Merge branch 'master' into doc/deployment

.github/labeler.yml

@@ -0,0 +1,5 @@
+# we have disabled GWASUI tests in CI due to ongoing change in the app
+# '@requires-cohort-middleware':
+#   - '**/*'
+'test-portal-homepageTest':
+  - '**/*'

.github/workflows/labeler.yml

@@ -0,0 +1,12 @@
+name: "Pull Request Labeler"
+on:
+  pull_request_target:
+    types: [opened]
+
+jobs:
+  triage:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/labeler@v3
+      with:
+        repo-token: "${{ secrets.GITHUB_TOKEN }}"

Dockerfile

@@ -1,14 +1,21 @@
-FROM quay.io/cdis/golang:1.18-bullseye as build-deps
+ARG AZLINUX_BASE_VERSION=master
+
+#FROM 707767160287.dkr.ecr.us-east-1.amazonaws.com/gen3/golang-build-base:${AZLINUX_BASE_VERSION} as base
+FROM --platform=$BUILDPLATFORM quay.io/cdis/golang-build-base:${AZLINUX_BASE_VERSION} as base
+
+ARG TARGETOS
+ARG TARGETARCH
+
+ENV appname=cohort-middleware
 
 ENV CGO_ENABLED=0
-ENV GOOS=linux
-ENV GOARCH=amd64
+ENV GOOS=${TARGETOS}
+ENV GOARCH=${TARGETARCH}
 
+FROM base as builder
 WORKDIR $GOPATH/src/github.com/uc-cdis/cohort-middleware/
 
-COPY go.mod .
-COPY go.sum .
-
+COPY go.mod go.sum ./
 RUN go mod download
 
 COPY . .
@@ -20,6 +27,6 @@ RUN GITCOMMIT=$(git rev-parse HEAD) \
     -o /cohort-middleware
 
 FROM scratch
-COPY --from=build-deps /etc/ssl/certs/ca-certificates.crt /etc/ssl/certs/
-COPY --from=build-deps /cohort-middleware /cohort-middleware
+COPY --from=builder /etc/pki/ca-trust/extracted/pem/tls-ca-bundle.pem /etc/ssl/certs/ca-certificates.crt
+COPY --from=builder /cohort-middleware /cohort-middleware
 CMD ["/cohort-middleware"]

Jenkinsfile

@@ -0,0 +1,4 @@
+#!groovy
+@Library('cdis-jenkins-lib@master') _
+testPipeline {
+}

go.mod

@@ -1,73 +1,59 @@
 module github.com/uc-cdis/cohort-middleware
 
-go 1.18
+go 1.20
 
 require (
-	github.com/gin-gonic/gin v1.7.4
+	github.com/gin-gonic/gin v1.9.1
+	github.com/montanaflynn/stats v0.6.6
 	github.com/spf13/viper v1.9.0
-	gorm.io/driver/postgres v1.2.0
-	gorm.io/driver/sqlserver v1.1.2
-	gorm.io/gorm v1.22.0
+	gorm.io/driver/postgres v1.4.6
+	gorm.io/driver/sqlserver v1.4.2
+	gorm.io/gorm v1.25.3
 )
 
 require (
-	github.com/DataDog/datadog-go v4.8.2+incompatible // indirect
-	github.com/DataDog/sketches-go v1.2.1 // indirect
-	github.com/Microsoft/go-winio v0.5.1 // indirect
-	github.com/google/uuid v1.3.0 // indirect
-	github.com/kr/pretty v0.3.0 // indirect
-	github.com/kr/text v0.2.0 // indirect
-	github.com/montanaflynn/stats v0.6.6 // indirect
-	github.com/philhofer/fwd v1.1.1 // indirect
-	github.com/rogpeppe/go-internal v1.8.0 // indirect
-	github.com/tinylib/msgp v1.1.6 // indirect
-	golang.org/x/mod v0.4.2 // indirect
-	golang.org/x/time v0.0.0-20210723032227-1f47c861a9ac // indirect
-	golang.org/x/tools v0.1.5 // indirect
-	golang.org/x/xerrors v0.0.0-20200804184101-5ec99f83aff1 // indirect
-)
-
-require (
-	github.com/denisenkom/go-mssqldb v0.11.0 // indirect
+	github.com/bytedance/sonic v1.9.1 // indirect
+	github.com/chenzhuoyu/base64x v0.0.0-20221115062448-fe3a3abad311 // indirect
 	github.com/fsnotify/fsnotify v1.5.1 // indirect
+	github.com/gabriel-vasile/mimetype v1.4.2 // indirect
 	github.com/gin-contrib/sse v0.1.0 // indirect
-	github.com/go-playground/locales v0.14.0 // indirect
-	github.com/go-playground/universal-translator v0.18.0 // indirect
-	github.com/go-playground/validator/v10 v10.9.0 // indirect
-	github.com/golang-sql/civil v0.0.0-20190719163853-cb61b32ac6fe // indirect
-	github.com/golang/protobuf v1.5.2 // indirect
+	github.com/go-playground/locales v0.14.1 // indirect
+	github.com/go-playground/universal-translator v0.18.1 // indirect
+	github.com/go-playground/validator/v10 v10.14.0 // indirect
+	github.com/goccy/go-json v0.10.2 // indirect
+	github.com/golang-sql/civil v0.0.0-20220223132316-b832511892a9 // indirect
+	github.com/golang-sql/sqlexp v0.1.0 // indirect
 	github.com/hashicorp/hcl v1.0.0 // indirect
-	github.com/jackc/chunkreader/v2 v2.0.1 // indirect
-	github.com/jackc/pgconn v1.10.0 // indirect
-	github.com/jackc/pgio v1.0.0 // indirect
 	github.com/jackc/pgpassfile v1.0.0 // indirect
-	github.com/jackc/pgproto3/v2 v2.1.1 // indirect
-	github.com/jackc/pgservicefile v0.0.0-20200714003250-2b9c44734f2b // indirect
-	github.com/jackc/pgtype v1.8.1 // indirect
-	github.com/jackc/pgx/v4 v4.13.0 // indirect
+	github.com/jackc/pgservicefile v0.0.0-20221227161230-091c0ba34f0a // indirect
+	github.com/jackc/pgx/v5 v5.2.0 // indirect
 	github.com/jinzhu/inflection v1.0.0 // indirect
-	github.com/jinzhu/now v1.1.2 // indirect
+	github.com/jinzhu/now v1.1.5 // indirect
 	github.com/json-iterator/go v1.1.12 // indirect
-	github.com/leodido/go-urn v1.2.1 // indirect
+	github.com/klauspost/cpuid/v2 v2.2.4 // indirect
+	github.com/leodido/go-urn v1.2.4 // indirect
 	github.com/magiconair/properties v1.8.5 // indirect
-	github.com/mattn/go-isatty v0.0.14 // indirect
+	github.com/mattn/go-isatty v0.0.19 // indirect
+	github.com/microsoft/go-mssqldb v0.19.0 // indirect
 	github.com/mitchellh/mapstructure v1.4.2 // indirect
 	github.com/modern-go/concurrent v0.0.0-20180306012644-bacd9c7ef1dd // indirect
 	github.com/modern-go/reflect2 v1.0.2 // indirect
-	github.com/niemeyer/pretty v0.0.0-20200227124842-a10e7caefd8e // indirect
 	github.com/pelletier/go-toml v1.9.4 // indirect
+	github.com/pelletier/go-toml/v2 v2.0.8 // indirect
 	github.com/spf13/afero v1.6.0 // indirect
 	github.com/spf13/cast v1.4.1 // indirect
 	github.com/spf13/jwalterweatherman v1.1.0 // indirect
 	github.com/spf13/pflag v1.0.5 // indirect
 	github.com/subosito/gotenv v1.2.0 // indirect
-	github.com/ugorji/go/codec v1.2.6 // indirect
-	golang.org/x/crypto v0.0.0-20210921155107-089bfa567519 // indirect
-	golang.org/x/sys v0.0.0-20211025201205-69cdffdb9359 // indirect
-	golang.org/x/text v0.3.7 // indirect
-	google.golang.org/protobuf v1.27.1 // indirect
-	gopkg.in/DataDog/dd-trace-go.v1 v1.33.0
-	gopkg.in/check.v1 v1.0.0-20201130134442-10cb98267c6c // indirect
+	github.com/twitchyliquid64/golang-asm v0.15.1 // indirect
+	github.com/ugorji/go/codec v1.2.11 // indirect
+	golang.org/x/arch v0.3.0 // indirect
+	golang.org/x/crypto v0.9.0 // indirect
+	golang.org/x/net v0.10.0 // indirect
+	golang.org/x/sys v0.8.0 // indirect
+	golang.org/x/text v0.9.0 // indirect
+	google.golang.org/protobuf v1.30.0 // indirect
 	gopkg.in/ini.v1 v1.63.2 // indirect
 	gopkg.in/yaml.v2 v2.4.0 // indirect
+	gopkg.in/yaml.v3 v3.0.1 // indirect
 )