DEVEX-2566: Add automation script to build and publish Copy File app

.github/workflows/build_publish_copy_app.yml

@@ -0,0 +1,54 @@
+name: Build & publish 'dxCompiler Copy File' app
+on:
+  workflow_dispatch:
+    inputs:
+      is-staging:
+        description: 'Deploy to staging? (true/false)'
+        required: false
+        type: choice
+        default: 'true'
+        options:
+          - 'true'
+          - 'false'
+      publish-app:
+        description: 'Publish app? (true/false)'
+        required: false
+        type: choice
+        default: 'false'
+        options:
+          - 'true'
+          - 'false'
+
+permissions:
+  contents: write
+  packages: read
+
+jobs:
+  deploy_app:
+    runs-on: ubuntu-24.04
+
+    steps:
+      - name: Checkout Repo
+        uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+        with:
+          ref: ${{ github.head_ref || github.ref_name }}
+
+      - name: Install dxpy
+        run: |
+          python3 -m pip install dxpy
+          which dx
+
+      - name: Login to platform
+        run: |
+          if [[ ${{ inputs.is-staging }} == "true" ]]; then
+            staging_param="--staging"
+          fi
+          token="${{ inputs.is-staging == 'true' && secrets.DX_STAGING_ROBOT_TOKEN || secrets.DX_PROD_RELEASE_TOKEN }}"
+          dx login --token $token --noprojects $staging_param
+
+      - name: Build and publish 'dxCompiler Copy File' app
+        run: |
+          if [[ ${{ inputs.publish-app }} == "true" ]]; then
+            publish_param="--publish"
+          fi
+          dx build --app --bill-to org-dnanexus_apps $publish_param scripts/dxcompiler_copy

doc/Developing.md

@@ -145,6 +145,11 @@ You should always run the unit tests after every successful compile. Generally,
 
 You need to have a DNAnexus account and be logged into DNAnexus via the command line before you can run the tests (`dx login`). Your default project has to be `dxCompiler_playground` upon login.
 
+```shell
+dx login --staging --noprojects --save --token=<your_staging_token_value>
+dx select project-Fy9QqgQ0yzZbg9KXKP4Jz6Yq
+```
+
 ### Running the integration tests
 
 Integration tests actually build and run apps/workflows on DNAnexus. These tests take much longer to run than the unit tests, and so typically you only run them before submitting a pull request. You can also submit a PR and trigger the integration tests via Github Actions.
@@ -268,4 +273,5 @@ dx api project-xxxx invite '{"invitee": "PUBLIC", "level": "VIEW"}'
 updated (one line change).
 * The app used for copying the assets to different regions during a release ([app-dxwdl_copy](/scripts/dxcompiler_copy)) 
 needs to be enabled in the new region (please update `regionalOptions`, `whatsNew`, and increment the `version` of the app).
+  * To publish `dxwdl_copy` app (`Copy file`) go to `Actions` > `Build & publish 'dxCompiler Copy File' app` and click `Run workflow` on the right side.
 * Update the script for [multi-region testing](/scripts/multi_region_tests.py#L24).

executorWdl/src/test/scala/dx/executor/wdl/WdlTaskExecutorTest.scala

@@ -327,7 +327,7 @@ class WdlTaskExecutorTest extends AnyFlatSpec with Matchers {
               }
               // sometimes it takes a while for the output file to close -
               // block here until the file is closed
-              if (!Iterator.range(0, 10).exists { i =>
+              if (!Iterator.range(0, 20).exists { i =>
                     if (i > 0) {
                       Thread.sleep(6000)
                     }