xml b/dsf-pseudonymization/pom.xml index 08a475225..f156ac720 100644 --- a/dsf-pseudonymization/pom.xml +++ b/dsf-pseudonymization/pom.xml @@ -8,7 +8,7 @@ org.highmed.dsf dsf-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-tools/dsf-tools-build-info-reader/pom.xml b/dsf-tools/dsf-tools-build-info-reader/pom.xml index 347886924..31147a656 100644 --- a/dsf-tools/dsf-tools-build-info-reader/pom.xml +++ b/dsf-tools/dsf-tools-build-info-reader/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-tools/dsf-tools-bundle-generator/pom.xml b/dsf-tools/dsf-tools-bundle-generator/pom.xml index 2e83f1ee0..18a345a32 100755 --- a/dsf-tools/dsf-tools-bundle-generator/pom.xml +++ b/dsf-tools/dsf-tools-bundle-generator/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-tools/dsf-tools-db-migration/pom.xml b/dsf-tools/dsf-tools-db-migration/pom.xml index 454b45aa9..f5ce1544a 100755 --- a/dsf-tools/dsf-tools-db-migration/pom.xml +++ b/dsf-tools/dsf-tools-db-migration/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-tools/dsf-tools-docker-secrets-reader/pom.xml b/dsf-tools/dsf-tools-docker-secrets-reader/pom.xml index 2a8711a06..0422adeb1 100644 --- a/dsf-tools/dsf-tools-docker-secrets-reader/pom.xml +++ b/dsf-tools/dsf-tools-docker-secrets-reader/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-tools/dsf-tools-documentation-generator/pom.xml b/dsf-tools/dsf-tools-documentation-generator/pom.xml index 8f7f56dc4..0e3a12e19 100644 --- a/dsf-tools/dsf-tools-documentation-generator/pom.xml +++ b/dsf-tools/dsf-tools-documentation-generator/pom.xml @@ -9,7 +9,7 @@ org.highmed.dsf dsf-tools-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-tools/dsf-tools-proxy-test/pom.xml b/dsf-tools/dsf-tools-proxy-test/pom.xml index 5686405d5..075a81d37 100755 --- a/dsf-tools/dsf-tools-proxy-test/pom.xml +++ b/dsf-tools/dsf-tools-proxy-test/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-tools/dsf-tools-test-data-generator/pom.xml b/dsf-tools/dsf-tools-test-data-generator/pom.xml index d02e2d6ea..4a8de1855 100755 --- a/dsf-tools/dsf-tools-test-data-generator/pom.xml +++ b/dsf-tools/dsf-tools-test-data-generator/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/dsf-tools/pom.xml b/dsf-tools/pom.xml index bdbccb3e4..595ab13e9 100755 --- a/dsf-tools/pom.xml +++ b/dsf-tools/pom.xml @@ -8,7 +8,7 @@ org.highmed.dsf dsf-pom - 0.6.0 + 0.7.0-SNAPSHOT diff --git a/pom.xml b/pom.xml index 2068ed28e..ba65d33da 100755 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.highmed.dsf dsf-pom - 0.6.0 + 0.7.0-SNAPSHOT pom @@ -30,7 +30,7 @@ 9.4.46.v20220331 2.35 1.18 - 5.3.19 + 5.3.20 5.1.0 2.3 @@ -131,7 +131,7 @@ org.postgresql postgresql - 42.3.4 + 42.3.6 @@ -206,12 +206,12 @@ com.fasterxml.jackson.core jackson-databind - 2.13.2.2 + 2.13.3 com.fasterxml.jackson.core jackson-annotations - 2.13.2 + 2.13.3 From 640be171481bfe121ce5a178753b5fe7cdf2dd27 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Mon, 13 Jun 2022 20:22:23 +0200 Subject: [PATCH 02/14] added dependencies needed for FHIR validation to dsf-bpe-process-base --- dsf-bpe/dsf-bpe-process-base/pom.xml | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/dsf-bpe/dsf-bpe-process-base/pom.xml b/dsf-bpe/dsf-bpe-process-base/pom.xml index 5742d8a3f..d5844ec56 100755 --- a/dsf-bpe/dsf-bpe-process-base/pom.xml +++ b/dsf-bpe/dsf-bpe-process-base/pom.xml @@ -19,6 +19,10 @@ org.highmed.dsf dsf-fhir-auth + + org.highmed.dsf + dsf-fhir-validation + org.highmed.dsf @@ -56,6 +60,10 @@ org.springframework spring-context + + org.springframework + spring-web + org.camunda.bpm camunda-engine @@ -65,11 +73,18 @@ commons-io commons-io + + org.apache.commons + commons-compress + de.hs-heilbronn.mi log4j2-utils - test + + + org.slf4j + jul-to-slf4j From 41ecabb76bc18438f1c9fe1d5114bee283d3b580 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Mon, 13 Jun 2022 20:23:49 +0200 Subject: [PATCH 03/14] modifications to enable extending snapshot generator classes --- .../dsf/fhir/validation/SnapshotGenerator.java | 13 ++++++++----- .../dsf/fhir/validation/SnapshotGeneratorImpl.java | 2 +- 2 files changed, 9 insertions(+), 6 deletions(-) diff --git a/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGenerator.java b/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGenerator.java index f2ffe050b..58eadac17 100755 --- a/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGenerator.java +++ b/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGenerator.java @@ -1,5 +1,7 @@ package org.highmed.dsf.fhir.validation; +import java.util.ArrayList; +import java.util.Collections; import java.util.List; import org.hl7.fhir.r4.model.StructureDefinition; @@ -7,15 +9,16 @@ public interface SnapshotGenerator { - class SnapshotWithValidationMessages + public class SnapshotWithValidationMessages { private final StructureDefinition snapshot; - private final List messages; + private final List messages = new ArrayList<>(); - SnapshotWithValidationMessages(StructureDefinition snapshot, List messages) + public SnapshotWithValidationMessages(StructureDefinition snapshot, List messages) { this.snapshot = snapshot; - this.messages = messages; + if (messages != null) + this.messages.addAll(messages); } public StructureDefinition getSnapshot() @@ -25,7 +28,7 @@ public StructureDefinition getSnapshot() public List getMessages() { - return messages; + return Collections.unmodifiableList(messages); } } diff --git a/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGeneratorImpl.java b/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGeneratorImpl.java index 733501854..695182aac 100755 --- a/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGeneratorImpl.java +++ b/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGeneratorImpl.java @@ -26,7 +26,7 @@ public SnapshotGeneratorImpl(FhirContext fhirContext, IValidationSupport validat worker = createWorker(fhirContext, validationSupport); } - protected HapiWorkerContext createWorker(FhirContext context, IValidationSupport validationSupport) + protected IWorkerContext createWorker(FhirContext context, IValidationSupport validationSupport) { HapiWorkerContext workerContext = new HapiWorkerContext(context, validationSupport); workerContext.setLocale(context.getLocalizer().getLocale()); From 2214ddb08ecc651b01f53ebd0d1652d0fa04fffc Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Sun, 19 Jun 2022 20:41:29 +0200 Subject: [PATCH 04/14] log message fix --- .../org/highmed/dsf/fhir/validation/SnapshotGeneratorImpl.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGeneratorImpl.java b/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGeneratorImpl.java index 695182aac..1ecdbd06f 100755 --- a/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGeneratorImpl.java +++ b/dsf-fhir/dsf-fhir-validation/src/main/java/org/highmed/dsf/fhir/validation/SnapshotGeneratorImpl.java @@ -65,7 +65,7 @@ public SnapshotWithValidationMessages generateSnapshot(StructureDefinition diffe differential.getIdElement().getIdPart(), differential.getUrl(), differential.getVersion()); else { - logger.warn("Snapshot not generated for StructureDefinition with id {}, url {}, version {}", + logger.warn("Snapshot generated with issues for StructureDefinition with id {}, url {}, version {}", differential.getIdElement().getIdPart(), differential.getUrl(), differential.getVersion()); messages.forEach(m -> logger.warn("Issue while generating snapshot: {} - {} - {}", m.getDisplay(), m.getLine(), m.getMessage())); From 08e308797565adacfcbdd7a88bff701d6cc01b28 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Sun, 19 Jun 2022 20:44:21 +0200 Subject: [PATCH 05/14] mechanism to correlate process instances with alternative business-key Using the new method createAndSaveAlternativeBusinessKey() in AbstractTaskMessageSend enables processes to create an alternative business key before sending a task to a target. Return task from the target with the alternative business key are correlated to the original process instance. --- .../org/highmed/dsf/bpe/ConstantsBase.java | 1 + .../fhir/task/AbstractTaskMessageSend.java | 31 ++++++++++++++++ .../highmed/dsf/fhir/task/TaskHandler.java | 37 ++++++++++++++----- 3 files changed, 59 insertions(+), 10 deletions(-) diff --git a/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ConstantsBase.java b/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ConstantsBase.java index 3798d121e..c3f473e34 100755 --- a/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ConstantsBase.java +++ b/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/bpe/ConstantsBase.java @@ -15,6 +15,7 @@ public interface ConstantsBase String BPMN_EXECUTION_VARIABLE_QUERY_PARAMETERS = "queryParameters"; String BPMN_EXECUTION_VARIABLE_TTP_IDENTIFIER = "ttpIdentifier"; String BPMN_EXECUTION_VARIABLE_LEADING_MEDIC_IDENTIFIER = "leadingMedicIdentifier"; + String BPMN_EXECUTION_VARIABLE_ALTERNATIVE_BUSINESS_KEY = "alternativeBusinessKey"; /** * Used to distinguish if I am at the moment in a process called by another process by a CallActivity or not diff --git a/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/fhir/task/AbstractTaskMessageSend.java b/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/fhir/task/AbstractTaskMessageSend.java index ff6efb569..0d76eff6c 100755 --- a/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/fhir/task/AbstractTaskMessageSend.java +++ b/dsf-bpe/dsf-bpe-process-base/src/main/java/org/highmed/dsf/fhir/task/AbstractTaskMessageSend.java @@ -1,5 +1,6 @@ package org.highmed.dsf.fhir.task; +import static org.highmed.dsf.bpe.ConstantsBase.BPMN_EXECUTION_VARIABLE_ALTERNATIVE_BUSINESS_KEY; import static org.highmed.dsf.bpe.ConstantsBase.BPMN_EXECUTION_VARIABLE_INSTANTIATES_URI; import static org.highmed.dsf.bpe.ConstantsBase.BPMN_EXECUTION_VARIABLE_MESSAGE_NAME; import static org.highmed.dsf.bpe.ConstantsBase.BPMN_EXECUTION_VARIABLE_PROFILE; @@ -14,6 +15,7 @@ import java.util.Date; import java.util.Objects; +import java.util.UUID; import java.util.stream.Stream; import org.camunda.bpm.engine.delegate.DelegateExecution; @@ -279,6 +281,35 @@ protected Stream getAdditionalInputParameters(DelegateExecut return Stream.empty(); } + /** + * Generates an alternative business-key and stores it as a process variable with name + * {@link ConstantsBase#BPMN_EXECUTION_VARIABLE_ALTERNATIVE_BUSINESS_KEY}
+ *
+ * Use this method in combination with overriding + * {@link #sendTask(Target, String, String, String, String, Stream)} to use an alternative business-key with the + * communication target. + * + * 
+	 * @Override
+	 * protected void sendTask(Target target, String instantiatesUri, String messageName, String businessKey,
+	 * 		String profile, Stream<ParameterComponent> additionalInputParameters)
+	 * {
+	 * 	String alternativeBusinesKey = createAndSaveAlternativeBusinessKey();
+	 * 	super.sendTask(target, instantiatesUri, messageName, alternativeBusinesKey, profile,
+	 * 			additionalInputParameters);
+	 * }
+	 *
+ * + * @return the alternative business-key stored as variable + * {@link ConstantsBase#BPMN_EXECUTION_VARIABLE_ALTERNATIVE_BUSINESS_KEY} + */ + protected final String createAndSaveAlternativeBusinessKey() + { + String alternativeBusinessKey = UUID.randomUUID().toString(); + execution.setVariable(BPMN_EXECUTION_VARIABLE_ALTERNATIVE_BUSINESS_KEY, alternativeBusinessKey); + return alternativeBusinessKey; + } + protected void sendTask(Target target, String instantiatesUri, String messageName, String businessKey, String profile, Stream additionalInputParameters) { diff --git a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/task/TaskHandler.java b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/task/TaskHandler.java index 752a5bfa4..c774f3363 100755 --- a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/task/TaskHandler.java +++ b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/task/TaskHandler.java @@ -1,5 +1,6 @@ package org.highmed.dsf.fhir.task; +import static org.highmed.dsf.bpe.ConstantsBase.BPMN_EXECUTION_VARIABLE_ALTERNATIVE_BUSINESS_KEY; import static org.highmed.dsf.bpe.ConstantsBase.BPMN_EXECUTION_VARIABLE_TASK; import static org.highmed.dsf.bpe.ConstantsBase.CODESYSTEM_HIGHMED_BPMN; import static org.highmed.dsf.bpe.ConstantsBase.CODESYSTEM_HIGHMED_BPMN_VALUE_BUSINESS_KEY; @@ -16,6 +17,7 @@ import java.util.regex.Matcher; import java.util.regex.Pattern; import java.util.stream.Collectors; +import java.util.stream.Stream; import org.camunda.bpm.engine.RepositoryService; import org.camunda.bpm.engine.RuntimeService; @@ -23,7 +25,6 @@ import org.camunda.bpm.engine.runtime.MessageCorrelationBuilder; import org.camunda.bpm.engine.runtime.ProcessInstance; import org.camunda.bpm.engine.runtime.ProcessInstanceQuery; -import org.camunda.bpm.engine.variable.Variables; import org.highmed.dsf.fhir.variables.FhirResourceValues; import org.highmed.fhir.client.FhirWebserviceClient; import org.hl7.fhir.r4.model.Task; @@ -159,27 +160,36 @@ protected void onMessage(String businessKey, String correlationKey, String proce else { List instances = getProcessInstanceQuery(processDefinition, businessKey).list(); + List instancesWithAlternativeBusinessKey = getAlternativeProcessInstanceQuery( + processDefinition, businessKey).list(); - if (instances.size() > 1) + if (instances.size() + instancesWithAlternativeBusinessKey.size() > 1) logger.warn("instance-ids {}", - instances.stream().map(ProcessInstance::getId).collect(Collectors.joining(", ", "[", "]"))); + Stream.concat(instances.stream(), instancesWithAlternativeBusinessKey.stream()) + .map(ProcessInstance::getId).collect(Collectors.joining(", ", "[", "]"))); - long instanceCount = getProcessInstanceQuery(processDefinition, businessKey).count(); - - if (instanceCount <= 0) + if (instances.size() + instancesWithAlternativeBusinessKey.size() <= 0) { runtimeService.createMessageCorrelation(messageName).processDefinitionId(processDefinition.getId()) .processInstanceBusinessKey(businessKey).setVariables(variables).correlateStartMessage(); } else { - MessageCorrelationBuilder correlation = runtimeService.createMessageCorrelation(messageName) - .setVariables(variables).processInstanceBusinessKey(businessKey); + MessageCorrelationBuilder correlation; + + if (instances.size() > 0) + correlation = runtimeService.createMessageCorrelation(messageName).setVariables(variables) + .processInstanceBusinessKey(businessKey); + else + correlation = runtimeService.createMessageCorrelation(messageName).setVariables(variables) + .processInstanceVariableEquals(BPMN_EXECUTION_VARIABLE_ALTERNATIVE_BUSINESS_KEY, + businessKey); if (correlationKey != null) - correlation = correlation - .localVariablesEqual(Map.of("correlationKey", Variables.stringValue(correlationKey))); + correlation = correlation.localVariableEquals("correlationKey", correlationKey); + // throws MismatchingMessageCorrelationException - if none or more than one execution or process + // definition is matched by the correlation correlation.correlate(); } } @@ -203,4 +213,11 @@ private ProcessInstanceQuery getProcessInstanceQuery(ProcessDefinition processDe return runtimeService.createProcessInstanceQuery().processDefinitionId(processDefinition.getId()) .processInstanceBusinessKey(businessKey); } + + private ProcessInstanceQuery getAlternativeProcessInstanceQuery(ProcessDefinition processDefinition, + String businessKey) + { + return runtimeService.createProcessInstanceQuery().processDefinitionId(processDefinition.getId()) + .variableValueEquals(BPMN_EXECUTION_VARIABLE_ALTERNATIVE_BUSINESS_KEY, businessKey); + } } From 04e344ea72b5d35ef02a72602f1af6db233f6f57 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Sun, 19 Jun 2022 22:51:36 +0200 Subject: [PATCH 06/14] request logging configurable, improved logging Requests and responses to local and remote DSF webservices can be enabled at the DSF BPE, same for remote DSF webservices at the DSF FHIR server. Webservice config now part of DSF FHIR/BPE startup log (level info). Improved status logging of websocket client at DSF BPE. Reduced log level to trace in AuthenticationFilterConfigImpl for messag about path needing authentication or not. --- .../highmed/dsf/bpe/start/ExampleStarter.java | 2 +- .../dsf/bpe/spring/config/FhirConfig.java | 55 ++++++++++++++++--- .../bpe/spring/config/PropertiesConfig.java | 42 ++++++++++---- .../fhir/client/FhirClientProviderImpl.java | 32 +++++------ .../AuthenticationFilterConfigImpl.java | 4 +- .../dsf/fhir/client/ClientProviderImpl.java | 7 ++- .../dsf/fhir/spring/config/ClientConfig.java | 26 ++++++++- .../fhir/spring/config/PropertiesConfig.java | 9 +++ .../dsf/fhir/client/ClientProviderTest.java | 3 +- .../integration/AbstractIntegrationTest.java | 2 +- .../fhir/client/AbstractJerseyClient.java | 16 +++++- .../client/FhirWebserviceClientJersey.java | 4 +- .../highmed/fhir/client/ClientEndpoint.java | 9 ++- .../fhir/client/WebsocketClientTyrus.java | 27 ++++++++- .../highmed/dsf/tools/proxy/TestClient.java | 3 +- 15 files changed, 182 insertions(+), 59 deletions(-) diff --git a/dsf-bpe/dsf-bpe-process-base/src/test/java/org/highmed/dsf/bpe/start/ExampleStarter.java b/dsf-bpe/dsf-bpe-process-base/src/test/java/org/highmed/dsf/bpe/start/ExampleStarter.java index 94629a2f8..2cf62b8fc 100644 --- a/dsf-bpe/dsf-bpe-process-base/src/test/java/org/highmed/dsf/bpe/start/ExampleStarter.java +++ b/dsf-bpe/dsf-bpe-process-base/src/test/java/org/highmed/dsf/bpe/start/ExampleStarter.java @@ -130,6 +130,6 @@ public FhirWebserviceClient createClient(String baseUrl) throws Exception ReferenceCleaner referenceCleaner = new ReferenceCleanerImpl(new ReferenceExtractorImpl()); return new FhirWebserviceClientJersey(baseUrl, trustStore, keyStore, certificatePassword, null, null, null, 0, - 0, null, context, referenceCleaner); + 0, false, null, context, referenceCleaner); } } diff --git a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/spring/config/FhirConfig.java b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/spring/config/FhirConfig.java index 2baeb1462..e5aaa995a 100755 --- a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/spring/config/FhirConfig.java +++ b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/spring/config/FhirConfig.java @@ -36,6 +36,9 @@ import org.highmed.dsf.fhir.websocket.FhirConnector; import org.highmed.dsf.fhir.websocket.FhirConnectorImpl; import org.highmed.dsf.fhir.websocket.LastEventTimeIo; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.InitializingBean; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; @@ -49,8 +52,10 @@ import de.rwh.utils.crypto.io.PemIo; @Configuration -public class FhirConfig +public class FhirConfig implements InitializingBean { + private static final Logger logger = LoggerFactory.getLogger(FhirConfig.class); + private static final BouncyCastleProvider provider = new BouncyCastleProvider(); @Autowired @@ -98,23 +103,24 @@ public FhirWebsocketClientProvider clientProvider() try { - KeyStore webserviceKeyStore = createKeyStore(propertiesConfig.getWebserviceClientCertificateFile(), - propertiesConfig.getWebserviceClientCertificatePrivateKeyFile(), - propertiesConfig.getWebserviceClientCertificatePrivateKeyFilePassword(), keyStorePassword); - KeyStore webserviceTrustStore = createTrustStore( - propertiesConfig.getWebserviceClientCertificateTrustStoreFile()); + KeyStore webserviceKeyStore = createKeyStore(propertiesConfig.getClientCertificateFile(), + propertiesConfig.getClientCertificatePrivateKeyFile(), + propertiesConfig.getClientCertificatePrivateKeyFilePassword(), keyStorePassword); + KeyStore webserviceTrustStore = createTrustStore(propertiesConfig.getClientCertificateTrustStoreFile()); return new FhirClientProviderImpl(fhirContext(), referenceCleaner(), propertiesConfig.getServerBaseUrl(), propertiesConfig.getWebserviceClientLocalReadTimeout(), propertiesConfig.getWebserviceClientLocalConnectTimeout(), propertiesConfig.getWebserviceClientLocalProxySchemeHostPort(), propertiesConfig.getWebserviceClientLocalProxyUsername(), - propertiesConfig.getWebserviceClientLocalProxyPassword(), webserviceTrustStore, webserviceKeyStore, + propertiesConfig.getWebserviceClientLocalProxyPassword(), + propertiesConfig.getWebserviceClientLocalVerbose(), webserviceTrustStore, webserviceKeyStore, keyStorePassword, propertiesConfig.getWebserviceClientRemoteReadTimeout(), propertiesConfig.getWebserviceClientRemoteConnectTimeout(), propertiesConfig.getWebserviceClientRemoteProxySchemeHostPort(), propertiesConfig.getWebserviceClientRemoteProxyUsername(), - propertiesConfig.getWebserviceClientRemoteProxyPassword(), getWebsocketUrl(), webserviceTrustStore, + propertiesConfig.getWebserviceClientRemoteProxyPassword(), + propertiesConfig.getWebserviceClientRemoteVerbose(), getWebsocketUrl(), webserviceTrustStore, webserviceKeyStore, keyStorePassword, propertiesConfig.getWebsocketClientProxySchemeHostPort(), propertiesConfig.getWebsocketClientProxyUsername(), propertiesConfig.getWebsocketClientProxyPassword()); @@ -211,4 +217,37 @@ public ReadAccessHelper readAccessHelper() { return new ReadAccessHelperImpl(); } + + @Override + public void afterPropertiesSet() throws Exception + { + logger.info( + "Local webservice client config: {trustStorePath: {}, certificatePath: {}, privateKeyPath: {}, privateKeyPassword: {}," + + " proxyUrl {}, proxyUsername {}, proxyPassword {}, serverBase: {}}", + propertiesConfig.getClientCertificateTrustStoreFile(), propertiesConfig.getClientCertificateFile(), + propertiesConfig.getClientCertificatePrivateKeyFile(), + propertiesConfig.getClientCertificatePrivateKeyFilePassword() != null ? "***" : "null", + propertiesConfig.getWebserviceClientLocalProxySchemeHostPort(), + propertiesConfig.getWebserviceClientLocalProxyUsername(), + propertiesConfig.getWebserviceClientLocalProxyPassword() != null ? "***" : "null", + propertiesConfig.getServerBaseUrl()); + logger.info( + "Local websocket client config: {trustStorePath: {}, certificatePath: {}, privateKeyPath: {}, privateKeyPassword: {}," + + " proxyUrl {}, proxyUsername {}, proxyPassword {}, websocketUrl: {}}", + propertiesConfig.getClientCertificateTrustStoreFile(), propertiesConfig.getClientCertificateFile(), + propertiesConfig.getClientCertificatePrivateKeyFile(), + propertiesConfig.getClientCertificatePrivateKeyFilePassword() != null ? "***" : "null", + propertiesConfig.getWebsocketClientProxySchemeHostPort(), + propertiesConfig.getWebsocketClientProxyUsername(), + propertiesConfig.getWebsocketClientProxyPassword() != null ? "***" : "null", getWebsocketUrl()); + logger.info( + "Remote webservice client config: {trustStorePath: {}, certificatePath: {}, privateKeyPath: {}, privateKeyPassword: {}," + + " proxyUrl {}, proxyUsername {}, proxyPassword {}}", + propertiesConfig.getClientCertificateTrustStoreFile(), propertiesConfig.getClientCertificateFile(), + propertiesConfig.getClientCertificatePrivateKeyFile(), + propertiesConfig.getClientCertificatePrivateKeyFilePassword() != null ? "***" : "null", + propertiesConfig.getWebserviceClientRemoteProxySchemeHostPort(), + propertiesConfig.getWebserviceClientRemoteProxyUsername(), + propertiesConfig.getWebserviceClientRemoteProxyPassword() != null ? "***" : "null"); + } } diff --git a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/spring/config/PropertiesConfig.java b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/spring/config/PropertiesConfig.java index 41d0d7478..8152a79de 100644 --- a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/spring/config/PropertiesConfig.java +++ b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/spring/config/PropertiesConfig.java @@ -44,19 +44,19 @@ public class PropertiesConfig @Documentation(required = true, description = "PEM encoded file with one or more trusted root certificates to validate server certificates for https connections to local and remote DSF FHIR servers", recommendation = "Use docker secret file to configure", example = "/run/secrets/app_client_trust_certificates.pem") @Value("${org.highmed.dsf.bpe.fhir.client.trust.certificates}") - private String webserviceClientCertificateTrustStoreFile; + private String clientCertificateTrustStoreFile; @Documentation(required = true, description = "PEM encoded file with local client certificate for https connections to local and remote DSF FHIR servers", recommendation = "Use docker secret file to configure", example = "/run/secrets/app_client_certificate.pem") @Value("${org.highmed.dsf.bpe.fhir.client.certificate}") - private String webserviceClientCertificateFile; + private String clientCertificateFile; @Documentation(required = true, description = "Private key corresponding to the local client certificate as PEM encoded file. Use ${env_variable}_PASSWORD* or *${env_variable}_PASSWORD_FILE* if private key is encrypted", recommendation = "Use docker secret file to configure", example = "/run/secrets/app_client_certificate_private_key.pem") @Value("${org.highmed.dsf.bpe.fhir.client.certificate.private.key}") - private String webserviceClientCertificatePrivateKeyFile; + private String clientCertificatePrivateKeyFile; @Documentation(description = "Password to decrypt the local client certificate encrypted private key", recommendation = "Use docker secret file to configure using *${env_variable}_FILE*", example = "/run/secrets/app_client_certificate_private_key.pem.password") @Value("${org.highmed.dsf.bpe.fhir.client.certificate.private.key.password:#{null}}") - private char[] webserviceClientCertificatePrivateKeyFilePassword; + private char[] clientCertificatePrivateKeyFilePassword; @Documentation(description = "The timeout in milliseconds until a reading a resource from a remote DSF FHIR server is aborted", recommendation = "Change default value only if timeout exceptions occur") @Value("${org.highmed.dsf.bpe.fhir.client.remote.timeout.read:60000}") @@ -78,6 +78,10 @@ public class PropertiesConfig @Value("${org.highmed.dsf.bpe.fhir.client.remote.proxy.password:#{null}}") private char[] webserviceClientRemoteProxyPassword; + @Documentation(description = "To enable verbose logging of requests to and replies from remote DSF FHIR servers, set to `true`") + @Value("${org.highmed.dsf.bpe.fhir.client.remote.verbose:false}") + private boolean webserviceClientRemoteVerbose; + @Documentation(required = true, description = "The base address of the local DSF FHIR server to read/store fhir resources", example = "https://foo.bar/fhir") @Value("${org.highmed.dsf.bpe.fhir.server.base.url}") private String serverBaseUrl; @@ -102,6 +106,10 @@ public class PropertiesConfig @Value("${org.highmed.dsf.bpe.fhir.client.local.proxy.password:#{null}}") private char[] webserviceClientLocalProxyPassword; + @Documentation(description = "To enable verbose logging of requests to and replies from the local DSF FHIR server, set to `true`") + @Value("${org.highmed.dsf.bpe.fhir.client.local.verbose:false}") + private boolean webserviceClientLocalVerbose; + @Documentation(description = "Proxy location, set if the DSF BPE server can reach internal servers via websocket, like the DSF FHIR server, only through a proxy", example = "http://proxy.foo:8080") @Value("${org.highmed.dsf.bpe.fhir.client.local.websocket.proxy.url:#{null}}") private String websocketClientProxySchemeHostPort; @@ -205,24 +213,24 @@ public String getOrganizationIdentifierValue() return organizationIdentifierValue; } - public String getWebserviceClientCertificateTrustStoreFile() + public String getClientCertificateTrustStoreFile() { - return webserviceClientCertificateTrustStoreFile; + return clientCertificateTrustStoreFile; } - public String getWebserviceClientCertificateFile() + public String getClientCertificateFile() { - return webserviceClientCertificateFile; + return clientCertificateFile; } - public String getWebserviceClientCertificatePrivateKeyFile() + public String getClientCertificatePrivateKeyFile() { - return webserviceClientCertificatePrivateKeyFile; + return clientCertificatePrivateKeyFile; } - public char[] getWebserviceClientCertificatePrivateKeyFilePassword() + public char[] getClientCertificatePrivateKeyFilePassword() { - return webserviceClientCertificatePrivateKeyFilePassword; + return clientCertificatePrivateKeyFilePassword; } public int getWebserviceClientRemoteReadTimeout() @@ -250,6 +258,11 @@ public char[] getWebserviceClientRemoteProxyPassword() return webserviceClientRemoteProxyPassword; } + public boolean getWebserviceClientRemoteVerbose() + { + return webserviceClientRemoteVerbose; + } + public String getServerBaseUrl() { return serverBaseUrl; @@ -280,6 +293,11 @@ public char[] getWebserviceClientLocalProxyPassword() return webserviceClientLocalProxyPassword; } + public boolean getWebserviceClientLocalVerbose() + { + return webserviceClientLocalVerbose; + } + public String getWebsocketClientProxySchemeHostPort() { return websocketClientProxySchemeHostPort; diff --git a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/client/FhirClientProviderImpl.java b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/client/FhirClientProviderImpl.java index 57dcfa944..09f0285de 100755 --- a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/client/FhirClientProviderImpl.java +++ b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/fhir/client/FhirClientProviderImpl.java @@ -34,6 +34,7 @@ public class FhirClientProviderImpl private final String localWebserviceProxySchemeHostPort; private final String localWebserviceProxyUsername; private final char[] localWebserviceProxyPassword; + private final boolean localWebserviceLogRequests; private final KeyStore webserviceTrustStore; private final KeyStore webserviceKeyStore; @@ -44,6 +45,7 @@ public class FhirClientProviderImpl private final String remoteWebserviceProxySchemeHostPort; private final String remoteWebserviceProxyUsername; private final char[] remoteWebserviceProxyPassword; + private final boolean remoteWebserviceLogRequests; private final String localWebsocketUrl; private final KeyStore localWebsocketTrustStore; @@ -57,10 +59,11 @@ public class FhirClientProviderImpl public FhirClientProviderImpl(FhirContext fhirContext, ReferenceCleaner referenceCleaner, String localWebserviceBaseUrl, int localWebserviceReadTimeout, int localWebserviceConnectTimeout, String localWebserviceProxySchemeHostPort, String localWebserviceProxyUsername, - char[] localWebserviceProxyPassword, KeyStore webserviceTrustStore, KeyStore webserviceKeyStore, - char[] webserviceKeyStorePassword, int remoteWebserviceReadTimeout, int remoteWebserviceConnectTimeout, - String remoteWebserviceProxySchemeHostPort, String remoteWebserviceProxyUsername, - char[] remoteWebserviceProxyPassword, String localWebsocketUrl, KeyStore localWebsocketTrustStore, + char[] localWebserviceProxyPassword, boolean localWebserviceLogRequests, KeyStore webserviceTrustStore, + KeyStore webserviceKeyStore, char[] webserviceKeyStorePassword, int remoteWebserviceReadTimeout, + int remoteWebserviceConnectTimeout, String remoteWebserviceProxySchemeHostPort, + String remoteWebserviceProxyUsername, char[] remoteWebserviceProxyPassword, + boolean remoteWebserviceLogRequests, String localWebsocketUrl, KeyStore localWebsocketTrustStore, KeyStore localWebsocketKeyStore, char[] localWebsocketKeyStorePassword, String localWebsocketProxySchemeHostPort, String localWebsocketProxyUsername, char[] localWebsocketProxyPassword) @@ -74,6 +77,7 @@ public FhirClientProviderImpl(FhirContext fhirContext, ReferenceCleaner referenc this.localWebserviceProxySchemeHostPort = localWebserviceProxySchemeHostPort; this.localWebserviceProxyUsername = localWebserviceProxyUsername; this.localWebserviceProxyPassword = localWebserviceProxyPassword; + this.localWebserviceLogRequests = localWebserviceLogRequests; this.webserviceTrustStore = webserviceTrustStore; this.webserviceKeyStore = webserviceKeyStore; @@ -84,6 +88,7 @@ public FhirClientProviderImpl(FhirContext fhirContext, ReferenceCleaner referenc this.remoteWebserviceProxySchemeHostPort = remoteWebserviceProxySchemeHostPort; this.remoteWebserviceProxyUsername = remoteWebserviceProxyUsername; this.remoteWebserviceProxyPassword = remoteWebserviceProxyPassword; + this.remoteWebserviceLogRequests = remoteWebserviceLogRequests; this.localWebsocketUrl = localWebsocketUrl; this.localWebsocketTrustStore = localWebsocketTrustStore; @@ -103,12 +108,6 @@ public void afterPropertiesSet() throws Exception throw new IllegalArgumentException("localReadTimeout < 0"); if (localWebserviceConnectTimeout < 0) throw new IllegalArgumentException("localConnectTimeout < 0"); - if (localWebserviceProxyPassword == null) - logger.info("localProxyPassword is null"); - if (localWebserviceProxyUsername == null) - logger.info("localProxyUsername is null"); - if (localWebserviceProxySchemeHostPort == null) - logger.info("localProxySchemeHostPort is null"); Objects.requireNonNull(webserviceTrustStore, "webserviceTrustStore"); Objects.requireNonNull(webserviceKeyStore, "webserviceKeyStore"); Objects.requireNonNull(webserviceKeyStorePassword, "webserviceKeyStorePassword"); @@ -116,12 +115,6 @@ public void afterPropertiesSet() throws Exception throw new IllegalArgumentException("remoteReadTimeout < 0"); if (remoteWebserviceConnectTimeout < 0) throw new IllegalArgumentException("remoteConnectTimeout < 0"); - if (remoteWebserviceProxyPassword == null) - logger.info("remoteProxyPassword is null"); - if (remoteWebserviceProxyUsername == null) - logger.info("remoteProxyUsername is null"); - if (remoteWebserviceProxySchemeHostPort == null) - logger.info("remoteProxySchemeHostPort is null"); Objects.requireNonNull(localWebsocketUrl, "localWebsocketUrl"); Objects.requireNonNull(localWebsocketTrustStore, "localWebsocketTrustStore"); Objects.requireNonNull(localWebsocketKeyStore, "localWebsocketKeyStore"); @@ -146,13 +139,14 @@ private FhirWebserviceClient getClient(String webserviceUrl) client = new FhirWebserviceClientJersey(webserviceUrl, webserviceTrustStore, webserviceKeyStore, webserviceKeyStorePassword, localWebserviceProxySchemeHostPort, localWebserviceProxyUsername, localWebserviceProxyPassword, localWebserviceConnectTimeout, - localWebserviceReadTimeout, null, fhirContext, referenceCleaner); + localWebserviceReadTimeout, localWebserviceLogRequests, null, fhirContext, + referenceCleaner); else client = new FhirWebserviceClientJersey(webserviceUrl, webserviceTrustStore, webserviceKeyStore, webserviceKeyStorePassword, remoteWebserviceProxySchemeHostPort, remoteWebserviceProxyUsername, remoteWebserviceProxyPassword, - remoteWebserviceConnectTimeout, remoteWebserviceReadTimeout, null, fhirContext, - referenceCleaner); + remoteWebserviceConnectTimeout, remoteWebserviceReadTimeout, remoteWebserviceLogRequests, + null, fhirContext, referenceCleaner); webserviceClientsByUrl.put(webserviceUrl, client); return client; diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/authentication/AuthenticationFilterConfigImpl.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/authentication/AuthenticationFilterConfigImpl.java index 87096638a..c05293551 100755 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/authentication/AuthenticationFilterConfigImpl.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/authentication/AuthenticationFilterConfigImpl.java @@ -43,12 +43,12 @@ public boolean needsAuthentication(HttpServletRequest request) if (pathsNotRequiringAuthentication.contains(path)) { - logger.debug("Request path: '{}' does not need authentication", path); + logger.trace("Request path: '{}' does not need authentication", path); return false; } else { - logger.debug("Request path: '{}' needs authentication", path); + logger.trace("Request path: '{}' needs authentication", path); return true; } } diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/client/ClientProviderImpl.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/client/ClientProviderImpl.java index 2f7a3b526..de88e22e3 100755 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/client/ClientProviderImpl.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/client/ClientProviderImpl.java @@ -28,6 +28,7 @@ public class ClientProviderImpl implements ClientProvider, InitializingBean private final String remoteProxySchemeHostPort; private final String remoteProxyUsername; private final char[] remoteProxyPassword; + private final boolean logRequests; private final FhirContext fhirContext; private final ReferenceCleaner referenceCleaner; private final EndpointDao endpointDao; @@ -36,7 +37,7 @@ public class ClientProviderImpl implements ClientProvider, InitializingBean public ClientProviderImpl(KeyStore webserviceTrustStore, KeyStore webserviceKeyStore, char[] webserviceKeyStorePassword, int remoteReadTimeout, int remoteConnectTimeout, String remoteProxySchemeHostPort, String remoteProxyUsername, char[] remoteProxyPassword, - FhirContext fhirContext, ReferenceCleaner referenceCleaner, EndpointDao endpointDao, + boolean logRequests, FhirContext fhirContext, ReferenceCleaner referenceCleaner, EndpointDao endpointDao, ExceptionHandler exceptionHandler) { this.webserviceTrustStore = webserviceTrustStore; @@ -47,6 +48,7 @@ public ClientProviderImpl(KeyStore webserviceTrustStore, KeyStore webserviceKeyS this.remoteProxySchemeHostPort = remoteProxySchemeHostPort; this.remoteProxyUsername = remoteProxyUsername; this.remoteProxyPassword = remoteProxyPassword; + this.logRequests = logRequests; this.fhirContext = fhirContext; this.referenceCleaner = referenceCleaner; this.endpointDao = endpointDao; @@ -73,7 +75,8 @@ public Optional getClient(String serverBase) { FhirWebserviceClient client = new FhirWebserviceClientJersey(serverBase, webserviceTrustStore, webserviceKeyStore, webserviceKeyStorePassword, remoteProxySchemeHostPort, remoteProxyUsername, - remoteProxyPassword, remoteConnectTimeout, remoteReadTimeout, null, fhirContext, referenceCleaner); + remoteProxyPassword, remoteConnectTimeout, remoteReadTimeout, logRequests, null, fhirContext, + referenceCleaner); return Optional.of(client); } diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/ClientConfig.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/ClientConfig.java index 4d8bb8bb8..a1d5ac549 100755 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/ClientConfig.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/ClientConfig.java @@ -17,6 +17,9 @@ import org.bouncycastle.pkcs.PKCSException; import org.highmed.dsf.fhir.client.ClientProvider; import org.highmed.dsf.fhir.client.ClientProviderImpl; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; +import org.springframework.beans.factory.InitializingBean; import org.springframework.beans.factory.annotation.Autowired; import org.springframework.context.annotation.Bean; import org.springframework.context.annotation.Configuration; @@ -26,8 +29,10 @@ import de.rwh.utils.crypto.io.PemIo; @Configuration -public class ClientConfig +public class ClientConfig implements InitializingBean { + private static final Logger logger = LoggerFactory.getLogger(ClientConfig.class); + private static final BouncyCastleProvider provider = new BouncyCastleProvider(); @Autowired @@ -62,8 +67,9 @@ public ClientProvider clientProvider() propertiesConfig.getWebserviceClientReadTimeout(), propertiesConfig.getWebserviceClientConnectTimeout(), propertiesConfig.getWebserviceClientProxyUrl(), propertiesConfig.getWebserviceClientProxyUsername(), - propertiesConfig.getWebserviceClientProxyPassword(), fhirConfig.fhirContext(), - referenceConfig.referenceCleaner(), daoConfig.endpointDao(), helperConfig.exceptionHandler()); + propertiesConfig.getWebserviceClientProxyPassword(), propertiesConfig.getWebserviceClientVerbose(), + fhirConfig.fhirContext(), referenceConfig.referenceCleaner(), daoConfig.endpointDao(), + helperConfig.exceptionHandler()); } catch (KeyStoreException | CertificateException | NoSuchAlgorithmException | IOException | PKCSException e) { @@ -101,4 +107,18 @@ private KeyStore createKeyStore(String certificateFile, String privateKeyFile, c return CertificateHelper.toJksKeyStore(privateKey, new Certificate[] { certificate }, subjectCommonName, keyStorePassword); } + + @Override + public void afterPropertiesSet() throws Exception + { + logger.info( + "Remote webservice client config: {trustStorePath: {}, certificatePath: {}, privateKeyPath: {}, privateKeyPassword: {}," + + " proxyUrl {}, proxyUsername {}, proxyPassword {}}", + propertiesConfig.getWebserviceClientCertificateTrustCertificatesFile(), + propertiesConfig.getWebserviceClientCertificateFile(), + propertiesConfig.getWebserviceClientCertificatePrivateKeyFile(), + propertiesConfig.getWebserviceClientCertificatePrivateKeyFilePassword() != null ? "***" : "null", + propertiesConfig.getWebserviceClientProxyUrl(), propertiesConfig.getWebserviceClientProxyUsername(), + propertiesConfig.getWebserviceClientProxyPassword() != null ? "***" : "null"); + } } diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/PropertiesConfig.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/PropertiesConfig.java index b2f15f1f6..6f1a6e39d 100644 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/PropertiesConfig.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/spring/config/PropertiesConfig.java @@ -96,6 +96,10 @@ public class PropertiesConfig @Value("${org.highmed.dsf.fhir.client.proxy.password:#{null}}") private char[] webserviceClientProxyPassword; + @Documentation(description = "To enable verbose logging of requests to and replies from remote DSF FHIR servers, set to `true`") + @Value("${org.highmed.dsf.fhir.client.verbose:false}") + private boolean webserviceClientVerbose; + @Documentation(description = "List of allowed CORS origins, used to set the *Access-Control-Allow-Origin* HTTP response header, which indicates whether the response can be shared with requesting code from the given origin; comma or space separated list, YAML block scalars supported") @Value("#{'${org.highmed.dsf.fhir.server.cors.origins:}'.trim().split('(,[ ]?)|(\\n)')}") private List allowedOrigins; @@ -209,6 +213,11 @@ public char[] getWebserviceClientProxyPassword() return webserviceClientProxyPassword; } + public boolean getWebserviceClientVerbose() + { + return webserviceClientVerbose; + } + public List getAllowedOrigins() { return Collections.unmodifiableList(allowedOrigins); diff --git a/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/client/ClientProviderTest.java b/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/client/ClientProviderTest.java index 0296722ba..1078e9e26 100755 --- a/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/client/ClientProviderTest.java +++ b/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/client/ClientProviderTest.java @@ -44,6 +44,7 @@ public void before() throws Exception char[] remoteProxyPassword = null; String remoteProxyUsername = null; String remoteProxySchemeHostPort = null; + boolean logRequests = false; FhirContext fhirContext = mock(FhirContext.class); referenceCleaner = mock(ReferenceCleaner.class); endpointDao = mock(EndpointDao.class); @@ -51,7 +52,7 @@ public void before() throws Exception provider = new ClientProviderImpl(webserviceTrustStore, webserviceKeyStore, webserviceKeyStorePassword, remoteReadTimeout, remoteConnectTimeout, remoteProxySchemeHostPort, remoteProxyUsername, - remoteProxyPassword, fhirContext, referenceCleaner, endpointDao, exceptionHandler); + remoteProxyPassword, logRequests, fhirContext, referenceCleaner, endpointDao, exceptionHandler); } @Test diff --git a/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/integration/AbstractIntegrationTest.java b/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/integration/AbstractIntegrationTest.java index 11dd3b3af..9ab605d77 100755 --- a/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/integration/AbstractIntegrationTest.java +++ b/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/integration/AbstractIntegrationTest.java @@ -155,7 +155,7 @@ private static FhirWebserviceClient createWebserviceClient(KeyStore trustStore, char[] keyStorePassword, FhirContext fhirContext, ReferenceCleaner referenceCleaner) { return new FhirWebserviceClientJersey(BASE_URL, trustStore, keyStore, keyStorePassword, null, null, null, 0, 0, - null, fhirContext, referenceCleaner); + false, null, fhirContext, referenceCleaner); } private static WebsocketClient createWebsocketClient(KeyStore trustStore, KeyStore keyStore, diff --git a/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/AbstractJerseyClient.java b/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/AbstractJerseyClient.java index e1960db07..b585cb6a9 100644 --- a/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/AbstractJerseyClient.java +++ b/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/AbstractJerseyClient.java @@ -3,6 +3,7 @@ import java.security.KeyStore; import java.util.List; import java.util.concurrent.TimeUnit; +import java.util.logging.Level; import javax.net.ssl.SSLContext; import javax.ws.rs.client.Client; @@ -15,11 +16,16 @@ import org.glassfish.jersey.client.ClientProperties; import org.glassfish.jersey.jackson.internal.jackson.jaxrs.json.JacksonJaxbJsonProvider; import org.glassfish.jersey.jackson.internal.jackson.jaxrs.json.JacksonJsonProvider; +import org.glassfish.jersey.logging.LoggingFeature; +import org.glassfish.jersey.logging.LoggingFeature.Verbosity; import com.fasterxml.jackson.databind.ObjectMapper; public class AbstractJerseyClient { + private static final java.util.logging.Logger requestDebugLogger = java.util.logging.Logger + .getLogger(AbstractJerseyClient.class.getName()); + private final Client client; private final String baseUrl; @@ -29,12 +35,12 @@ public AbstractJerseyClient(String baseUrl, KeyStore trustStore, KeyStore keySto ObjectMapper objectMapper, List componentsToRegister) { this(baseUrl, trustStore, keyStore, keyStorePassword, null, null, null, 0, 0, objectMapper, - componentsToRegister); + componentsToRegister, false); } public AbstractJerseyClient(String baseUrl, KeyStore trustStore, KeyStore keyStore, char[] keyStorePassword, String proxySchemeHostPort, String proxyUserName, char[] proxyPassword, int connectTimeout, int readTimeout, - ObjectMapper objectMapper, List componentsToRegister) + ObjectMapper objectMapper, List componentsToRegister, boolean logRequests) { SSLContext sslContext = null; if (trustStore != null && keyStore == null && keyStorePassword == null) @@ -68,6 +74,12 @@ else if (trustStore != null && keyStore != null && keyStorePassword != null) if (componentsToRegister != null) componentsToRegister.forEach(builder::register); + if (logRequests) + { + builder = builder.register(new LoggingFeature(requestDebugLogger, Level.FINE, Verbosity.PAYLOAD_ANY, + LoggingFeature.DEFAULT_MAX_ENTITY_SIZE)); + } + client = builder.build(); this.baseUrl = baseUrl.endsWith("/") ? baseUrl : baseUrl + "/"; diff --git a/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/FhirWebserviceClientJersey.java b/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/FhirWebserviceClientJersey.java index e9ad1a751..0e676b685 100755 --- a/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/FhirWebserviceClientJersey.java +++ b/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/FhirWebserviceClientJersey.java @@ -117,10 +117,10 @@ public class FhirWebserviceClientJersey extends AbstractJerseyClient implements public FhirWebserviceClientJersey(String baseUrl, KeyStore trustStore, KeyStore keyStore, char[] keyStorePassword, String proxySchemeHostPort, String proxyUserName, char[] proxyPassword, int connectTimeout, int readTimeout, - ObjectMapper objectMapper, FhirContext fhirContext, ReferenceCleaner referenceCleaner) + boolean logRequests, ObjectMapper objectMapper, FhirContext fhirContext, ReferenceCleaner referenceCleaner) { super(baseUrl, trustStore, keyStore, keyStorePassword, proxySchemeHostPort, proxyUserName, proxyPassword, - connectTimeout, readTimeout, objectMapper, components(fhirContext)); + connectTimeout, readTimeout, objectMapper, components(fhirContext), logRequests); this.referenceCleaner = referenceCleaner; diff --git a/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/ClientEndpoint.java b/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/ClientEndpoint.java index 057354f67..93b8ba1a5 100755 --- a/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/ClientEndpoint.java +++ b/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/ClientEndpoint.java @@ -35,7 +35,8 @@ public ClientEndpoint(Runnable reconnector, String subscriptionIdPart) @Override public void onOpen(Session session, EndpointConfig config) { - logger.debug("Websocket onOpen"); + logger.info("Websocket connected {uri: {}, session-id: {}}", session.getRequestURI().toString(), + session.getId()); session.addMessageHandler(new MessageHandler.Whole() // don't use lambda { @@ -77,7 +78,8 @@ else if (domainResourceHandler != null && parserFactory != null) @Override public void onClose(Session session, CloseReason closeReason) { - logger.info("Websocket onClose {}", closeReason.getReasonPhrase()); + logger.info("Websocket closed {uri: {}, session-id: {}}: {}", session.getRequestURI().toString(), + session.getId(), closeReason.getReasonPhrase()); if (CloseReason.CloseCodes.CANNOT_ACCEPT.equals(closeReason.getCloseCode())) { @@ -89,7 +91,8 @@ public void onClose(Session session, CloseReason closeReason) @Override public void onError(Session session, Throwable throwable) { - logger.warn("Websocket onError", throwable); + logger.warn("Websocket closed with error {uri: " + session.getRequestURI().toString() + ", session-id: " + + session.getId() + "}: {}", throwable); } public void setDomainResourceHandler(Consumer handler, Supplier parser) diff --git a/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/WebsocketClientTyrus.java b/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/WebsocketClientTyrus.java index 8f5801f35..44089532f 100755 --- a/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/WebsocketClientTyrus.java +++ b/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/WebsocketClientTyrus.java @@ -35,15 +35,38 @@ public class WebsocketClientTyrus implements WebsocketClient @Override public boolean onConnectFailure(Exception exception) { - logger.warn("onConnectFailure {}: {}", exception.getClass().getName(), exception.getMessage()); + logger.warn("Websocket connection failure: {}", getMessages(exception)); logger.debug("onConnectFailure", exception); return true; } + private String getMessages(Exception e) + { + StringBuilder b = new StringBuilder(); + if (e != null) + { + if (e.getMessage() != null) + b.append(e.getMessage()); + + Throwable cause = e.getCause(); + while (cause != null) + { + if (cause.getMessage() != null) + { + b.append(' '); + b.append(cause.getMessage()); + } + + cause = cause.getCause(); + } + } + return b.toString(); + } + @Override public boolean onDisconnect(CloseReason closeReason) { - logger.warn("OnDisconnect {}", closeReason.getReasonPhrase()); + logger.debug("onDisconnect {}", closeReason.getReasonPhrase()); return !closed; } }; diff --git a/dsf-tools/dsf-tools-proxy-test/src/main/java/org/highmed/dsf/tools/proxy/TestClient.java b/dsf-tools/dsf-tools-proxy-test/src/main/java/org/highmed/dsf/tools/proxy/TestClient.java index d6e8f24fe..ffefe0978 100755 --- a/dsf-tools/dsf-tools-proxy-test/src/main/java/org/highmed/dsf/tools/proxy/TestClient.java +++ b/dsf-tools/dsf-tools-proxy-test/src/main/java/org/highmed/dsf/tools/proxy/TestClient.java @@ -15,7 +15,8 @@ public class TestClient extends AbstractJerseyClient public TestClient(String baseUrl, String proxySchemeHostPort, String proxyUserName, char[] proxyPassword) { - super(baseUrl, null, null, null, proxySchemeHostPort, proxyUserName, proxyPassword, 5_000, 5_000, null, null); + super(baseUrl, null, null, null, proxySchemeHostPort, proxyUserName, proxyPassword, 5_000, 5_000, null, null, + true); logger.info("baseUrl: {}", baseUrl); logger.info("proxySchemeHostPort: {}", proxySchemeHostPort); From 62cbf600ea04426ae82a3644febbcce252b4c657 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Sun, 19 Jun 2022 23:42:36 +0200 Subject: [PATCH 07/14] improved log message --- .../main/java/org/highmed/fhir/client/WebsocketClientTyrus.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/WebsocketClientTyrus.java b/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/WebsocketClientTyrus.java index 44089532f..d461da0c7 100755 --- a/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/WebsocketClientTyrus.java +++ b/dsf-fhir/dsf-fhir-websocket-client/src/main/java/org/highmed/fhir/client/WebsocketClientTyrus.java @@ -35,7 +35,7 @@ public class WebsocketClientTyrus implements WebsocketClient @Override public boolean onConnectFailure(Exception exception) { - logger.warn("Websocket connection failure: {}", getMessages(exception)); + logger.warn("Websocket connection failed: {}", getMessages(exception)); logger.debug("onConnectFailure", exception); return true; } From c8e5b0ccd3e83e33b4568dc4d982b0b1bf071c94 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Sun, 19 Jun 2022 23:42:53 +0200 Subject: [PATCH 08/14] verbose log level to info, added missing logger config --- .../org/highmed/fhir/client/AbstractJerseyClient.java | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/AbstractJerseyClient.java b/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/AbstractJerseyClient.java index b585cb6a9..eef20700e 100644 --- a/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/AbstractJerseyClient.java +++ b/dsf-fhir/dsf-fhir-webservice-client/src/main/java/org/highmed/fhir/client/AbstractJerseyClient.java @@ -23,8 +23,12 @@ public class AbstractJerseyClient { - private static final java.util.logging.Logger requestDebugLogger = java.util.logging.Logger - .getLogger(AbstractJerseyClient.class.getName()); + private static final java.util.logging.Logger requestDebugLogger; + static + { + requestDebugLogger = java.util.logging.Logger.getLogger(AbstractJerseyClient.class.getName()); + requestDebugLogger.setLevel(Level.INFO); + } private final Client client; private final String baseUrl; @@ -76,7 +80,7 @@ else if (trustStore != null && keyStore != null && keyStorePassword != null) if (logRequests) { - builder = builder.register(new LoggingFeature(requestDebugLogger, Level.FINE, Verbosity.PAYLOAD_ANY, + builder = builder.register(new LoggingFeature(requestDebugLogger, Level.INFO, Verbosity.PAYLOAD_ANY, LoggingFeature.DEFAULT_MAX_ENTITY_SIZE)); } From 335487a012787dd53eeea6e4768a02bba030d137 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Mon, 20 Jun 2022 00:49:47 +0200 Subject: [PATCH 09/14] ui fixes, bookmarks for two word ressources, download filenames --- .../src/main/resources/static/bookmarks.js | 4 +-- .../src/main/resources/static/tabs.js | 30 +++++++++---------- 2 files changed, 17 insertions(+), 17 deletions(-) diff --git a/dsf-fhir/dsf-fhir-server/src/main/resources/static/bookmarks.js b/dsf-fhir/dsf-fhir-server/src/main/resources/static/bookmarks.js index 1b3972785..1c97d31c2 100644 --- a/dsf-fhir/dsf-fhir-server/src/main/resources/static/bookmarks.js +++ b/dsf-fhir/dsf-fhir-server/src/main/resources/static/bookmarks.js @@ -95,9 +95,9 @@ function saveBookmarks(bookmarks) { } function getResourceType(url) { - const regex = new RegExp('(?:(?:[A-Za-z0-9\-\\\.\:\%\$]*\/)+)?' + const regex = new RegExp('(?:(?:http|https):\/\/(?:[A-Za-z0-9\-\\\.\:\%\$]*\/)+)?' + '(Account|ActivityDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EffectEvidenceSynthesis|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|InsurancePlan|Invoice|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationStatement|MedicinalProduct|MedicinalProductAuthorization|MedicinalProductContraindication|MedicinalProductIndication|MedicinalProductIngredient|MedicinalProductInteraction|MedicinalProductManufactured|MedicinalProductPackaged|MedicinalProductPharmaceutical|MedicinalProductUndesirableEffect|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RelatedPerson|RequestGroup|ResearchDefinition|ResearchElementDefinition|ResearchStudy|ResearchSubject|RiskAssessment|RiskEvidenceSynthesis|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SubstanceSpecification|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|ValueSet|VerificationResult|VisionPrescription)' - + '(?:.*)'); + + '(?:[\/?#](?:.*)?)?$'); const match = regex.exec(url); if (match != null) return match[1]; diff --git a/dsf-fhir/dsf-fhir-server/src/main/resources/static/tabs.js b/dsf-fhir/dsf-fhir-server/src/main/resources/static/tabs.js index 564d224e5..56a74d9e0 100644 --- a/dsf-fhir/dsf-fhir-server/src/main/resources/static/tabs.js +++ b/dsf-fhir/dsf-fhir-server/src/main/resources/static/tabs.js @@ -50,36 +50,36 @@ function getDownloadFileName(lang) { } else { //Resource - if (resourceType[0] !== undefined && resourceType[1] === undefined && resourceType[2] === undefined && resourceType[3] === undefined) { - return resourceType[0] + '_Search.' + lang; + if (resourceType[1] !== undefined && resourceType[2] === undefined && resourceType[3] === undefined && resourceType[4] === undefined) { + return resourceType[1] + '_Search.' + lang; } //Resource/_history - else if (resourceType[0] !== undefined && resourceType[1] === undefined && resourceType[2] !== undefined && resourceType[3] === undefined) { - return resourceType[0] + '_History.' + lang; + else if (resourceType[1] !== undefined && resourceType[2] === undefined && resourceType[3] !== undefined && resourceType[4] === undefined) { + return resourceType[1] + '_History.' + lang; } //Resource/id - else if (resourceType[0] !== undefined && resourceType[1] !== undefined && resourceType[2] === undefined && resourceType[3] === undefined) { - return resourceType[0] + '_' + resourceType[1].substring(1) + '.' + lang; + else if (resourceType[1] !== undefined && resourceType[2] !== undefined && resourceType[3] === undefined && resourceType[4] === undefined) { + return resourceType[1] + '_' + resourceType[2].replace('/','') + '.' + lang; } //Resource/id/_history - else if (resourceType[0] !== undefined && resourceType[1] !== undefined && resourceType[2] !== undefined && resourceType[3] === undefined) { - return resourceType[0] + '_' + resourceType[1].substring(1) + '_History.' + lang; + else if (resourceType[1] !== undefined && resourceType[2] !== undefined && resourceType[3] !== undefined && resourceType[4] === undefined) { + return resourceType[1] + '_' + resourceType[2].replace('/','') + '_History.' + lang; } //Resource/id/_history/version - else if (resourceType[0] !== undefined && resourceType[1] !== undefined && resourceType[2] !== undefined && resourceType[3] !== undefined) { - return resourceType[0] + '_' + resourceType[1].substring(1) + '_v' + resourceType[3].substring(1) + '.' + lang; + else if (resourceType[1] !== undefined && resourceType[2] !== undefined && resourceType[3] !== undefined && resourceType[4] !== undefined) { + return resourceType[1] + '_' + resourceType[2].replace('/','') + '_v' + resourceType[4].replace('/','') + '.' + lang; } } } function getResourceTypeForCurrentUrl() { const url = window.location.pathname; - const regex = new RegExp('(([A-Za-z0-9\-\\\.\:\%\$]*\/)+)?' - + '(Account|ActivityDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EffectEvidenceSynthesis|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|InsurancePlan|Invoice|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationStatement|MedicinalProduct|MedicinalProductAuthorization|MedicinalProductContraindication|MedicinalProductIndication|MedicinalProductIngredient|MedicinalProductInteraction|MedicinalProductManufactured|MedicinalProductPackaged|MedicinalProductPharmaceutical|MedicinalProductUndesirableEffect|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RelatedPerson|RequestGroup|ResearchDefinition|ResearchElementDefinition|ResearchStudy|ResearchSubject|RiskAssessment|RiskEvidenceSynthesis|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SubstanceSpecification|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|ValueSet|VerificationResult|VisionPrescription)' - + '(\/[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12})?(\/_history)?(\/[0-9]+)?.*'); + const regex = new RegExp('(?:(?:[A-Za-z0-9\-\\\.\:\%\$]*\/)+)?' + + '(Account|ActivityDefinition|AdverseEvent|AllergyIntolerance|Appointment|AppointmentResponse|AuditEvent|Basic|Binary|BiologicallyDerivedProduct|BodyStructure|Bundle|CapabilityStatement|CarePlan|CareTeam|CatalogEntry|ChargeItem|ChargeItemDefinition|Claim|ClaimResponse|ClinicalImpression|CodeSystem|Communication|CommunicationRequest|CompartmentDefinition|Composition|ConceptMap|Condition|Consent|Contract|Coverage|CoverageEligibilityRequest|CoverageEligibilityResponse|DetectedIssue|Device|DeviceDefinition|DeviceMetric|DeviceRequest|DeviceUseStatement|DiagnosticReport|DocumentManifest|DocumentReference|EffectEvidenceSynthesis|Encounter|Endpoint|EnrollmentRequest|EnrollmentResponse|EpisodeOfCare|EventDefinition|Evidence|EvidenceVariable|ExampleScenario|ExplanationOfBenefit|FamilyMemberHistory|Flag|Goal|GraphDefinition|Group|GuidanceResponse|HealthcareService|ImagingStudy|Immunization|ImmunizationEvaluation|ImmunizationRecommendation|ImplementationGuide|InsurancePlan|Invoice|Library|Linkage|List|Location|Measure|MeasureReport|Media|Medication|MedicationAdministration|MedicationDispense|MedicationKnowledge|MedicationRequest|MedicationStatement|MedicinalProduct|MedicinalProductAuthorization|MedicinalProductContraindication|MedicinalProductIndication|MedicinalProductIngredient|MedicinalProductInteraction|MedicinalProductManufactured|MedicinalProductPackaged|MedicinalProductPharmaceutical|MedicinalProductUndesirableEffect|MessageDefinition|MessageHeader|MolecularSequence|NamingSystem|NutritionOrder|Observation|ObservationDefinition|OperationDefinition|OperationOutcome|Organization|OrganizationAffiliation|Patient|PaymentNotice|PaymentReconciliation|Person|PlanDefinition|Practitioner|PractitionerRole|Procedure|Provenance|Questionnaire|QuestionnaireResponse|RelatedPerson|RequestGroup|ResearchDefinition|ResearchElementDefinition|ResearchStudy|ResearchSubject|RiskAssessment|RiskEvidenceSynthesis|Schedule|SearchParameter|ServiceRequest|Slot|Specimen|SpecimenDefinition|StructureDefinition|StructureMap|Subscription|Substance|SubstanceNucleicAcid|SubstancePolymer|SubstanceProtein|SubstanceReferenceInformation|SubstanceSourceMaterial|SubstanceSpecification|SupplyDelivery|SupplyRequest|Task|TerminologyCapabilities|TestReport|TestScript|ValueSet|VerificationResult|VisionPrescription)' + + '(?:(?:\/([A-Za-z0-9\-\.]{1,64}))?(?:\/(_history)(?:\/([0-9]{1,64}))?)?)?(?:\\?.*)?$'); const match = regex.exec(url); - if (match != null && match.length == 7) - return [match[3], match[4], match[5], match[6]]; + if (match != null) + return match; else return null; } \ No newline at end of file From 137328f82dc165029011c866fce28b885e9d290a Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Mon, 20 Jun 2022 15:00:46 +0200 Subject: [PATCH 10/14] reduced log level from warn to debug No resource may be found locally, when removing (excluding) a process that was never deployed. --- .../org/highmed/dsf/bpe/service/FhirResourceHandlerImpl.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/service/FhirResourceHandlerImpl.java b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/service/FhirResourceHandlerImpl.java index d24df8990..81d4fde55 100644 --- a/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/service/FhirResourceHandlerImpl.java +++ b/dsf-bpe/dsf-bpe-server/src/main/java/org/highmed/dsf/bpe/service/FhirResourceHandlerImpl.java @@ -355,7 +355,7 @@ private Stream getCurrentOrOldResources( List resources = dbResourcesByProcess.get(process); if (resources == null) { - logger.warn("No resources found in BPE DB for process {}", process); + logger.debug("No resources found in BPE DB for process {}", process); resources = Collections.emptyList(); } From 8f318175e9278eec057e12eb4c98b8025a71967d Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Mon, 20 Jun 2022 20:41:10 +0200 Subject: [PATCH 11/14] adds mechanism to disable literal external reference checks Adds a rule for skipping checks of literal external references in Task.input for Task with status `failed` and `completed`. --- .../dao/command/CheckReferencesCommand.java | 45 +++++++- .../fhir/dao/command/CommandFactoryImpl.java | 11 +- .../fhir/dao/command/ReferencesHelper.java | 5 +- .../dao/command/ReferencesHelperImpl.java | 7 +- .../impl/AbstractResourceServiceImpl.java | 43 ++++++- .../fhir/webservice/impl/TaskServiceImpl.java | 28 +++++ .../fhir/integration/TaskIntegrationTest.java | 106 +++++++++++++++++- 7 files changed, 228 insertions(+), 17 deletions(-) diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/CheckReferencesCommand.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/CheckReferencesCommand.java index c7089aefd..91395cf3d 100644 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/CheckReferencesCommand.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/CheckReferencesCommand.java @@ -2,6 +2,7 @@ import java.sql.Connection; import java.sql.SQLException; +import java.util.EnumSet; import java.util.Map; import javax.ws.rs.WebApplicationException; @@ -14,23 +15,36 @@ import org.highmed.dsf.fhir.prefer.PreferReturnType; import org.highmed.dsf.fhir.service.ReferenceExtractor; import org.highmed.dsf.fhir.service.ReferenceResolver; +import org.highmed.dsf.fhir.service.ResourceReference; +import org.highmed.dsf.fhir.service.ResourceReference.ReferenceType; import org.highmed.dsf.fhir.validation.SnapshotGenerator; import org.hl7.fhir.r4.model.Bundle; import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; +import org.hl7.fhir.r4.model.Bundle.HTTPVerb; import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.Resource; +import org.hl7.fhir.r4.model.Task; +import org.hl7.fhir.r4.model.Task.TaskStatus; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class CheckReferencesCommand> extends AbstractCommandWithResource implements Command { + private static final Logger logger = LoggerFactory.getLogger(CheckReferencesCommand.class); + + private final HTTPVerb verb; + public CheckReferencesCommand(int index, User user, PreferReturnType returnType, Bundle bundle, - BundleEntryComponent entry, String serverBase, AuthorizationHelper authorizationHelper, R resource, D dao, - ExceptionHandler exceptionHandler, ParameterConverter parameterConverter, + BundleEntryComponent entry, String serverBase, AuthorizationHelper authorizationHelper, R resource, + HTTPVerb verb, D dao, ExceptionHandler exceptionHandler, ParameterConverter parameterConverter, ResponseGenerator responseGenerator, ReferenceExtractor referenceExtractor, ReferenceResolver referenceResolver) { super(4, index, user, returnType, bundle, entry, serverBase, authorizationHelper, resource, dao, exceptionHandler, parameterConverter, responseGenerator, referenceExtractor, referenceResolver); + + this.verb = verb; } @Override @@ -38,6 +52,31 @@ public void execute(Map idTranslationTable, Connection connectio ValidationHelper validationHelper, SnapshotGenerator snapshotGenerator) throws SQLException, WebApplicationException { - referencesHelper.checkReferences(idTranslationTable, connection); + referencesHelper.checkReferences(idTranslationTable, connection, this::checkReferenceAfterUpdate); + } + + // See also TaskServiceImpl#checkReferenceAfterUpdate + // See also AbstractResourceServiceImpl#checkReferenceAfterUpdate + // See also AbstractResourceServiceImpl#checkReferenceAfterCreate + private boolean checkReferenceAfterUpdate(ResourceReference ref) + { + if (resource instanceof Task && HTTPVerb.PUT.equals(verb)) + { + Task task = (Task) resource; + if (EnumSet.of(TaskStatus.COMPLETED, TaskStatus.FAILED).contains(task.getStatus())) + { + ReferenceType refType = ref.getType(serverBase); + if ("Task.input".equals(ref.getLocation()) && ReferenceType.LITERAL_EXTERNAL.equals(refType)) + { + logger.warn("Skipping check of {} reference '{}' at {} in resource with {}, version {}", refType, + ref.getReference().getReference(), "Task.input", resource.getIdElement().getIdPart(), + // we are checking against the pre-update resource + resource.getIdElement().getVersionIdPartAsLong() + 1); + return false; + } + } + } + + return true; } } diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/CommandFactoryImpl.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/CommandFactoryImpl.java index 41ecac316..4bd0b638b 100755 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/CommandFactoryImpl.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/CommandFactoryImpl.java @@ -29,6 +29,7 @@ import org.highmed.dsf.fhir.validation.SnapshotGenerator; import org.hl7.fhir.r4.model.Bundle; import org.hl7.fhir.r4.model.Bundle.BundleEntryComponent; +import org.hl7.fhir.r4.model.Bundle.HTTPVerb; import org.hl7.fhir.r4.model.Resource; import org.hl7.fhir.r4.model.StructureDefinition; import org.springframework.beans.factory.InitializingBean; @@ -246,11 +247,11 @@ protected Stream createCommand(int index, User user, PreferReturnType r case POST: // create Command post = post(index, user, returnType, bundle, entry, (Resource) entry.getResource()); return resolveReferences(post, index, user, returnType, bundle, entry, - (Resource) entry.getResource()); + (Resource) entry.getResource(), HTTPVerb.POST); case PUT: // update Command put = put(index, user, returnType, bundle, entry, (Resource) entry.getResource()); return resolveReferences(put, index, user, returnType, bundle, entry, - (Resource) entry.getResource()); + (Resource) entry.getResource(), HTTPVerb.PUT); default: throw new BadBundleException("Request method " + entry.getRequest().getMethod() + " at index " + index + " not supported with resource"); @@ -262,7 +263,7 @@ protected Stream createCommand(int index, User user, PreferReturnType r } private Stream resolveReferences(Command cmd, int index, User user, - PreferReturnType returnType, Bundle bundle, BundleEntryComponent entry, R resource) + PreferReturnType returnType, Bundle bundle, BundleEntryComponent entry, R resource, HTTPVerb verb) { @SuppressWarnings("unchecked") Optional> dao = (Optional>) daoProvider @@ -273,8 +274,8 @@ private Stream resolveReferences(Command cmd, int return dao .map(d -> Stream.of(cmd, new CheckReferencesCommand>(index, user, returnType, bundle, entry, - serverBase, authorizationHelper, resource, d, exceptionHandler, parameterConverter, - responseGenerator, referenceExtractor, referenceResolver))) + serverBase, authorizationHelper, resource, verb, d, exceptionHandler, + parameterConverter, responseGenerator, referenceExtractor, referenceResolver))) .orElseThrow(() -> new IllegalStateException( "Resource of type " + resource.getClass().getName() + " not supported")); } diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/ReferencesHelper.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/ReferencesHelper.java index e74a397f3..57f8969df 100644 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/ReferencesHelper.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/ReferencesHelper.java @@ -2,9 +2,11 @@ import java.sql.Connection; import java.util.Map; +import java.util.function.Predicate; import javax.ws.rs.WebApplicationException; +import org.highmed.dsf.fhir.service.ResourceReference; import org.hl7.fhir.r4.model.IdType; import org.hl7.fhir.r4.model.Resource; @@ -15,5 +17,6 @@ void resolveTemporaryAndConditionalReferencesOrLiteralInternalRelatedArtifactOrA void resolveLogicalReferences(Connection connection) throws WebApplicationException; - void checkReferences(Map idTranslationTable, Connection connection) throws WebApplicationException; + void checkReferences(Map idTranslationTable, Connection connection, + Predicate checkReference) throws WebApplicationException; } \ No newline at end of file diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/ReferencesHelperImpl.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/ReferencesHelperImpl.java index 40ce75978..7af0b1d7f 100644 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/ReferencesHelperImpl.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/command/ReferencesHelperImpl.java @@ -6,6 +6,7 @@ import java.util.function.BiConsumer; import java.util.function.Consumer; import java.util.function.Function; +import java.util.function.Predicate; import java.util.function.Supplier; import javax.ws.rs.WebApplicationException; @@ -203,10 +204,10 @@ private Optional resolveLogicalReference(ResourceReference ref } @Override - public void checkReferences(Map idTranslationTable, Connection connection) - throws WebApplicationException + public void checkReferences(Map idTranslationTable, Connection connection, + Predicate checkReference) throws WebApplicationException { - referenceExtractor.getReferences(resource) + referenceExtractor.getReferences(resource).filter(checkReference) .filter(ref -> referenceResolver.referenceCanBeChecked(ref, connection)).forEach(ref -> { Optional outcome = checkReference(idTranslationTable, connection, ref); diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/webservice/impl/AbstractResourceServiceImpl.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/webservice/impl/AbstractResourceServiceImpl.java index ac21ce573..ccdd7f1fc 100755 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/webservice/impl/AbstractResourceServiceImpl.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/webservice/impl/AbstractResourceServiceImpl.java @@ -20,6 +20,7 @@ import java.util.Optional; import java.util.UUID; import java.util.function.Consumer; +import java.util.function.Predicate; import java.util.stream.Collectors; import javax.ws.rs.WebApplicationException; @@ -35,6 +36,7 @@ import org.highmed.dsf.fhir.authorization.AuthorizationRule; import org.highmed.dsf.fhir.authorization.AuthorizationRuleProvider; import org.highmed.dsf.fhir.dao.ResourceDao; +import org.highmed.dsf.fhir.dao.command.CheckReferencesCommand; import org.highmed.dsf.fhir.event.EventGenerator; import org.highmed.dsf.fhir.event.EventHandler; import org.highmed.dsf.fhir.help.ExceptionHandler; @@ -168,7 +170,7 @@ public Response create(R resource, UriInfo uri, HttpHeaders headers) R created = dao.createWithTransactionAndId(connection, resource, UUID.randomUUID()); - checkReferences(resource, connection); + checkReferences(resource, connection, ref -> checkReferenceAfterCreate(resource, ref)); connection.commit(); @@ -198,6 +200,22 @@ public Response create(R resource, UriInfo uri, HttpHeaders headers) .tag(new EntityTag(createdResource.getMeta().getVersionId(), true)).build(); } + /** + * Override this method to exclude references from being checked after a create, add similar rule to + * {@link CheckReferencesCommand} + * + * @param created + * not null + * @param ref + * not null + * @return true if a reference should be checked + * @see CheckReferencesCommand + */ + protected boolean checkReferenceAfterCreate(R created, ResourceReference ref) + { + return true; + } + private URI toLocation(R resource) { return UriBuilder.fromUri(serverBase).path(resource.getResourceType().name()) @@ -236,9 +254,10 @@ private Optional resolveLogicalReference(Resource resource, Re return Optional.of(responseGenerator.referenceTargetNotFoundLocallyByIdentifier(resource, reference)); } - private void checkReferences(Resource resource, Connection connection) throws WebApplicationException + private void checkReferences(Resource resource, Connection connection, Predicate checkReference) + throws WebApplicationException { - referenceExtractor.getReferences(resource) + referenceExtractor.getReferences(resource).filter(checkReference) .filter(ref -> referenceResolver.referenceCanBeChecked(ref, connection)).forEach(ref -> { Optional outcome = checkReference(resource, connection, ref); @@ -494,7 +513,7 @@ public Response update(String id, R resource, UriInfo uri, HttpHeaders headers) R updated = dao.update(resource, ifMatch.orElse(null)); - checkReferences(resource, connection); + checkReferences(resource, connection, ref -> checkReferenceAfterUpdate(updated, ref)); connection.commit(); @@ -525,6 +544,22 @@ public Response update(String id, R resource, UriInfo uri, HttpHeaders headers) .tag(new EntityTag(updatedResource.getMeta().getVersionId(), true)).build(); } + /** + * Override this method to exclude references from being checked after an update, add similar rule to + * {@link CheckReferencesCommand} + * + * @param updated + * not null + * @param ref + * not null + * @return true if a reference should be checked + * @see CheckReferencesCommand + */ + protected boolean checkReferenceAfterUpdate(R updated, ResourceReference ref) + { + return true; + } + /** * Override to modify the given resource before db update, throw {@link WebApplicationException} to interrupt the * normal flow. Path id vs. resource.id.idPart is checked before this method is called diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/webservice/impl/TaskServiceImpl.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/webservice/impl/TaskServiceImpl.java index 67da122a4..8b3c7c79f 100755 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/webservice/impl/TaskServiceImpl.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/webservice/impl/TaskServiceImpl.java @@ -1,5 +1,7 @@ package org.highmed.dsf.fhir.webservice.impl; +import java.util.EnumSet; + import org.highmed.dsf.fhir.authorization.AuthorizationRuleProvider; import org.highmed.dsf.fhir.dao.TaskDao; import org.highmed.dsf.fhir.event.EventGenerator; @@ -11,12 +13,19 @@ import org.highmed.dsf.fhir.service.ReferenceCleaner; import org.highmed.dsf.fhir.service.ReferenceExtractor; import org.highmed.dsf.fhir.service.ReferenceResolver; +import org.highmed.dsf.fhir.service.ResourceReference; +import org.highmed.dsf.fhir.service.ResourceReference.ReferenceType; import org.highmed.dsf.fhir.validation.ResourceValidator; import org.highmed.dsf.fhir.webservice.specification.TaskService; import org.hl7.fhir.r4.model.Task; +import org.hl7.fhir.r4.model.Task.TaskStatus; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; public class TaskServiceImpl extends AbstractResourceServiceImpl implements TaskService { + private static final Logger logger = LoggerFactory.getLogger(TaskServiceImpl.class); + public TaskServiceImpl(String path, String serverBase, int defaultPageCount, TaskDao dao, ResourceValidator validator, EventHandler eventHandler, ExceptionHandler exceptionHandler, EventGenerator eventGenerator, ResponseGenerator responseGenerator, ParameterConverter parameterConverter, @@ -28,4 +37,23 @@ public TaskServiceImpl(String path, String serverBase, int defaultPageCount, Tas eventGenerator, responseGenerator, parameterConverter, referenceExtractor, referenceResolver, referenceCleaner, authorizationRuleProvider, historyService); } + + // See also CheckReferencesCommand#checkReferenceAfterUpdate + @Override + protected boolean checkReferenceAfterUpdate(Task updated, ResourceReference ref) + { + if (EnumSet.of(TaskStatus.COMPLETED, TaskStatus.FAILED).contains(updated.getStatus())) + { + ReferenceType refType = ref.getType(serverBase); + if ("Task.input".equals(ref.getLocation()) && ReferenceType.LITERAL_EXTERNAL.equals(refType)) + { + logger.warn("Skipping check of {} reference '{}' at {} in resource with {}, version {}", refType, + ref.getReference().getReference(), "Task.input", updated.getIdElement().getIdPart(), + updated.getIdElement().getVersionIdPart()); + return false; + } + } + + return super.checkReferenceAfterUpdate(updated, ref); + } } diff --git a/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/integration/TaskIntegrationTest.java b/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/integration/TaskIntegrationTest.java index 8d3c4c6a9..ef9fea0ed 100755 --- a/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/integration/TaskIntegrationTest.java +++ b/dsf-fhir/dsf-fhir-server/src/test/java/org/highmed/dsf/fhir/integration/TaskIntegrationTest.java @@ -1,11 +1,16 @@ package org.highmed.dsf.fhir.integration; -import static org.junit.Assert.*; +import static org.junit.Assert.assertEquals; +import static org.junit.Assert.assertFalse; +import static org.junit.Assert.assertNotNull; +import static org.junit.Assert.assertTrue; +import static org.junit.Assert.fail; import java.io.IOException; import java.io.InputStream; import java.nio.file.Files; import java.nio.file.Paths; +import java.sql.Connection; import java.util.Arrays; import java.util.Collections; import java.util.Date; @@ -17,9 +22,16 @@ import javax.ws.rs.WebApplicationException; import javax.ws.rs.core.Response.Status; +import org.apache.commons.dbcp2.BasicDataSource; import org.highmed.dsf.fhir.authentication.OrganizationProvider; +import org.highmed.dsf.fhir.authentication.User; import org.highmed.dsf.fhir.dao.OrganizationDao; import org.highmed.dsf.fhir.dao.TaskDao; +import org.highmed.dsf.fhir.dao.command.ReferencesHelperImpl; +import org.highmed.dsf.fhir.help.ResponseGenerator; +import org.highmed.dsf.fhir.service.ReferenceCleaner; +import org.highmed.dsf.fhir.service.ReferenceExtractor; +import org.highmed.dsf.fhir.service.ReferenceResolver; import org.highmed.fhir.client.FhirWebserviceClient; import org.hl7.fhir.r4.model.ActivityDefinition; import org.hl7.fhir.r4.model.Bundle; @@ -1057,4 +1069,96 @@ public void testSearchByProfile() throws Exception assertEquals(task2.getMeta().getProfile().get(0).getValue(), result6.getEntry().get(0).getResource().getMeta().getProfile().get(0).getValue()); } + + @Test + public void testUpdateTaskFromInProgressToCompletedWithNonExistingInputReferenceToExternalBinary() throws Exception + { + ActivityDefinition ad2 = readActivityDefinition("highmed-test-activity-definition2-0.5.0.xml"); + ActivityDefinition createdAd2 = getWebserviceClient().create(ad2); + assertNotNull(createdAd2); + assertNotNull(createdAd2.getIdElement().getIdPart()); + + StructureDefinition testTaskProfile = readTestTaskProfile(); + StructureDefinition createdTestTaskProfile = getWebserviceClient().create(testTaskProfile); + assertNotNull(createdTestTaskProfile); + assertNotNull(createdTestTaskProfile.getIdElement().getIdPart()); + + Task task = readTestTask("External_Test_Organization", "Test_Organization"); + task.setStatus(TaskStatus.INPROGRESS); + task.addInput().setValue(new Reference("https://localhost:80010/fhir/Binary/" + UUID.randomUUID().toString())) + .getType().getCodingFirstRep().setSystem("http://test.com/fhir/CodeSystem/test").setCode("binary-ref"); + + TaskDao taskDao = getSpringWebApplicationContext().getBean(TaskDao.class); + Task created = taskDao.create(task); + + ReferenceCleaner cleaner = getSpringWebApplicationContext().getBean(ReferenceCleaner.class); + cleaner.cleanLiteralReferences(created); + + created.setStatus(TaskStatus.COMPLETED); + + Task updatedTask = getWebserviceClient().update(created); + assertNotNull(updatedTask); + assertNotNull(updatedTask.getIdElement().getIdPart()); + } + + @Test + public void testUpdateTaskFromInProgressToCompletedWithNonExistingInputReferenceToExternalBinaryViaBundle() + throws Exception + { + ActivityDefinition ad2 = readActivityDefinition("highmed-test-activity-definition2-0.5.0.xml"); + ActivityDefinition createdAd2 = getWebserviceClient().create(ad2); + assertNotNull(createdAd2); + assertNotNull(createdAd2.getIdElement().getIdPart()); + + StructureDefinition testTaskProfile = readTestTaskProfile(); + StructureDefinition createdTestTaskProfile = getWebserviceClient().create(testTaskProfile); + assertNotNull(createdTestTaskProfile); + assertNotNull(createdTestTaskProfile.getIdElement().getIdPart()); + + Task task = readTestTask("External_Test_Organization", "Test_Organization"); + task.setStatus(TaskStatus.INPROGRESS); + task.addInput().setValue(new Reference("https://localhost:80010/fhir/Binary/" + UUID.randomUUID().toString())) + .getType().getCodingFirstRep().setSystem("http://test.com/fhir/CodeSystem/test").setCode("binary-ref"); + + OrganizationProvider organizationProvider = getSpringWebApplicationContext() + .getBean(OrganizationProvider.class); + ReferenceExtractor referenceExtractor = getSpringWebApplicationContext().getBean(ReferenceExtractor.class); + ReferenceResolver referenceResolver = getSpringWebApplicationContext().getBean(ReferenceResolver.class); + ResponseGenerator responseGenerator = getSpringWebApplicationContext().getBean(ResponseGenerator.class); + BasicDataSource dataSource = getSpringWebApplicationContext().getBean("dataSource", BasicDataSource.class); + + ReferencesHelperImpl referencesHelper = new ReferencesHelperImpl<>(0, + User.local(organizationProvider.getLocalOrganization().get()), task, BASE_URL, referenceExtractor, + referenceResolver, responseGenerator); + try (Connection connection = dataSource.getConnection()) + { + System.out.println(fhirContext.newJsonParser().encodeResourceToString(task)); + referencesHelper.resolveLogicalReferences(connection); + System.out.println(fhirContext.newJsonParser().encodeResourceToString(task)); + } + + TaskDao taskDao = getSpringWebApplicationContext().getBean(TaskDao.class); + Task created = taskDao.create(task); + + ReferenceCleaner referenceCleaner = getSpringWebApplicationContext().getBean(ReferenceCleaner.class); + referenceCleaner.cleanLiteralReferences(created); + created.setStatus(TaskStatus.COMPLETED); + + Bundle bundle = new Bundle(); + bundle.setType(BundleType.TRANSACTION); + BundleEntryComponent entry = bundle.addEntry() + .setFullUrl(created.getIdElement().withServerBase(BASE_URL, "Task").toVersionless().getValue()); + entry.setResource(created).getRequest().setMethod(HTTPVerb.PUT) + .setUrl("Task/" + created.getIdElement().getIdPart()); + + Bundle response = getWebserviceClient().postBundle(bundle); + assertNotNull(response); + assertEquals(BundleType.TRANSACTIONRESPONSE, response.getType()); + assertTrue(response.hasEntry()); + assertEquals(1, response.getEntry().size()); + assertTrue(response.getEntryFirstRep().hasResponse()); + assertEquals("200 OK", response.getEntryFirstRep().getResponse().getStatus()); + assertTrue(response.getEntryFirstRep().hasResource()); + assertTrue(response.getEntryFirstRep().getResource() instanceof Task); + } } From 8ff49514c655955c419e10344e1c3b176e3140c1 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Mon, 20 Jun 2022 21:24:03 +0200 Subject: [PATCH 12/14] dependency version upgrades --- .../dsf/fhir/dao/jdbc/AbstractResourceDaoJdbc.java | 2 +- pom.xml | 8 +++++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/AbstractResourceDaoJdbc.java b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/AbstractResourceDaoJdbc.java index 24b19f98d..df33dbe41 100755 --- a/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/AbstractResourceDaoJdbc.java +++ b/dsf-fhir/dsf-fhir-server/src/main/java/org/highmed/dsf/fhir/dao/jdbc/AbstractResourceDaoJdbc.java @@ -846,7 +846,7 @@ private void getResources(ResultSet result, int columnIndex, List it = array.iterator(); while (it.hasNext()) diff --git a/pom.xml b/pom.xml index ba65d33da..3377ec066 100755 --- a/pom.xml +++ b/pom.xml @@ -30,7 +30,7 @@ 9.4.46.v20220331 2.35 1.18 - 5.3.20 + 5.3.21 5.1.0 2.3 @@ -342,6 +342,12 @@ guava 31.1-jre + + com.google.code.gson + gson + 2.9.0 + + From 6308552cd883b1f585807a0cfec3841225bcf301 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Mon, 20 Jun 2022 21:55:37 +0200 Subject: [PATCH 13/14] update release date --- CITATION.cff | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CITATION.cff b/CITATION.cff index eb1d288ce..eb673bad8 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -25,7 +25,7 @@ preferred-citation: type: proceedings title: "HiGHmed Data Sharing Framework (HiGHmed DSF)" version: 0.7.0 -date-released: 2022-06-12 +date-released: 2022-06-20 url: https://github.com/highmed/highmed-dsf/wiki repository-code: https://github.com/highmed/highmed-dsf repository-artifact: https://github.com/highmed/highmed-dsf/releases From 90c54e39fc39af2cadd91e2f09a78d526d4d26e6 Mon Sep 17 00:00:00 2001 From: Hauke Hund Date: Tue, 21 Jun 2022 20:25:06 +0200 Subject: [PATCH 14/14] 0.7.0 release --- CITATION.cff | 2 +- dsf-bpe/dsf-bpe-process-base/pom.xml | 2 +- dsf-bpe/dsf-bpe-server-jetty/pom.xml | 2 +- dsf-bpe/dsf-bpe-server/pom.xml | 2 +- dsf-bpe/dsf-bpe-webservice-client/pom.xml | 2 +- dsf-bpe/pom.xml | 2 +- dsf-consent/dsf-consent-client-stub/pom.xml | 2 +- dsf-consent/dsf-consent-client/pom.xml | 2 +- dsf-consent/pom.xml | 2 +- dsf-fhir/dsf-fhir-auth/pom.xml | 2 +- dsf-fhir/dsf-fhir-rest-adapter/pom.xml | 2 +- dsf-fhir/dsf-fhir-server-jetty/pom.xml | 2 +- dsf-fhir/dsf-fhir-server/pom.xml | 2 +- dsf-fhir/dsf-fhir-validation/pom.xml | 4 ++-- dsf-fhir/dsf-fhir-webservice-client/pom.xml | 2 +- dsf-fhir/dsf-fhir-websocket-client/pom.xml | 2 +- dsf-fhir/pom.xml | 2 +- dsf-mpi/dsf-mpi-client-pdq/pom.xml | 2 +- dsf-mpi/dsf-mpi-client-stub/pom.xml | 2 +- dsf-mpi/dsf-mpi-client/pom.xml | 2 +- dsf-mpi/pom.xml | 2 +- dsf-openehr/dsf-openehr-client-impl/pom.xml | 2 +- dsf-openehr/dsf-openehr-client-stub/pom.xml | 2 +- dsf-openehr/dsf-openehr-client/pom.xml | 2 +- dsf-openehr/dsf-openehr-model/pom.xml | 2 +- dsf-openehr/pom.xml | 2 +- dsf-pseudonymization/dsf-pseudonymization-base/pom.xml | 2 +- dsf-pseudonymization/dsf-pseudonymization-client-stub/pom.xml | 2 +- dsf-pseudonymization/dsf-pseudonymization-client/pom.xml | 2 +- dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml | 2 +- dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml | 2 +- dsf-pseudonymization/pom.xml | 2 +- dsf-tools/dsf-tools-build-info-reader/pom.xml | 2 +- dsf-tools/dsf-tools-bundle-generator/pom.xml | 2 +- dsf-tools/dsf-tools-db-migration/pom.xml | 2 +- dsf-tools/dsf-tools-docker-secrets-reader/pom.xml | 2 +- dsf-tools/dsf-tools-documentation-generator/pom.xml | 2 +- dsf-tools/dsf-tools-proxy-test/pom.xml | 2 +- dsf-tools/dsf-tools-test-data-generator/pom.xml | 2 +- dsf-tools/pom.xml | 2 +- pom.xml | 2 +- 41 files changed, 42 insertions(+), 42 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index eb673bad8..263b525b8 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -25,7 +25,7 @@ preferred-citation: type: proceedings title: "HiGHmed Data Sharing Framework (HiGHmed DSF)" version: 0.7.0 -date-released: 2022-06-20 +date-released: 2022-06-21 url: https://github.com/highmed/highmed-dsf/wiki repository-code: https://github.com/highmed/highmed-dsf repository-artifact: https://github.com/highmed/highmed-dsf/releases diff --git a/dsf-bpe/dsf-bpe-process-base/pom.xml b/dsf-bpe/dsf-bpe-process-base/pom.xml index d5844ec56..21610d117 100755 --- a/dsf-bpe/dsf-bpe-process-base/pom.xml +++ b/dsf-bpe/dsf-bpe-process-base/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-bpe-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-bpe/dsf-bpe-server-jetty/pom.xml b/dsf-bpe/dsf-bpe-server-jetty/pom.xml index 06464732e..346a9ec47 100755 --- a/dsf-bpe/dsf-bpe-server-jetty/pom.xml +++ b/dsf-bpe/dsf-bpe-server-jetty/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-bpe-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-bpe/dsf-bpe-server/pom.xml b/dsf-bpe/dsf-bpe-server/pom.xml index d9cdbb2f8..2f3fce2cb 100755 --- a/dsf-bpe/dsf-bpe-server/pom.xml +++ b/dsf-bpe/dsf-bpe-server/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-bpe-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-bpe/dsf-bpe-webservice-client/pom.xml b/dsf-bpe/dsf-bpe-webservice-client/pom.xml index 7bb961c9e..3d1893a3c 100755 --- a/dsf-bpe/dsf-bpe-webservice-client/pom.xml +++ b/dsf-bpe/dsf-bpe-webservice-client/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-bpe-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-bpe/pom.xml b/dsf-bpe/pom.xml index b81e1db76..f9335c981 100755 --- a/dsf-bpe/pom.xml +++ b/dsf-bpe/pom.xml @@ -8,7 +8,7 @@ org.highmed.dsf dsf-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-consent/dsf-consent-client-stub/pom.xml b/dsf-consent/dsf-consent-client-stub/pom.xml index 67b09bd04..503255081 100644 --- a/dsf-consent/dsf-consent-client-stub/pom.xml +++ b/dsf-consent/dsf-consent-client-stub/pom.xml @@ -9,7 +9,7 @@ dsf-consent-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-consent/dsf-consent-client/pom.xml b/dsf-consent/dsf-consent-client/pom.xml index daca69c3f..027058c9b 100644 --- a/dsf-consent/dsf-consent-client/pom.xml +++ b/dsf-consent/dsf-consent-client/pom.xml @@ -9,7 +9,7 @@ dsf-consent-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-consent/pom.xml b/dsf-consent/pom.xml index 81cb8ff4c..8438de4aa 100644 --- a/dsf-consent/pom.xml +++ b/dsf-consent/pom.xml @@ -10,7 +10,7 @@ dsf-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-fhir/dsf-fhir-auth/pom.xml b/dsf-fhir/dsf-fhir-auth/pom.xml index 0295db58a..c93e33d7b 100644 --- a/dsf-fhir/dsf-fhir-auth/pom.xml +++ b/dsf-fhir/dsf-fhir-auth/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-fhir/dsf-fhir-rest-adapter/pom.xml b/dsf-fhir/dsf-fhir-rest-adapter/pom.xml index 42f92179e..58597c8a6 100755 --- a/dsf-fhir/dsf-fhir-rest-adapter/pom.xml +++ b/dsf-fhir/dsf-fhir-rest-adapter/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-fhir/dsf-fhir-server-jetty/pom.xml b/dsf-fhir/dsf-fhir-server-jetty/pom.xml index 2aa7c5b0c..55f8ff78d 100755 --- a/dsf-fhir/dsf-fhir-server-jetty/pom.xml +++ b/dsf-fhir/dsf-fhir-server-jetty/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-fhir/dsf-fhir-server/pom.xml b/dsf-fhir/dsf-fhir-server/pom.xml index 2b4a8e966..15329c722 100755 --- a/dsf-fhir/dsf-fhir-server/pom.xml +++ b/dsf-fhir/dsf-fhir-server/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-fhir/dsf-fhir-validation/pom.xml b/dsf-fhir/dsf-fhir-validation/pom.xml index 609bfdb1f..f9ef2bdca 100644 --- a/dsf-fhir/dsf-fhir-validation/pom.xml +++ b/dsf-fhir/dsf-fhir-validation/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.7.0-SNAPSHOT + 0.7.0 @@ -93,7 +93,7 @@ - diff --git a/dsf-fhir/dsf-fhir-webservice-client/pom.xml b/dsf-fhir/dsf-fhir-webservice-client/pom.xml index 398cc7b5c..8a0da2e6e 100755 --- a/dsf-fhir/dsf-fhir-webservice-client/pom.xml +++ b/dsf-fhir/dsf-fhir-webservice-client/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-fhir/dsf-fhir-websocket-client/pom.xml b/dsf-fhir/dsf-fhir-websocket-client/pom.xml index f0294dfc3..f5828e649 100755 --- a/dsf-fhir/dsf-fhir-websocket-client/pom.xml +++ b/dsf-fhir/dsf-fhir-websocket-client/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-fhir-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-fhir/pom.xml b/dsf-fhir/pom.xml index 00f2a5019..9147cb5ae 100755 --- a/dsf-fhir/pom.xml +++ b/dsf-fhir/pom.xml @@ -8,7 +8,7 @@ org.highmed.dsf dsf-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-mpi/dsf-mpi-client-pdq/pom.xml b/dsf-mpi/dsf-mpi-client-pdq/pom.xml index b3a7a43a9..a2fd8907a 100644 --- a/dsf-mpi/dsf-mpi-client-pdq/pom.xml +++ b/dsf-mpi/dsf-mpi-client-pdq/pom.xml @@ -9,7 +9,7 @@ dsf-mpi-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-mpi/dsf-mpi-client-stub/pom.xml b/dsf-mpi/dsf-mpi-client-stub/pom.xml index 90505a9b4..50589e69d 100644 --- a/dsf-mpi/dsf-mpi-client-stub/pom.xml +++ b/dsf-mpi/dsf-mpi-client-stub/pom.xml @@ -9,7 +9,7 @@ dsf-mpi-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-mpi/dsf-mpi-client/pom.xml b/dsf-mpi/dsf-mpi-client/pom.xml index e37c298e7..b9001f5fa 100644 --- a/dsf-mpi/dsf-mpi-client/pom.xml +++ b/dsf-mpi/dsf-mpi-client/pom.xml @@ -9,7 +9,7 @@ dsf-mpi-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-mpi/pom.xml b/dsf-mpi/pom.xml index 55652ab8d..a6a247fd5 100644 --- a/dsf-mpi/pom.xml +++ b/dsf-mpi/pom.xml @@ -10,7 +10,7 @@ dsf-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-openehr/dsf-openehr-client-impl/pom.xml b/dsf-openehr/dsf-openehr-client-impl/pom.xml index c9df348c3..a06dcb7dc 100644 --- a/dsf-openehr/dsf-openehr-client-impl/pom.xml +++ b/dsf-openehr/dsf-openehr-client-impl/pom.xml @@ -9,7 +9,7 @@ dsf-openehr-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-openehr/dsf-openehr-client-stub/pom.xml b/dsf-openehr/dsf-openehr-client-stub/pom.xml index eb42fa82d..64e51b14f 100644 --- a/dsf-openehr/dsf-openehr-client-stub/pom.xml +++ b/dsf-openehr/dsf-openehr-client-stub/pom.xml @@ -8,7 +8,7 @@ dsf-openehr-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-openehr/dsf-openehr-client/pom.xml b/dsf-openehr/dsf-openehr-client/pom.xml index 5d6973fcb..68608f0aa 100644 --- a/dsf-openehr/dsf-openehr-client/pom.xml +++ b/dsf-openehr/dsf-openehr-client/pom.xml @@ -8,7 +8,7 @@ dsf-openehr-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-openehr/dsf-openehr-model/pom.xml b/dsf-openehr/dsf-openehr-model/pom.xml index 284c3be4d..ea657afa1 100644 --- a/dsf-openehr/dsf-openehr-model/pom.xml +++ b/dsf-openehr/dsf-openehr-model/pom.xml @@ -8,7 +8,7 @@ dsf-openehr-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-openehr/pom.xml b/dsf-openehr/pom.xml index ed6907b0f..ebc9f7c79 100755 --- a/dsf-openehr/pom.xml +++ b/dsf-openehr/pom.xml @@ -10,7 +10,7 @@ dsf-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml index 95819d0ee..9af74e8fd 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-base/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-pseudonymization-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-pseudonymization/dsf-pseudonymization-client-stub/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-client-stub/pom.xml index b55bcfda7..ab174b257 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-client-stub/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-client-stub/pom.xml @@ -9,7 +9,7 @@ dsf-pseudonymization-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-pseudonymization/dsf-pseudonymization-client/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-client/pom.xml index d3f2bbe35..9ca985988 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-client/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-client/pom.xml @@ -9,7 +9,7 @@ dsf-pseudonymization-pom org.highmed.dsf - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml index 8713cc96d..b522db305 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-medic/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-pseudonymization-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml b/dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml index f1fe03fcd..f6d3dbad3 100644 --- a/dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml +++ b/dsf-pseudonymization/dsf-pseudonymization-ttp/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-pseudonymization-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-pseudonymization/pom.xml b/dsf-pseudonymization/pom.xml index f156ac720..b7c6ed798 100644 --- a/dsf-pseudonymization/pom.xml +++ b/dsf-pseudonymization/pom.xml @@ -8,7 +8,7 @@ org.highmed.dsf dsf-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-tools/dsf-tools-build-info-reader/pom.xml b/dsf-tools/dsf-tools-build-info-reader/pom.xml index 31147a656..972e812d8 100644 --- a/dsf-tools/dsf-tools-build-info-reader/pom.xml +++ b/dsf-tools/dsf-tools-build-info-reader/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-tools/dsf-tools-bundle-generator/pom.xml b/dsf-tools/dsf-tools-bundle-generator/pom.xml index 18a345a32..2bf548612 100755 --- a/dsf-tools/dsf-tools-bundle-generator/pom.xml +++ b/dsf-tools/dsf-tools-bundle-generator/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-tools/dsf-tools-db-migration/pom.xml b/dsf-tools/dsf-tools-db-migration/pom.xml index f5ce1544a..2306a5d5d 100755 --- a/dsf-tools/dsf-tools-db-migration/pom.xml +++ b/dsf-tools/dsf-tools-db-migration/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-tools/dsf-tools-docker-secrets-reader/pom.xml b/dsf-tools/dsf-tools-docker-secrets-reader/pom.xml index 0422adeb1..c6fd2658a 100644 --- a/dsf-tools/dsf-tools-docker-secrets-reader/pom.xml +++ b/dsf-tools/dsf-tools-docker-secrets-reader/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-tools/dsf-tools-documentation-generator/pom.xml b/dsf-tools/dsf-tools-documentation-generator/pom.xml index 0e3a12e19..309c9ac11 100644 --- a/dsf-tools/dsf-tools-documentation-generator/pom.xml +++ b/dsf-tools/dsf-tools-documentation-generator/pom.xml @@ -9,7 +9,7 @@ org.highmed.dsf dsf-tools-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-tools/dsf-tools-proxy-test/pom.xml b/dsf-tools/dsf-tools-proxy-test/pom.xml index 075a81d37..34306cce3 100755 --- a/dsf-tools/dsf-tools-proxy-test/pom.xml +++ b/dsf-tools/dsf-tools-proxy-test/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-tools/dsf-tools-test-data-generator/pom.xml b/dsf-tools/dsf-tools-test-data-generator/pom.xml index 4a8de1855..8d4968fd8 100755 --- a/dsf-tools/dsf-tools-test-data-generator/pom.xml +++ b/dsf-tools/dsf-tools-test-data-generator/pom.xml @@ -7,7 +7,7 @@ org.highmed.dsf dsf-tools-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/dsf-tools/pom.xml b/dsf-tools/pom.xml index 595ab13e9..d61f03611 100755 --- a/dsf-tools/pom.xml +++ b/dsf-tools/pom.xml @@ -8,7 +8,7 @@ org.highmed.dsf dsf-pom - 0.7.0-SNAPSHOT + 0.7.0 diff --git a/pom.xml b/pom.xml index 3377ec066..916f78483 100755 --- a/pom.xml +++ b/pom.xml @@ -4,7 +4,7 @@ org.highmed.dsf dsf-pom - 0.7.0-SNAPSHOT + 0.7.0 pom