Merge branch 'master' into 789-capture-wave-metrics-by-container-arch…

…itecture

.github/workflows/typespec.yml

@@ -7,10 +7,12 @@ on:
       - '**'
     paths :
       - 'typespec/**'
+      - VERSION
   pull_request:
     types: [opened, reopened, synchronize]
     paths:
       - 'typespec/**'
+      - VERSION
 
 permissions:
   contents: read
@@ -30,11 +32,26 @@ jobs:
           node-version : '20.9.0'
 
       - name : Install tsp
-        run : npm install -g @typespec/compiler
+        run : npm install -g @typespec/compiler@0.64.0
 
       - name : Validate tsp files
         run : |
           cd typespec
           tsp install
           tsp compile .
 
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{secrets.TOWER_CI_AWS_ACCESS}}
+          aws-secret-access-key: ${{secrets.TOWER_CI_AWS_SECRET}}
+          aws-region: eu-west-1
+
+      - name : Login to Amazon ECR
+        id : login-ecr
+        uses : aws-actions/amazon-ecr-login@v1
+
+      - name: Release OpenAPI docs
+        if: "contains(github.event.head_commit.message, '[release]')"
+        run: |
+          bash typespec/tag-and-push-openapi.sh

VERSION

@@ -1 +1 @@
-1.16.8
+1.17.0

build.gradle

@@ -34,10 +34,10 @@ dependencies {
     compileOnly 'io.micronaut:micronaut-inject-groovy'
     compileOnly 'io.micronaut:micronaut-http-validation'
     implementation 'jakarta.persistence:jakarta.persistence-api:3.0.0'
-    api 'io.seqera:lib-mail:1.2.1'
-    api 'io.seqera:lib-pool:1.0.0'
-    api 'io.seqera:wave-api:0.14.0'
-    api 'io.seqera:wave-utils:0.15.0'
+    implementation 'io.seqera:lib-mail:1.2.1'
+    implementation 'io.seqera:lib-pool:1.0.0'
+    implementation 'io.seqera:wave-api:0.14.0'
+    implementation 'io.seqera:wave-utils:0.15.0'
     implementation 'io.seqera:lib-crypto:1.0.0'
     implementation 'io.micronaut:micronaut-http-client'
     implementation 'io.micronaut:micronaut-jackson-databind'

buildSrc/src/main/groovy/io.seqera.wave.groovy-common-conventions.gradle

@@ -13,18 +13,12 @@ repositories {
 }
 
 java {
+    // these settings apply to all jvm tooling, including groovy
     toolchain {
         languageVersion = JavaLanguageVersion.of(21)
     }
-}
-
-compileJava {
-    options.release.set(17)
-}
-
-tasks.withType(GroovyCompile).configureEach {
-    sourceCompatibility = '17'
-    targetCompatibility = '17'
+    sourceCompatibility = 17
+    targetCompatibility = 17
 }
 
 group = 'io.seqera'

buildSrc/src/main/groovy/io.seqera.wave.java-library-conventions.gradle

@@ -15,18 +15,12 @@ repositories {
 }
 
 java {
+    // these settings apply to all jvm tooling, including groovy
     toolchain {
         languageVersion = JavaLanguageVersion.of(21)
     }
-}
-
-compileJava {
-    options.release.set(17)
-}
-
-tasks.withType(GroovyCompile).configureEach {
-    sourceCompatibility = '17'
-    targetCompatibility = '17'
+    sourceCompatibility = 17
+    targetCompatibility = 17
 }
 
 test {

changelog.txt

@@ -1,4 +1,12 @@
 # Wave changelog
+1.17.0 - 30 Jan 2025
+- Ignore URI dependencies in Conda envs when generating image hash (#786) [c097c8a2]
+- Render html from openapi spec generated by typespec (#707) [d3dfee9a]
+- Disable proxy cache by default [c91fc31f]
+- Update gradle deps [8a2e4209]
+- Bump buildkit to version 0.18.2 (#787) [facbf99c]
+- Bump java settings [1f6b94da]
+
 1.16.8 - 20 Jab 2025
 - Add TraceContextFilter logging context propagation [396c10c2]
 - Improve Proxy cache configuration [163e605f]

configuration.md → docs/configuration.mdx

@@ -1,10 +1,10 @@
 # Wave Application Configuration
 
-Set Wave configuration values using environment variables or in [`config.yml`](./config.yml) configuration file
+Set Wave configuration values using environment variables or in [`config.yml`](https://github.com/seqeralabs/wave/blob/master/config.yml) configuration file
 
 ### config.yml configuration
 
-Declare YAML configuration values in [`config.yml`](./config.yml)
+Declare YAML configuration values in [`config.yml`](https://github.com/seqeralabs/wave/blob/master/config.yml)
 ```
 wave:
     mail:
@@ -39,7 +39,7 @@ The generic format for the attributes is `wave.registries.<registry_name>.userna
 You need to specify all the repositories you will use in the respective wave installation.
 Below are the standard format for known registries, but you can change registry name `(azurecr.io)` to specific one like `seqeralabs.azurecr.io `.
 
-**Note**: Container registry credentials can be defined in [`config.yml`](./config.yml) too. These configurations are important for the wave authentication to the repositories used to push or pull artifacts.
+**Note**: Container registry credentials can be defined in [`config.yml`](https://github.com/seqeralabs/wave/blob/master/config.yml) too. These configurations are important for the wave authentication to the repositories used to push or pull artifacts.
 
 - **`wave.registries.default`**: the default Docker registry for Wave. The default is `docker.io`, and it represents the Docker Hub. *Optional*.
 

docs/metrics.mdx

@@ -1,6 +1,4 @@
----
-title: Usage metrics
----
+# Usage metrics
 
 Wave uses Redis to store its usage metrics for a specific date and/or a specific organization.
 

src/main/groovy/io/seqera/util/trace/TraceElapsedTimeInterceptor.groovy

@@ -55,7 +55,7 @@ class TraceElapsedTimeInterceptor implements MethodInterceptor<Object,Object> {
         finally {
             final delta = System.currentTimeMillis() - begin
             if( delta>=threshold ) {
-                log.warn(msg(delta,context,result))
+                log.debug(msg(delta,context,result))
             }
         }
     }

src/main/groovy/io/seqera/wave/configuration/ProxyCacheConfig.groovy

@@ -41,7 +41,7 @@ class ProxyCacheConfig {
     @Value('${wave.proxy-cache.max-size:10000}')
     private int maxSize
 
-    @Value('${wave.proxy-cache.enabled:true}')
+    @Value('${wave.proxy-cache.enabled:false}')
     private boolean enabled
 
     Duration getDuration() {

src/main/groovy/io/seqera/wave/controller/ServiceInfoController.groovy

@@ -59,4 +59,9 @@ class ServiceInfoController {
                 : HttpResponse.badRequest()
     }
 
+    @Get(uri = "/openapi")
+    HttpResponse getOpenAPI() {
+        HttpResponse.redirect(URI.create("/openapi/"))
+    }
+
 }

src/main/groovy/io/seqera/wave/filter/TraceSlowEndpointPublisher.java

@@ -106,7 +106,7 @@ public void onComplete() {
     protected void traceResponse(HttpResponse<?> response) {
         final long delta = System.currentTimeMillis()-begin;
         if( delta>=duration.toMillis() )
-            log.warn("Slow request detected - elapsed time: {}\n{}", Duration.ofMillis(delta), dumpRequest(request,response));
+            log.debug("Slow request detected - elapsed time: {}\n{}", Duration.ofMillis(delta), dumpRequest(request,response));
     }
 
     @CompileStatic

src/main/groovy/io/seqera/wave/util/ContainerHelper.groovy

@@ -204,6 +204,9 @@ class ContainerHelper {
                     //strip `pip:` prefix
                     if( it.startsWith('pip:') && it.length()>4 && it[4]!=':')
                         it = it.substring(4)
+                    // ignore http based dependencies
+                    if( it.startsWith('https://') || it.startsWith('http://'))
+                        continue
                     // strip channel prefix
                     final int p=it.indexOf('::')
                     if( p!=-1 )

src/test/groovy/io/seqera/wave/controller/ServiceInfoControllerTest.groovy

@@ -0,0 +1,44 @@
+/*
+ *  Wave, containers provisioning service
+ *  Copyright (c) 2024, Seqera Labs
+ *
+ *  This program is free software: you can redistribute it and/or modify
+ *  it under the terms of the GNU Affero General Public License as published by
+ *  the Free Software Foundation, either version 3 of the License, or
+ *  (at your option) any later version.
+ *
+ *  This program is distributed in the hope that it will be useful,
+ *  but WITHOUT ANY WARRANTY; without even the implied warranty of
+ *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ *  GNU Affero General Public License for more details.
+ *
+ *  You should have received a copy of the GNU Affero General Public License
+ *  along with this program.  If not, see <https://www.gnu.org/licenses/>.
+ */
+
+package io.seqera.wave.controller
+
+import spock.lang.Specification
+
+import io.micronaut.http.HttpResponse
+import io.micronaut.http.HttpStatus
+
+/**
+ *
+ * @author Munish Chouhan <[email protected]>
+ */
+class ServiceInfoControllerTest extends Specification {
+
+    def 'should redirect to /openapi/'() {
+        given:
+        def controller = new ServiceInfoController()
+
+        when:
+        HttpResponse response = controller.getOpenAPI()
+
+        then:
+        response.status == HttpStatus.MOVED_PERMANENTLY
+        response.header('Location') == '/openapi/'
+    }
+
+}

src/test/groovy/io/seqera/wave/util/ContainerHelperTest.groovy

@@ -494,6 +494,27 @@ class ContainerHelperTest extends Specification {
                   - pandas==2.2.2
                   - numpy=1.0
             '''.stripIndent(true)
+    @Shared def GIT1 = '''\
+                channels:
+                - bioconda
+                - conda-forge
+                dependencies:
+                - pip
+                - pip:
+                  - "https://github.com/seqeralabs/seqera-kit/archive/dev.zip"
+            '''.stripIndent(true)
+    @Shared def GIT2 = '''\
+                channels:
+                - bioconda
+                - conda-forge
+                dependencies:
+                - bwa
+                - pip
+                - pip:
+                  - "https://github.com/seqeralabs/seqera-kit/archive/dev.zip"
+                  - "https://github.com/seqeralabs/seqera-kit/archive/dev2.zip"
+                  - "https://github.com/seqeralabs/seqera-kit/archive/dev3.zip"
+            '''.stripIndent(true)
 
     @Unroll
     def 'should make request target with name strategy' () {
@@ -546,6 +567,16 @@ class ContainerHelperTest extends Specification {
         'DOCKER'      | 'foo.com/build'   | '123'     | PIP2 | 'tagPrefix'   | 'foo.com/build:pip_pandas-2.2.2_numpy-1.0--123'
         'DOCKER'      | 'foo.com/build'   | '123'     | PIP2 | 'imageSuffix' | 'foo.com/build/pip_pandas_numpy:123'
         'DOCKER'      | 'foo.com/build'   | '123'     | PIP2 | 'none'        | 'foo.com/build:123'
+        and:
+        'DOCKER'      | 'foo.com/build'   | '123'     | GIT1 | null          | 'foo.com/build:pip--123'
+        'DOCKER'      | 'foo.com/build'   | '123'     | GIT1 | 'tagPrefix'   | 'foo.com/build:pip--123'
+        'DOCKER'      | 'foo.com/build'   | '123'     | GIT1 | 'imageSuffix' | 'foo.com/build/pip:123'
+        'DOCKER'      | 'foo.com/build'   | '123'     | GIT1 | 'none'        | 'foo.com/build:123'
+        and:
+        'DOCKER'      | 'foo.com/build'   | '123'     | GIT2 | null          | 'foo.com/build:bwa_pip--123'
+        'DOCKER'      | 'foo.com/build'   | '123'     | GIT2 | 'tagPrefix'   | 'foo.com/build:bwa_pip--123'
+        'DOCKER'      | 'foo.com/build'   | '123'     | GIT2 | 'imageSuffix' | 'foo.com/build/bwa_pip:123'
+        'DOCKER'      | 'foo.com/build'   | '123'     | GIT2 | 'none'        | 'foo.com/build:123'
 
     }
 
@@ -571,4 +602,5 @@ class ContainerHelperTest extends Specification {
         thrown(BadRequestException)
 
     }
+
 }

typespec/Dockerfile

@@ -0,0 +1,10 @@
+FROM nginxinc/nginx-unprivileged:alpine
+
+# Copy index.html and openapi.yaml to the Nginx html directory
+COPY index.html /usr/share/nginx/html/openapi/index.html
+COPY tsp-output/@typespec/openapi3/openapi.yaml /usr/share/nginx/html/openapi/openapi.yaml
+
+# Expose port 8080
+EXPOSE 8080
+
+CMD ["nginx", "-g", "daemon off;"]

typespec/index.html

@@ -0,0 +1,28 @@
+<!DOCTYPE html>
+<html lang="en">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Wave API Documentation</title>
+    <link rel="stylesheet" href="https://unpkg.com/swagger-ui-dist/swagger-ui.css">
+</head>
+<body>
+<div id="swagger-ui"></div>
+<script src="https://unpkg.com/swagger-ui-dist/swagger-ui-bundle.js"></script>
+<script src="https://unpkg.com/swagger-ui-dist/swagger-ui-standalone-preset.js"></script>
+<script>
+    window.onload = function() {
+        const ui = SwaggerUIBundle({
+            url: "openapi.yaml",
+            dom_id: '#swagger-ui',
+            presets: [
+                SwaggerUIBundle.presets.apis,
+                SwaggerUIStandalonePreset
+            ],
+            layout: "BaseLayout"
+        });
+        window.ui = ui;
+    };
+</script>
+</body>
+</html>

typespec/main.tsp

@@ -1,4 +1,5 @@
 import "@typespec/http";
 import "@typespec/rest";
 import "@typespec/openapi3";
+import "@typespec/versioning";
 import "./routes.tsp";

typespec/package.json

@@ -1,12 +1,12 @@
 {
   "name": "wave",
-  "version": "1.8.2",
+  "version": "1.16.7",
   "type": "module",
   "dependencies": {
-    "@typespec/compiler": "latest",
-    "@typespec/http": "latest",
-    "@typespec/rest": "latest",
-    "@typespec/openapi3": "latest"
+    "@typespec/compiler": "0.64.0",
+    "@typespec/http": "0.64.0",
+    "@typespec/openapi3": "0.64.0",
+    "@typespec/rest": "0.64.0"
   },
   "private": true
-}
+}

typespec/routes.tsp

@@ -2,12 +2,19 @@ import "./models/models.tsp";
 
 using TypeSpec.Http;
 using TypeSpec.Rest;
+using TypeSpec.Versioning;
 
+@versioned(wave.Versions)
 @service({
-  title: "Wave service",
+  title: "Wave service"
 })
-@server("https://wave.seqera.io", "wave endopint")
+@server("https://wave.dev-tower.net", "wave dev endpoint")
+@server("https://wave.stage-seqera.io", "wave stage endpoint")
+@server("https://wave.seqera.io", "wave prod endpoint")
 namespace wave {
+    enum Versions {
+      v1: "0.0.0",
+    }
   @route("/v1alpha2/container")
   interface  ContainerService {