Merge pull request #12 from mrtamm/dev-builtin-htsget-crypt4gh

Built-in Htsget and Crypt4gh for the HTSGET storage

Dockerfile

@@ -11,8 +11,7 @@ COPY . .
 RUN --mount=type=cache,target=/root/.cache/go-build make build
 
 # final stage
-FROM debian
-RUN apt-get update && apt-get install -y --no-install-recommends curl python3-pip && pip3 install htsget crypt4gh --break-system-packages && rm -rf ~/.cache
+FROM alpine
 WORKDIR /opt/funnel
 VOLUME /opt/funnel/funnel-work-dir
 EXPOSE 8000 9090

Dockerfile.dind

@@ -12,7 +12,6 @@ RUN --mount=type=cache,target=/root/.cache/go-build make build
 
 # final stage
 FROM docker:dind
-RUN apk add --update --no-cache curl python3 py3-pip && pip3 install htsget crypt4gh --break-system-packages
 WORKDIR /opt/funnel
 VOLUME /opt/funnel/funnel-work-dir
 EXPOSE 8000 9090

Dockerfile.dind-rootless

@@ -11,7 +11,7 @@ COPY . .
 RUN --mount=type=cache,target=/root/.cache/go-build make build
 
 # final stage
-FROM docker:stable-dind-rootless
+FROM docker:dind-rootless
 WORKDIR /opt/funnel
 VOLUME /opt/funnel/funnel-work-dir
 EXPOSE 8000 9090

config/config.go

@@ -390,13 +390,14 @@ func (h FTPStorage) Valid() bool {
 	return !h.Disabled
 }
 
-// HTSGETStorage configures the http storage backend.
+// HTSGETStorage configures the storage backend for the HTSGET protocol.
 type HTSGETStorage struct {
+	// Controls whether HTSGET storage is disabled (defaults to false)
 	Disabled bool
 	// Actual protocol for fetching the resource (defaults to 'https')
 	Protocol string
-	// Whether Funnel should generate and send its crypt4gh public key (default: false)
-	SendPublicKey bool
+	// Timeout for each HTSGET request (defaults to 30 seconds)
+	Timeout Duration
 }
 
 // Valid validates the HTSGETStorage configuration.

config/default-config.yaml

@@ -396,4 +396,4 @@ FTPStorage:
 HTSGETStorage:
   Disabled: false
   Protocol: https
-  SendPublicKey: false
+  Timeout: 30s

go.mod

@@ -41,6 +41,7 @@ require (
 	github.com/spf13/cobra v1.8.0
 	github.com/spf13/pflag v1.0.5
 	github.com/stretchr/testify v1.9.0
+	golang.org/x/crypto v0.19.0
 	golang.org/x/net v0.21.0
 	golang.org/x/oauth2 v0.17.0
 	golang.org/x/term v0.17.0
@@ -156,7 +157,6 @@ require (
 	go.opentelemetry.io/otel/metric v1.24.0 // indirect
 	go.opentelemetry.io/otel/sdk v1.24.0 // indirect
 	go.opentelemetry.io/otel/trace v1.24.0 // indirect
-	golang.org/x/crypto v0.19.0 // indirect
 	golang.org/x/sync v0.6.0 // indirect
 	golang.org/x/sys v0.17.0 // indirect
 	golang.org/x/text v0.14.0 // indirect