Skip to content

CORE-382: delete Data Library #1623

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 18 commits into from
Apr 15, 2025
Merged

CORE-382: delete Data Library #1623

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
18 commits
Select commit Hold shift + click to select a range
f53467b
first pass, deleting code
davidangb Apr 9, 2025
3f23a87
delete-workspace is now a passthrough
davidangb Apr 9, 2025
cd20bcc
remove elastic client and lucene queryparser
davidangb Apr 9, 2025
330f937
remove netty-handler
davidangb Apr 9, 2025
12ca5d5
remove log4j
davidangb Apr 9, 2025
d297de2
remove json-schema
davidangb Apr 9, 2025
9501769
remove json-lenses
davidangb Apr 9, 2025
4e22f5c
delete ElasticSearch model
davidangb Apr 9, 2025
bd7c331
delete some curator/admin library features
davidangb Apr 9, 2025
6a5c025
remove more models and json codecs
davidangb Apr 9, 2025
8f49dd8
delete more config and unused
davidangb Apr 9, 2025
ecddb18
clone-workspace is now passthrough
davidangb Apr 9, 2025
c5c4afa
remove catalog APIs
davidangb Apr 10, 2025
96be0dc
updateAttributes is a passthrough
davidangb Apr 10, 2025
b79c145
fix updateAttributes unit tests
davidangb Apr 10, 2025
66fb4e5
remove catalog url
davidangb Apr 10, 2025
ef58dda
remove commented code; rename method
davidangb Apr 10, 2025
e9efd3a
scalafmt
davidangb Apr 10, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 0 additions & 15 deletions local-dev/templates/firecloud-orchestration.conf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -132,21 +132,6 @@ shibboleth {
publicKeyUrl = "https://broad-shibboleth-prod.appspot.com/dev/public-key.pem"
}

elasticsearch {
urls = "elasticsearch5a1.dsde-dev.broadinstitute.org:9300,elasticsearch5a2.dsde-dev.broadinstitute.org:9300,elasticsearch5a3.dsde-dev.broadinstitute.org:9300"
clusterName = "elasticsearch5a"
index = "library"
ontologyIndex = "ontology"
discoverGroupNames = ["all_broad_users","demo_users","GP_DataDelivery_TaskTeam"]
shareLogIndex = "sharelog"
maxAutocomplete = 1000
}

duos {
baseOntologyUrl = "https://consent-ontology.dsde-dev.broadinstitute.org"
dulvn = 4
}

Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Once this PR is deployed to prod, I'll follow up with another PR to remove these config stanzas from terra-helmfile.

notification {
fullyQualifiedNotificationTopic = "projects/broad-dsde-dev/topics/workbench-notifications-local"
}
Expand Down
25 changes: 0 additions & 25 deletions project/Dependencies.scala
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,6 @@ object Dependencies {
val akkaHttpV = "10.6.3"
val jacksonV = "2.18.3"
val jacksonHotfixV = "2.18.3" // for when only some of the Jackson libs have hotfix releases
val nettyV = "4.1.119.Final"
Copy link
Contributor Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

all of the libraries removed in this PR are no longer needed, given all the code deletion.

val workbenchLibsHash = "70c7d82" // see https://github.com/broadinstitute/workbench-libs readme for hash values

val excludeAkkaActor = ExclusionRule(organization = "com.typesafe.akka", name = "akka-actor_2.13")
Expand Down Expand Up @@ -33,15 +32,6 @@ object Dependencies {
)

val rootDependencies: Seq[ModuleID] = Seq(
// proactively pull in latest versions of these libraries, instead of relying on the versions
// specified as transitive dependencies, due to OWASP DependencyCheck warnings for earlier versions.
// TODO: can these move to sbt's dependencyOverrides?
"io.netty" % "netty-handler" % nettyV, // netty is needed by the Elasticsearch client at runtime
"org.apache.lucene" % "lucene-queryparser" % "6.6.6", // pin to this version; it's the latest compatible with our elasticsearch client
// END transitive dependency overrides

// elasticsearch requires log4j, but we redirect log4j to logback
"org.apache.logging.log4j" % "log4j-to-slf4j" % "2.24.3",
"ch.qos.logback" % "logback-classic" % "1.5.18",
"io.sentry" % "sentry-logback" % "8.6.0",
"com.typesafe.scala-logging" %% "scala-logging" % "3.9.5",
Expand Down Expand Up @@ -77,27 +67,12 @@ object Dependencies {
"com.typesafe.akka" %% "akka-testkit" % akkaV % "test",
"com.typesafe.akka" %% "akka-http-testkit" % akkaHttpV % "test",

"net.virtual-void" %% "json-lenses" % "0.6.2" % "test",

"org.elasticsearch.client" % "transport" % "5.6.16" // pin to this version; it's the latest compatible with our elasticsearch server
exclude("io.netty", "netty-codec")
exclude("io.netty", "netty-transport")
exclude("io.netty", "netty-resolver")
exclude("io.netty", "netty-buffer")
exclude("io.netty", "netty-common")
exclude("io.netty", "netty-codec-http")
exclude("io.netty", "netty-handler")
exclude("com.fasterxml.jackson.dataformat", "jackson-dataformat-cbor")
exclude("org.apache.logging.log4j", "log4j-api")
exclude("org.apache.logging.log4j", "log4j-core"),

"com.github.jwt-scala" %% "jwt-core" % "10.0.4",
// javax.mail is used only by MethodRepository.validatePublicOrEmail(). Consider
// refactoring that method to remove this entire dependency.
"com.sun.mail" % "javax.mail" % "1.6.2"
exclude("javax.activation", "activation"),
"com.univocity" % "univocity-parsers" % "2.9.1",
"com.github.erosb" % "everit-json-schema" % "1.14.5",
"com.github.pathikrit" %% "better-files" % "3.9.2",

"org.scalatest" %% "scalatest" % "3.2.19" % "test",
Expand Down
Loading
Loading