Merge pull request #288 from umccr/feat/simple-locations

feat: path-based locations

htsget-config/examples/config-files/basic.toml

@@ -1,18 +1,8 @@
 # An example of running htsget-rs.
-# Run with `cargo run --all-features -- --config htsget-config/examples/config-files/basic.toml`
+# Run with `cargo run -p htsget-axum --all-features -- --config htsget-config/examples/config-files/basic.toml`
 
 ticket_server_addr = "127.0.0.1:8080"
 data_server_addr = "127.0.0.1:8081"
 
-# Serve data locally from the `data` directory.
-[[resolvers]]
-regex = '.*'
-substitution_string = '$0'
-storage.backend = 'Local'
-
-# Serve data from S3 if the id is prefixed with `example_bucket`.
-[[resolvers]]
-regex = '^(example_bucket)/(?P<key>.*)$'
-substitution_string = '$key'
-storage.backend = 'S3'
-# Uses the first capture group in the regex as the bucket.
+# Serve data locally from the `data` directory or from an S3 bucket called `bucket` depending on the prefix.
+locations = [ "file://data/file_prefix", "s3://bucket/s3_prefix" ]

htsget-config/examples/config-files/c4gh.toml

@@ -1,23 +1,19 @@
 # An example of running htsget-rs with Crypt4GH enabled.
-# Run with `cargo run -p htsget-axum --features experimental -- --config htsget-config/examples/config-files/c4gh.toml`
+# Run with `cargo run -p htsget-axum --features experimental,s3-storage -- --config htsget-config/examples/config-files/c4gh.toml`
 
-ticket_server_addr = "127.0.0.1:8080"
-data_server_addr = "127.0.0.1:8081"
+ticket_server.addr = "127.0.0.1:8080"
+data_server.addr = "127.0.0.1:8081"
 
-[[resolvers]]
+[[locations]]
 regex = ".*"
 substitution_string = "$0"
+backend.kind = "File"
 
-[resolvers.storage]
-backend = 'Local'
+backend.keys.kind = "File"
+backend.keys.private = "data/c4gh/keys/bob.sec" # pragma: allowlist secret
+backend.keys.public = "data/c4gh/keys/alice.pub"
 
-[resolvers.storage.keys]
-location = "Local"
-private_key = "data/c4gh/keys/bob.sec" # pragma: allowlist secret
-recipient_public_key = "data/c4gh/keys/alice.pub"
-
-# Or, use AWS secrets manager to store keys.
-#[resolvers.storage.keys]
-#location = "SecretsManager"
-#private_key = "htsget/test_c4gh_private_key" # pragma: allowlist secret
-#recipient_public_key = "htsget/test_c4gh_public_key"
+## Or, use AWS secrets manager to store keys.
+#backend.keys.kind = "SecretsManager"
+#backend.keys.private = "htsget/test_c4gh_private_key" # pragma: allowlist secret
+#backend.keys.public = "htsget/test_c4gh_public_key"

htsget-config/examples/config-files/default.toml

@@ -1,40 +1,37 @@
 # Config generated by running `cargo run -p htsget-axum -- -p`
 
 formatting_style = "Full"
-ticket_server_addr = "127.0.0.1:8080"
-ticket_server_cors_allow_credentials = false
-ticket_server_cors_allow_origins = ["http://localhost:8080"]
-ticket_server_cors_allow_headers = "All"
-ticket_server_cors_allow_methods = "All"
-ticket_server_cors_max_age = 86400
-ticket_server_cors_expose_headers = []
-data_server_enabled = true
-data_server_addr = "127.0.0.1:8081"
-data_server_local_path = "./"
-data_server_serve_at = ""
-data_server_cors_allow_credentials = false
-data_server_cors_allow_origins = ["http://localhost:8080"]
-data_server_cors_allow_headers = "All"
-data_server_cors_allow_methods = "All"
-data_server_cors_max_age = 86400
-data_server_cors_expose_headers = []
-
-[[resolvers]]
-regex = ".*"
-substitution_string = "$0"
-storage = "Local"
-
-[resolvers.allow_guard]
-allow_reference_names = "All"
-allow_fields = "All"
-allow_tags = "All"
-allow_formats = [
-    "BAM",
-    "CRAM",
-    "VCF",
-    "BCF",
-]
-allow_classes = [
-    "body",
-    "header",
-]
+
+[ticket_server]
+addr = "127.0.0.1:8080"
+
+[ticket_server.cors]
+allow_credentials = false
+allow_origins = "Mirror"
+allow_headers = "Mirror"
+allow_methods = "Mirror"
+max_age = 2592000
+expose_headers = "All"
+
+[data_server]
+addr = "127.0.0.1:8081"
+local_path = "./"
+
+[data_server.cors]
+allow_credentials = false
+allow_origins = "Mirror"
+allow_headers = "Mirror"
+allow_methods = "Mirror"
+max_age = 2592000
+expose_headers = "All"
+
+[service_info]
+
+[[locations]]
+prefix = ""
+
+[locations.backend]
+kind = "File"
+scheme = "HTTP"
+authority = "127.0.0.1:8081"
+local_path = "./"

htsget-config/examples/config-files/s3_storage.toml

@@ -1,19 +1,18 @@
 # An example for a server which uses s3 storage with data located in "bucket".
 # Run with `cargo run -p htsget-axum --features s3-storage -- --config htsget-config/examples/config-files/s3_storage.toml`
 
-ticket_server_cors_allow_headers = "All"
-ticket_server_cors_allow_methods = "All"
-ticket_server_cors_allow_credentials = true
-ticket_server_cors_max_age = 300
+ticket_server.cors.allow_headers = "All"
+ticket_server.cors.allow_methods = "All"
+ticket_server.cors.allow_credentials = false
+ticket_server.cors.max_age = 300
 
-data_server_enabled = false
+data_server = "None"
 
-[[resolvers]]
-regex = '^(bucket)/(?P<key>.*)$'
-substitution_string = '$key'
-storage.backend = 'S3'
+locations = "s3://bucket"
 
-# Or, set the bucket manually
-#[resolvers.storage]
-#backend = 'S3'
-#bucket = 'bucket'
+## Or, set using regex locations
+#[[locations]]
+#regex = "^(bucket)/(?P<key>.*)$"
+#substitution_string = "$key"
+#backend.kind = "S3"
+#backend.bucket = "bucket"

htsget-config/examples/config-files/tls_data_server.toml

@@ -1,16 +1,17 @@
 # An example config file for a TLS data server that uses a local storage backend.
 # Run with `cargo run -p htsget-axum -- --config htsget-config/examples/config-files/tls_data_server.toml`
 
-ticket_server_addr = "0.0.0.0:8080"
-data_server_addr = "0.0.0.0:8081"
-data_server_cors_allow_origins = "All"
-data_server_tls.cert = "cert.pem"
-data_server_tls.key = "key.pem"
+ticket_server.addr = "0.0.0.0:8080"
+data_server.addr = "0.0.0.0:8081"
+data_server.cors.allow_origins = "All"
+data_server.tls.cert = "cert.pem"
+data_server.tls.key = "key.pem"
 
-[[resolvers]]
-regex = ".*"
-substitution_string = "$0"
+locations = "file://data"
 
-[resolvers.storage]
-backend = 'Local'
-use_data_server_config = true
+## Or, set using regex locations
+#[[locations]]
+#regex = ".*"
+#substitution_string = "$0"
+#backend.kind = "File"
+#backend.local_path = "data"

htsget-config/examples/config-files/tls_ticket_server.toml

@@ -1,16 +1,17 @@
 # An example config file for a TLS ticket server that uses S3 as a storage backend.
 # Run with `cargo run -p htsget-axum --features s3-storage -- --config htsget-config/examples/config-files/tls_ticket_server.toml`
 
-ticket_server_addr = "0.0.0.0:8080"
-ticket_server_cors_allow_origins = "All"
-ticket_server_tls.cert = "cert.pem"
-ticket_server_tls.key = "key.pem"
-data_server_addr = "0.0.0.0:8081"
+ticket_server.addr = "0.0.0.0:8080"
+ticket_server.cors_allow_origins = "All"
+ticket_server.tls.cert = "cert.pem"
+ticket_server.tls.key = "key.pem"
+data_server.addr = "0.0.0.0:8081"
 
-[[resolvers]]
-regex = ".*"
-substitution_string = "$0"
+locations = "s3://bucket"
 
-[resolvers.storage]
-backend = 'S3'
-bucket = "bucket"
+## Or, set using regex locations
+#[[locations]]
+#regex = ".*"
+#substitution_string = "$0"
+#backend.kind = "S3"
+#backend.bucket = "bucket"

htsget-config/examples/config-files/url_storage.toml

@@ -3,27 +3,29 @@
 # `cargo run -p htsget-axum --features url-storage -- --config htsget-config/examples/config-files/url_storage.toml`
 # in the project directory.
 
-ticket_server_addr = "127.0.0.1:8082"
-ticket_server_cors_allow_origins = "All"
+ticket_server.addr = "127.0.0.1:8082"
+ticket_server.cors.allow_origins = "All"
 
-ticket_server_cert = "cert.pem"
-ticket_server_key = "key.pem"
+ticket_server.tls.cert = "cert.pem"
+ticket_server.tls.key = "key.pem"
 
-data_server_enabled = false
+data_server = "None"
 
-[[resolvers]]
-regex = ".*"
-substitution_string = "$0"
+locations = "https://127.0.0.1:8081"
 
-[resolvers.storage]
-backend = 'Url'
-url = "http://127.0.0.1:8081"
-response_url = "https://127.0.0.1:8081"
-forward_headers = true
-
-# Set client authentication
-#tls.key = "key.pem"
-#tls.cert = "cert.pem"
-
-# Set root certificates
-#tls.root_store = "cert.pem"
+## Or, set using regex locations
+#[[locations]]
+#regex = ".*"
+#substitution_string = "$0"
+#
+#backend.kind = "Url"
+#backend.url = "http://127.0.0.1:8081"
+#backend.response_url = "https://127.0.0.1:8081"
+#backend.forward_headers = true
+#
+## Set client authentication
+#backend.tls.key = "key.pem"
+#backend.tls.cert = "cert.pem"
+#
+## Set root certificates
+#backend.tls.root_store = "root.crt"