Updating all submodules to latest stable release (#254)

* Updating federation * Update opa * Update htsget * Updating federation * Update opa * Update htsget * Update candig-data-portal * Update stable_pr_template.md
CanDIG · Jul 22, 2023 · d707e04 · d707e04
1 parent 15db896
commit d707e04
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diff --git a/PULL_REQUEST_TEMPLATE/stable_pr_template.md b/PULL_REQUEST_TEMPLATE/stable_pr_template.md
@@ -17,7 +17,7 @@ Add a summary description of the main user-facing changes made in this release,
 
 ### Other changes
 
-- [] All submodule versions have been updated in etc/env/example.env
-- [] Submodules point to latest stable release on each repo
-- [] Appropriate integration tests have been made to validate the changes
-- [] Passes integration tests on a development instance
+- [ ] All submodule versions have been updated in etc/env/example.env
+- [ ] Submodules point to latest stable release on each repo
+- [ ] Appropriate integration tests have been made to validate the changes
+- [ ] Passes integration tests on a development instance
diff --git a/etc/env/example.env b/etc/env/example.env
@@ -68,7 +68,7 @@ MINIO_SELF_CERT=0
 
 
 # htsget
-HTSGET_VERSION=v2.1.0
+HTSGET_VERSION=v2.2.0
 HTSGET_PRIVATE_URL=http://htsget:3000
 HTSGET_PUBLIC_URL=${TYK_LOGIN_TARGET_URL}/${TYK_HTSGET_API_LISTEN_PATH}
 HTSGET_PORT=3333
@@ -113,7 +113,7 @@ TOIL_WORKER_PORT=5051
 
 
 # federation
-FEDERATION_VERSION=v1.0.0
+FEDERATION_VERSION=v1.0.1
 FEDERATION_IP=0.0.0.0
 FEDERATION_PORT=4232
 FEDERATION_SERVICE_URL=http://${CANDIG_DOMAIN}:${FEDERATION_PORT}
@@ -261,7 +261,7 @@ VAULT_SERVICE_URL=http://vault:8200
 
 
 # OPA
-OPA_VERSION=v1.3.2
+OPA_VERSION=v1.3.3
 OPA_PORT=8181
 OPA_LOG_LEVEL=debug
 OPA_URL=http://${CANDIG_DOMAIN}:${OPA_PORT}
@@ -270,7 +270,7 @@ OPA_SITE_ADMIN_KEY=site_admin
 
 
 # candig-data-server (previously mcode)
-CANDIG_DATA_PORTAL_VERSION=v0.1.9
+CANDIG_DATA_PORTAL_VERSION=v1.0.0
 CANDIG_DATA_PORTAL_PORT=2543
 CANDIG_DATA_PORTAL_URL=http://${CANDIG_DOMAIN}:${CANDIG_DATA_PORTAL_PORT}/data-portal
 CANDIG_DATA_PORTAL_PRIVATE_URL=http://candig-data-portal:3000

diff --git a/lib/candig-data-portal/candig-data-portal b/lib/candig-data-portal/candig-data-portal
diff --git a/lib/federation/federation b/lib/federation/federation
diff --git a/lib/htsget/htsget_app b/lib/htsget/htsget_app
diff --git a/lib/opa/opa b/lib/opa/opa
+1 −1		src/store/constant.js
+4 −4		src/views/clinicalGenomic/widgets/patientCountSingle.js
+3 −3		src/views/clinicalGenomic/widgets/patientCounts.js
+1 −1		src/views/clinicalGenomic/widgets/patientView.js
+62 −58		src/views/summary/CustomOfflineChart.js
+4 −1		src/views/summary/summary.js
+165 −0		LICENSE
+1 −1		htsget_server/beacon_openapi.yaml
+20 −2		htsget_server/drs_openapi.yaml
+8 −1		htsget_server/drs_operations.py
+4 −1		htsget_server/variants.py
+131 −33		tests/test_htsget_server.py