Develop->Master #360

bio-boris · 2020-10-14T15:22:10Z

No description provided.

changes to templates, code parser, and test data

Also, there are a few other test files that should all be changed and tested together...

…est token in the test_local folder

Check KBASE_TEST_TOKEN env var if no dev token is found

…ompliant

…h spaces

…trieval of information from git.properties file.

…tarting kb-sdk. Add release notes. Fix KBase report class name error in Java version.

Let's skip ci this time.

Java edits for kb-sdk 1.3

Update Dockerfile

Makefile template change for develop branch.

Adding kb-sdk image build and upload to Dockerhub to GitHub actions

Remove outdated sdkbase directory and docs

…cfg file Remove extra step of adding in the test token to the test.cfg file in the github actions Improve error message text with information about where the kbase test token may be found Update release notes; bump version number.

Update entrypoint script to force root user

Removing "-t" flag to allow github actions to run kb-sdk

DEVOPS-1197: Add GHA actions

…r available

Update module_test_python_client.vm.properties

…at no longer exists

Fixing kb_sdk tests, slimming down dockerfile

Updating Dockerfile to enable `docker buildx`

363 python Server.py file adds extraneous quotes to error messages

github-advanced-security · 2025-02-21T18:10:53Z

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.github/workflows/basic_sdk_functionality_tests.yml

+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04, ubuntu-latest]
+        language: [perl, python, java]
+        test_type: [base] #, example]
+        auth: [token, env_var]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      # build kb-sdk from source and test basic functions
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 8.0.362+9
+
+      - name: Build with Ant
+        run: |
+          make
+
+      - name: Add bin to $PATH
+        run: |
+          echo "$GITHUB_WORKSPACE/bin" >> $GITHUB_PATH
+
+      - name: checking kb-sdk functions
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          env
+          kb-sdk help
+          kb-sdk version
+
+      # the following steps create a KBase app using the SDK
+      # and runs some checks to ensure the app generated
+      # is functional and that the SDK can test it.
+      - name: init base repo
+        if: matrix.test_type == 'base'
+        env:
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          kb-sdk init -l $LANGUAGE_TOKEN -u user SampleApp
+
+      - name: init example repo
+        if: matrix.test_type == 'example'
+        env:
+          LANGUAGE_TOKEN: ${{ matrix.language }}
+        run: |
+          kb-sdk init -l $LANGUAGE_TOKEN -u user --example SampleApp
+
+      - name: test ${{ matrix.test_type }} repo, using test.cfg for auth
+        if: matrix.auth == 'token'
+        run: |
+          cd SampleApp
+          kb-sdk test || true
+
+      - name: test ${{ matrix.test_type }} repo, using test.cfg for auth, add env var to test.cfg
+        if: matrix.auth == 'token'
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+        run: |
+          cd SampleApp
+          sed -i "s/test_token=/test_token=$KBASE_TEST_TOKEN/" test_local/test.cfg
+          kb-sdk test
+
+      - name: test ${{ matrix.test_type }} repo, using env var for auth
+        if: matrix.auth == 'env_var'
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+        run: |
+          cd SampleApp
+          kb-sdk test
+
+      - name: make resulting app available as artefact in case of failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: kbaseapp-${{ matrix.language }}-${{ matrix.test_type }}-${{ matrix.os }}
+          path: SampleApp
+
+
+  test_existing_repos:


.github/workflows/basic_sdk_functionality_tests.yml

+    if: "!contains(github.event.head_commit.message, 'skip ci')"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-20.04, ubuntu-latest]
+        # TODO: add a Java app. WsLargeDataIO does not currently build as it relies on a Java
+        # repo that no longer exists.
+        app: [KBaseReport]  # , WsLargeDataIO]
+        auth: [token, env_var]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+
+      - name: Set up JDK 1.8
+        uses: actions/setup-java@v3
+        with:
+          distribution: temurin
+          java-version: 8.0.362+9
+
+      - name: Build with Ant
+        run: |
+          make
+
+      - name: Add bin to $PATH
+        run: |
+          echo "$GITHUB_WORKSPACE/bin" >> $GITHUB_PATH
+
+      - name: checking basic kb-sdk functions
+        run: |
+          env
+          kb-sdk help
+          kb-sdk version
+
+      # the following steps check out and run the tests of an existing KBase app
+      - name: Checkout existing kbase module ${{ matrix.app }}
+        uses: actions/checkout@v3
+        with:
+          repository: kbaseapps/${{ matrix.app }}
+          path: kbase_app
+
+      - name: run repo tests, using test.cfg for auth
+        if: matrix.auth == 'token'
+        run: |
+          cd kbase_app
+          kb-sdk test || true
+
+      - name: run repo tests, using test.cfg for auth
+        if: matrix.auth == 'token'
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+        run: |
+          cd kbase_app
+          sed -i "s/test_token=/test_token=$KBASE_TEST_TOKEN/" test_local/test.cfg
+          kb-sdk test
+
+      - name: run repo tests, using env var for auth
+        if: matrix.auth == 'env_var'
+        env:
+          KBASE_TEST_TOKEN: ${{ secrets.KBASE_TEST_TOKEN }}
+        run: |
+          cd kbase_app
+          kb-sdk test
+
+      - name: make resulting app available as artefact in case of failure
+        if: ${{ failure() }}
+        uses: actions/upload-artifact@v3
+        with:
+          name: kbaseapp-${{ matrix.app }}-${{ matrix.os }}
+          path: kbase_app


.github/workflows/manual-build.yml

+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}-develop'
+      tags: br-${{ github.ref_name }}
+    secrets: inherit


.github/workflows/pr_build.yml

+    if: github.base_ref == 'develop' && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_build.yml@main
+    secrets: inherit
+  build-develop-merge:


.github/workflows/pr_build.yml

+    if: github.base_ref == 'develop' && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}-develop'
+      tags: pr-${{ github.event.number }},latest
+    secrets: inherit
+  build-main-open:


.github/workflows/pr_build.yml

+    if: (github.base_ref == 'main' || github.base_ref == 'master') && github.event.pull_request.merged == true
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: pr-${{ github.event.number }},latest-rc
+    secrets: inherit
+  trivy-scans:


.github/workflows/pr_build.yml

+    if: (github.base_ref == 'develop' || github.base_ref == 'main' || github.base_ref == 'master' ) && github.event.pull_request.merged == false
+    uses: kbase/.github/.github/workflows/reusable_trivy-scans.yml@main
+    secrets: inherit


.github/workflows/release-main.yml

+    uses: kbase/.github/.github/workflows/reusable_validate-branch.yml@main
+    with:
+      build_branch: '${{ github.event.release.target_commitish }}'
+  validate-release-tag:


.github/workflows/release-main.yml

+    needs: check-source-branch
+    uses: kbase/.github/.github/workflows/reusable_validate-release-tag.yml@main
+    with:
+      release_tag: '${{ github.event.release.tag_name }}'
+  build-push:


.github/workflows/release-main.yml

+    needs: validate-release-tag
+    uses: kbase/.github/.github/workflows/reusable_build-push.yml@main
+    with:
+      name: '${{ github.event.repository.name }}'
+      tags: '${{ github.event.release.tag_name }},latest'
+    secrets: inherit


eapearson and others added 30 commits January 23, 2020 06:27

make generated python code pep8 compliant

965cc0c

changes to templates, code parser, and test data

revert test file change, not necessary and can't be tested.

e3684ed

Also, there are a few other test files that should all be changed and tested together...

Allow KBASE_TEST_TOKEN env var to be used as well as hardcoding the t…

4d7bdb7

…est token in the test_local folder

Adding KBASE_TEST_TOKEN to entrypoint

fa01d62

Removing stray "D" from env var

ef10268

Merge pull request #346 from ialarmedalien/kbase_test_token_env_var

2ea5555

Check KBASE_TEST_TOKEN env var if no dev token is found

Merge remote-tracking branch 'origin/develop' into make-python-pep8-c…

b1c51ba

…ompliant

Whitespace changes only: removing trailing spaces, replacing tabs wit…

35e7479

…h spaces

Typo in error message

8d0e981

Adding build date/time to kb-sdk. Failing earlier in kb-sdk test.

2a7474a

Adding actions file

7e58f55

Adding in Java example generate/test to github actions; DRYing out re…

835b9cc

…trieval of information from git.properties file.

Updating actions to create a build/test matrix. Report version when s…

9ac1aba

…tarting kb-sdk. Add release notes. Fix KBase report class name error in Java version.

Updating release notes with more specific details

2384e3b

Reworded release notes message.

48f8e29

Let's skip ci this time.

Die if the git.properties file cannot be found

c3e81fb

Merge pull request #350 from ialarmedalien/java_edits_for_kb_sdk_1.3

ad5e402

Java edits for kb-sdk 1.3

Update dockerfile with updated dependencies

2813c80

Bump version to 1.2.3

965b840

Merge pull request #352 from ialarmedalien/update_Dockerfile

8fc4c60

Update Dockerfile

try removing sdkbase dir

76e3728

jsf-nose-mod

5be329c

Merge pull request #355 from kbase/jsfillman-patch-1

782e415

Makefile template change for develop branch.

Adding kb-sdk image build and upload to Dockerhub to GitHub actions

b7b7d16

Merge pull request #354 from kbase/autobuild_docker_images

ebfcf73

Adding kb-sdk image build and upload to Dockerhub to GitHub actions

Merge branch 'develop' into remove_sdkbase_dir

c03ad16

Merge pull request #353 from kbase/remove_sdkbase_dir

7df70d8

Remove outdated sdkbase directory and docs

Test both env var and test.cfg-based auth

0325651

Merge branch 'develop' into make-python-pep8-compliant

492c5f7

ialarmedalien and others added 28 commits October 14, 2020 13:59

Merge pull request #359 from kbase/force_root_user

0f955f3

Update entrypoint script to force root user

Merge branch 'master' into develop

cf29601

Removing "-t" flag to allow github actions to run kb-sdk

2eacd99

Merge pull request #362 from kbase/remove_-t_flag

07a0a3c

Removing "-t" flag to allow github actions to run kb-sdk

Update module_test_python_client.vm.properties

401b3d7

Update python_server.vm.properties

29d1ee5

Create manual-build.yml

6eecbf5

Create pr_build.yml

e9dd950

Create release-main.yml

03c6a09

Update kb_sdk-actions.yml

8b2d1e6

Merge pull request #369 from kbase/add_gha_build

f22afe7

DEVOPS-1197: Add GHA actions

Merge branch 'develop' into issue_347_with_updated_kb-sdk

f7f7f26

Fixing kb_sdk tests, slimming down dockerfile

dad228a

removing travis file, updating test workflow to remove push to github

830e4af

adding missing distro tag to java action

c1b938c

fix java action again

13caa04

update to using two most recent ubuntus

3acd45d

disable generating the example module as the software dep is no longe…

28f15f5

…r available

Merge pull request #367 from kbase/issue_347_with_updated_kb-sdk

85bc764

Update module_test_python_client.vm.properties

Disable testing of WSLargeDataIO as it relies on a Java repository th…

edd9146

…at no longer exists

disable WsLargeDataIO tests

8f14d80

Renaming workflow file, adding comments about what tests are doing

1a1e51e

Update python_server.vm.properties

89e620e

Merge pull request #370 from kbase/fix_actions

2501e08

Fixing kb_sdk tests, slimming down dockerfile

Merge branch 'develop' into adjust_repr_use

ad8134e

Updating docker install to enable docker buildx

0ab2a97

Merge pull request #366 from kbase/DEVOPS-765-add_buildx

3a7e1b2

Updating Dockerfile to enable `docker buildx`

Merge pull request #371 from kbase/adjust_repr_use

cedcfc2

363 python Server.py file adds extraneous quotes to error messages

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Develop->Master #360

Develop->Master #360

bio-boris commented Oct 14, 2020

github-advanced-security bot commented Feb 21, 2025

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Develop->Master #360

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