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Merge branch 'develop' into da_CORE-207_tsvOptimizations
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@davidangb
davidangb authored Dec 17, 2024
2 parents 5a22ef9 + b081de4 commit 323ad5d
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Showing 19 changed files with 107 additions and 910 deletions.
7 changes: 1 addition & 6 deletions src/main/scala/org/broadinstitute/dsde/firecloud/FireCloudApiService.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,6 @@ trait FireCloudApiService
with RegisterApiService
with WorkspaceApiService
with MethodConfigurationApiService
with SubmissionApiService
with StatusApiService
with MethodsApiService
with UserApiService
Expand All @@ -80,7 +79,6 @@ trait FireCloudApiService
with CromIamApiService
with HealthApiService
with StaticNotebooksApiService
with PerimeterApiService
with PassthroughApiService {

override lazy val log = LoggerFactory.getLogger(getClass)
Expand Down Expand Up @@ -179,11 +177,9 @@ trait FireCloudApiService
profileRoutes ~
cromIamApiServiceRoutes ~
methodConfigurationRoutes ~
submissionServiceRoutes ~
nihRoutes ~
shareLogServiceRoutes ~
staticNotebooksRoutes ~
perimeterServiceRoutes
staticNotebooksRoutes
}

val routeWrappers: Directive[Unit] =
Expand All @@ -195,7 +191,6 @@ trait FireCloudApiService

def route: server.Route = routeWrappers {
cromIamEngineRoutes ~
tosRoutes ~
exportEntitiesRoutes ~
cromIamEngineRoutes ~
exportEntitiesRoutes ~
Expand Down
42 changes: 1 addition & 41 deletions src/main/scala/org/broadinstitute/dsde/firecloud/service/FireCloudDirectives.scala
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@@ -1,8 +1,7 @@
package org.broadinstitute.dsde.firecloud.service

import akka.http.scaladsl.client.RequestBuilding
import akka.http.scaladsl.model.headers.{`Content-Type`, Authorization}
import akka.http.scaladsl.model.{HttpMethod, Uri}
import akka.http.scaladsl.model.Uri
import akka.http.scaladsl.server.{Directives, Route}
import org.broadinstitute.dsde.firecloud.utils.RestJsonClient
import org.parboiled.common.FileUtils
Expand All @@ -20,51 +19,12 @@ object FireCloudDirectiveUtils {
}
toUri(path).toString
}

// TODO: should this pass through any other headers, such as Cookie?
/* This list controls which headers from the original request are passed through to the
* target service. It is important that some headers are NOT passed through:
* - if the Host header is passed through, it will not match the target service's host,
* and some servers - notably App Engine - will reject the request.
* - if headers that control the http protocol such as Accept-Encoding or Connection
* are passed through, they may not reflect reality. The original request may have
* come from a browser that supports different encodings or connection protocols
* than the service-to-service request we're about to make.
* - if headers that inform the target such as User-Agent, Referer or X-Forwarded-For
* are passed through, they will be misleading, as they reflect the original request
* and not the service-to-service request we're about to make.
*/
final val allowedPassthroughHeaders = List(Authorization, `Content-Type`).map(_.lowercaseName)

}

trait FireCloudDirectives extends Directives with RequestBuilding with RestJsonClient {

def passthrough(unencodedPath: String, methods: HttpMethod*): Route =
passthrough(Uri(unencodedPath), methods: _*)

// Danger: it is a common mistake to pass in a URI that omits the query parameters included in the original request to Orch.
// To preserve the query, extract it and attach it to the passthrough URI using `.withQuery(query)`.
def passthrough(uri: Uri, methods: HttpMethod*): Route = methods map { inMethod =>
generateExternalHttpRequestForMethod(uri, inMethod)
} reduce (_ ~ _)

def encodeUri(path: String): String = FireCloudDirectiveUtils.encodeUri(path)

private def generateExternalHttpRequestForMethod(uri: Uri, inMethod: HttpMethod) =
method(inMethod) { requestContext =>
val outgoingRequest = requestContext.request
.withUri(uri)
.withHeaders(
requestContext.request.headers.filter(hdr =>
FireCloudDirectiveUtils.allowedPassthroughHeaders.contains(hdr.lowercaseName())
)
)
requestContext.complete(
unAuthedRequest(outgoingRequest)
) // NOTE: This is actually AUTHED because we pass through the Authorization header
}

def withResourceFileContents(path: String)(innerRoute: String => Route): Route =
innerRoute(FileUtils.readAllTextFromResource(path))

Expand Down
14 changes: 1 addition & 13 deletions src/main/scala/org/broadinstitute/dsde/firecloud/webservice/CromIamApiService.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,6 @@ trait CromIamApiService
with StreamingPassthrough {

lazy val workflowRoot: String = FireCloudConfig.CromIAM.authUrl + "/workflows/v1"
lazy val womtoolRoute: String = FireCloudConfig.CromIAM.authUrl + "/womtool/v1"
lazy val engineRoot: String = FireCloudConfig.CromIAM.baseUrl + "/engine/v1"
lazy val rawlsWorkflowRoot: String = FireCloudConfig.Rawls.authUrl + "/workflows"

Expand Down Expand Up @@ -46,18 +45,7 @@ trait CromIamApiService
streamingPassthrough(Uri.Path(localBase) -> Uri(workflowRoot))
}

val womToolRoute: Route =
pathPrefix("womtool" / Segment) { _ =>
path("describe") {
pathEnd {
post {
passthrough(s"$womtoolRoute/describe", HttpMethods.POST)
}
}
}
}

val cromIamApiServiceRoutes = rawlsServiceRoute ~ cromIamServiceRoutes ~ womToolRoute
val cromIamApiServiceRoutes = rawlsServiceRoute ~ cromIamServiceRoutes

val cromIamEngineRoutes: Route =
pathPrefix("engine" / Segment) { _ =>
Expand Down
123 changes: 45 additions & 78 deletions ...in/scala/org/broadinstitute/dsde/firecloud/webservice/MethodConfigurationApiService.scala
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Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,7 @@ import org.broadinstitute.dsde.firecloud.FireCloudConfig
import org.broadinstitute.dsde.firecloud.model.ModelJsonProtocol._
import org.broadinstitute.dsde.firecloud.model._
import org.broadinstitute.dsde.firecloud.service.FireCloudDirectives
import org.broadinstitute.dsde.firecloud.utils.{RestJsonClient, StandardUserInfoDirectives}
import org.broadinstitute.dsde.firecloud.utils.{RestJsonClient, StandardUserInfoDirectives, StreamingPassthrough}
import org.broadinstitute.dsde.rawls.model.WorkspaceName
import org.slf4j.LoggerFactory

Expand Down Expand Up @@ -93,100 +93,67 @@ trait MethodConfigurationApiService
extends FireCloudDirectives
with SprayJsonSupport
with StandardUserInfoDirectives
with StreamingPassthrough
with RestJsonClient {

final private val ApiPrefix = "workspaces"
lazy val log = LoggerFactory.getLogger(getClass)

val methodConfigurationRoutes: Route = requireUserInfo() { userInfo =>
path("template") {
passthrough(MethodConfigurationApiService.remoteTemplateURL, HttpMethods.POST)
} ~
path("inputsOutputs") {
passthrough(MethodConfigurationApiService.remoteInputsOutputsURL, HttpMethods.POST)
} ~
pathPrefix(ApiPrefix) {
pathPrefix(Segment / Segment / "method_configs") { (workspaceNamespace, workspaceName) =>
path("copyFromMethodRepo") {
post {
entity(as[CopyConfigurationIngest]) { ingest =>
val copyMethodConfig = new MethodConfigurationCopy(
methodRepoName = ingest.configurationName,
methodRepoNamespace = ingest.configurationNamespace,
methodRepoSnapshotId = ingest.configurationSnapshotId,
destination = Option(
MethodConfigurationId(
name = ingest.destinationName,
namespace = ingest.destinationNamespace,
workspaceName = Option(WorkspaceName(namespace = workspaceNamespace, name = workspaceName))
)
pathPrefix(ApiPrefix) {
pathPrefix(Segment / Segment / "method_configs") { (workspaceNamespace, workspaceName) =>
path("copyFromMethodRepo") {
post {
entity(as[CopyConfigurationIngest]) { ingest =>
val copyMethodConfig = new MethodConfigurationCopy(
methodRepoName = ingest.configurationName,
methodRepoNamespace = ingest.configurationNamespace,
methodRepoSnapshotId = ingest.configurationSnapshotId,
destination = Option(
MethodConfigurationId(
name = ingest.destinationName,
namespace = ingest.destinationNamespace,
workspaceName = Option(WorkspaceName(namespace = workspaceNamespace, name = workspaceName))
)
)
val extReq = Post(MethodConfigurationApiService.remoteCopyFromMethodRepoConfigUrl, copyMethodConfig)
)
val extReq = Post(MethodConfigurationApiService.remoteCopyFromMethodRepoConfigUrl, copyMethodConfig)

complete(userAuthedRequest(extReq)(userInfo))
}
complete(userAuthedRequest(extReq)(userInfo))
}
} ~ path("copyToMethodRepo") {
post {
entity(as[PublishConfigurationIngest]) { ingest =>
val copyMethodConfig = new MethodConfigurationPublish(
methodRepoName = ingest.configurationName,
methodRepoNamespace = ingest.configurationNamespace,
source = Option(
MethodConfigurationId(name = ingest.sourceName,
namespace = ingest.sourceNamespace,
workspaceName =
Option(WorkspaceName(namespace = workspaceNamespace, name = workspaceName))
)
}
} ~ path("copyToMethodRepo") {
post {
entity(as[PublishConfigurationIngest]) { ingest =>
val copyMethodConfig = new MethodConfigurationPublish(
methodRepoName = ingest.configurationName,
methodRepoNamespace = ingest.configurationNamespace,
source = Option(
MethodConfigurationId(name = ingest.sourceName,
namespace = ingest.sourceNamespace,
workspaceName =
Option(WorkspaceName(namespace = workspaceNamespace, name = workspaceName))
)
)
val extReq = Post(MethodConfigurationApiService.remoteCopyToMethodRepoConfigUrl, copyMethodConfig)
)
val extReq = Post(MethodConfigurationApiService.remoteCopyToMethodRepoConfigUrl, copyMethodConfig)

complete(userAuthedRequest(extReq)(userInfo))
}
complete(userAuthedRequest(extReq)(userInfo))
}
} ~ pathPrefix(Segment / Segment) { (configNamespace, configName) =>
pathEnd {
passthrough(
encodeUri(
MethodConfigurationApiService.remoteMethodConfigUrl(workspaceNamespace,
workspaceName,
configNamespace,
configName
)
),
HttpMethods.GET,
HttpMethods.PUT,
HttpMethods.POST,
HttpMethods.DELETE
)
} ~
path("rename") {
passthrough(encodeUri(
MethodConfigurationApiService.remoteMethodConfigRenameUrl(workspaceNamespace,
workspaceName,
configNamespace,
configName
)
),
HttpMethods.POST
)
} ~
path("validate") {
passthrough(encodeUri(
MethodConfigurationApiService.remoteMethodConfigValidateUrl(workspaceNamespace,
workspaceName,
configNamespace,
configName
)
),
HttpMethods.GET
)
}
}
} ~ pathPrefix(Segment / Segment) { (configNamespace, configName) =>
streamingPassthrough(
encodeUri(
MethodConfigurationApiService.remoteMethodConfigUrl(workspaceNamespace,
workspaceName,
configNamespace,
configName
)
)
)
}
}
}
}

}
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