diff --git a/charts/onco-analytics-on-fhir/Chart.lock b/charts/onco-analytics-on-fhir/Chart.lock index 0afe9a70..31e79056 100644 --- a/charts/onco-analytics-on-fhir/Chart.lock +++ b/charts/onco-analytics-on-fhir/Chart.lock @@ -1,15 +1,15 @@ dependencies: - name: akhq repository: https://akhq.io/ - version: 0.24.0 + version: 0.25.1 - name: stream-processors repository: https://miracum.github.io/charts - version: 1.6.0 + version: 1.7.25 - name: hapi-fhir-jpaserver repository: https://hapifhir.github.io/hapi-fhir-jpaserver-starter - version: 0.15.0 + version: 0.17.1 - name: fhir-gateway repository: https://miracum.github.io/charts - version: 6.2.0 -digest: sha256:a8beeea01663ba075258174948eee1c377bdbf1cb70252c01e188003f477bd18 -generated: "2024-02-22T07:51:46.369204628Z" + version: 6.3.52 +digest: sha256:6606fa0516f16822903b855cf1d2a04e3e1cae80b8b90e2c7cd60ccd345df6ae +generated: "2024-12-03T16:32:37.799596789Z" diff --git a/charts/onco-analytics-on-fhir/Chart.yaml b/charts/onco-analytics-on-fhir/Chart.yaml index c2b632de..67200f33 100644 --- a/charts/onco-analytics-on-fhir/Chart.yaml +++ b/charts/onco-analytics-on-fhir/Chart.yaml @@ -8,19 +8,19 @@ dependencies: - name: akhq condition: akhq.enabled repository: https://akhq.io/ - version: 0.24.0 + version: 0.25.1 - condition: stream-processors.enabled name: stream-processors repository: https://miracum.github.io/charts - version: 1.6.0 + version: 1.7.25 - condition: hapi-fhir-jpaserver.enabled name: hapi-fhir-jpaserver repository: https://hapifhir.github.io/hapi-fhir-jpaserver-starter - version: 0.15.0 + version: 0.17.1 - condition: fhir-gateway.enabled name: fhir-gateway repository: https://miracum.github.io/charts - version: 6.2.0 + version: 6.3.52 # x-release-please-start-version version: 2.3.1 appVersion: 2.3.1 diff --git a/charts/onco-analytics-on-fhir/values.yaml b/charts/onco-analytics-on-fhir/values.yaml index 2ed0da0e..addb40ca 100644 --- a/charts/onco-analytics-on-fhir/values.yaml +++ b/charts/onco-analytics-on-fhir/values.yaml @@ -107,7 +107,7 @@ stream-processors: image: registry: ghcr.io repository: miracum/kafka-fhir-to-server - tag: v2.0.6@sha256:155859d275b636e356a99dac3592aa602eef6b68a8f1fe82f7e9670e2be1ef33 + tag: v2.2.1@sha256:c23d6e12f3cb63500384ff4fd4e69dc4feaef162e9250ecf66cde0080b42544e pullPolicy: IfNotPresent env: - name: FHIR_URL @@ -137,7 +137,7 @@ stream-processors: image: registry: ghcr.io repository: miracum/obds-to-fhir - tag: v2.0.15@sha256:c359ef5449068ff0c1231c3ee237801f2fb76932ab9a16386813d02c07ac9f7d + tag: v2.1.0@sha256:6752d517b423388cce447aaca75a714034bc0a7c0f545c9111d5e45a126fab89 pullPolicy: IfNotPresent env: - name: OPENTRACING_JAEGER_ENABLED diff --git a/charts/prerequisites/Chart.lock b/charts/prerequisites/Chart.lock index 37fe327d..2a0dca04 100644 --- a/charts/prerequisites/Chart.lock +++ b/charts/prerequisites/Chart.lock @@ -1,6 +1,6 @@ dependencies: - name: strimzi-kafka-operator repository: oci://quay.io/strimzi-helm - version: 0.39.0 -digest: sha256:c986c32b5483a8d395c49960c179f12d775ce5ef2c55ac5cb63f376d9fc97660 -generated: "2024-01-11T20:52:49.55346174Z" + version: 0.44.0 +digest: sha256:04c48bb66f6b9e8cfd36ef49ea9859d397d4497c9107dd046b498431da6bbe57 +generated: "2024-12-03T16:33:06.398655703Z" diff --git a/charts/prerequisites/Chart.yaml b/charts/prerequisites/Chart.yaml index 6c13c04f..b1ce5396 100644 --- a/charts/prerequisites/Chart.yaml +++ b/charts/prerequisites/Chart.yaml @@ -7,7 +7,7 @@ kubeVersion: ">= 1.21.0" dependencies: - name: strimzi-kafka-operator repository: oci://quay.io/strimzi-helm - version: 0.39.0 + version: 0.44.0 # x-release-please-start-version version: 2.3.1 appVersion: 2.3.1 diff --git a/docker-compose/compose.fhir-server.yaml b/docker-compose/compose.fhir-server.yaml index 754e0594..8d170cdd 100644 --- a/docker-compose/compose.fhir-server.yaml +++ b/docker-compose/compose.fhir-server.yaml @@ -35,7 +35,7 @@ services: - "8082:8080" fhir-db: - image: docker.io/library/postgres:15.6@sha256:1ebd963e5c598f944a4e9ba27de4c95289d663dcc73731025aa53c5254094d8f + image: docker.io/library/postgres:15.10@sha256:6cbdd616ae7ea61fa88873fdab529b3fd141b8a8311bfe4e6e62575f643f88fe restart: unless-stopped deploy: resources: diff --git a/docker-compose/compose.full.yaml b/docker-compose/compose.full.yaml index 9c398852..bd1e6166 100644 --- a/docker-compose/compose.full.yaml +++ b/docker-compose/compose.full.yaml @@ -1,6 +1,6 @@ services: kafka: - image: docker.io/bitnami/kafka:3.6.1@sha256:b5254050e61d1912ed9cf3f7107adc6a21ff29d85047b46d7b6df57cf25fa2f7 + image: docker.io/bitnami/kafka:3.9.0@sha256:978583d0859444d3bc6b6592b38b5af5a834d473db51441071a20e67e0afb945 restart: unless-stopped cap_drop: - ALL @@ -25,7 +25,7 @@ services: - "kafka_data:/bitnami:rw" kafka-connect: - image: ghcr.io/miracum/util-images/cricketeerone-kafka-connect:v1.6.0@sha256:5d4c79d5b9d64562d8906aec14c66ed5f48ddb0f9e7f12949547ab89b69e3f0f + image: ghcr.io/miracum/util-images/cricketeerone-kafka-connect:v1.6.2@sha256:66fa69028dffe5aabe2323a782aa365fbe45394393f8da53cc283375bc910399 restart: unless-stopped cap_drop: - ALL @@ -52,7 +52,7 @@ services: - 8083:8083 akhq: - image: docker.io/tchiotludo/akhq:0.24.0@sha256:6ccf8323ae6e93a893107f857cd9f7210add3569743b2c8528c6567967cc636f + image: docker.io/tchiotludo/akhq:0.25.1@sha256:cfaef8f419c4e4b78c583597d6428b63166e90eeb194af890264d68051a22180 restart: unless-stopped cap_drop: - ALL diff --git a/docker-compose/compose.obds-to-fhir.yaml b/docker-compose/compose.obds-to-fhir.yaml index 61bf0105..789c55aa 100644 --- a/docker-compose/compose.obds-to-fhir.yaml +++ b/docker-compose/compose.obds-to-fhir.yaml @@ -1,6 +1,6 @@ services: obds-to-fhir: - image: ghcr.io/bzkf/obds-to-fhir:v2.2.0@sha256:b5d264c849fb5a19d8af1677b6f9adc26d70108c22e4f2753d0b2472da39f038 + image: ghcr.io/bzkf/obds-to-fhir:v2.2.3@sha256:fc22d3986e57475f6586da2035c7e8d407bb04b1449b94bee16edd4e0a92e674 restart: unless-stopped cap_drop: - ALL diff --git a/docker-compose/compose.pseudonymization.yaml b/docker-compose/compose.pseudonymization.yaml index b73d50f7..1f06edb4 100644 --- a/docker-compose/compose.pseudonymization.yaml +++ b/docker-compose/compose.pseudonymization.yaml @@ -1,6 +1,6 @@ services: fhir-gateway: - image: ghcr.io/miracum/fhir-gateway:v3.12.8@sha256:2cf2d887b25594c04af3d6be302f8ccaea12dee90965fe4e2f81d24786ac3b6d + image: ghcr.io/miracum/fhir-gateway:v3.14.2@sha256:4a8d63755d26dbc81b2fc59afd15b7792fc73a23d76501b4a2433a93e8e9d100 restart: unless-stopped cap_drop: - ALL @@ -32,7 +32,7 @@ services: SERVICES_KAFKA_GENERATE_OUTPUT_TOPIC_REPLACE_WITH: "fhir.pseudonymized." fhir-pseudonymizer: - image: ghcr.io/miracum/fhir-pseudonymizer:v2.21.6@sha256:f250919efe324d31d9d442058256d6af58c0ea26980fc5852544a93cf8a71b1d + image: ghcr.io/miracum/fhir-pseudonymizer:v2.22.1@sha256:ce25487f1cab422bdb4d36231fd0f89d66a41a518a7823abfd03953b16e4719a restart: unless-stopped cap_drop: - ALL diff --git a/docker-compose/datashield/compose.datashield.yaml b/docker-compose/datashield/compose.datashield.yaml index ca39de81..22cf948d 100644 --- a/docker-compose/datashield/compose.datashield.yaml +++ b/docker-compose/datashield/compose.datashield.yaml @@ -1,6 +1,6 @@ services: opal: - image: docker.io/obiba/opal:4.6@sha256:50abaa400d5b474981c951719301ce4f3c9f5058090cc878e5e82b1b35342881 + image: docker.io/obiba/opal:4.7@sha256:37acba4b52d91d93fd30bba78fd306d96901b33d214f2ba02048e5f29961008e restart: unless-stopped ipc: none security_opt: @@ -32,7 +32,7 @@ services: - rock-2 opal-db: - image: docker.io/library/postgres:16.2@sha256:4aea012537edfad80f98d870a36e6b90b4c09b27be7f4b4759d72db863baeebb + image: docker.io/library/postgres:16.6@sha256:5620f242bbc0e17478556102327e7efcf60ab48de3607c9e0ea98800841785ec restart: unless-stopped ipc: private security_opt: diff --git a/src/decompose_xmls/compose.yaml b/src/decompose_xmls/compose.yaml index 398a25ee..5c4bb044 100644 --- a/src/decompose_xmls/compose.yaml +++ b/src/decompose_xmls/compose.yaml @@ -12,7 +12,7 @@ services: - ./output-obds-reports:/app/output-obds-reports:rw kafka: - image: docker.io/bitnami/kafka:3.6.1@sha256:b5254050e61d1912ed9cf3f7107adc6a21ff29d85047b46d7b6df57cf25fa2f7 + image: docker.io/bitnami/kafka:3.9.0@sha256:978583d0859444d3bc6b6592b38b5af5a834d473db51441071a20e67e0afb945 restart: unless-stopped profiles: - kafka @@ -33,7 +33,7 @@ services: # KAFKA_CFG_ADVERTISED_LISTENERS: LISTENER_DOCKER_INTERNAL://kafka:19092,LISTENER_DOCKER_EXTERNAL://${DOCKER_HOST_IP:-127.0.0.1}:9092 akhq: - image: docker.io/tchiotludo/akhq:0.24.0@sha256:6ccf8323ae6e93a893107f857cd9f7210add3569743b2c8528c6567967cc636f + image: docker.io/tchiotludo/akhq:0.25.1@sha256:cfaef8f419c4e4b78c583597d6428b63166e90eeb194af890264d68051a22180 restart: unless-stopped profiles: - kafka diff --git a/src/decompose_xmls/requirements-test.txt b/src/decompose_xmls/requirements-test.txt index 32e2f5c3..1374c8ca 100644 --- a/src/decompose_xmls/requirements-test.txt +++ b/src/decompose_xmls/requirements-test.txt @@ -1,3 +1,3 @@ pytest==7.4.4 -syrupy==4.6.1 +syrupy==4.8.0 pytest-cov==4.1.0 diff --git a/src/decompose_xmls/requirements.txt b/src/decompose_xmls/requirements.txt index 0eb22420..6c1e1bb2 100644 --- a/src/decompose_xmls/requirements.txt +++ b/src/decompose_xmls/requirements.txt @@ -1,3 +1,3 @@ -pydantic==1.10.14 -confluent-kafka==2.3.0 -regex==2024.5.15 +pydantic==1.10.19 +confluent-kafka==2.6.1 +regex==2024.11.6 diff --git a/src/obds_fhir_to_opal/plots/requirements.txt b/src/obds_fhir_to_opal/plots/requirements.txt index 86d5fa5f..7288e201 100644 --- a/src/obds_fhir_to_opal/plots/requirements.txt +++ b/src/obds_fhir_to_opal/plots/requirements.txt @@ -1,8 +1,8 @@ ipykernel==6.29.5 -ipython==8.26.0 -matplotlib==3.9.1 +ipython==8.30.0 +matplotlib==3.9.3 matplotlib-inline==0.1.7 numpy==1.26.4 -pandas==2.2.0 +pandas==2.2.3 seaborn==0.13.2 diff --git a/src/obds_fhir_to_opal/requirements.txt b/src/obds_fhir_to_opal/requirements.txt index e3292cd6..4917a675 100644 --- a/src/obds_fhir_to_opal/requirements.txt +++ b/src/obds_fhir_to_opal/requirements.txt @@ -1,6 +1,6 @@ pathling==6.2.1 -pydantic==1.10.14 +pydantic==1.10.19 pyspark==3.3.4 -pandas==2.2.0 +pandas==2.2.3 python-dateutil==2.9.0.post0 xlsxwriter==3.2.0