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Built-in Htsget and Crypt4gh for the HTSGET storage #12

Merged
merged 11 commits into from
Sep 5, 2024
Merged

Built-in Htsget and Crypt4gh for the HTSGET storage #12

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e822a48
Fix: send full public-key file to htsget
mrtamm May 23, 2024
a3c83a4
HTSGET client + Crypt4gh decryption
mrtamm Aug 1, 2024
0c45c6e
Remove htsget from Docker build
mrtamm Aug 1, 2024
0005ab8
Update htsget storage documentation
mrtamm Aug 1, 2024
d279b5d
Fix: Docker dind image tags
mrtamm Aug 5, 2024
c8641ea
Logging and minor fixes
mrtamm Aug 5, 2024
d740d99
Fix command completed log message
mrtamm Aug 5, 2024
5097d81
Add Crypt4gh content decryption tests
mrtamm Aug 6, 2024
6d3dc37
Add tests for the IsCrypt4ghFile() function
mrtamm Aug 6, 2024
0ed77cd
Merge branch 'master' into dev-builtin-htsget-crypt4gh
mrtamm Aug 6, 2024
b923c22
Editorial changes: comments, docs
mrtamm Aug 7, 2024
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3 changes: 1 addition & 2 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -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
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1 change: 0 additions & 1 deletion Dockerfile.dind
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Expand Up @@ -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
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2 changes: 1 addition & 1 deletion Dockerfile.dind-rootless
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Expand Up @@ -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
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7 changes: 4 additions & 3 deletions config/config.go
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Expand Up @@ -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.
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2 changes: 1 addition & 1 deletion config/default-config.yaml
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Expand Up @@ -396,4 +396,4 @@ FTPStorage:
HTSGETStorage:
Disabled: false
Protocol: https
SendPublicKey: false
Timeout: 30s
2 changes: 1 addition & 1 deletion go.mod
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Expand Up @@ -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
Expand Down Expand Up @@ -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
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